Date: 2021-07-22 18:32:45 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 375915 rows and 492 columns.
#> Performed in total 81200 partitions.
#> There are 40 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, 492 cols
#> |-- 01, 154 cols, 3093 signatures
#> | |-- 011, 95 cols, 1365 signatures
#> | | |-- 0111, 38 cols, 8709 signatures
#> | | | |-- 01111, 16 cols, 0 signatures (c)
#> | | | |-- 01112, 8 cols (b)
#> | | | |-- 01113, 3 cols (b)
#> | | | `-- 01114, 11 cols (b)
#> | | |-- 0112, 27 cols, 183 signatures (c)
#> | | `-- 0113, 30 cols, 5918 signatures
#> | | |-- 01131, 8 cols (b)
#> | | |-- 01132, 11 cols (b)
#> | | |-- 01133, 8 cols (b)
#> | | `-- 01134, 3 cols (b)
#> | |-- 012, 37 cols, 4296 signatures
#> | | |-- 0121, 16 cols, 709 signatures (c)
#> | | |-- 0122, 15 cols, 1363 signatures
#> | | | |-- 01221, 10 cols (b)
#> | | | `-- 01222, 5 cols (b)
#> | | `-- 0123, 6 cols (b)
#> | `-- 013, 22 cols, 121 signatures (c)
#> |-- 02, 220 cols, 3141 signatures
#> | |-- 021, 68 cols, 3497 signatures
#> | | |-- 0211, 27 cols, 65 signatures (c)
#> | | |-- 0212, 25 cols, 3568 signatures
#> | | | |-- 02121, 6 cols (b)
#> | | | |-- 02122, 8 cols (b)
#> | | | |-- 02123, 7 cols (b)
#> | | | `-- 02124, 4 cols (b)
#> | | `-- 0213, 16 cols, 168 signatures (c)
#> | |-- 022, 61 cols, 3199 signatures
#> | | |-- 0221, 29 cols, 889 signatures (c)
#> | | |-- 0222, 21 cols, 3921 signatures
#> | | | |-- 02221, 14 cols, 319 signatures (c)
#> | | | |-- 02222, 5 cols (b)
#> | | | `-- 02223, 2 cols (b)
#> | | `-- 0223, 11 cols (b)
#> | `-- 023, 91 cols, 2248 signatures
#> | |-- 0231, 50 cols, 3755 signatures
#> | | |-- 02311, 17 cols, 463 signatures (c)
#> | | |-- 02312, 12 cols, 4 signatures (c)
#> | | |-- 02313, 9 cols (b)
#> | | `-- 02314, 12 cols, 341 signatures (c)
#> | `-- 0232, 41 cols, 2566 signatures
#> | |-- 02321, 18 cols, 113 signatures (c)
#> | |-- 02322, 18 cols, 30 signatures (c)
#> | `-- 02323, 5 cols (b)
#> |-- 03, 44 cols, 3054 signatures
#> | |-- 031, 22 cols, 2965 signatures
#> | | |-- 0311, 15 cols, 26 signatures (c)
#> | | |-- 0312, 2 cols (b)
#> | | `-- 0313, 5 cols (b)
#> | `-- 032, 22 cols, 1644 signatures
#> | |-- 0321, 3 cols (b)
#> | |-- 0322, 15 cols, 0 signatures (c)
#> | |-- 0323, 2 cols (b)
#> | `-- 0324, 2 cols (b)
#> `-- 04, 74 cols, 457 signatures (c)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375915 492
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "01111" "01112" "01113" "01114" "0112" "0113" "01131" "01132"
#> [13] "01133" "01134" "012" "0121" "0122" "01221" "01222" "0123" "013" "02" "021" "0211"
#> [25] "0212" "02121" "02122" "02123" "02124" "0213" "022" "0221" "0222" "02221" "02222" "02223"
#> [37] "0223" "023" "0231" "02311" "02312" "02313" "02314" "0232" "02321" "02322" "02323" "03"
#> [49] "031" "0311" "0312" "0313" "032" "0321" "0322" "0323" "0324" "04"
all_leaves(res_rh)
#> [1] "01111" "01112" "01113" "01114" "0112" "01131" "01132" "01133" "01134" "0121" "01221" "01222"
#> [13] "0123" "013" "0211" "02121" "02122" "02123" "02124" "0213" "0221" "02221" "02222" "02223"
#> [25] "0223" "02311" "02312" "02313" "02314" "02321" "02322" "02323" "0311" "0312" "0313" "0321"
#> [37] "0322" "0323" "0324" "04"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 4 492 19867 5.28e-02 FALSE
#> 2 01 SD:skmeans 2 3 154 3093 8.23e-03 FALSE
#> 3 011 ATC:kmeans 3 3 95 1365 3.63e-03 FALSE
#> 4 0111 ATC:skmeans 4 4 38 8709 2.32e-02 FALSE
#> 5 01111 ATC:kmeans 5 2 16 0 0.00e+00 TRUE
#> 6 01112 not applied 5 NA 8 NA NA TRUE
#> 7 01113 not applied 5 NA 3 NA NA TRUE
#> 8 01114 not applied 5 NA 11 NA NA TRUE
#> 9 0112 ATC:kmeans 4 2 27 183 4.87e-04 TRUE
#> 10 0113 ATC:skmeans 4 4 30 5918 1.57e-02 FALSE
#> 11 01131 not applied 5 NA 8 NA NA TRUE
#> 12 01132 not applied 5 NA 11 NA NA TRUE
#> 13 01133 not applied 5 NA 8 NA NA TRUE
#> 14 01134 not applied 5 NA 3 NA NA TRUE
#> 15 012 ATC:kmeans 3 3 37 4296 1.14e-02 FALSE
#> 16 0121 ATC:skmeans 4 4 16 709 1.89e-03 TRUE
#> 17 0122 ATC:kmeans 4 2 15 1363 3.63e-03 FALSE
#> 18 01221 not applied 5 NA 10 NA NA TRUE
#> 19 01222 not applied 5 NA 5 NA NA TRUE
#> 20 0123 not applied 4 NA 6 NA NA TRUE
#> 21 013 SD:kmeans 3 2 22 121 3.22e-04 TRUE
#> 22 02 ATC:kmeans 2 3 220 3141 8.36e-03 FALSE
#> 23 021 ATC:skmeans 3 3 68 3497 9.30e-03 FALSE
#> 24 0211 ATC:skmeans 4 2 27 65 1.73e-04 TRUE
#> 25 0212 ATC:skmeans 4 4 25 3568 9.49e-03 FALSE
#> 26 02121 not applied 5 NA 6 NA NA TRUE
#> 27 02122 not applied 5 NA 8 NA NA TRUE
#> 28 02123 not applied 5 NA 7 NA NA TRUE
#> 29 02124 not applied 5 NA 4 NA NA TRUE
#> 30 0213 ATC:skmeans 4 3 16 168 4.47e-04 TRUE
#> 31 022 SD:skmeans 3 3 61 3199 8.51e-03 FALSE
#> 32 0221 SD:kmeans 4 2 29 889 2.36e-03 TRUE
#> 33 0222 ATC:skmeans 4 3 21 3921 1.04e-02 FALSE
#> 34 02221 ATC:skmeans 5 2 14 319 8.49e-04 TRUE
#> 35 02222 not applied 5 NA 5 NA NA TRUE
#> 36 02223 not applied 5 NA 2 NA NA TRUE
#> 37 0223 not applied 4 NA 11 NA NA TRUE
#> 38 023 SD:kmeans 3 2 91 2248 5.98e-03 FALSE
#> 39 0231 ATC:skmeans 4 4 50 3755 9.99e-03 FALSE
#> 40 02311 ATC:skmeans 5 3 17 463 1.23e-03 TRUE
#> 41 02312 ATC:kmeans 5 3 12 4 1.06e-05 TRUE
#> 42 02313 not applied 5 NA 9 NA NA TRUE
#> 43 02314 ATC:skmeans 5 3 12 341 9.07e-04 TRUE
#> 44 0232 ATC:skmeans 4 3 41 2566 6.83e-03 FALSE
#> 45 02321 ATC:kmeans 5 2 18 113 3.01e-04 TRUE
#> 46 02322 ATC:skmeans 5 2 18 30 7.98e-05 TRUE
#> 47 02323 not applied 5 NA 5 NA NA TRUE
#> 48 03 SD:kmeans 2 2 44 3054 8.12e-03 FALSE
#> 49 031 ATC:kmeans 3 3 22 2965 7.89e-03 FALSE
#> 50 0311 ATC:skmeans 4 3 15 26 6.92e-05 TRUE
#> 51 0312 not applied 4 NA 2 NA NA TRUE
#> 52 0313 not applied 4 NA 5 NA NA TRUE
#> 53 032 ATC:skmeans 3 4 22 1644 4.37e-03 FALSE
#> 54 0321 not applied 4 NA 3 NA NA TRUE
#> 55 0322 ATC:skmeans 4 2 15 0 0.00e+00 TRUE
#> 56 0323 not applied 4 NA 2 NA NA TRUE
#> 57 0324 not applied 4 NA 2 NA NA TRUE
#> 58 04 ATC:kmeans 2 2 74 457 1.22e-03 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 | 6 | 0.90 | 0.89 | 0.95 | 492 | * | |
| Node01 | SD:skmeans | 3 | 0.94 | 0.97 | 0.96 | 154 | * | |
| Node011 | ATC:kmeans | 3 | 0.94 | 0.97 | 0.99 | 95 | * | |
| Node0111 | ATC:skmeans | 5 | 0.97 | 0.96 | 0.97 | 38 | ** | |
| Node01111-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 0.91 | 0.96 | 16 | ** |
| Node01112-leaf | not applied | ✓ (b) | 8 | |||||
| Node01113-leaf | not applied | ✓ (b) | 3 | |||||
| Node01114-leaf | not applied | ✓ (b) | 11 | |||||
| Node0112-leaf | ATC:kmeans | ✓ (c) | 2 | 0.64 | 0.96 | 0.97 | 27 | |
| Node0113 | ATC:skmeans | 4 | 1.00 | 0.98 | 0.99 | 30 | ** | |
| Node01131-leaf | not applied | ✓ (b) | 8 | |||||
| Node01132-leaf | not applied | ✓ (b) | 11 | |||||
| Node01133-leaf | not applied | ✓ (b) | 8 | |||||
| Node01134-leaf | not applied | ✓ (b) | 3 | |||||
| Node012 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 37 | ** | |
| Node0121-leaf | ATC:skmeans | ✓ (c) | 4 | 1.00 | 1.00 | 1.00 | 16 | ** |
| Node0122 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 15 | ** | |
| Node01221-leaf | not applied | ✓ (b) | 10 | |||||
| Node01222-leaf | not applied | ✓ (b) | 5 | |||||
| Node0123-leaf | not applied | ✓ (b) | 6 | |||||
| Node013-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 1.00 | 22 | ** |
| Node02 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.99 | 220 | ** | |
| Node021 | ATC:skmeans | 3 | 1.00 | 0.99 | 0.99 | 68 | ** | |
| Node0211-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 27 | ** |
| Node0212 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 25 | ** | |
| Node02121-leaf | not applied | ✓ (b) | 6 | |||||
| Node02122-leaf | not applied | ✓ (b) | 8 | |||||
| Node02123-leaf | not applied | ✓ (b) | 7 | |||||
| Node02124-leaf | not applied | ✓ (b) | 4 | |||||
| Node0213-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.99 | 1.00 | 16 | ** |
| Node022 | SD:skmeans | 3 | 1.00 | 0.98 | 0.97 | 61 | ** | |
| Node0221-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 0.99 | 29 | ** |
| Node0222 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 21 | ** | |
| Node02221-leaf | ATC:skmeans | ✓ (c) | 8 | 0.90 | 0.48 | 0.93 | 14 | * |
| Node02222-leaf | not applied | ✓ (b) | 5 | |||||
| Node02223-leaf | not applied | ✓ (b) | 2 | |||||
| Node0223-leaf | not applied | ✓ (b) | 11 | |||||
| Node023 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 91 | ** | |
| Node0231 | ATC:skmeans | 4 | 1.00 | 0.96 | 0.98 | 50 | ** | |
| Node02311-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 17 | ** |
| Node02312-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 0.92 | 1.00 | 12 | ** |
| Node02313-leaf | not applied | ✓ (b) | 9 | |||||
| Node02314-leaf | ATC:skmeans | ✓ (c) | 8 | 0.92 | 0.52 | 0.93 | 12 | * |
| Node0232 | ATC:skmeans | 3 | 1.00 | 0.96 | 0.99 | 41 | ** | |
| Node02321-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 18 | ** |
| Node02322-leaf | ATC:skmeans | ✓ (c) | 2 | 0.84 | 0.95 | 0.97 | 18 | |
| Node02323-leaf | not applied | ✓ (b) | 5 | |||||
| Node03 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 44 | ** | |
| Node031 | ATC:kmeans | 7 | 0.93 | 0.84 | 0.92 | 22 | * | |
| Node0311-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.99 | 0.99 | 15 | ** |
| Node0312-leaf | not applied | ✓ (b) | 2 | |||||
| Node0313-leaf | not applied | ✓ (b) | 5 | |||||
| Node032 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 22 | ** | |
| Node0321-leaf | not applied | ✓ (b) | 3 | |||||
| Node0322-leaf | ATC:skmeans | ✓ (c) | 4 | 1.00 | 0.91 | 0.98 | 15 | ** |
| Node0323-leaf | not applied | ✓ (b) | 2 | |||||
| Node0324-leaf | not applied | ✓ (b) | 2 | |||||
| Node04-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 74 | ** |
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 = 1363))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1365))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1644))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2248))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2566))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2965))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3054))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3093))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3141))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3199))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3497))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3568))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3755))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3921))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4296))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5918))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8709))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 19867))
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 = 1363))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02314" "02321" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "0321" "013" "0112" "04" "02311" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "0321" "04" "01221" "01221" "0324"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "0322" "0213" "0112" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "02314" "02312" "0211" "01111"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "0112" "01132" "02321" "02323"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "0112" "0123" "02322" "01114" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02321" "0112" "0112" "01222" "0211" "02311"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "0112" "01134" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "0311" "0221" "02123" "02221" "0311"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01221" "02321" "02322" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01132" "0213" "04" "02314" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02313" "01222" "04" "04" "04" "0112"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02313" "02311" "013" "0312" "02312" "01131"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "0311" "0211" "0211" "04" "0221" "02313"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "0312" "02221" "0223" "01221" "0112" "02321"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "02311" "04" "02313" "01114"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "0313" "01132" "01132" "02322" "04" "01113"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02323" "0211" "0121" "0221" "0322" "0322"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "01222" "01111" "0311" "0311" "02311"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "0322" "0112" "04" "01132" "02311" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "0112" "01114" "0211" "01221" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02321" "0221" "01133" "02323" "04" "0112"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "0112" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "02321" "0221" "0221" "0324" "02322"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01131" "02311" "0112" "04" "01114" "01131"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "02322" "01133" "01221" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "0322" "01112" "02314" "02321" "01111"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02314" "01133" "02314" "013" "0311" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02321" "01112" "02123" "02321" "0322" "02321"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "01111" "0223" "02312" "0311"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02312" "0322" "0213" "01112" "04" "02311"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "0323" "01131" "02312" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02313" "04" "0322" "02313" "0311" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01112" "04" "0322" "0223" "0112" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "02322" "0221" "02322" "01111"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02313" "02322" "013" "04" "02312" "0313"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "01134" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "02322" "02311"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02312" "0322" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "0313" "02123" "04" "02124" "01111" "02322"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "02313" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01111" "02322" "02321" "04" "0112" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02311" "0221" "0121" "0112" "01132" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01112" "02124" "02321" "04" "01133" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "02311" "0211" "02323"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "0311" "01112"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "01111" "02314" "0112"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01114" "0223" "0112" "04" "02121" "02322"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "0112" "0221" "0221" "01114" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "0311" "0121" "01133" "04" "01132" "02312"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "0322" "013" "02221" "0121" "02323" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01114" "04" "04" "0313" "013" "0112"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01133" "04" "02223" "02222" "02311" "02311"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01221" "01131" "013" "02122" "01111" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01111" "0313" "02312" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01221" "01114" "0221" "02312" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "0112" "04" "02311" "02311" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "01114" "0221" "0211" "01221" "01134"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "01133" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01111" "04" "0112" "02321"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "0311" "04" "02311" "04" "04" "02312"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01131" "0211" "02314" "01132" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02314" "0211" "0123" "01133" "0112" "01221"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "0322" "02123" "0112" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02314" "0213" "04" "04" "04" "02313"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "02321" "0311" "01132"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "02321" "01131" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "02322" "0321" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "01222" "02314" "01113" "0213" "0311"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "01111" "02121" "02122" "02321" "02314"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "01111" "0322" "02311" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "02322" "0213" "013" "01113" "01114"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "02322" "0311" "0221" "01111"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01131" "0322" "013" "02122" "0121" "0323"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "0311" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02322" "04" "01111" "04" "02322" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01132" "01111" "01112" "01132" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "02312" "0211" "013" "0112" "01114"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "02321" "02221" "0221" "01222" "0112"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "01112" "04" "0322" "04" "02322"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1365))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02314" "02321" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "0321" "013" "0112" "04" "02311" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "0321" "04" "0122" "0122" "0324"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "0322" "0213" "0112" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "02314" "02312" "0211" "01111"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "0112" "01132" "02321" "02323"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "0112" "0123" "02322" "01114" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02321" "0112" "0112" "0122" "0211" "02311"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "0112" "01134" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "0311" "0221" "02123" "02221" "0311"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "0122" "02321" "02322" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01132" "0213" "04" "02314" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02313" "0122" "04" "04" "04" "0112"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02313" "02311" "013" "0312" "02312" "01131"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "0311" "0211" "0211" "04" "0221" "02313"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "0312" "02221" "0223" "0122" "0112" "02321"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "02311" "04" "02313" "01114"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "0313" "01132" "01132" "02322" "04" "01113"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02323" "0211" "0121" "0221" "0322" "0322"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "0122" "01111" "0311" "0311" "02311"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "0322" "0112" "04" "01132" "02311" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "0112" "01114" "0211" "0122" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02321" "0221" "01133" "02323" "04" "0112"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "0112" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "02321" "0221" "0221" "0324" "02322"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01131" "02311" "0112" "04" "01114" "01131"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "02322" "01133" "0122" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "0322" "01112" "02314" "02321" "01111"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02314" "01133" "02314" "013" "0311" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02321" "01112" "02123" "02321" "0322" "02321"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "01111" "0223" "02312" "0311"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02312" "0322" "0213" "01112" "04" "02311"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "0323" "01131" "02312" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02313" "04" "0322" "02313" "0311" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01112" "04" "0322" "0223" "0112" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "02322" "0221" "02322" "01111"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02313" "02322" "013" "04" "02312" "0313"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "01134" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "02322" "02311"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02312" "0322" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "0313" "02123" "04" "02124" "01111" "02322"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "02313" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01111" "02322" "02321" "04" "0112" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02311" "0221" "0121" "0112" "01132" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01112" "02124" "02321" "04" "01133" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "02311" "0211" "02323"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "0311" "01112"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "01111" "02314" "0112"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01114" "0223" "0112" "04" "02121" "02322"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "0112" "0221" "0221" "01114" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "0311" "0121" "01133" "04" "01132" "02312"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "0322" "013" "02221" "0121" "02323" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01114" "04" "04" "0313" "013" "0112"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01133" "04" "02223" "02222" "02311" "02311"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "0122" "01131" "013" "02122" "01111" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01111" "0313" "02312" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0122" "01114" "0221" "02312" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "0112" "04" "02311" "02311" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "01114" "0221" "0211" "0122" "01134"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "01133" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01111" "04" "0112" "02321"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "0311" "04" "02311" "04" "04" "02312"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01131" "0211" "02314" "01132" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02314" "0211" "0123" "01133" "0112" "0122"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "0322" "02123" "0112" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02314" "0213" "04" "04" "04" "02313"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "02321" "0311" "01132"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "02321" "01131" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "02322" "0321" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "0122" "02314" "01113" "0213" "0311"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "01111" "02121" "02122" "02321" "02314"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "01111" "0322" "02311" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "02322" "0213" "013" "01113" "01114"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "02322" "0311" "0221" "01111"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01131" "0322" "013" "02122" "0121" "0323"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "0311" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02322" "04" "01111" "04" "02322" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01132" "01111" "01112" "01132" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "02312" "0211" "013" "0112" "01114"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "02321" "02221" "0221" "0122" "0112"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "01112" "04" "0322" "04" "02322"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1644))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02314" "02321" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "0321" "013" "011" "04" "02311" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "0321" "04" "0122" "0122" "0324"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "0322" "0213" "011" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "02314" "02312" "0211" "011"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "011" "011" "02321" "02323"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "011" "0123" "02322" "011" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02321" "011" "011" "0122" "0211" "02311"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "011" "011" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "0311" "0221" "02123" "02221" "0311"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "0122" "02321" "02322" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "011" "0213" "04" "02314" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02313" "0122" "04" "04" "04" "011"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02313" "02311" "013" "0312" "02312" "011"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "0311" "0211" "0211" "04" "0221" "02313"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "0312" "02221" "0223" "0122" "011" "02321"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "02311" "04" "02313" "011"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "0313" "011" "011" "02322" "04" "011"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02323" "0211" "0121" "0221" "0322" "0322"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "0122" "011" "0311" "0311" "02311"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "0322" "011" "04" "011" "02311" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "011" "011" "0211" "0122" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02321" "0221" "011" "02323" "04" "011"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "011" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "02321" "0221" "0221" "0324" "02322"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "011" "02311" "011" "04" "011" "011"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "02322" "011" "0122" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "0322" "011" "02314" "02321" "011"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02314" "011" "02314" "013" "0311" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02321" "011" "02123" "02321" "0322" "02321"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "011" "0223" "02312" "0311"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02312" "0322" "0213" "011" "04" "02311"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "0323" "011" "02312" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02313" "04" "0322" "02313" "0311" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "011" "04" "0322" "0223" "011" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "02322" "0221" "02322" "011"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02313" "02322" "013" "04" "02312" "0313"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "011" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "02322" "02311"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02312" "0322" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "0313" "02123" "04" "02124" "011" "02322"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "02313" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "011" "02322" "02321" "04" "011" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02311" "0221" "0121" "011" "011" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "011" "02124" "02321" "04" "011" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "02311" "0211" "02323"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "0311" "011"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "011" "02314" "011"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "011" "0223" "011" "04" "02121" "02322"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "011" "0221" "0221" "011" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "0311" "0121" "011" "04" "011" "02312"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "0322" "013" "02221" "0121" "02323" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "011" "04" "04" "0313" "013" "011"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "011" "04" "02223" "02222" "02311" "02311"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "0122" "011" "013" "02122" "011" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "011" "0313" "02312" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0122" "011" "0221" "02312" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "011" "04" "02311" "02311" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "011" "0221" "0211" "0122" "011"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "011" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "011" "04" "011" "02321"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "0311" "04" "02311" "04" "04" "02312"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "011" "0211" "02314" "011" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02314" "0211" "0123" "011" "011" "0122"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "0322" "02123" "011" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02314" "0213" "04" "04" "04" "02313"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "02321" "0311" "011"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "02321" "011" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "02322" "0321" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "0122" "02314" "011" "0213" "0311"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "011" "02121" "02122" "02321" "02314"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "011" "0322" "02311" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "02322" "0213" "013" "011" "011"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "02322" "0311" "0221" "011"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "011" "0322" "013" "02122" "0121" "0323"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "0311" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02322" "04" "011" "04" "02322" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "011" "011" "011" "011" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "02312" "0211" "013" "011" "011"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "02321" "02221" "0221" "0122" "011"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "011" "04" "0322" "04" "02322"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2248))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02314" "02321" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "032" "013" "011" "04" "02311" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "032" "04" "0122" "0122" "032"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "032" "0213" "011" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "02314" "02312" "0211" "011"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "011" "011" "02321" "02323"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "011" "0123" "02322" "011" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02321" "011" "011" "0122" "0211" "02311"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "011" "011" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "0311" "0221" "02123" "02221" "0311"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "0122" "02321" "02322" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "011" "0213" "04" "02314" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02313" "0122" "04" "04" "04" "011"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02313" "02311" "013" "0312" "02312" "011"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "0311" "0211" "0211" "04" "0221" "02313"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "0312" "02221" "0223" "0122" "011" "02321"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "02311" "04" "02313" "011"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "0313" "011" "011" "02322" "04" "011"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02323" "0211" "0121" "0221" "032" "032"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "0122" "011" "0311" "0311" "02311"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "032" "011" "04" "011" "02311" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "011" "011" "0211" "0122" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02321" "0221" "011" "02323" "04" "011"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "011" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "02321" "0221" "0221" "032" "02322"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "011" "02311" "011" "04" "011" "011"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "02322" "011" "0122" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "032" "011" "02314" "02321" "011"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02314" "011" "02314" "013" "0311" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02321" "011" "02123" "02321" "032" "02321"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "011" "0223" "02312" "0311"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02312" "032" "0213" "011" "04" "02311"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "032" "011" "02312" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02313" "04" "032" "02313" "0311" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "011" "04" "032" "0223" "011" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "02322" "0221" "02322" "011"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02313" "02322" "013" "04" "02312" "0313"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "011" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "02322" "02311"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02312" "032" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "0313" "02123" "04" "02124" "011" "02322"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "02313" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "011" "02322" "02321" "04" "011" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02311" "0221" "0121" "011" "011" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "011" "02124" "02321" "04" "011" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "02311" "0211" "02323"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "0311" "011"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "011" "02314" "011"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "011" "0223" "011" "04" "02121" "02322"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "011" "0221" "0221" "011" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "0311" "0121" "011" "04" "011" "02312"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "032" "013" "02221" "0121" "02323" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "011" "04" "04" "0313" "013" "011"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "011" "04" "02223" "02222" "02311" "02311"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "0122" "011" "013" "02122" "011" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "011" "0313" "02312" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0122" "011" "0221" "02312" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "011" "04" "02311" "02311" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "011" "0221" "0211" "0122" "011"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "011" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "011" "04" "011" "02321"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "0311" "04" "02311" "04" "04" "02312"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "011" "0211" "02314" "011" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02314" "0211" "0123" "011" "011" "0122"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "032" "02123" "011" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02314" "0213" "04" "04" "04" "02313"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "02321" "0311" "011"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "02321" "011" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "02322" "032" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "0122" "02314" "011" "0213" "0311"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "011" "02121" "02122" "02321" "02314"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "011" "032" "02311" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "02322" "0213" "013" "011" "011"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "02322" "0311" "0221" "011"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "011" "032" "013" "02122" "0121" "032"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "0311" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02322" "04" "011" "04" "02322" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "011" "011" "011" "011" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "02312" "0211" "013" "011" "011"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "02321" "02221" "0221" "0122" "011"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "011" "04" "032" "04" "02322"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2566))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "023" "023" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "032" "013" "011" "04" "023" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "032" "04" "0122" "0122" "032"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "032" "0213" "011" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "023" "023" "0211" "011"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "011" "011" "023" "023"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "011" "0123" "023" "011" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "023" "011" "011" "0122" "0211" "023"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "011" "011" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "0311" "0221" "02123" "02221" "0311"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "0122" "023" "023" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "011" "0213" "04" "023" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "023" "0122" "04" "04" "04" "011"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "023" "023" "013" "0312" "023" "011"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "0311" "0211" "0211" "04" "0221" "023"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "0312" "02221" "0223" "0122" "011" "023"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "023" "04" "023" "011"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "0313" "011" "011" "023" "04" "011"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "023" "0211" "0121" "0221" "032" "032"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "0122" "011" "0311" "0311" "023"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "032" "011" "04" "011" "023" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "011" "011" "0211" "0122" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "023" "0221" "011" "023" "04" "011"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "011" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "023" "0221" "0221" "032" "023"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "011" "023" "011" "04" "011" "011"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "023" "011" "0122" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "032" "011" "023" "023" "011"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "023" "011" "023" "013" "0311" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "023" "011" "02123" "023" "032" "023"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "011" "0223" "023" "0311"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "023" "032" "0213" "011" "04" "023"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "032" "011" "023" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "023" "04" "032" "023" "0311" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "011" "04" "032" "0223" "011" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "023" "0221" "023" "011"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "023" "023" "013" "04" "023" "0313"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "011" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "023" "023"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "023" "032" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "0313" "02123" "04" "02124" "011" "023"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "023" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "011" "023" "023" "04" "011" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "023" "0221" "0121" "011" "011" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "011" "02124" "023" "04" "011" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "023" "0211" "023"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "0311" "011"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "011" "023" "011"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "011" "0223" "011" "04" "02121" "023"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "011" "0221" "0221" "011" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "0311" "0121" "011" "04" "011" "023"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "032" "013" "02221" "0121" "023" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "011" "04" "04" "0313" "013" "011"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "011" "04" "02223" "02222" "023" "023"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "0122" "011" "013" "02122" "011" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "011" "0313" "023" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0122" "011" "0221" "023" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "011" "04" "023" "023" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "011" "0221" "0211" "0122" "011"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "011" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "011" "04" "011" "023"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "0311" "04" "023" "04" "04" "023"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "011" "0211" "023" "011" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "023" "0211" "0123" "011" "011" "0122"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "032" "02123" "011" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "023" "0213" "04" "04" "04" "023"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "023" "0311" "011"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "023" "011" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "023" "032" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "0122" "023" "011" "0213" "0311"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "011" "02121" "02122" "023" "023"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "011" "032" "023" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "023" "0213" "013" "011" "011"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "023" "0311" "0221" "011"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "011" "032" "013" "02122" "0121" "032"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "0311" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "023" "04" "011" "04" "023" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "011" "011" "011" "011" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "023" "0211" "013" "011" "011"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "023" "02221" "0221" "0122" "011"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "011" "04" "032" "04" "023"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2965))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "023" "023" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "032" "013" "011" "04" "023" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "032" "04" "0122" "0122" "032"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "032" "0213" "011" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "023" "023" "0211" "011"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "011" "011" "023" "023"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "011" "0123" "023" "011" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "023" "011" "011" "0122" "0211" "023"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "011" "011" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "0311" "0221" "02123" "02221" "0311"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "0122" "023" "023" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "011" "0213" "04" "023" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "023" "0122" "04" "04" "04" "011"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "023" "023" "013" "0312" "023" "011"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "0311" "0211" "0211" "04" "0221" "023"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "0312" "02221" "0223" "0122" "011" "023"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "023" "04" "023" "011"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "0313" "011" "011" "023" "04" "011"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "023" "0211" "0121" "0221" "032" "032"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "0122" "011" "0311" "0311" "023"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "032" "011" "04" "011" "023" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "011" "011" "0211" "0122" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "023" "0221" "011" "023" "04" "011"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "011" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "023" "0221" "0221" "032" "023"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "011" "023" "011" "04" "011" "011"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "023" "011" "0122" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "032" "011" "023" "023" "011"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "023" "011" "023" "013" "0311" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "023" "011" "02123" "023" "032" "023"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "011" "0223" "023" "0311"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "023" "032" "0213" "011" "04" "023"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "032" "011" "023" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "023" "04" "032" "023" "0311" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "011" "04" "032" "0223" "011" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "023" "0221" "023" "011"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "023" "023" "013" "04" "023" "0313"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "011" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "023" "023"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "023" "032" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "0313" "02123" "04" "02124" "011" "023"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "023" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "011" "023" "023" "04" "011" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "023" "0221" "0121" "011" "011" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "011" "02124" "023" "04" "011" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "023" "0211" "023"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "0311" "011"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "011" "023" "011"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "011" "0223" "011" "04" "02121" "023"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "011" "0221" "0221" "011" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "0311" "0121" "011" "04" "011" "023"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "032" "013" "02221" "0121" "023" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "011" "04" "04" "0313" "013" "011"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "011" "04" "02223" "02222" "023" "023"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "0122" "011" "013" "02122" "011" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "011" "0313" "023" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0122" "011" "0221" "023" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "011" "04" "023" "023" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "011" "0221" "0211" "0122" "011"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "011" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "011" "04" "011" "023"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "0311" "04" "023" "04" "04" "023"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "011" "0211" "023" "011" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "023" "0211" "0123" "011" "011" "0122"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "032" "02123" "011" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "023" "0213" "04" "04" "04" "023"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "023" "0311" "011"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "023" "011" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "023" "032" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "0122" "023" "011" "0213" "0311"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "011" "02121" "02122" "023" "023"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "011" "032" "023" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "023" "0213" "013" "011" "011"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "023" "0311" "0221" "011"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "011" "032" "013" "02122" "0121" "032"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "0311" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "023" "04" "011" "04" "023" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "011" "011" "011" "011" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "023" "0211" "013" "011" "011"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "023" "02221" "0221" "0122" "011"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "011" "04" "032" "04" "023"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3054))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "023" "023" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "032" "013" "011" "04" "023" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "032" "04" "0122" "0122" "032"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "032" "0213" "011" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "023" "023" "0211" "011"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "011" "011" "023" "023"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "011" "0123" "023" "011" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "023" "011" "011" "0122" "0211" "023"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "011" "011" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "031" "0221" "02123" "02221" "031"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "0122" "023" "023" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "011" "0213" "04" "023" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "023" "0122" "04" "04" "04" "011"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "023" "023" "013" "031" "023" "011"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "031" "0211" "0211" "04" "0221" "023"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "031" "02221" "0223" "0122" "011" "023"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "023" "04" "023" "011"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "031" "011" "011" "023" "04" "011"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "023" "0211" "0121" "0221" "032" "032"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "0122" "011" "031" "031" "023"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "032" "011" "04" "011" "023" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "011" "011" "0211" "0122" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "023" "0221" "011" "023" "04" "011"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "011" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "023" "0221" "0221" "032" "023"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "011" "023" "011" "04" "011" "011"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "023" "011" "0122" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "032" "011" "023" "023" "011"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "023" "011" "023" "013" "031" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "023" "011" "02123" "023" "032" "023"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "011" "0223" "023" "031"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "023" "032" "0213" "011" "04" "023"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "032" "011" "023" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "023" "04" "032" "023" "031" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "011" "04" "032" "0223" "011" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "023" "0221" "023" "011"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "023" "023" "013" "04" "023" "031"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "011" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "023" "023"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "023" "032" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "031" "02123" "04" "02124" "011" "023"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "023" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "011" "023" "023" "04" "011" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "023" "0221" "0121" "011" "011" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "011" "02124" "023" "04" "011" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "023" "0211" "023"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "031" "011"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "011" "023" "011"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "011" "0223" "011" "04" "02121" "023"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "011" "0221" "0221" "011" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "031" "0121" "011" "04" "011" "023"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "032" "013" "02221" "0121" "023" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "011" "04" "04" "031" "013" "011"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "011" "04" "02223" "02222" "023" "023"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "0122" "011" "013" "02122" "011" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "011" "031" "023" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0122" "011" "0221" "023" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "011" "04" "023" "023" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "011" "0221" "0211" "0122" "011"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "011" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "011" "04" "011" "023"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "031" "04" "023" "04" "04" "023"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "011" "0211" "023" "011" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "023" "0211" "0123" "011" "011" "0122"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "032" "02123" "011" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "023" "0213" "04" "04" "04" "023"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "023" "031" "011"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "023" "011" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "023" "032" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "0122" "023" "011" "0213" "031"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "011" "02121" "02122" "023" "023"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "011" "032" "023" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "023" "0213" "013" "011" "011"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "023" "031" "0221" "011"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "011" "032" "013" "02122" "0121" "032"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "031" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "023" "04" "011" "04" "023" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "011" "011" "011" "011" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "023" "0211" "013" "011" "011"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "023" "02221" "0221" "0122" "011"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "011" "04" "032" "04" "023"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3093))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "023" "023" "0211" "04" "013" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "013" "011" "04" "023" "013"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "0121" "03" "04" "0122" "0122" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "03" "0213" "011" "013"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "023" "023" "0211" "011"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "0121" "011" "011" "023" "023"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "011" "0123" "023" "011" "0121"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "023" "011" "011" "0122" "0211" "023"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "011" "011" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "03" "0221" "02123" "02221" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "0122" "023" "023" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "011" "0213" "04" "023" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "023" "0122" "04" "04" "04" "011"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "023" "023" "013" "03" "023" "011"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "0211" "0211" "04" "0221" "023"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02221" "0223" "0122" "011" "023"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "023" "04" "023" "011"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "011" "011" "023" "04" "011"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "023" "0211" "0121" "0221" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "013" "0122" "011" "03" "03" "023"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "011" "04" "011" "023" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "011" "011" "0211" "0122" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "023" "0221" "011" "023" "04" "011"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "011" "0121" "04" "04" "04" "0121"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "023" "0221" "0221" "03" "023"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "011" "023" "011" "04" "011" "011"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "023" "011" "0122" "0121"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "013" "03" "011" "023" "023" "011"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "023" "011" "023" "013" "03" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "023" "011" "02123" "023" "03" "023"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "011" "0223" "023" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "023" "03" "0213" "011" "04" "023"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "03" "011" "023" "0123" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "023" "04" "03" "023" "03" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "011" "04" "03" "0223" "011" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "023" "0221" "023" "011"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "023" "023" "013" "04" "023" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "0123" "04" "02222" "011" "013" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "0121" "013" "0213" "0221" "023" "023"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "023" "03" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02123" "04" "02124" "011" "023"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "023" "0121" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "011" "023" "023" "04" "011" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "023" "0221" "0121" "011" "011" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "011" "02124" "023" "04" "011" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "023" "0211" "023"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "0123" "02122" "0221" "02123" "03" "011"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "0121" "011" "023" "011"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "011" "0223" "011" "04" "02121" "023"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "011" "0221" "0221" "011" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "0121" "011" "04" "011" "023"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "013" "02221" "0121" "023" "0123"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "011" "04" "04" "03" "013" "011"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "011" "04" "02223" "02222" "023" "023"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "0122" "011" "013" "02122" "011" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "011" "03" "023" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0122" "011" "0221" "023" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "011" "04" "023" "023" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "011" "0221" "0211" "0122" "011"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "013" "02121" "02124" "011" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "011" "04" "011" "023"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "023" "04" "04" "023"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "011" "0211" "023" "011" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "023" "0211" "0123" "011" "011" "0122"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02123" "011" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "023" "0213" "04" "04" "04" "023"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "013" "04" "023" "03" "011"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "0121" "023" "011" "0121"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "023" "03" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "013" "0122" "023" "011" "0213" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "011" "02121" "02122" "023" "023"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "011" "03" "023" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "013" "023" "0213" "013" "011" "011"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "013" "04" "023" "03" "0221" "011"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "011" "03" "013" "02122" "0121" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "03" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "023" "04" "011" "04" "023" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "011" "011" "011" "011" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "023" "0211" "013" "011" "011"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "023" "02221" "0221" "0122" "011"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "011" "04" "03" "04" "023"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3141))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "023" "023" "0211" "04" "01" "0211"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "023" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "0211" "0221" "03" "0213" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "023" "023" "0211" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "0213" "0221" "02221" "02123" "04" "0221"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "023" "023"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "023" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "023" "01" "01" "01" "0211" "023"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "0221" "04" "04" "01" "01" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "0213" "03" "0221" "02123" "02221" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "023" "023" "0211" "0223" "0223"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "0213" "04" "023" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "023" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "023" "023" "01" "03" "023" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "0211" "0211" "04" "0221" "023"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02221" "0223" "01" "01" "023"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "023" "04" "023" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "023" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "023" "0211" "01" "0221" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "023"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "023" "0221"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "0211" "01" "0211"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "023" "0221" "01" "023" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "0221" "023" "0221" "0221" "03" "023"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "023" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "023" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "023" "023" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "023" "01" "023" "01" "03" "0211"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "023" "01" "02123" "023" "03" "023"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "01" "0223" "023" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "023" "03" "0213" "01" "04" "023"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "0211" "03" "01" "023" "01" "0223"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "023" "04" "03" "023" "03" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "0223" "01" "0221"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "0213" "0213" "023" "0221" "023" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "023" "023" "01" "04" "023" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02222" "01" "01" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "0213" "0221" "023" "023"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "023" "03" "02122" "0223" "04" "0221"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02123" "04" "02124" "01" "023"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "0211" "0223" "023" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "023" "023" "04" "01" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "023" "0221" "01" "01" "01" "0223"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02124" "023" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "0213" "0211" "023" "0211" "023"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02122" "0221" "02123" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "023" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "0223" "01" "04" "02121" "023"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "0221" "01" "0221" "0221" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "023"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02221" "01" "023" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02223" "02222" "023" "023"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02122" "01" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "023" "02221" "0211" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "0221" "023" "0213" "0211"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "023" "023" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "01" "0221" "0211" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "0223" "01" "02121" "02124" "01" "0221"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "023"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "023" "04" "04" "023"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "0211" "023" "01" "04" "0211"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "023" "0211" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02123" "01" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "023" "0213" "04" "04" "04" "023"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "0213" "01" "04" "023" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "0221" "01" "023" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "0211" "0213" "0211" "023" "03" "0213"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "023" "01" "0213" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "01" "02121" "02122" "023" "023"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "01" "03" "023" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "023" "0213" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "023" "03" "0221" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02122" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "03" "0221" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "023" "04" "01" "04" "023" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "0211" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "0221" "023" "0211" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "0211" "023" "02221" "0221" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "01" "04" "03" "04" "023"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3199))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02221" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02221" "02123" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02221"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02123" "02221" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02221" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02221" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02221" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02123" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02221" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02222" "01" "01" "02223"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02122" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02123" "04" "02124" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02124" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02221" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02122" "02" "02123" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02121" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02221" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02223" "02222" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02122" "01" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02221" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02221"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02222" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02121" "02124" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02123" "01" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "01" "02121" "02122" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02222" "02122" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02122" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "03" "02" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02222"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02221" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02221" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3497))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02123" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02123" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02123" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02123"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02122" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02123" "04" "02124" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02124"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02124" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02122" "02" "02123" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02121" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02122" "01" "02121"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02121" "02124" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02123" "01" "02121" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02122" "01" "02121" "02122" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02122" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02122" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02121" "04" "04" "03" "02" "02122"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3568))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02" "04" "02" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02" "02" "02" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02" "01" "02"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02" "01" "02" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02" "04" "04" "03" "02" "02"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3755))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02" "04" "02" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02" "02" "02" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02" "01" "02"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02" "01" "02" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02" "04" "04" "03" "02" "02"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3921))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02" "04" "02" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02" "02" "02" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02" "01" "02"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02" "01" "02" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02" "04" "04" "03" "02" "02"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4296))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02" "04" "02" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02" "02" "02" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02" "01" "02"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02" "01" "02" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02" "04" "04" "03" "02" "02"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5918))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02" "04" "02" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02" "02" "02" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02" "01" "02"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02" "01" "02" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02" "04" "04" "03" "02" "02"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8709))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02" "04" "02" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02" "02" "02" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02" "01" "02"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02" "01" "02" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02" "04" "04" "03" "02" "02"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 19867))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.86.8278.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.97.A4M1.01 TCGA.55.6975.01 TCGA.99.8033.01 TCGA.78.7149.01 TCGA.50.6597.01 TCGA.69.8255.01
#> "03" "01" "01" "04" "02" "01"
#> TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.78.7162.01 TCGA.75.7025.01 TCGA.44.2659.11
#> "01" "03" "04" "01" "01" "03"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.55.8096.01 TCGA.93.A4JQ.01
#> "02" "02" "03" "02" "01" "01"
#> TCGA.86.6851.01 TCGA.62.8398.01 TCGA.J2.A4AG.01 TCGA.MP.A4TK.01 TCGA.L9.A443.01 TCGA.55.8208.01
#> "02" "04" "02" "02" "02" "01"
#> TCGA.MN.A4N5.01 TCGA.64.5775.01 TCGA.62.8394.01 TCGA.05.4405.01 TCGA.97.8176.01 TCGA.05.5428.01
#> "02" "02" "02" "02" "04" "02"
#> TCGA.50.5931.01 TCGA.49.AAR4.01 TCGA.64.1679.01 TCGA.55.6984.01 TCGA.MN.A4N1.01 TCGA.91.6847.01
#> "04" "01" "01" "01" "02" "02"
#> TCGA.86.8358.01 TCGA.49.AARO.01 TCGA.75.6206.01 TCGA.MP.A4TC.01 TCGA.49.6744.01 TCGA.L9.A743.01
#> "04" "01" "01" "02" "01" "01"
#> TCGA.05.4410.01 TCGA.86.7954.01 TCGA.55.7910.01 TCGA.64.5778.01 TCGA.62.A46Y.01 TCGA.55.6982.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.55.6642.01 TCGA.44.6144.01 TCGA.05.4415.01 TCGA.44.A479.01 TCGA.55.8087.01 TCGA.50.6673.01
#> "02" "04" "04" "01" "01" "02"
#> TCGA.55.8207.01 TCGA.44.2662.11 TCGA.86.6562.01 TCGA.05.4425.01 TCGA.86.8074.01 TCGA.50.5930.11
#> "02" "03" "02" "02" "02" "03"
#> TCGA.55.8091.01 TCGA.55.7727.01 TCGA.MP.A4SW.01 TCGA.67.6216.01 TCGA.55.8203.01 TCGA.J2.8194.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.44.2668.01 TCGA.44.7660.01 TCGA.55.A57B.01 TCGA.55.8507.01
#> "04" "01" "02" "04" "02" "04"
#> TCGA.NJ.A4YI.01 TCGA.49.AAR0.01 TCGA.86.8281.01 TCGA.91.6831.01 TCGA.75.7027.01 TCGA.44.A4SU.01
#> "02" "01" "04" "04" "04" "01"
#> TCGA.L9.A444.01 TCGA.86.8668.01 TCGA.50.5072.01 TCGA.55.8512.01 TCGA.44.A47G.01 TCGA.91.6849.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.44.6146.11 TCGA.55.6986.01 TCGA.44.2665.01 TCGA.86.8279.01 TCGA.05.5425.01 TCGA.62.A46R.01
#> "03" "02" "02" "04" "02" "02"
#> TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.69.8254.01 TCGA.53.7624.01 TCGA.75.5125.01
#> "03" "02" "02" "01" "01" "02"
#> TCGA.86.8054.01 TCGA.L4.A4E5.01 TCGA.44.6775.01 TCGA.55.7913.01 TCGA.55.7911.01 TCGA.55.8621.01
#> "04" "02" "02" "04" "02" "01"
#> TCGA.49.6745.11 TCGA.S2.AA1A.01 TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.78.8640.01 TCGA.44.7670.01
#> "03" "01" "01" "02" "04" "01"
#> TCGA.69.7760.01 TCGA.95.7948.01 TCGA.97.A4M5.01 TCGA.55.A4DG.01 TCGA.55.7816.01 TCGA.50.6593.11
#> "02" "02" "01" "02" "03" "03"
#> TCGA.86.7711.01 TCGA.05.5423.01 TCGA.MP.A4TJ.01 TCGA.44.2656.11 TCGA.44.6778.11 TCGA.55.6985.01
#> "01" "01" "01" "03" "03" "02"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.55.8615.01 TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.91.6829.01
#> "03" "01" "04" "01" "02" "02"
#> TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01 TCGA.99.7458.01 TCGA.91.A4BD.01 TCGA.38.6178.01
#> "04" "01" "01" "02" "01" "02"
#> TCGA.44.A47B.01 TCGA.78.7542.01 TCGA.55.7573.01 TCGA.05.5429.01 TCGA.78.7633.01 TCGA.86.7953.01
#> "02" "02" "01" "02" "04" "01"
#> TCGA.55.6970.01 TCGA.78.7160.01 TCGA.50.5946.02 TCGA.50.5946.01 TCGA.50.5066.02 TCGA.50.5066.01
#> "01" "01" "04" "04" "04" "01"
#> TCGA.97.8179.01 TCGA.86.A4JF.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.44.2665.11 TCGA.75.5122.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.97.7938.01 TCGA.49.AARE.01 TCGA.55.7726.01 TCGA.91.8499.01 TCGA.MP.A4TH.01 TCGA.91.8496.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.69.7764.01 TCGA.95.7043.01 TCGA.86.7701.01 TCGA.49.4512.01 TCGA.L9.A50W.01 TCGA.50.8460.01
#> "04" "02" "02" "01" "01" "01"
#> TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.55.7281.01 TCGA.78.7535.01 TCGA.86.8671.01
#> "01" "03" "01" "02" "02" "01"
#> TCGA.50.6592.01 TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.97.A4M0.01
#> "02" "01" "02" "01" "03" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.78.7153.01 TCGA.78.8660.01 TCGA.44.2655.11 TCGA.55.7907.01
#> "02" "01" "02" "02" "03" "02"
#> TCGA.49.6767.01 TCGA.78.7155.01 TCGA.91.6835.01 TCGA.50.5051.01 TCGA.78.7540.01 TCGA.50.5939.11
#> "02" "04" "01" "02" "02" "03"
#> TCGA.95.A4VN.01 TCGA.44.6145.11 TCGA.44.A47F.01 TCGA.55.A48Z.01 TCGA.44.8119.01 TCGA.69.8253.01
#> "02" "03" "02" "01" "04" "02"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.50.5942.01 TCGA.50.6590.01 TCGA.78.7148.01 TCGA.80.5608.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.55.8205.01 TCGA.44.7669.01 TCGA.50.6594.11 TCGA.99.8025.01 TCGA.44.2668.11 TCGA.55.7283.01
#> "02" "04" "03" "02" "03" "02"
#> TCGA.91.6830.01 TCGA.86.8055.01 TCGA.49.4488.11 TCGA.78.7159.01 TCGA.44.6774.01 TCGA.44.8120.01
#> "01" "04" "03" "02" "01" "02"
#> TCGA.69.7763.01 TCGA.64.5815.01 TCGA.69.7761.01 TCGA.73.A9RS.01 TCGA.69.7978.01 TCGA.55.8299.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01 TCGA.55.A490.01 TCGA.83.5908.01 TCGA.55.6980.01
#> "02" "02" "01" "04" "02" "03"
#> TCGA.44.6146.01 TCGA.86.8669.01 TCGA.95.7039.01 TCGA.62.8397.01 TCGA.91.6848.01 TCGA.71.6725.01
#> "01" "04" "02" "01" "01" "02"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.91.7771.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.78.7146.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.69.7974.01 TCGA.78.7161.01 TCGA.55.8614.01 TCGA.97.7937.01
#> "02" "03" "02" "02" "04" "02"
#> TCGA.49.AARR.01 TCGA.62.A46V.01 TCGA.75.5147.01 TCGA.49.6745.01 TCGA.55.6979.01 TCGA.55.8089.01
#> "03" "02" "04" "02" "01" "02"
#> TCGA.55.8094.01 TCGA.55.7574.01 TCGA.44.5644.01 TCGA.55.8511.01 TCGA.50.8459.01 TCGA.44.7671.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.78.8648.01 TCGA.91.A4BC.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.49.6743.01 TCGA.86.8673.01
#> "01" "02" "02" "04" "01" "02"
#> TCGA.73.7499.01 TCGA.L9.A7SV.01 TCGA.97.A4LX.01 TCGA.38.4631.01 TCGA.99.AA5R.01 TCGA.05.4390.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.MP.A4T7.01 TCGA.69.7765.01 TCGA.95.8494.01 TCGA.97.8171.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "01" "02" "02" "04" "01" "04"
#> TCGA.69.7979.01 TCGA.62.A46P.01 TCGA.78.7158.01 TCGA.69.7980.01 TCGA.97.8547.01 TCGA.05.4433.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.50.5932.01 TCGA.97.8175.01 TCGA.50.7109.01 TCGA.44.A47A.01 TCGA.73.4676.11 TCGA.NJ.A55O.01
#> "01" "02" "02" "02" "03" "01"
#> TCGA.55.8508.01 TCGA.78.7220.01 TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.44.6147.01 TCGA.86.8075.01
#> "04" "04" "01" "01" "02" "01"
#> TCGA.55.7724.01 TCGA.75.6211.01 TCGA.55.8510.01 TCGA.55.8085.01 TCGA.55.8090.01 TCGA.86.8073.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.91.6828.01 TCGA.49.4514.01 TCGA.05.4396.01 TCGA.MN.A4N4.01 TCGA.55.8204.01 TCGA.44.5643.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.75.7031.01 TCGA.50.5044.01 TCGA.64.5781.01
#> "03" "01" "01" "04" "01" "02"
#> TCGA.73.4658.11 TCGA.05.5420.01 TCGA.NJ.A4YF.01 TCGA.49.AAR3.01 TCGA.78.7154.01 TCGA.05.4384.01
#> "03" "01" "02" "01" "02" "01"
#> TCGA.55.6971.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.50.5939.01 TCGA.O1.A52J.01
#> "01" "04" "04" "03" "01" "01"
#> TCGA.91.8497.01 TCGA.78.7167.01 TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.MP.A4T2.01 TCGA.86.7714.01 TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01
#> "01" "01" "01" "02" "01" "02"
#> TCGA.49.4487.01 TCGA.50.5933.11 TCGA.55.A493.01 TCGA.78.7147.01 TCGA.75.5126.01 TCGA.50.6591.01
#> "01" "03" "02" "02" "02" "04"
#> TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.NJ.A4YQ.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.55.8514.01 TCGA.50.5944.01 TCGA.49.AAR9.01 TCGA.50.6594.01 TCGA.86.8056.01 TCGA.95.A4VK.01
#> "04" "01" "04" "02" "02" "02"
#> TCGA.49.4488.01 TCGA.55.7728.01 TCGA.55.7994.01 TCGA.67.6215.01 TCGA.78.7537.01 TCGA.55.8097.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.MP.A5C7.01 TCGA.05.4424.01 TCGA.55.7227.01 TCGA.MP.A4TI.01 TCGA.44.5645.01 TCGA.35.5375.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.75.6214.01 TCGA.80.5611.01 TCGA.49.AAQV.01 TCGA.49.6742.01 TCGA.73.7498.01 TCGA.38.4632.01
#> "04" "04" "01" "04" "01" "02"
#> TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.MP.A4T6.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "03" "04" "02" "04" "04" "02"
#> TCGA.97.7547.01 TCGA.86.A4P7.01 TCGA.49.6761.01 TCGA.93.7348.01 TCGA.99.8032.01 TCGA.50.5935.01
#> "01" "02" "02" "01" "04" "02"
#> TCGA.55.6981.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.97.8174.01
#> "02" "02" "01" "01" "01" "01"
#> TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.91.6840.01 TCGA.62.A472.01 TCGA.64.5779.01
#> "04" "03" "02" "01" "02" "04"
#> TCGA.05.4417.01 TCGA.67.4679.01 TCGA.64.5774.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.97.7554.01
#> "02" "02" "04" "04" "04" "02"
#> TCGA.MP.A4SY.01 TCGA.93.A4JP.01 TCGA.55.5899.01 TCGA.95.8039.01 TCGA.44.6144.11 TCGA.50.5941.01
#> "02" "01" "04" "02" "03" "01"
#> TCGA.62.8399.01 TCGA.95.7562.01 TCGA.75.7030.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01
#> "04" "02" "01" "02" "01" "01"
#> TCGA.80.5607.01 TCGA.93.8067.01 TCGA.62.8395.01 TCGA.86.8672.01 TCGA.75.6212.01 TCGA.44.2666.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.50.5930.01 TCGA.55.7284.01 TCGA.44.6777.01 TCGA.44.6776.01 TCGA.55.6983.01 TCGA.50.5932.11
#> "01" "01" "02" "01" "02" "03"
#> TCGA.69.A59K.01 TCGA.50.5055.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.73.4676.01 TCGA.91.6836.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.55.8616.01 TCGA.38.7271.01 TCGA.50.5045.01 TCGA.44.6147.11 TCGA.55.A491.01 TCGA.78.7150.01
#> "02" "02" "01" "03" "02" "04"
#> TCGA.86.8674.01 TCGA.55.6978.01 TCGA.NJ.A4YG.01 TCGA.44.A4SS.01 TCGA.55.A492.01 TCGA.53.7626.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.55.6969.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11 TCGA.MP.A4SV.01 TCGA.50.6595.01
#> "01" "04" "02" "03" "02" "01"
#> TCGA.55.6543.01 TCGA.50.6592.11 TCGA.50.5049.01 TCGA.73.4658.01 TCGA.97.A4M2.01 TCGA.55.8513.01
#> "01" "03" "01" "02" "01" "03"
#> TCGA.44.7659.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.NJ.A55R.01 TCGA.86.A456.01
#> "02" "04" "04" "03" "02" "02"
#> TCGA.97.A4M7.01 TCGA.78.7536.01 TCGA.L9.A8F4.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01
#> "02" "04" "01" "04" "02" "02"
#> TCGA.50.5068.01 TCGA.MP.A4T4.01 TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.71.8520.01 TCGA.86.7955.01
#> "01" "01" "01" "01" "02" "04"
#> TCGA.55.7815.01 TCGA.44.7672.01 TCGA.97.8172.01 TCGA.55.6987.01 TCGA.64.1681.01 TCGA.95.A4VP.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.05.5715.01 TCGA.78.7152.01 TCGA.78.7539.01 TCGA.62.A46S.01 TCGA.95.7947.01 TCGA.J2.8192.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.78.7145.01 TCGA.50.6593.01 TCGA.69.7973.01 TCGA.50.6591.11 TCGA.86.7713.01 TCGA.55.8302.01
#> "02" "01" "04" "03" "04" "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 = 1363),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1363),
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 = 1365),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1365),
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 = 1644),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1644),
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 = 2248),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2248),
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 = 2566),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2566),
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 = 2965),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2965),
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 = 3054),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3054),
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 = 3093),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3093),
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 = 3141),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3141),
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 = 3199),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3199),
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 = 3497),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3497),
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 = 3568),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3568),
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 = 3755),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3755),
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 = 3921),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3921),
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 = 4296),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4296),
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 = 5918),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5918),
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 = 8709),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8709),
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 = 19867),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 19867),
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 = 1363))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1365))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1644))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2248))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2566))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2965))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3054))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3093))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3141))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3199))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3497))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3568))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3755))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3921))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4296))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5918))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8709))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 19867))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 , Node04-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 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 492 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.988 0.995 0.4490 0.552 0.552
#> 3 3 1.000 0.972 0.989 0.2881 0.717 0.549
#> 4 4 0.993 0.958 0.984 0.1671 0.857 0.680
#> 5 5 0.784 0.853 0.922 0.1427 0.819 0.508
#> 6 6 0.901 0.895 0.949 0.0573 0.887 0.569
#> 7 7 0.899 0.859 0.927 0.0220 0.954 0.765
#> 8 8 0.884 0.779 0.891 0.0207 0.965 0.799
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 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.44.4112.01 2 0.000 0.996 0.00 1.00
#> TCGA.NJ.A4YP.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8278.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A470.01 2 0.904 0.528 0.32 0.68
#> TCGA.44.6778.01 1 0.000 0.994 1.00 0.00
#> TCGA.49.AARQ.01 2 0.000 0.996 0.00 1.00
#> TCGA.97.A4M1.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.6975.01 2 0.402 0.910 0.08 0.92
#> TCGA.99.8033.01 1 0.000 0.994 1.00 0.00
#> TCGA.78.7149.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.6597.01 2 0.000 0.996 0.00 1.00
#> TCGA.69.8255.01 1 0.000 0.994 1.00 0.00
#> TCGA.69.8453.01 2 0.000 0.996 0.00 1.00
#> TCGA.97.8552.01 1 0.000 0.994 1.00 0.00
#> TCGA.53.A4EZ.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7162.01 1 0.000 0.994 1.00 0.00
#> TCGA.75.7025.01 1 0.000 0.994 1.00 0.00
#> TCGA.44.2659.11 1 0.000 0.994 1.00 0.00
#> TCGA.62.A46U.01 2 0.000 0.996 0.00 1.00
#> TCGA.MP.A4T8.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.5645.11 1 0.000 0.994 1.00 0.00
#> TCGA.93.A4JN.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8096.01 1 0.000 0.994 1.00 0.00
#> TCGA.93.A4JQ.01 1 0.000 0.994 1.00 0.00
#> TCGA.86.6851.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.8398.01 1 0.000 0.994 1.00 0.00
#> TCGA.J2.A4AG.01 2 0.000 0.996 0.00 1.00
#> TCGA.MP.A4TK.01 2 0.000 0.996 0.00 1.00
#> TCGA.L9.A443.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8208.01 1 0.000 0.994 1.00 0.00
#> TCGA.MN.A4N5.01 2 0.000 0.996 0.00 1.00
#> TCGA.64.5775.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.8394.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.4405.01 2 0.000 0.996 0.00 1.00
#> TCGA.97.8176.01 1 0.000 0.994 1.00 0.00
#> TCGA.05.5428.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5931.01 1 0.000 0.994 1.00 0.00
#> TCGA.49.AAR4.01 2 0.000 0.996 0.00 1.00
#> TCGA.64.1679.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.6984.01 2 0.000 0.996 0.00 1.00
#> TCGA.MN.A4N1.01 2 0.000 0.996 0.00 1.00
#> TCGA.91.6847.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8358.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.AARO.01 2 0.000 0.996 0.00 1.00
#> TCGA.75.6206.01 1 0.000 0.994 1.00 0.00
#> TCGA.MP.A4TC.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.6744.01 2 0.000 0.996 0.00 1.00
#> TCGA.L9.A743.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.4410.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.7954.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.7910.01 1 0.000 0.994 1.00 0.00
#> TCGA.64.5778.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A46Y.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6982.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6642.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.6144.01 1 0.000 0.994 1.00 0.00
#> TCGA.05.4415.01 1 0.795 0.688 0.76 0.24
#> TCGA.44.A479.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.8087.01 1 0.000 0.994 1.00 0.00
#> TCGA.50.6673.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8207.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.2662.11 1 0.000 0.994 1.00 0.00
#> TCGA.86.6562.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.4425.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8074.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5930.11 1 0.000 0.994 1.00 0.00
#> TCGA.55.8091.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.7727.01 2 0.000 0.996 0.00 1.00
#> TCGA.MP.A4SW.01 2 0.000 0.996 0.00 1.00
#> TCGA.67.6216.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8203.01 2 0.000 0.996 0.00 1.00
#> TCGA.J2.8194.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6968.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8619.01 1 0.000 0.994 1.00 0.00
#> TCGA.44.2668.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.7660.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.A57B.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8507.01 2 0.000 0.996 0.00 1.00
#> TCGA.NJ.A4YI.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.AAR0.01 1 0.000 0.994 1.00 0.00
#> TCGA.86.8281.01 2 0.000 0.996 0.00 1.00
#> TCGA.91.6831.01 2 0.000 0.996 0.00 1.00
#> TCGA.75.7027.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.A4SU.01 2 0.971 0.331 0.40 0.60
#> TCGA.L9.A444.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8668.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5072.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.8512.01 1 0.000 0.994 1.00 0.00
#> TCGA.44.A47G.01 2 0.000 0.996 0.00 1.00
#> TCGA.91.6849.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.6146.11 1 0.000 0.994 1.00 0.00
#> TCGA.55.6986.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.2665.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8279.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.5425.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A46R.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.6148.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.A494.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.3917.01 2 0.000 0.996 0.00 1.00
#> TCGA.69.8254.01 2 0.000 0.996 0.00 1.00
#> TCGA.53.7624.01 1 0.000 0.994 1.00 0.00
#> TCGA.75.5125.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8054.01 2 0.000 0.996 0.00 1.00
#> TCGA.L4.A4E5.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.6775.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.7913.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.7911.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8621.01 1 0.000 0.994 1.00 0.00
#> TCGA.49.6745.11 1 0.000 0.994 1.00 0.00
#> TCGA.S2.AA1A.01 1 0.000 0.994 1.00 0.00
#> TCGA.MP.A4T9.01 1 0.000 0.994 1.00 0.00
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#> TCGA.75.6212.01 1 0.000 0.994 1.00 0.00
#> TCGA.44.2666.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5930.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.7284.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.6777.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.6776.01 1 0.680 0.783 0.82 0.18
#> TCGA.55.6983.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5932.11 1 0.000 0.994 1.00 0.00
#> TCGA.69.A59K.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5055.01 1 0.000 0.994 1.00 0.00
#> TCGA.95.7567.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.AARN.01 2 0.000 0.996 0.00 1.00
#> TCGA.73.4676.01 2 0.000 0.996 0.00 1.00
#> TCGA.91.6836.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8616.01 2 0.000 0.996 0.00 1.00
#> TCGA.38.7271.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5045.01 1 0.000 0.994 1.00 0.00
#> TCGA.44.6147.11 1 0.000 0.994 1.00 0.00
#> TCGA.55.A491.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7150.01 1 0.000 0.994 1.00 0.00
#> TCGA.86.8674.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.6978.01 2 0.000 0.996 0.00 1.00
#> TCGA.NJ.A4YG.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.A4SS.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.A492.01 2 0.000 0.996 0.00 1.00
#> TCGA.53.7626.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6969.01 1 0.634 0.811 0.84 0.16
#> TCGA.78.7166.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.A48Y.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.5643.11 1 0.000 0.994 1.00 0.00
#> TCGA.MP.A4SV.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.6595.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.6543.01 1 0.000 0.994 1.00 0.00
#> TCGA.50.6592.11 1 0.000 0.994 1.00 0.00
#> TCGA.50.5049.01 2 0.000 0.996 0.00 1.00
#> TCGA.73.4658.01 2 0.000 0.996 0.00 1.00
#> TCGA.97.A4M2.01 1 0.000 0.994 1.00 0.00
#> TCGA.55.8513.01 1 0.000 0.994 1.00 0.00
#> TCGA.44.7659.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.8402.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.7995.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.5420.11 1 0.000 0.994 1.00 0.00
#> TCGA.NJ.A55R.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.A456.01 2 0.000 0.996 0.00 1.00
#> TCGA.97.A4M7.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7536.01 2 0.000 0.996 0.00 1.00
#> TCGA.L9.A8F4.01 1 0.000 0.994 1.00 0.00
#> TCGA.78.7156.01 1 0.000 0.994 1.00 0.00
#> TCGA.44.7662.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8506.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.5068.01 2 0.000 0.996 0.00 1.00
#> TCGA.MP.A4T4.01 2 0.000 0.996 0.00 1.00
#> TCGA.53.7813.01 2 0.000 0.996 0.00 1.00
#> TCGA.NJ.A55A.01 1 0.000 0.994 1.00 0.00
#> TCGA.71.8520.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.7955.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.7815.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.7672.01 2 0.000 0.996 0.00 1.00
#> TCGA.97.8172.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6987.01 2 0.000 0.996 0.00 1.00
#> TCGA.64.1681.01 1 0.000 0.994 1.00 0.00
#> TCGA.95.A4VP.01 1 0.000 0.994 1.00 0.00
#> TCGA.05.5715.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7152.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7539.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A46S.01 2 0.000 0.996 0.00 1.00
#> TCGA.95.7947.01 2 0.000 0.996 0.00 1.00
#> TCGA.J2.8192.01 1 0.000 0.994 1.00 0.00
#> TCGA.78.7145.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.6593.01 2 0.000 0.996 0.00 1.00
#> TCGA.69.7973.01 2 0.000 0.996 0.00 1.00
#> TCGA.50.6591.11 1 0.000 0.994 1.00 0.00
#> TCGA.86.7713.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8302.01 2 0.000 0.996 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.4112.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.NJ.A4YP.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8278.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.62.A470.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.44.6778.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.49.AARQ.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.97.A4M1.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.55.6975.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.99.8033.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.78.7149.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.6597.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.69.8255.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.69.8453.01 1 0.4291 0.732 0.82 0.18 0.00
#> TCGA.97.8552.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.53.A4EZ.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.78.7162.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.75.7025.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.44.2659.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.62.A46U.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.MP.A4T8.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.5645.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.93.A4JN.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8096.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.86.6851.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.62.8398.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.J2.A4AG.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.MP.A4TK.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.L9.A443.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8208.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.MN.A4N5.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.64.5775.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.62.8394.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.05.4405.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.97.8176.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.05.5428.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.5931.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.49.AAR4.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.64.1679.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.6984.01 2 0.0892 0.971 0.02 0.98 0.00
#> TCGA.MN.A4N1.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.91.6847.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8358.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.49.AARO.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.75.6206.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.MP.A4TC.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.49.6744.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.L9.A743.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.05.4410.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.7954.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.7910.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.64.5778.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.62.A46Y.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.6982.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.6642.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.6144.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.05.4415.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.44.A479.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.50.6673.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8207.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.2662.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.86.6562.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.05.4425.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8074.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.5930.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.55.8091.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.7727.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.MP.A4SW.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.67.6216.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8203.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.J2.8194.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.6968.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8619.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.44.2668.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.7660.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.A57B.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8507.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.NJ.A4YI.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.49.AAR0.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.86.8281.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.91.6831.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.75.7027.01 1 0.1529 0.934 0.96 0.04 0.00
#> TCGA.44.A4SU.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.L9.A444.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8668.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.5072.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.8512.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.44.A47G.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.91.6849.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.44.6146.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.55.6986.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.2665.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8279.01 2 0.0892 0.971 0.02 0.98 0.00
#> TCGA.05.5425.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.62.A46R.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.6148.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.55.A494.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.3917.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.69.8254.01 2 0.2066 0.922 0.06 0.94 0.00
#> TCGA.53.7624.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.75.5125.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8054.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.L4.A4E5.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.6775.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.7913.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.7911.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8621.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.49.6745.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.S2.AA1A.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.MP.A4T9.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.6712.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.8640.01 2 0.2066 0.925 0.06 0.94 0.00
#> TCGA.44.7670.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.95.7948.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.97.A4M5.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.55.A4DG.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.7816.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.50.6593.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.86.7711.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.05.5423.01 1 0.4555 0.699 0.80 0.20 0.00
#> TCGA.MP.A4TJ.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.44.2656.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.44.6778.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.55.6985.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.38.4631.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.L9.A5IP.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.8615.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.93.7347.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.MP.A4TF.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.91.6829.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.62.A471.01 1 0.5706 0.480 0.68 0.32 0.00
#> TCGA.49.4490.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.97.8177.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.99.7458.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.91.A4BD.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.38.6178.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.A47B.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.7542.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.7573.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.05.5429.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.7633.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.86.7953.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.6970.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.50.5946.02 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.50.5946.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.50.5066.02 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.5066.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.97.8179.01 2 0.0892 0.971 0.02 0.98 0.00
#> TCGA.86.A4JF.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8092.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.2665.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.75.5122.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.97.7938.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.49.AARE.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.7726.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.91.8499.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.MP.A4TH.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.69.7764.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.95.7043.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.7701.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.49.4512.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.L9.A50W.01 1 0.3340 0.826 0.88 0.12 0.00
#> TCGA.50.8460.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.55.8505.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.86.A4P8.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.67.6217.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.55.7281.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.7535.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8671.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.50.6592.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.97.7546.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.44.7661.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.95.7944.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.38.4632.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.97.A4M0.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.5933.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.86.8280.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.78.7153.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.2655.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.55.7907.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.49.6767.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.7155.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.91.6835.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.5051.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.7540.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.5939.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.95.A4VN.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.6145.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.44.A47F.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.A48Z.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.44.8119.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.69.8253.01 2 0.2066 0.922 0.06 0.94 0.00
#> TCGA.J2.A4AE.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.75.6203.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.50.5942.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.50.6590.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.78.7148.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.80.5608.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.55.8205.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.7669.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.50.6594.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.99.8025.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.44.2668.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.55.7283.01 2 0.0000 0.993 0.00 1.00 0.00
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#> TCGA.62.A46S.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.95.7947.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.J2.8192.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.78.7145.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.50.6593.01 2 0.0892 0.971 0.02 0.98 0.00
#> TCGA.69.7973.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.50.6591.11 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.86.7713.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.8302.01 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.44.4112.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.NJ.A4YP.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8278.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.62.A470.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.44.6778.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.49.AARQ.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.97.A4M1.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.55.6975.01 1 0.4790 0.3875 0.62 0.00 0.00 0.38
#> TCGA.99.8033.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.78.7149.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.50.6597.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.69.8255.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.69.8453.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.97.8552.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.53.A4EZ.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.78.7162.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.75.7025.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.2659.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.62.A46U.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T8.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.5645.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.93.A4JN.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8096.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.86.6851.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.62.8398.01 4 0.1211 0.9328 0.04 0.00 0.00 0.96
#> TCGA.J2.A4AG.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TK.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.L9.A443.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8208.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.MN.A4N5.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.64.5775.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.62.8394.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.05.4405.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.97.8176.01 4 0.0707 0.9505 0.02 0.00 0.00 0.98
#> TCGA.05.5428.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.50.5931.01 4 0.2345 0.8636 0.10 0.00 0.00 0.90
#> TCGA.49.AAR4.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.64.1679.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.6984.01 1 0.1211 0.9266 0.96 0.04 0.00 0.00
#> TCGA.MN.A4N1.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.91.6847.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8358.01 4 0.0707 0.9451 0.00 0.02 0.00 0.98
#> TCGA.49.AARO.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.49.6744.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.05.4410.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.7954.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.7910.01 1 0.3801 0.7129 0.78 0.00 0.00 0.22
#> TCGA.64.5778.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.62.A46Y.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.6982.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.6642.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.6144.01 4 0.2921 0.8113 0.14 0.00 0.00 0.86
#> TCGA.05.4415.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.44.A479.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.50.6673.01 2 0.0707 0.9663 0.00 0.98 0.00 0.02
#> TCGA.55.8207.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.2662.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.86.6562.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.05.4425.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8074.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.50.5930.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.55.8091.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.7727.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.67.6216.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8203.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.J2.8194.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.6968.01 4 0.4134 0.5664 0.00 0.26 0.00 0.74
#> TCGA.55.8619.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.2668.01 2 0.4624 0.4792 0.34 0.66 0.00 0.00
#> TCGA.44.7660.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.55.A57B.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8507.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.NJ.A4YI.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.49.AAR0.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.86.8281.01 4 0.3610 0.7200 0.20 0.00 0.00 0.80
#> TCGA.91.6831.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.75.7027.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.44.A4SU.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.L9.A444.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8668.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.50.5072.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.8512.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.44.A47G.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.91.6849.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.6146.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.55.6986.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.2665.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8279.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.05.5425.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.62.A46R.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.6148.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.55.A494.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.3917.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.69.8254.01 1 0.0707 0.9508 0.98 0.02 0.00 0.00
#> TCGA.53.7624.01 1 0.4713 0.4379 0.64 0.00 0.00 0.36
#> TCGA.75.5125.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8054.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.L4.A4E5.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.6775.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.7913.01 4 0.3172 0.7800 0.16 0.00 0.00 0.84
#> TCGA.55.7911.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8621.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.49.6745.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T9.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.6712.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.8640.01 4 0.0707 0.9451 0.00 0.02 0.00 0.98
#> TCGA.44.7670.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.95.7948.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.97.A4M5.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.A4DG.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.7816.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.50.6593.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.86.7711.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.05.5423.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TJ.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.2656.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.44.6778.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.55.6985.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.38.4631.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.L9.A5IP.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.8615.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.93.7347.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TF.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.91.6829.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.62.A471.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.49.4490.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.97.8177.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.99.7458.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.91.A4BD.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.38.6178.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.A47B.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7542.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.7573.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.05.5429.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7633.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.86.7953.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.6970.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.50.5946.02 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.50.5946.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.50.5066.02 4 0.0707 0.9452 0.00 0.02 0.00 0.98
#> TCGA.50.5066.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.97.8179.01 2 0.4406 0.5705 0.00 0.70 0.00 0.30
#> TCGA.86.A4JF.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8092.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.2665.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.75.5122.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.97.7938.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.49.AARE.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.7726.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.91.8499.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.MP.A4TH.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.69.7764.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.95.7043.01 2 0.1211 0.9463 0.00 0.96 0.00 0.04
#> TCGA.86.7701.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.49.4512.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 1 0.2011 0.8757 0.92 0.08 0.00 0.00
#> TCGA.50.8460.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.8505.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.86.A4P8.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.67.6217.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.7281.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7535.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8671.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.50.6592.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.97.7546.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.7661.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.95.7944.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.38.4632.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.50.5933.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.86.8280.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.78.7153.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.2655.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.55.7907.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.49.6767.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7155.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.91.6835.01 1 0.1637 0.9014 0.94 0.06 0.00 0.00
#> TCGA.50.5051.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7540.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.50.5939.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.95.A4VN.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.6145.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.44.A47F.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.A48Z.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.8119.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.69.8253.01 2 0.4994 0.0636 0.48 0.52 0.00 0.00
#> TCGA.J2.A4AE.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.75.6203.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.50.5942.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.50.6590.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7148.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.80.5608.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8205.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.7669.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.50.6594.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.2668.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.91.6830.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.86.8055.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.49.4488.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.78.7159.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.44.6774.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.8120.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.69.7763.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.64.5815.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.69.7761.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.73.A9RS.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.69.7978.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.8299.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.44.8117.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TD.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.49.AAR2.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.55.A490.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.83.5908.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.55.6980.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.44.6146.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.86.8669.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.95.7039.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.62.8397.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.91.6848.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.71.6725.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.97.7552.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.50.5936.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
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#> TCGA.55.6987.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.64.1681.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.05.5715.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7152.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.78.7539.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.62.A46S.01 2 0.3172 0.8041 0.00 0.84 0.00 0.16
#> TCGA.95.7947.01 1 0.4948 0.2177 0.56 0.00 0.00 0.44
#> TCGA.J2.8192.01 1 0.0000 0.9731 1.00 0.00 0.00 0.00
#> TCGA.78.7145.01 2 0.0000 0.9861 0.00 1.00 0.00 0.00
#> TCGA.50.6593.01 1 0.2345 0.8478 0.90 0.10 0.00 0.00
#> TCGA.69.7973.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.50.6591.11 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.86.7713.01 4 0.0000 0.9660 0.00 0.00 0.00 1.00
#> TCGA.55.8302.01 2 0.0000 0.9861 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.44.4112.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.NJ.A4YP.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.8278.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.62.A470.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6778.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARQ.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.97.A4M1.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6975.01 1 0.4060 0.4582 0.64 0.00 0.00 0.36 0.00
#> TCGA.99.8033.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7149.01 4 0.2516 0.8342 0.00 0.14 0.00 0.86 0.00
#> TCGA.50.6597.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.69.8255.01 1 0.0609 0.9221 0.98 0.00 0.00 0.02 0.00
#> TCGA.69.8453.01 5 0.1410 0.8751 0.06 0.00 0.00 0.00 0.94
#> TCGA.97.8552.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.53.A4EZ.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.7162.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.7025.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2659.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.62.A46U.01 2 0.3274 0.8396 0.00 0.78 0.00 0.00 0.22
#> TCGA.MP.A4T8.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.5645.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.93.A4JN.01 5 0.4302 -0.2405 0.00 0.48 0.00 0.00 0.52
#> TCGA.55.8096.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.6851.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.8398.01 4 0.3684 0.5757 0.28 0.00 0.00 0.72 0.00
#> TCGA.J2.A4AG.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.MP.A4TK.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.L9.A443.01 2 0.3109 0.8571 0.00 0.80 0.00 0.00 0.20
#> TCGA.55.8208.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N5.01 2 0.2732 0.8867 0.00 0.84 0.00 0.00 0.16
#> TCGA.64.5775.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.8394.01 2 0.4302 -0.0710 0.00 0.52 0.00 0.00 0.48
#> TCGA.05.4405.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.97.8176.01 4 0.4287 0.0848 0.46 0.00 0.00 0.54 0.00
#> TCGA.05.5428.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.5931.01 1 0.3424 0.6803 0.76 0.00 0.00 0.24 0.00
#> TCGA.49.AAR4.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.64.1679.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6984.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.MN.A4N1.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.91.6847.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8358.01 4 0.3684 0.6759 0.00 0.28 0.00 0.72 0.00
#> TCGA.49.AARO.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.75.6206.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.6744.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.L9.A743.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.05.4410.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.7954.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7910.01 1 0.2280 0.8280 0.88 0.00 0.00 0.12 0.00
#> TCGA.64.5778.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.62.A46Y.01 5 0.0609 0.8789 0.00 0.02 0.00 0.00 0.98
#> TCGA.55.6982.01 2 0.4060 0.6374 0.00 0.64 0.00 0.00 0.36
#> TCGA.55.6642.01 2 0.4675 0.2733 0.00 0.60 0.00 0.02 0.38
#> TCGA.44.6144.01 1 0.3983 0.5036 0.66 0.00 0.00 0.34 0.00
#> TCGA.05.4415.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.A479.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6673.01 2 0.6254 0.1374 0.00 0.50 0.00 0.16 0.34
#> TCGA.55.8207.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.44.2662.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.6562.01 5 0.2280 0.8253 0.00 0.12 0.00 0.00 0.88
#> TCGA.05.4425.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.8074.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5930.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8091.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7727.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.MP.A4SW.01 2 0.4060 0.6375 0.00 0.64 0.00 0.00 0.36
#> TCGA.67.6216.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.8203.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
#> TCGA.J2.8194.01 2 0.1043 0.8401 0.00 0.96 0.00 0.04 0.00
#> TCGA.55.6968.01 4 0.3424 0.7282 0.00 0.24 0.00 0.76 0.00
#> TCGA.55.8619.01 1 0.4060 0.3646 0.64 0.00 0.00 0.00 0.36
#> TCGA.44.2668.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.7660.01 4 0.2020 0.8229 0.10 0.00 0.00 0.90 0.00
#> TCGA.55.A57B.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.8507.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.NJ.A4YI.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.49.AAR0.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8281.01 4 0.4287 0.0912 0.00 0.00 0.00 0.54 0.46
#> TCGA.91.6831.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.75.7027.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.A4SU.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A444.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.8668.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.5072.01 1 0.2516 0.8051 0.86 0.00 0.00 0.14 0.00
#> TCGA.55.8512.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A47G.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.91.6849.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.44.6146.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6986.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.2665.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.86.8279.01 4 0.2516 0.8342 0.00 0.14 0.00 0.86 0.00
#> TCGA.05.5425.01 5 0.6146 0.3954 0.00 0.20 0.00 0.24 0.56
#> TCGA.62.A46R.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.44.6148.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.A494.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.3917.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.8254.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.53.7624.01 1 0.2732 0.7837 0.84 0.00 0.00 0.16 0.00
#> TCGA.75.5125.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.8054.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.L4.A4E5.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6775.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.7913.01 4 0.5130 0.5878 0.10 0.00 0.00 0.68 0.22
#> TCGA.55.7911.01 2 0.3274 0.8396 0.00 0.78 0.00 0.00 0.22
#> TCGA.55.8621.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T9.01 1 0.4060 0.3646 0.64 0.00 0.00 0.00 0.36
#> TCGA.55.6712.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.78.8640.01 4 0.4170 0.7670 0.00 0.14 0.00 0.78 0.08
#> TCGA.44.7670.01 1 0.1410 0.8887 0.94 0.00 0.00 0.06 0.00
#> TCGA.69.7760.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.95.7948.01 2 0.1043 0.8816 0.00 0.96 0.00 0.00 0.04
#> TCGA.97.A4M5.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A4DG.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.7816.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6593.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.7711.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5423.01 5 0.1732 0.8656 0.08 0.00 0.00 0.00 0.92
#> TCGA.MP.A4TJ.01 1 0.1043 0.8990 0.96 0.00 0.00 0.00 0.04
#> TCGA.44.2656.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6778.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6985.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.38.4631.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8615.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.93.7347.01 5 0.4060 0.5143 0.36 0.00 0.00 0.00 0.64
#> TCGA.MP.A4TF.01 5 0.2516 0.8073 0.00 0.14 0.00 0.00 0.86
#> TCGA.91.6829.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A471.01 4 0.0609 0.8970 0.00 0.02 0.00 0.98 0.00
#> TCGA.49.4490.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.8177.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.7458.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.91.A4BD.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.A47B.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.78.7542.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7573.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.78.7633.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.7953.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6970.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5946.02 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5946.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5066.02 4 0.2516 0.8342 0.00 0.14 0.00 0.86 0.00
#> TCGA.50.5066.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.8179.01 5 0.3868 0.7596 0.00 0.14 0.00 0.06 0.80
#> TCGA.86.A4JF.01 5 0.3424 0.5561 0.00 0.24 0.00 0.00 0.76
#> TCGA.55.8092.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.2665.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.75.5122.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.97.7938.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.49.AARE.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7726.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.91.8499.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TH.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7764.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.95.7043.01 2 0.1732 0.8035 0.00 0.92 0.00 0.08 0.00
#> TCGA.86.7701.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.49.4512.01 1 0.4060 0.3625 0.64 0.00 0.00 0.00 0.36
#> TCGA.L9.A50W.01 5 0.0609 0.8899 0.02 0.00 0.00 0.00 0.98
#> TCGA.50.8460.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.55.8505.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P8.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.67.6217.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.55.7281.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.78.7535.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.8671.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.50.6592.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.97.7546.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.95.7944.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.38.4632.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.50.5933.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.8280.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7153.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.78.8660.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.44.2655.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7907.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
#> TCGA.49.6767.01 5 0.2516 0.8073 0.00 0.14 0.00 0.00 0.86
#> TCGA.78.7155.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.91.6835.01 5 0.0609 0.8899 0.02 0.00 0.00 0.00 0.98
#> TCGA.50.5051.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7540.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.50.5939.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.A4VN.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.6145.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A47F.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.A48Z.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.8119.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.69.8253.01 5 0.0609 0.8899 0.02 0.00 0.00 0.00 0.98
#> TCGA.J2.A4AE.01 2 0.3274 0.8396 0.00 0.78 0.00 0.00 0.22
#> TCGA.75.6203.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5942.01 1 0.0609 0.9190 0.98 0.00 0.00 0.00 0.02
#> TCGA.50.6590.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.78.7148.01 1 0.1043 0.9060 0.96 0.00 0.00 0.04 0.00
#> TCGA.80.5608.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8205.01 2 0.2732 0.8867 0.00 0.84 0.00 0.00 0.16
#> TCGA.44.7669.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.6594.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
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#> TCGA.86.8673.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
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#> TCGA.50.8457.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.55.6972.01 1 0.3424 0.6804 0.76 0.00 0.00 0.24 0.00
#> TCGA.69.7979.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
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#> TCGA.69.7980.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.8547.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
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#> TCGA.50.5932.01 1 0.5646 0.2305 0.52 0.00 0.00 0.40 0.08
#> TCGA.97.8175.01 2 0.2732 0.8867 0.00 0.84 0.00 0.00 0.16
#> TCGA.50.7109.01 5 0.6184 0.0989 0.00 0.14 0.00 0.38 0.48
#> TCGA.44.A47A.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
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#> TCGA.78.7220.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
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#> TCGA.75.6211.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8510.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.55.8085.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
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#> TCGA.44.5643.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
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#> TCGA.50.5044.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.64.5781.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
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#> TCGA.49.AAR3.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.78.7154.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
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#> TCGA.55.6971.01 5 0.3109 0.7732 0.20 0.00 0.00 0.00 0.80
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#> TCGA.78.7537.01 5 0.1043 0.8835 0.04 0.00 0.00 0.00 0.96
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#> TCGA.50.5932.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.50.5055.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.49.AARN.01 2 0.3274 0.8396 0.00 0.78 0.00 0.00 0.22
#> TCGA.73.4676.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
#> TCGA.91.6836.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.55.8616.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
#> TCGA.38.7271.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.5045.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.A491.01 2 0.1043 0.8816 0.00 0.96 0.00 0.00 0.04
#> TCGA.78.7150.01 4 0.0609 0.8914 0.02 0.00 0.00 0.98 0.00
#> TCGA.86.8674.01 1 0.1732 0.8696 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.6978.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.NJ.A4YG.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.A4SS.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A492.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.53.7626.01 5 0.1043 0.8836 0.04 0.00 0.00 0.00 0.96
#> TCGA.55.6969.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7166.01 1 0.4302 0.1244 0.52 0.00 0.00 0.48 0.00
#> TCGA.55.A48Y.01 5 0.1043 0.8796 0.00 0.04 0.00 0.00 0.96
#> TCGA.44.5643.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6595.01 5 0.4182 0.4219 0.40 0.00 0.00 0.00 0.60
#> TCGA.55.6543.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6592.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5049.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.73.4658.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.97.A4M2.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8513.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7659.01 2 0.3109 0.8571 0.00 0.80 0.00 0.00 0.20
#> TCGA.62.8402.01 4 0.2516 0.8342 0.00 0.14 0.00 0.86 0.00
#> TCGA.55.7995.01 4 0.2516 0.8342 0.00 0.14 0.00 0.86 0.00
#> TCGA.05.5420.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.86.A456.01 2 0.3274 0.8396 0.00 0.78 0.00 0.00 0.22
#> TCGA.97.A4M7.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.78.7536.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.L9.A8F4.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7156.01 1 0.4182 0.3654 0.60 0.00 0.00 0.40 0.00
#> TCGA.44.7662.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.8506.01 2 0.0609 0.8765 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.5068.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.MP.A4T4.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.53.7813.01 5 0.0609 0.8899 0.02 0.00 0.00 0.00 0.98
#> TCGA.NJ.A55A.01 5 0.4060 0.5143 0.36 0.00 0.00 0.00 0.64
#> TCGA.71.8520.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.86.7955.01 4 0.2516 0.8342 0.00 0.14 0.00 0.86 0.00
#> TCGA.55.7815.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.7672.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.97.8172.01 2 0.4287 0.4128 0.00 0.54 0.00 0.00 0.46
#> TCGA.55.6987.01 5 0.2516 0.8324 0.14 0.00 0.00 0.00 0.86
#> TCGA.64.1681.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5715.01 2 0.2732 0.8870 0.00 0.84 0.00 0.00 0.16
#> TCGA.78.7152.01 2 0.2516 0.8979 0.00 0.86 0.00 0.00 0.14
#> TCGA.78.7539.01 2 0.0000 0.8692 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46S.01 5 0.4676 0.6900 0.00 0.14 0.00 0.12 0.74
#> TCGA.95.7947.01 5 0.3291 0.8048 0.04 0.00 0.00 0.12 0.84
#> TCGA.J2.8192.01 1 0.0000 0.9367 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7145.01 5 0.2516 0.8073 0.00 0.14 0.00 0.00 0.86
#> TCGA.50.6593.01 5 0.0000 0.8949 0.00 0.00 0.00 0.00 1.00
#> TCGA.69.7973.01 4 0.0609 0.8919 0.00 0.00 0.00 0.98 0.02
#> TCGA.50.6591.11 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.7713.01 4 0.0000 0.9037 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8302.01 5 0.0000 0.8949 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.44.4112.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YP.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8278.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A470.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6778.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARQ.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M1.01 3 0.2454 0.7983 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.55.6975.01 4 0.2048 0.8201 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.99.8033.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7149.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.6597.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.8255.01 1 0.2048 0.8724 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.69.8453.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.97.8552.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.53.A4EZ.01 4 0.3819 0.7290 0.00 0.00 0.00 0.70 0.02 0.28
#> TCGA.78.7162.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7025.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2659.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46U.01 2 0.0937 0.9178 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.MP.A4T8.01 2 0.3797 0.1537 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.44.5645.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.93.A4JN.01 2 0.1556 0.8824 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.8096.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.6851.01 6 0.1267 0.8739 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.62.8398.01 4 0.0547 0.9022 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.J2.A4AG.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TK.01 5 0.0937 0.9135 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.L9.A443.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.8208.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N5.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.64.5775.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.62.8394.01 6 0.0547 0.8774 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.05.4405.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.8176.01 4 0.0547 0.9022 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.05.5428.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5931.01 4 0.1556 0.8547 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.49.AAR4.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.64.1679.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6984.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MN.A4N1.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6847.01 6 0.1814 0.8632 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.86.8358.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.AARO.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.75.6206.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.49.6744.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.L9.A743.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.05.4410.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.7954.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7910.01 1 0.3198 0.6830 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.64.5778.01 5 0.0547 0.9349 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.62.A46Y.01 2 0.2454 0.8027 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.55.6982.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.6642.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.6144.01 4 0.0547 0.9022 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.05.4415.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A479.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6673.01 6 0.0547 0.8699 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.55.8207.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2662.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.6562.01 6 0.3797 0.2790 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.05.4425.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8074.01 6 0.2260 0.8440 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.50.5930.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8091.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7727.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.67.6216.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8203.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J2.8194.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.6968.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.8619.01 5 0.3851 0.2148 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.44.2668.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.7660.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.A57B.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8507.01 4 0.1814 0.8875 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.NJ.A4YI.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8281.01 5 0.4377 0.6458 0.00 0.00 0.00 0.16 0.72 0.12
#> TCGA.91.6831.01 4 0.0937 0.9065 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.75.7027.01 4 0.3309 0.7405 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.44.A4SU.01 1 0.0547 0.9609 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.L9.A444.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8668.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5072.01 1 0.2260 0.8501 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.55.8512.01 3 0.0937 0.9390 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.44.A47G.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.91.6849.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6146.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6986.01 2 0.2631 0.7807 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.44.2665.01 5 0.0937 0.9137 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.86.8279.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.05.5425.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.62.A46R.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6148.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A494.01 6 0.2260 0.8454 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.44.3917.01 6 0.3076 0.7621 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.69.8254.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.53.7624.01 1 0.3828 0.2673 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.75.5125.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8054.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.L4.A4E5.01 6 0.2260 0.8469 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.44.6775.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.7913.01 5 0.2631 0.7851 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.55.7911.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.8621.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T9.01 5 0.3756 0.3896 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.55.6712.01 2 0.2941 0.7337 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.78.8640.01 6 0.0547 0.8656 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.44.7670.01 1 0.2454 0.8267 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.69.7760.01 5 0.1267 0.9057 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.95.7948.01 2 0.0937 0.9093 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.97.A4M5.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A4DG.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7816.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6593.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.7711.01 1 0.0547 0.9609 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.05.5423.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TJ.01 1 0.2260 0.8092 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.44.2656.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6778.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6985.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.38.4631.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.0937 0.9461 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.55.8615.01 4 0.2941 0.8105 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.93.7347.01 5 0.2260 0.8240 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.MP.A4TF.01 6 0.1814 0.8117 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.91.6829.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.62.A471.01 4 0.3309 0.7404 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.49.4490.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8177.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.7458.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.91.A4BD.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 2 0.2454 0.8027 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.44.A47B.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7542.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.55.7573.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7633.01 4 0.1267 0.9021 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.86.7953.01 1 0.0937 0.9336 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.55.6970.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5946.02 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5946.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5066.02 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.5066.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8179.01 6 0.3828 0.1706 0.00 0.00 0.00 0.00 0.44 0.56
#> TCGA.86.A4JF.01 2 0.2048 0.8439 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.55.8092.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.75.6207.01 2 0.3864 -0.0878 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.44.2665.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.5122.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.97.7938.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.49.AARE.01 6 0.2048 0.8553 0.00 0.12 0.00 0.00 0.00 0.88
#> TCGA.55.7726.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.91.8499.01 4 0.0547 0.9085 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.MP.A4TH.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7764.01 4 0.2048 0.8798 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.95.7043.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.86.7701.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 5 0.3756 0.3886 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.L9.A50W.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.8460.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8505.01 1 0.0547 0.9609 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.86.A4P8.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.6217.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.7281.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7535.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8671.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.6592.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.97.7546.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.95.7944.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4632.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8280.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7153.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2655.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7907.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6767.01 6 0.0547 0.8656 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.78.7155.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.6835.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5051.01 6 0.0937 0.8761 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.78.7540.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5939.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.95.A4VN.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6145.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A47F.01 5 0.1267 0.9057 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.55.A48Z.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8119.01 4 0.1814 0.8875 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.69.8253.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.J2.A4AE.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.75.6203.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5942.01 1 0.1814 0.8626 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.50.6590.01 2 0.2631 0.7807 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.78.7148.01 1 0.0547 0.9609 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.80.5608.01 6 0.1267 0.8729 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.55.8205.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7669.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6594.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2668.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6830.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8055.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.4488.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7159.01 6 0.0547 0.8759 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.44.6774.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8120.01 6 0.2048 0.7996 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.69.7763.01 5 0.2048 0.8248 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.64.5815.01 5 0.0547 0.9317 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.69.7761.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.73.A9RS.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.69.7978.01 2 0.2454 0.8027 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.55.8299.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8117.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR2.01 1 0.1267 0.9295 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.55.A490.01 6 0.2941 0.6606 0.00 0.00 0.00 0.22 0.00 0.78
#> TCGA.83.5908.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.6980.01 3 0.3309 0.6187 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.44.6146.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8669.01 4 0.2793 0.8273 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.95.7039.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.8397.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6848.01 5 0.0937 0.9192 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.71.6725.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.97.7552.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5936.01 1 0.2048 0.8721 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.91.7771.01 5 0.1267 0.9057 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.86.8359.01 6 0.1267 0.8352 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.55.8301.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.7146.01 6 0.1556 0.8691 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.44.3918.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5935.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7974.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.78.7161.01 6 0.2454 0.8338 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.55.8614.01 4 0.1267 0.9025 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.97.7937.01 2 0.3864 -0.0878 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.49.AARR.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.5147.01 4 0.0547 0.9085 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.49.6745.01 2 0.1556 0.8824 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.6979.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8094.01 4 0.1814 0.8875 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.55.7574.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.5644.01 6 0.2260 0.8454 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.55.8511.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.7671.01 4 0.5292 0.6119 0.00 0.00 0.00 0.60 0.22 0.18
#> TCGA.78.8648.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 5 0.1556 0.8902 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.44.2656.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.J2.A4AD.01 4 0.0937 0.8884 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.49.6743.01 5 0.0547 0.9337 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.86.8673.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 5 0.1267 0.9057 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.L9.A7SV.01 6 0.0547 0.8759 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.97.A4LX.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4631.01 1 0.2454 0.8267 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.99.AA5R.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4390.01 6 0.1556 0.8691 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.MP.A4T7.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.69.7765.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.95.8494.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.8171.01 4 0.3679 0.8058 0.00 0.00 0.00 0.76 0.04 0.20
#> TCGA.50.8457.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.6972.01 4 0.1556 0.8575 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.69.7979.01 6 0.1814 0.8632 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.62.A46P.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7980.01 6 0.1814 0.8630 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.97.8547.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.05.4433.01 2 0.3198 0.6803 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.50.5932.01 4 0.5457 0.6384 0.04 0.00 0.00 0.64 0.22 0.10
#> TCGA.97.8175.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.50.7109.01 6 0.0547 0.8656 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.44.A47A.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8508.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.78.7220.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.93.A4JO.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6145.01 5 0.2631 0.7791 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.44.6147.01 5 0.3076 0.6590 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.86.8075.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7724.01 5 0.2454 0.8017 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.75.6211.01 6 0.2631 0.8199 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.55.8510.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8085.01 4 0.2941 0.8105 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.55.8090.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.91.6828.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4514.01 5 0.3578 0.5280 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.05.4396.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.MN.A4N4.01 2 0.3409 0.5021 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.55.8204.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.5643.01 4 0.0937 0.9037 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.L4.A4E6.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8076.01 5 0.1556 0.8838 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7031.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5044.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.64.5781.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.73.4658.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.5420.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.AAR3.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.7154.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4384.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6971.01 5 0.1556 0.8843 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.55.A4DF.01 4 0.0937 0.9065 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.44.7667.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.6148.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5939.01 1 0.0937 0.9334 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.O1.A52J.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.7167.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.78.8662.01 6 0.2260 0.8454 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.05.4427.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.78.7143.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 6 0.3409 0.5239 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.MP.A4T2.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7714.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8585.01 1 0.0547 0.9609 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.75.6205.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.99.8028.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A493.01 5 0.2631 0.7472 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.78.7147.01 6 0.3076 0.7620 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.75.5126.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.6591.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8206.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7553.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 6 0.2631 0.8199 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.NJ.A4YQ.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.NJ.A7XG.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.A48X.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8514.01 4 0.1267 0.9021 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.50.5944.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR9.01 4 0.0547 0.9085 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.50.6594.01 5 0.3076 0.6845 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.86.8056.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VK.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.4488.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.55.7728.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7994.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.6215.01 2 0.1267 0.9006 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.78.7537.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8097.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.05.4424.01 1 0.0547 0.9609 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.7227.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.MP.A4TI.01 5 0.0547 0.9317 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.44.5645.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.35.5375.01 6 0.0547 0.8774 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.75.6214.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.80.5611.01 4 0.2631 0.8356 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.49.AAQV.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6742.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.7498.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4632.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5936.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4B.A93V.01 4 0.0937 0.8921 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.MP.A4T6.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4D0.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.62.A46O.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6779.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.49.6761.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.7348.01 5 0.2454 0.8017 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.99.8032.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.5935.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.6981.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.8655.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7163.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7941.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TA.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8174.01 5 0.3797 0.3346 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.75.5146.01 4 0.4475 0.7015 0.00 0.00 0.00 0.70 0.20 0.10
#> TCGA.50.5931.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7914.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6840.01 1 0.3198 0.6835 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.62.A472.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.64.5779.01 4 0.1267 0.9021 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.05.4417.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.4679.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.64.5774.01 4 0.1556 0.8958 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.55.8620.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.7570.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.7554.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SY.01 2 0.2631 0.7807 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.93.A4JP.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.5899.01 4 0.3076 0.7622 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.95.8039.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6144.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5941.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.62.8399.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.7562.01 6 0.2941 0.7845 0.00 0.22 0.00 0.00 0.00 0.78
#> TCGA.75.7030.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7576.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.38.A44F.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.80.5607.01 2 0.1556 0.8824 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.93.8067.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.8395.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6212.01 3 0.2631 0.7737 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.44.2666.01 2 0.2793 0.7563 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.50.5930.01 1 0.0547 0.9609 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.7284.01 5 0.0547 0.9349 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.44.6777.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6776.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6983.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5932.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.73.4676.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6836.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.38.7271.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5045.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A491.01 2 0.3706 0.2957 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.78.7150.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8674.01 1 0.2048 0.8724 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.55.6978.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.NJ.A4YG.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.A4SS.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A492.01 5 0.2454 0.8093 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.53.7626.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.6969.01 1 0.1480 0.9345 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.78.7166.01 4 0.0000 0.9083 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.A48Y.01 5 0.1267 0.9057 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.44.5643.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 6 0.2793 0.8052 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.50.6595.01 5 0.2454 0.8017 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.55.6543.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6592.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5049.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.73.4658.01 2 0.2793 0.7563 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.97.A4M2.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8513.01 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.62.8402.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.7995.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.05.5420.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.A456.01 2 0.0547 0.9333 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.97.A4M7.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.7536.01 4 0.1556 0.8958 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.L9.A8F4.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7156.01 4 0.0937 0.8908 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.44.7662.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8506.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4T4.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.53.7813.01 5 0.0547 0.9349 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.NJ.A55A.01 5 0.2260 0.8240 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.71.8520.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.7955.01 6 0.0000 0.8751 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.7815.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.7672.01 2 0.2793 0.7563 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.97.8172.01 2 0.1814 0.8641 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.55.6987.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.64.1681.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5715.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7152.01 2 0.0000 0.9433 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 6 0.2454 0.8338 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.62.A46S.01 6 0.0547 0.8656 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.95.7947.01 5 0.1267 0.9057 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.J2.8192.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7145.01 6 0.0937 0.8589 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.50.6593.01 5 0.0000 0.9479 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.69.7973.01 4 0.4244 0.7710 0.00 0.00 0.00 0.72 0.08 0.20
#> TCGA.50.6591.11 3 0.0000 0.9812 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.7713.01 4 0.2793 0.8273 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.55.8302.01 2 0.3409 0.6095 0.00 0.70 0.00 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.44.4112.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YP.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8278.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A470.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.44.6778.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARQ.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M1.01 3 0.2832 0.6641 0.24 0.00 0.76 0.00 0.00 0.00 0.00
#> TCGA.55.6975.01 4 0.4003 0.4595 0.32 0.00 0.00 0.64 0.00 0.04 0.00
#> TCGA.99.8033.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7149.01 7 0.1433 0.7666 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.50.6597.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.8255.01 1 0.2832 0.7283 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.69.8453.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.8552.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.53.A4EZ.01 6 0.1363 0.7724 0.00 0.00 0.00 0.04 0.02 0.94 0.00
#> TCGA.78.7162.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7025.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2659.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46U.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T8.01 2 0.3526 0.6549 0.00 0.76 0.00 0.00 0.00 0.06 0.18
#> TCGA.44.5645.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JN.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8096.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.6851.01 7 0.1886 0.8198 0.00 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.62.8398.01 4 0.4640 0.5511 0.18 0.00 0.00 0.64 0.00 0.18 0.00
#> TCGA.J2.A4AG.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TK.01 5 0.1166 0.9019 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.L9.A443.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8208.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N5.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.5775.01 7 0.2278 0.8381 0.00 0.04 0.00 0.00 0.00 0.08 0.88
#> TCGA.62.8394.01 6 0.0504 0.7780 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.05.4405.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8176.01 4 0.0863 0.8134 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.1166 0.9152 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.50.5931.01 4 0.0504 0.8224 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.49.AAR4.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.64.1679.01 1 0.1433 0.8998 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.55.6984.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MN.A4N1.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6847.01 6 0.3244 0.6136 0.00 0.04 0.00 0.00 0.00 0.78 0.18
#> TCGA.86.8358.01 6 0.2259 0.6667 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.49.AARO.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0504 0.9356 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.6744.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.L9.A743.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.05.4410.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7954.01 1 0.1433 0.9016 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.55.7910.01 4 0.3562 -0.0977 0.50 0.00 0.00 0.50 0.00 0.00 0.00
#> TCGA.64.5778.01 5 0.2569 0.7935 0.00 0.00 0.00 0.02 0.84 0.14 0.00
#> TCGA.62.A46Y.01 2 0.0504 0.9489 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.6982.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6642.01 6 0.0504 0.7780 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.44.6144.01 4 0.0863 0.8134 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.05.4415.01 4 0.0000 0.8264 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A479.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6673.01 7 0.2163 0.8160 0.00 0.00 0.00 0.00 0.02 0.10 0.88
#> TCGA.55.8207.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2662.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.6562.01 6 0.1886 0.7563 0.00 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.05.4425.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8074.01 6 0.2163 0.7266 0.00 0.02 0.00 0.00 0.00 0.88 0.10
#> TCGA.50.5930.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8091.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7727.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.6216.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8203.01 2 0.0504 0.9510 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.J2.8194.01 6 0.2422 0.6552 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.55.6968.01 6 0.1166 0.7485 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.55.8619.01 5 0.3358 0.4699 0.36 0.00 0.00 0.00 0.64 0.00 0.00
#> TCGA.44.2668.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7660.01 4 0.0504 0.8303 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.A57B.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8507.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.NJ.A4YI.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 1 0.0863 0.9247 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.86.8281.01 6 0.3617 0.7056 0.00 0.00 0.00 0.08 0.16 0.76 0.00
#> TCGA.91.6831.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.75.7027.01 6 0.3867 0.6452 0.00 0.00 0.00 0.14 0.00 0.74 0.12
#> TCGA.44.A4SU.01 1 0.2081 0.8519 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.L9.A444.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8668.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5072.01 1 0.3139 0.6268 0.70 0.00 0.00 0.30 0.00 0.00 0.00
#> TCGA.55.8512.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.6849.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6146.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6986.01 2 0.0863 0.9281 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.44.2665.01 5 0.1433 0.8806 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.86.8279.01 6 0.0504 0.7718 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.05.5425.01 6 0.0504 0.7780 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.62.A46R.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6148.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A494.01 7 0.3221 0.6786 0.00 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.44.3917.01 2 0.4990 0.2551 0.00 0.58 0.00 0.00 0.00 0.22 0.20
#> TCGA.69.8254.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.53.7624.01 4 0.3413 0.3225 0.38 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.75.5125.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8054.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.L4.A4E5.01 6 0.3052 0.6206 0.00 0.02 0.00 0.00 0.00 0.78 0.20
#> TCGA.44.6775.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7913.01 6 0.2906 0.7109 0.00 0.00 0.00 0.02 0.18 0.80 0.00
#> TCGA.55.7911.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8621.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T9.01 5 0.3139 0.5898 0.30 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.55.6712.01 2 0.2081 0.7972 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.78.8640.01 6 0.0504 0.7780 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.44.7670.01 1 0.2832 0.7312 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.69.7760.01 6 0.2708 0.6817 0.00 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.95.7948.01 2 0.0504 0.9498 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.97.A4M5.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A4DG.01 2 0.1166 0.9152 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.55.7816.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6593.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.7711.01 1 0.1671 0.8845 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.05.5423.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TJ.01 1 0.0863 0.9112 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.44.2656.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6778.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6985.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.38.4631.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.2081 0.8520 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.55.8615.01 6 0.3867 0.6452 0.00 0.00 0.00 0.14 0.00 0.74 0.12
#> TCGA.93.7347.01 5 0.1671 0.8664 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.MP.A4TF.01 6 0.2569 0.7435 0.00 0.00 0.00 0.00 0.14 0.84 0.02
#> TCGA.91.6829.01 7 0.2829 0.8240 0.00 0.08 0.00 0.00 0.00 0.08 0.84
#> TCGA.62.A471.01 6 0.3687 0.6680 0.00 0.00 0.00 0.12 0.00 0.76 0.12
#> TCGA.49.4490.01 1 0.1433 0.8998 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.97.8177.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.7458.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.A4BD.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 2 0.0504 0.9489 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.44.A47B.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7542.01 7 0.2278 0.8381 0.00 0.04 0.00 0.00 0.00 0.08 0.88
#> TCGA.55.7573.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7633.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.86.7953.01 1 0.1664 0.8882 0.92 0.00 0.00 0.02 0.06 0.00 0.00
#> TCGA.55.6970.01 1 0.0504 0.9356 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5946.02 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.50.5946.01 4 0.1671 0.8199 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.50.5066.02 6 0.0000 0.7718 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5066.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8179.01 6 0.2259 0.7306 0.00 0.00 0.00 0.00 0.16 0.84 0.00
#> TCGA.86.A4JF.01 2 0.0504 0.9489 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.8092.01 7 0.2278 0.8381 0.00 0.04 0.00 0.00 0.00 0.08 0.88
#> TCGA.75.6207.01 7 0.2512 0.8056 0.00 0.10 0.00 0.00 0.00 0.04 0.86
#> TCGA.44.2665.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.5122.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.7938.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.AARE.01 6 0.4030 0.5119 0.00 0.12 0.00 0.00 0.00 0.72 0.16
#> TCGA.55.7726.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.8499.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.MP.A4TH.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7764.01 6 0.3358 0.4413 0.00 0.00 0.00 0.36 0.00 0.64 0.00
#> TCGA.95.7043.01 6 0.3047 0.4839 0.00 0.00 0.00 0.00 0.00 0.72 0.28
#> TCGA.86.7701.01 2 0.0863 0.9321 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.49.4512.01 5 0.3496 0.3133 0.42 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.L9.A50W.01 5 0.0863 0.9257 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.50.8460.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8505.01 1 0.2081 0.8519 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.86.A4P8.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.6217.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7281.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7535.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8671.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6592.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.7546.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.7944.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4632.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8280.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7153.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2655.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7907.01 2 0.0504 0.9510 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.49.6767.01 6 0.0504 0.7780 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.78.7155.01 4 0.0504 0.8303 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.91.6835.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5051.01 6 0.2422 0.6552 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.78.7540.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5939.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VN.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6145.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47F.01 6 0.2832 0.6609 0.00 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.55.A48Z.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8119.01 4 0.2569 0.8001 0.00 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.69.8253.01 5 0.0504 0.9418 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.J2.A4AE.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6203.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5942.01 1 0.2572 0.7015 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.50.6590.01 2 0.0863 0.9281 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.78.7148.01 1 0.2259 0.8315 0.84 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.80.5608.01 6 0.2259 0.6789 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.55.8205.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7669.01 4 0.0504 0.8303 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.6594.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2668.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6830.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8055.01 4 0.1006 0.8190 0.02 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.49.4488.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7159.01 7 0.2832 0.7652 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.44.6774.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8120.01 6 0.2163 0.7624 0.00 0.00 0.00 0.00 0.10 0.88 0.02
#> TCGA.69.7763.01 5 0.1671 0.8560 0.00 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.64.5815.01 5 0.1433 0.8806 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.69.7761.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.A9RS.01 6 0.0504 0.7681 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.69.7978.01 2 0.0504 0.9489 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.8299.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8117.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR2.01 1 0.2572 0.7849 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.55.A490.01 7 0.1006 0.7433 0.00 0.00 0.00 0.02 0.00 0.02 0.96
#> TCGA.83.5908.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6980.01 3 0.3221 0.5393 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.44.6146.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8669.01 6 0.3867 0.6455 0.00 0.00 0.00 0.14 0.00 0.74 0.12
#> TCGA.95.7039.01 2 0.1166 0.9152 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.62.8397.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6848.01 5 0.3691 0.7662 0.08 0.00 0.00 0.06 0.80 0.06 0.00
#> TCGA.71.6725.01 7 0.2278 0.8381 0.00 0.04 0.00 0.00 0.00 0.08 0.88
#> TCGA.97.7552.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5936.01 1 0.2422 0.8089 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.91.7771.01 6 0.2832 0.6609 0.00 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.86.8359.01 6 0.0863 0.7796 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.55.8301.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7146.01 7 0.3221 0.6786 0.00 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.44.3918.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5935.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7974.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7161.01 7 0.4146 0.7581 0.00 0.08 0.00 0.00 0.00 0.24 0.68
#> TCGA.55.8614.01 4 0.3358 0.3669 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.97.7937.01 7 0.3526 0.7426 0.00 0.18 0.00 0.00 0.00 0.06 0.76
#> TCGA.49.AARR.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5147.01 4 0.1433 0.7929 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.49.6745.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8094.01 4 0.3417 0.6978 0.00 0.00 0.00 0.72 0.00 0.02 0.26
#> TCGA.55.7574.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.5644.01 7 0.3519 0.7867 0.00 0.04 0.00 0.00 0.00 0.22 0.74
#> TCGA.55.8511.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7671.01 6 0.3867 0.7022 0.00 0.00 0.00 0.14 0.12 0.74 0.00
#> TCGA.78.8648.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 6 0.2708 0.6815 0.00 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.44.2656.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J2.A4AD.01 4 0.0504 0.8227 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.49.6743.01 5 0.0504 0.9427 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.86.8673.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 6 0.2572 0.6998 0.00 0.00 0.00 0.00 0.20 0.80 0.00
#> TCGA.L9.A7SV.01 7 0.1433 0.8201 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.97.A4LX.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4631.01 1 0.2832 0.7299 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.99.AA5R.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4390.01 7 0.3221 0.6786 0.00 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.MP.A4T7.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7765.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.8494.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8171.01 6 0.3244 0.7027 0.00 0.00 0.00 0.18 0.04 0.78 0.00
#> TCGA.50.8457.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6972.01 4 0.0863 0.8134 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.69.7979.01 6 0.2422 0.6552 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.62.A46P.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7980.01 6 0.0504 0.7686 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.97.8547.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 2 0.3770 0.6488 0.00 0.74 0.00 0.00 0.08 0.18 0.00
#> TCGA.50.5932.01 6 0.3745 0.6235 0.00 0.00 0.00 0.26 0.04 0.70 0.00
#> TCGA.97.8175.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.7109.01 6 0.0504 0.7780 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.44.A47A.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8508.01 6 0.2259 0.6789 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.78.7220.01 4 0.0504 0.8303 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.93.A4JO.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6145.01 5 0.1671 0.8670 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.44.6147.01 5 0.3294 0.4717 0.00 0.34 0.00 0.00 0.66 0.00 0.00
#> TCGA.86.8075.01 1 0.0504 0.9360 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.7724.01 5 0.1671 0.8664 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.75.6211.01 7 0.4243 0.7628 0.00 0.10 0.00 0.00 0.00 0.22 0.68
#> TCGA.55.8510.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8085.01 6 0.3687 0.6680 0.00 0.00 0.00 0.12 0.00 0.76 0.12
#> TCGA.55.8090.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 5 0.1433 0.8806 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.91.6828.01 2 0.3968 0.0718 0.00 0.54 0.00 0.00 0.00 0.02 0.44
#> TCGA.49.4514.01 1 0.5128 0.3774 0.56 0.00 0.00 0.02 0.32 0.10 0.00
#> TCGA.05.4396.01 7 0.2278 0.8381 0.00 0.04 0.00 0.00 0.00 0.08 0.88
#> TCGA.MN.A4N4.01 2 0.2313 0.8494 0.00 0.88 0.00 0.00 0.00 0.06 0.06
#> TCGA.55.8204.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.5643.01 4 0.2832 0.6032 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.L4.A4E6.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8076.01 5 0.1166 0.9076 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7031.01 4 0.0000 0.8264 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5044.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.64.5781.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.4658.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 6 0.2081 0.6974 0.00 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.49.AAR3.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7154.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4384.01 1 0.1433 0.9044 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.55.6971.01 5 0.0504 0.9423 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.55.A4DF.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.44.7667.01 6 0.2081 0.7120 0.00 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.44.6148.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5939.01 1 0.1928 0.8690 0.90 0.00 0.00 0.02 0.08 0.00 0.00
#> TCGA.O1.A52J.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7167.01 7 0.1166 0.7509 0.00 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.78.8662.01 7 0.2569 0.8259 0.00 0.02 0.00 0.00 0.00 0.14 0.84
#> TCGA.05.4427.01 7 0.2278 0.8381 0.00 0.04 0.00 0.00 0.00 0.08 0.88
#> TCGA.78.7143.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 6 0.0863 0.7796 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.MP.A4T2.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7714.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8585.01 1 0.1671 0.8845 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.75.6205.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.99.8028.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 5 0.2708 0.6785 0.00 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.78.7147.01 7 0.4146 0.6754 0.00 0.24 0.00 0.00 0.00 0.08 0.68
#> TCGA.75.5126.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6591.01 4 0.0000 0.8264 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8206.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7553.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 7 0.4243 0.7628 0.00 0.10 0.00 0.00 0.00 0.22 0.68
#> TCGA.NJ.A4YQ.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.NJ.A7XG.01 5 0.0504 0.9414 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.55.A48X.01 5 0.0504 0.9412 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.55.8514.01 4 0.3606 0.6490 0.00 0.00 0.00 0.68 0.00 0.02 0.30
#> TCGA.50.5944.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR9.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.50.6594.01 6 0.1671 0.7652 0.00 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.86.8056.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VK.01 6 0.2422 0.6552 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.49.4488.01 7 0.4348 0.7526 0.00 0.14 0.00 0.00 0.00 0.18 0.68
#> TCGA.55.7728.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7994.01 2 0.3496 0.2190 0.00 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.67.6215.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7537.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8097.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 6 0.2259 0.6789 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.05.4424.01 1 0.1671 0.8845 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.55.7227.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 5 0.1433 0.8806 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.44.5645.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.35.5375.01 6 0.2572 0.6292 0.00 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.75.6214.01 7 0.1433 0.7666 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.80.5611.01 4 0.3770 0.7296 0.00 0.00 0.00 0.74 0.00 0.08 0.18
#> TCGA.49.AAQV.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6742.01 4 0.0000 0.8264 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.7498.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4632.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5936.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4B.A93V.01 4 0.4003 0.4311 0.04 0.00 0.00 0.64 0.00 0.32 0.00
#> TCGA.MP.A4T6.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4D0.01 6 0.0504 0.7716 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.62.A46O.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.44.6779.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.6761.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.7348.01 5 0.1671 0.8664 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.99.8032.01 6 0.0000 0.7718 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5935.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6981.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.8655.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7163.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7941.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TA.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8174.01 1 0.3047 0.5726 0.72 0.00 0.00 0.00 0.28 0.00 0.00
#> TCGA.75.5146.01 6 0.4615 0.5076 0.00 0.00 0.00 0.30 0.10 0.60 0.00
#> TCGA.50.5931.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7914.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6840.01 4 0.3558 -0.0228 0.48 0.00 0.00 0.52 0.00 0.00 0.00
#> TCGA.62.A472.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.5779.01 4 0.4177 0.7067 0.00 0.00 0.00 0.70 0.00 0.18 0.12
#> TCGA.05.4417.01 2 0.1671 0.8638 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.67.4679.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.64.5774.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.55.8620.01 7 0.1886 0.8182 0.00 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.55.7570.01 4 0.0504 0.8303 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.97.7554.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SY.01 2 0.0504 0.9489 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.93.A4JP.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.5899.01 7 0.3994 -0.2993 0.00 0.00 0.00 0.48 0.00 0.02 0.50
#> TCGA.95.8039.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6144.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5941.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.62.8399.01 4 0.0504 0.8303 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.95.7562.01 7 0.4789 0.6076 0.00 0.26 0.00 0.00 0.00 0.14 0.60
#> TCGA.75.7030.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7576.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.38.A44F.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.80.5607.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.8067.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8395.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6212.01 3 0.2945 0.6368 0.26 0.00 0.74 0.00 0.00 0.00 0.00
#> TCGA.44.2666.01 2 0.1671 0.8535 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.50.5930.01 1 0.1671 0.8845 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.55.7284.01 5 0.2259 0.7841 0.00 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.44.6777.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6776.01 1 0.1433 0.9016 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.55.6983.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5932.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0863 0.9113 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.01 2 0.1166 0.9152 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.91.6836.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 2 0.1166 0.9152 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.38.7271.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5045.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A491.01 6 0.3546 0.1088 0.00 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.78.7150.01 4 0.0504 0.8303 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.86.8674.01 1 0.2708 0.7574 0.78 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.55.6978.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.NJ.A4YG.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A4SS.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A492.01 6 0.2376 0.7522 0.00 0.00 0.00 0.02 0.12 0.86 0.00
#> TCGA.53.7626.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6969.01 1 0.2259 0.8315 0.84 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.78.7166.01 4 0.0504 0.8227 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.55.A48Y.01 6 0.2945 0.6380 0.00 0.00 0.00 0.00 0.26 0.74 0.00
#> TCGA.44.5643.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 7 0.2278 0.8381 0.00 0.04 0.00 0.00 0.00 0.08 0.88
#> TCGA.50.6595.01 5 0.1671 0.8664 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.55.6543.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6592.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5049.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.4658.01 2 0.0863 0.9281 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.97.A4M2.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8513.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8402.01 6 0.2081 0.6886 0.00 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.55.7995.01 6 0.0000 0.7718 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.05.5420.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.A456.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7536.01 4 0.2376 0.8114 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.L9.A8F4.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7156.01 4 0.0863 0.8134 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.44.7662.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8506.01 2 0.1166 0.9152 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.50.5068.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T4.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.53.7813.01 6 0.3294 0.5438 0.00 0.00 0.00 0.00 0.34 0.66 0.00
#> TCGA.NJ.A55A.01 5 0.1671 0.8664 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.71.8520.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7955.01 7 0.0863 0.7782 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.55.7815.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7672.01 2 0.1166 0.9054 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.97.8172.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6987.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.64.1681.01 1 0.1166 0.9148 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5715.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7152.01 2 0.0000 0.9667 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 7 0.4535 0.7277 0.00 0.12 0.00 0.00 0.00 0.24 0.64
#> TCGA.62.A46S.01 6 0.0863 0.7796 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.95.7947.01 6 0.3606 0.5771 0.00 0.00 0.00 0.02 0.30 0.68 0.00
#> TCGA.J2.8192.01 1 0.0000 0.9457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7145.01 6 0.0863 0.7794 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.50.6593.01 5 0.0000 0.9582 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7973.01 6 0.3244 0.7123 0.00 0.00 0.00 0.18 0.04 0.78 0.00
#> TCGA.50.6591.11 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.7713.01 6 0.4030 0.6181 0.00 0.00 0.00 0.16 0.00 0.72 0.12
#> TCGA.55.8302.01 2 0.2572 0.7043 0.00 0.80 0.00 0.00 0.20 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.44.4112.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YP.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8278.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A470.01 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.44.6778.01 1 0.2406 0.7658 0.80 0.00 0.00 0.20 0.00 0.00 0.00 0.00
#> TCGA.49.AARQ.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M1.01 3 0.3329 0.0494 0.48 0.00 0.52 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6975.01 4 0.2114 0.5999 0.00 0.00 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.99.8033.01 1 0.1804 0.8365 0.90 0.00 0.00 0.08 0.00 0.02 0.00 0.00
#> TCGA.78.7149.01 8 0.3015 0.3537 0.00 0.00 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.50.6597.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.8255.01 4 0.2114 0.6700 0.16 0.00 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.69.8453.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.8552.01 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.A4EZ.01 6 0.0471 0.7366 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.78.7162.01 1 0.1765 0.8382 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.75.7025.01 1 0.0471 0.8813 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.44.2659.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46U.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T8.01 7 0.3237 0.4119 0.00 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.44.5645.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JN.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.8096.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.1947 0.8269 0.86 0.00 0.00 0.14 0.00 0.00 0.00 0.00
#> TCGA.86.6851.01 7 0.2267 0.7398 0.00 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.62.8398.01 4 0.3514 0.4121 0.00 0.00 0.00 0.64 0.00 0.34 0.00 0.02
#> TCGA.J2.A4AG.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TK.01 5 0.1341 0.8555 0.00 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.L9.A443.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8208.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N5.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.5775.01 7 0.2719 0.7473 0.00 0.02 0.00 0.00 0.00 0.00 0.80 0.18
#> TCGA.62.8394.01 6 0.1947 0.7306 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.05.4405.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8176.01 4 0.1091 0.6461 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.05.5428.01 2 0.3083 0.4267 0.00 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.50.5931.01 4 0.1947 0.6030 0.00 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.49.AAR4.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.64.1679.01 1 0.2938 0.5165 0.70 0.00 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.55.6984.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MN.A4N1.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6847.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.86.8358.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.49.AARO.01 5 0.0471 0.9207 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.75.6206.01 1 0.2025 0.8420 0.88 0.00 0.00 0.10 0.00 0.02 0.00 0.00
#> TCGA.MP.A4TC.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.6744.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.4410.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7954.01 1 0.1563 0.8323 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.55.7910.01 4 0.2406 0.6631 0.20 0.00 0.00 0.80 0.00 0.00 0.00 0.00
#> TCGA.64.5778.01 5 0.4199 0.1941 0.00 0.00 0.00 0.06 0.52 0.42 0.00 0.00
#> TCGA.62.A46Y.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.6982.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.6642.01 6 0.1947 0.7297 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.44.6144.01 4 0.0471 0.6644 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.05.4415.01 4 0.3170 0.5127 0.00 0.00 0.00 0.76 0.00 0.04 0.00 0.20
#> TCGA.44.A479.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6673.01 7 0.3036 0.7250 0.00 0.00 0.00 0.00 0.00 0.04 0.78 0.18
#> TCGA.55.8207.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2662.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.6562.01 6 0.1275 0.7138 0.00 0.00 0.00 0.02 0.04 0.94 0.00 0.00
#> TCGA.05.4425.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8074.01 6 0.3385 0.6539 0.00 0.08 0.00 0.00 0.00 0.76 0.16 0.00
#> TCGA.50.5930.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8091.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.55.7727.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.6216.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8203.01 2 0.0471 0.9386 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.J2.8194.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.55.6968.01 6 0.2406 0.7098 0.00 0.00 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.55.8619.01 1 0.2756 0.5492 0.74 0.00 0.00 0.00 0.26 0.00 0.00 0.00
#> TCGA.44.2668.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7660.01 4 0.2534 0.5303 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.55.A57B.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8507.01 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.NJ.A4YI.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 1 0.2406 0.7651 0.80 0.00 0.00 0.20 0.00 0.00 0.00 0.00
#> TCGA.86.8281.01 6 0.1607 0.7034 0.00 0.00 0.00 0.04 0.04 0.92 0.00 0.00
#> TCGA.91.6831.01 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.75.7027.01 8 0.3618 0.4473 0.00 0.00 0.00 0.02 0.00 0.38 0.00 0.60
#> TCGA.44.A4SU.01 4 0.3862 0.4907 0.36 0.00 0.00 0.60 0.00 0.04 0.00 0.00
#> TCGA.L9.A444.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8668.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5072.01 4 0.1947 0.6739 0.14 0.00 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.55.8512.01 3 0.2224 0.7902 0.12 0.00 0.86 0.02 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.6849.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6146.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6986.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.44.2665.01 5 0.0808 0.8993 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.86.8279.01 6 0.0471 0.7259 0.00 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.05.5425.01 6 0.0471 0.7366 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.62.A46R.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6148.01 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A494.01 7 0.1563 0.6933 0.00 0.00 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.44.3917.01 7 0.3594 0.5261 0.00 0.28 0.00 0.00 0.00 0.04 0.68 0.00
#> TCGA.69.8254.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.53.7624.01 4 0.2132 0.6702 0.08 0.00 0.00 0.88 0.00 0.00 0.00 0.04
#> TCGA.75.5125.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8054.01 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.L4.A4E5.01 6 0.4588 0.3885 0.00 0.12 0.00 0.00 0.00 0.54 0.34 0.00
#> TCGA.44.6775.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7913.01 6 0.0941 0.7219 0.00 0.00 0.00 0.02 0.02 0.96 0.00 0.00
#> TCGA.55.7911.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8621.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T9.01 1 0.2650 0.5807 0.76 0.00 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.55.6712.01 2 0.2406 0.6933 0.00 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.78.8640.01 6 0.1947 0.7297 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.44.7670.01 4 0.2650 0.6530 0.24 0.00 0.00 0.76 0.00 0.00 0.00 0.00
#> TCGA.69.7760.01 6 0.0808 0.7300 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.95.7948.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M5.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.55.A4DG.01 2 0.3015 0.4741 0.00 0.68 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.55.7816.01 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6593.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7711.01 4 0.3272 0.2690 0.42 0.00 0.00 0.58 0.00 0.00 0.00 0.00
#> TCGA.05.5423.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TJ.01 1 0.0808 0.8571 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.44.2656.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6778.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6985.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.38.4631.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A5IP.01 4 0.3618 0.4648 0.38 0.00 0.00 0.60 0.00 0.02 0.00 0.00
#> TCGA.55.8615.01 8 0.3658 0.4175 0.00 0.00 0.00 0.02 0.00 0.40 0.00 0.58
#> TCGA.93.7347.01 5 0.1765 0.8237 0.12 0.00 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.MP.A4TF.01 6 0.2482 0.7025 0.00 0.00 0.00 0.02 0.06 0.88 0.02 0.02
#> TCGA.91.6829.01 7 0.2648 0.7553 0.00 0.08 0.00 0.00 0.00 0.00 0.84 0.08
#> TCGA.62.A471.01 8 0.3690 0.3750 0.00 0.00 0.00 0.02 0.00 0.42 0.00 0.56
#> TCGA.49.4490.01 1 0.3272 0.1388 0.58 0.00 0.00 0.42 0.00 0.00 0.00 0.00
#> TCGA.97.8177.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.7458.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.A4BD.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.44.A47B.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7542.01 7 0.2719 0.7473 0.00 0.02 0.00 0.00 0.00 0.00 0.80 0.18
#> TCGA.55.7573.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7633.01 8 0.2569 0.7253 0.00 0.00 0.00 0.16 0.00 0.02 0.00 0.82
#> TCGA.86.7953.01 1 0.3397 0.7449 0.80 0.00 0.00 0.10 0.06 0.04 0.00 0.00
#> TCGA.55.6970.01 1 0.1557 0.8494 0.92 0.00 0.00 0.06 0.00 0.02 0.00 0.00
#> TCGA.78.7160.01 1 0.1563 0.8515 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.50.5946.02 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.50.5946.01 8 0.3237 0.3962 0.00 0.00 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.50.5066.02 6 0.0808 0.7382 0.00 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.50.5066.01 1 0.1947 0.8269 0.86 0.00 0.00 0.14 0.00 0.00 0.00 0.00
#> TCGA.97.8179.01 6 0.1557 0.7002 0.00 0.00 0.00 0.02 0.06 0.92 0.00 0.00
#> TCGA.86.A4JF.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8092.01 7 0.2719 0.7473 0.00 0.02 0.00 0.00 0.00 0.00 0.80 0.18
#> TCGA.75.6207.01 7 0.2888 0.7488 0.00 0.04 0.00 0.00 0.00 0.00 0.80 0.16
#> TCGA.44.2665.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5122.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.7938.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AARE.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.55.7726.01 5 0.0941 0.9077 0.02 0.00 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.91.8499.01 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.MP.A4TH.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7764.01 6 0.4059 0.3454 0.00 0.00 0.00 0.28 0.00 0.64 0.00 0.08
#> TCGA.95.7043.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.86.7701.01 2 0.1275 0.9013 0.00 0.94 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.49.4512.01 1 0.3015 0.4509 0.68 0.00 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.L9.A50W.01 5 0.1563 0.8494 0.00 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.50.8460.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8505.01 4 0.3272 0.2690 0.42 0.00 0.00 0.58 0.00 0.00 0.00 0.00
#> TCGA.86.A4P8.01 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.6217.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7281.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7535.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8671.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6592.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.7546.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.95.7944.01 1 0.1765 0.8431 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.38.4632.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8280.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7153.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2655.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7907.01 2 0.0808 0.9204 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.49.6767.01 6 0.1947 0.7297 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.78.7155.01 4 0.2534 0.5303 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.91.6835.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5051.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.78.7540.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5939.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VN.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6145.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47F.01 6 0.1091 0.7194 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.55.A48Z.01 1 0.1563 0.8366 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.44.8119.01 8 0.2114 0.7274 0.00 0.00 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.69.8253.01 5 0.2650 0.6732 0.00 0.00 0.00 0.00 0.76 0.24 0.00 0.00
#> TCGA.J2.A4AE.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6203.01 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5942.01 1 0.1947 0.7339 0.86 0.00 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.50.6590.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.78.7148.01 4 0.3142 0.4217 0.36 0.00 0.00 0.64 0.00 0.00 0.00 0.00
#> TCGA.80.5608.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.55.8205.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7669.01 4 0.2534 0.5303 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.50.6594.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2668.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6830.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8055.01 4 0.2719 0.5860 0.00 0.00 0.00 0.80 0.00 0.18 0.00 0.02
#> TCGA.49.4488.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7159.01 7 0.1091 0.7320 0.00 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.44.6774.01 1 0.0808 0.8704 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.44.8120.01 6 0.2025 0.6896 0.00 0.00 0.00 0.00 0.10 0.88 0.02 0.00
#> TCGA.69.7763.01 5 0.2534 0.6593 0.00 0.22 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.64.5815.01 5 0.0808 0.8993 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.69.7761.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.A9RS.01 6 0.1947 0.7297 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.69.7978.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.8299.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8117.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR2.01 4 0.2267 0.6625 0.18 0.00 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.55.A490.01 8 0.2756 0.4618 0.00 0.00 0.00 0.00 0.00 0.00 0.26 0.74
#> TCGA.83.5908.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6980.01 3 0.3971 0.1754 0.42 0.00 0.54 0.04 0.00 0.00 0.00 0.00
#> TCGA.44.6146.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8669.01 8 0.3618 0.4546 0.00 0.00 0.00 0.02 0.00 0.38 0.00 0.60
#> TCGA.95.7039.01 2 0.3142 0.3762 0.00 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.62.8397.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6848.01 5 0.4952 0.2181 0.00 0.00 0.00 0.30 0.50 0.20 0.00 0.00
#> TCGA.71.6725.01 7 0.2719 0.7473 0.00 0.02 0.00 0.00 0.00 0.00 0.80 0.18
#> TCGA.97.7552.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5936.01 4 0.2267 0.6625 0.18 0.00 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.91.7771.01 6 0.0808 0.7300 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.86.8359.01 6 0.0471 0.7366 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.55.8301.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7146.01 7 0.1341 0.7161 0.00 0.00 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.44.3918.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5935.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7974.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7161.01 7 0.1091 0.7320 0.00 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.55.8614.01 6 0.4873 0.0298 0.00 0.00 0.00 0.36 0.00 0.48 0.00 0.16
#> TCGA.97.7937.01 7 0.2725 0.7217 0.00 0.14 0.00 0.00 0.00 0.00 0.82 0.04
#> TCGA.49.AARR.01 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5147.01 4 0.4096 0.5219 0.02 0.00 0.00 0.68 0.00 0.24 0.00 0.06
#> TCGA.49.6745.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.6979.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8094.01 8 0.1091 0.7171 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.55.7574.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.5644.01 7 0.1091 0.7320 0.00 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.55.8511.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7671.01 6 0.2071 0.6879 0.00 0.00 0.00 0.04 0.02 0.90 0.00 0.04
#> TCGA.78.8648.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 6 0.0941 0.7361 0.00 0.00 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.44.2656.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J2.A4AD.01 4 0.2025 0.6264 0.02 0.00 0.00 0.88 0.00 0.00 0.00 0.10
#> TCGA.49.6743.01 5 0.3185 0.7792 0.08 0.00 0.00 0.06 0.82 0.04 0.00 0.00
#> TCGA.86.8673.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 6 0.0471 0.7311 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.L9.A7SV.01 7 0.2406 0.7271 0.00 0.00 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.97.A4LX.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.38.4631.01 4 0.2650 0.6519 0.24 0.00 0.00 0.76 0.00 0.00 0.00 0.00
#> TCGA.99.AA5R.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4390.01 7 0.1091 0.7320 0.00 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.MP.A4T7.01 5 0.0471 0.9207 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.69.7765.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.8494.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8171.01 6 0.1275 0.7133 0.00 0.00 0.00 0.04 0.02 0.94 0.00 0.00
#> TCGA.50.8457.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6972.01 4 0.0471 0.6644 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.69.7979.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.62.A46P.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7980.01 6 0.2267 0.7184 0.00 0.00 0.00 0.00 0.00 0.82 0.18 0.00
#> TCGA.97.8547.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 2 0.3675 0.4651 0.00 0.66 0.00 0.00 0.00 0.30 0.04 0.00
#> TCGA.50.5932.01 6 0.3514 0.3283 0.00 0.00 0.00 0.34 0.02 0.64 0.00 0.00
#> TCGA.97.8175.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.7109.01 6 0.0471 0.7366 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.44.A47A.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8508.01 6 0.3193 0.5595 0.00 0.00 0.00 0.00 0.00 0.62 0.38 0.00
#> TCGA.78.7220.01 4 0.2534 0.5303 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.93.A4JO.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6145.01 5 0.3083 0.5160 0.34 0.00 0.00 0.00 0.66 0.00 0.00 0.00
#> TCGA.44.6147.01 5 0.3193 0.3907 0.00 0.38 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.86.8075.01 1 0.2534 0.6822 0.78 0.00 0.00 0.22 0.00 0.00 0.00 0.00
#> TCGA.55.7724.01 5 0.3142 0.4720 0.36 0.00 0.00 0.00 0.64 0.00 0.00 0.00
#> TCGA.75.6211.01 7 0.1275 0.7420 0.00 0.02 0.00 0.00 0.00 0.04 0.94 0.00
#> TCGA.55.8510.01 5 0.0471 0.9207 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.55.8085.01 8 0.3658 0.4175 0.00 0.00 0.00 0.02 0.00 0.40 0.00 0.58
#> TCGA.55.8090.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 5 0.1765 0.8055 0.00 0.12 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.91.6828.01 7 0.3142 0.4936 0.00 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.49.4514.01 6 0.6318 -0.0383 0.30 0.00 0.00 0.10 0.30 0.30 0.00 0.00
#> TCGA.05.4396.01 7 0.2719 0.7473 0.00 0.02 0.00 0.00 0.00 0.00 0.80 0.18
#> TCGA.MN.A4N4.01 7 0.3329 0.1397 0.00 0.48 0.00 0.00 0.00 0.00 0.52 0.00
#> TCGA.55.8204.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.5643.01 4 0.4943 0.1369 0.00 0.00 0.00 0.48 0.00 0.34 0.00 0.18
#> TCGA.L4.A4E6.01 3 0.0471 0.9405 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8076.01 5 0.2267 0.7549 0.18 0.00 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7031.01 4 0.1947 0.6030 0.00 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.50.5044.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.64.5781.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.4658.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.01 1 0.1765 0.8382 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 6 0.3083 0.6031 0.00 0.00 0.00 0.00 0.00 0.66 0.34 0.00
#> TCGA.49.AAR3.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7154.01 2 0.0808 0.9204 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.05.4384.01 1 0.4141 0.3478 0.56 0.00 0.00 0.38 0.00 0.06 0.00 0.00
#> TCGA.55.6971.01 5 0.2404 0.7884 0.14 0.00 0.00 0.00 0.84 0.02 0.00 0.00
#> TCGA.55.A4DF.01 8 0.3291 0.6127 0.00 0.00 0.00 0.28 0.00 0.02 0.00 0.70
#> TCGA.44.7667.01 6 0.4380 0.5488 0.00 0.00 0.00 0.00 0.00 0.58 0.32 0.10
#> TCGA.44.6148.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5939.01 1 0.4097 0.6691 0.70 0.00 0.00 0.20 0.08 0.02 0.00 0.00
#> TCGA.O1.A52J.01 1 0.1341 0.8474 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7167.01 8 0.2650 0.4826 0.00 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.78.8662.01 7 0.0000 0.7460 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.05.4427.01 7 0.2719 0.7473 0.00 0.02 0.00 0.00 0.00 0.00 0.80 0.18
#> TCGA.78.7143.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 6 0.0471 0.7311 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.1947 0.8269 0.86 0.00 0.00 0.14 0.00 0.00 0.00 0.00
#> TCGA.86.7714.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8585.01 4 0.3272 0.2690 0.42 0.00 0.00 0.58 0.00 0.00 0.00 0.00
#> TCGA.75.6205.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.8028.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 5 0.1947 0.7778 0.00 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.78.7147.01 7 0.2267 0.6915 0.00 0.18 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.75.5126.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6591.01 4 0.2267 0.5697 0.00 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.55.8206.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.97.7553.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 7 0.1275 0.7420 0.00 0.02 0.00 0.00 0.00 0.04 0.94 0.00
#> TCGA.NJ.A4YQ.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A7XG.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A48X.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8514.01 8 0.1091 0.6708 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.50.5944.01 1 0.0471 0.8799 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.49.AAR9.01 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.50.6594.01 6 0.0941 0.7361 0.00 0.00 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.86.8056.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VK.01 6 0.3237 0.5404 0.00 0.00 0.00 0.00 0.00 0.60 0.40 0.00
#> TCGA.49.4488.01 7 0.2719 0.6910 0.00 0.18 0.00 0.00 0.00 0.02 0.80 0.00
#> TCGA.55.7728.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7994.01 2 0.3333 -0.1087 0.00 0.50 0.00 0.00 0.00 0.00 0.50 0.00
#> TCGA.67.6215.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.78.7537.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8097.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.05.4424.01 4 0.3299 0.2013 0.44 0.00 0.00 0.56 0.00 0.00 0.00 0.00
#> TCGA.55.7227.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 5 0.0808 0.8995 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.44.5645.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.35.5375.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.75.6214.01 8 0.2852 0.4245 0.00 0.00 0.00 0.00 0.00 0.00 0.28 0.72
#> TCGA.80.5611.01 8 0.1765 0.7265 0.00 0.00 0.00 0.12 0.00 0.00 0.00 0.88
#> TCGA.49.AAQV.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6742.01 4 0.1765 0.6158 0.00 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.73.7498.01 1 0.0808 0.8723 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.38.4632.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5936.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4B.A93V.01 4 0.4877 0.2479 0.06 0.00 0.00 0.48 0.00 0.42 0.00 0.04
#> TCGA.MP.A4T6.01 2 0.0471 0.9386 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.86.A4D0.01 6 0.2534 0.6987 0.00 0.00 0.00 0.00 0.00 0.78 0.22 0.00
#> TCGA.62.A46O.01 8 0.3193 0.4669 0.00 0.00 0.00 0.38 0.00 0.00 0.00 0.62
#> TCGA.44.6779.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.6761.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.7348.01 5 0.3237 0.3754 0.40 0.00 0.00 0.00 0.60 0.00 0.00 0.00
#> TCGA.99.8032.01 6 0.1091 0.7384 0.00 0.00 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.50.5935.01 5 0.2406 0.7190 0.00 0.00 0.00 0.00 0.80 0.20 0.00 0.00
#> TCGA.55.6981.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.8655.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7163.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.97.7941.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 1 0.1765 0.8184 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.97.8174.01 1 0.3385 0.6816 0.76 0.00 0.00 0.08 0.16 0.00 0.00 0.00
#> TCGA.75.5146.01 6 0.4537 0.0532 0.00 0.00 0.00 0.40 0.10 0.50 0.00 0.00
#> TCGA.50.5931.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7914.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6840.01 4 0.2025 0.6747 0.10 0.00 0.00 0.88 0.00 0.00 0.00 0.02
#> TCGA.62.A472.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.5779.01 8 0.3594 0.5826 0.00 0.00 0.00 0.04 0.00 0.28 0.00 0.68
#> TCGA.05.4417.01 2 0.1275 0.9013 0.00 0.94 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.67.4679.01 5 0.0471 0.9208 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.64.5774.01 8 0.2114 0.7274 0.00 0.00 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.55.8620.01 7 0.2267 0.7282 0.00 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.55.7570.01 4 0.2534 0.5303 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.97.7554.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SY.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.93.A4JP.01 1 0.1765 0.8382 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.55.5899.01 8 0.1563 0.6381 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.95.8039.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6144.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5941.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.8399.01 4 0.2534 0.5303 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.95.7562.01 7 0.3830 0.6997 0.00 0.16 0.00 0.00 0.00 0.02 0.74 0.08
#> TCGA.75.7030.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.55.7576.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.38.A44F.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.80.5607.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.93.8067.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8395.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6212.01 1 0.3015 0.5192 0.68 0.00 0.32 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2666.01 2 0.1563 0.8420 0.00 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.50.5930.01 4 0.3272 0.2690 0.42 0.00 0.00 0.58 0.00 0.00 0.00 0.00
#> TCGA.55.7284.01 5 0.3618 0.3743 0.00 0.00 0.00 0.02 0.60 0.38 0.00 0.00
#> TCGA.44.6777.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6776.01 1 0.3975 0.4759 0.66 0.00 0.00 0.26 0.00 0.08 0.00 0.00
#> TCGA.55.6983.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5932.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.01 2 0.3083 0.4267 0.00 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.91.6836.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 2 0.3193 0.3179 0.00 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.38.7271.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5045.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A491.01 6 0.4511 0.2314 0.00 0.38 0.00 0.00 0.00 0.52 0.10 0.00
#> TCGA.78.7150.01 4 0.2534 0.5303 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.86.8674.01 4 0.2114 0.6700 0.16 0.00 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YG.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A4SS.01 1 0.2534 0.7550 0.78 0.00 0.00 0.22 0.00 0.00 0.00 0.00
#> TCGA.55.A492.01 6 0.0941 0.7219 0.00 0.00 0.00 0.02 0.02 0.96 0.00 0.00
#> TCGA.53.7626.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6969.01 4 0.3095 0.6190 0.24 0.00 0.00 0.74 0.00 0.02 0.00 0.00
#> TCGA.78.7166.01 4 0.0808 0.6501 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.A48Y.01 6 0.2569 0.5950 0.00 0.00 0.00 0.02 0.16 0.82 0.00 0.00
#> TCGA.44.5643.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 7 0.2719 0.7473 0.00 0.02 0.00 0.00 0.00 0.00 0.80 0.18
#> TCGA.50.6595.01 5 0.3015 0.5522 0.32 0.00 0.00 0.00 0.68 0.00 0.00 0.00
#> TCGA.55.6543.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6592.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5049.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.4658.01 2 0.1091 0.8938 0.00 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.97.A4M2.01 1 0.1341 0.8599 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.55.8513.01 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8402.01 6 0.3272 0.5157 0.00 0.00 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.55.7995.01 6 0.1947 0.7297 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.05.5420.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.A456.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7536.01 8 0.2267 0.7240 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.L9.A8F4.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7156.01 4 0.0000 0.6561 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7662.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8506.01 2 0.3083 0.4267 0.00 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.50.5068.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T4.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.53.7813.01 6 0.3198 0.5325 0.00 0.00 0.00 0.00 0.26 0.72 0.02 0.00
#> TCGA.NJ.A55A.01 5 0.2114 0.7773 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.71.8520.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7955.01 8 0.3083 0.3128 0.00 0.00 0.00 0.00 0.00 0.00 0.34 0.66
#> TCGA.55.7815.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7672.01 2 0.1947 0.7857 0.00 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.97.8172.01 2 0.0471 0.9380 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.6987.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.64.1681.01 1 0.2981 0.6598 0.76 0.00 0.00 0.22 0.00 0.02 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.8854 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5715.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7152.01 2 0.0000 0.9540 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 7 0.1091 0.7320 0.00 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.62.A46S.01 6 0.0471 0.7366 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.95.7947.01 6 0.1804 0.6841 0.00 0.00 0.00 0.02 0.08 0.90 0.00 0.00
#> TCGA.J2.8192.01 1 0.1341 0.8474 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.78.7145.01 6 0.1408 0.7282 0.00 0.00 0.00 0.02 0.02 0.94 0.02 0.00
#> TCGA.50.6593.01 5 0.0000 0.9354 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7973.01 6 0.0471 0.7259 0.00 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.50.6591.11 3 0.0000 0.9650 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7713.01 6 0.3570 0.1718 0.00 0.00 0.00 0.02 0.00 0.62 0.00 0.36
#> TCGA.55.8302.01 2 0.2406 0.6934 0.00 0.80 0.00 0.00 0.20 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node031 , Node032 .
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 154 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 0.4763 0.524 0.524
#> 3 3 0.944 0.973 0.961 0.1276 0.931 0.868
#> 4 4 0.758 0.837 0.895 0.1370 0.998 0.996
#> 5 5 0.733 0.731 0.862 0.0903 0.868 0.709
#> 6 6 0.650 0.750 0.859 0.0772 0.914 0.747
#> 7 7 0.581 0.675 0.801 0.0250 0.973 0.909
#> 8 8 0.612 0.630 0.789 0.0336 0.988 0.959
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.44.6778.01 2 0 1 0 1
#> TCGA.55.6975.01 2 0 1 0 1
#> TCGA.99.8033.01 1 0 1 1 0
#> TCGA.69.8255.01 2 0 1 0 1
#> TCGA.69.8453.01 2 0 1 0 1
#> TCGA.78.7162.01 2 0 1 0 1
#> TCGA.75.7025.01 2 0 1 0 1
#> TCGA.55.8096.01 1 0 1 1 0
#> TCGA.93.A4JQ.01 2 0 1 0 1
#> TCGA.55.8208.01 1 0 1 1 0
#> TCGA.49.AAR4.01 2 0 1 0 1
#> TCGA.64.1679.01 1 0 1 1 0
#> TCGA.55.6984.01 1 0 1 1 0
#> TCGA.49.AARO.01 1 0 1 1 0
#> TCGA.75.6206.01 2 0 1 0 1
#> TCGA.49.6744.01 1 0 1 1 0
#> TCGA.L9.A743.01 2 0 1 0 1
#> TCGA.86.7954.01 1 0 1 1 0
#> TCGA.55.7910.01 1 0 1 1 0
#> TCGA.64.5778.01 2 0 1 0 1
#> TCGA.44.A479.01 1 0 1 1 0
#> TCGA.55.8087.01 1 0 1 1 0
#> TCGA.55.8091.01 2 0 1 0 1
#> TCGA.55.8619.01 1 0 1 1 0
#> TCGA.49.AAR0.01 2 0 1 0 1
#> TCGA.44.A4SU.01 1 0 1 1 0
#> TCGA.50.5072.01 2 0 1 0 1
#> TCGA.91.6849.01 1 0 1 1 0
#> TCGA.69.8254.01 2 0 1 0 1
#> TCGA.53.7624.01 1 0 1 1 0
#> TCGA.55.8621.01 1 0 1 1 0
#> TCGA.S2.AA1A.01 1 0 1 1 0
#> TCGA.MP.A4T9.01 1 0 1 1 0
#> TCGA.44.7670.01 1 0 1 1 0
#> TCGA.97.A4M5.01 2 0 1 0 1
#> TCGA.86.7711.01 2 0 1 0 1
#> TCGA.05.5423.01 2 0 1 0 1
#> TCGA.MP.A4TJ.01 1 0 1 1 0
#> TCGA.L9.A5IP.01 1 0 1 1 0
#> TCGA.93.7347.01 1 0 1 1 0
#> TCGA.49.4490.01 1 0 1 1 0
#> TCGA.97.8177.01 1 0 1 1 0
#> TCGA.91.A4BD.01 2 0 1 0 1
#> TCGA.55.7573.01 1 0 1 1 0
#> TCGA.86.7953.01 1 0 1 1 0
#> TCGA.55.6970.01 1 0 1 1 0
#> TCGA.78.7160.01 2 0 1 0 1
#> TCGA.50.5066.01 2 0 1 0 1
#> TCGA.97.7938.01 1 0 1 1 0
#> TCGA.55.7726.01 1 0 1 1 0
#> TCGA.MP.A4TH.01 1 0 1 1 0
#> TCGA.91.8496.01 1 0 1 1 0
#> TCGA.49.4512.01 1 0 1 1 0
#> TCGA.L9.A50W.01 2 0 1 0 1
#> TCGA.50.8460.01 2 0 1 0 1
#> TCGA.55.8505.01 2 0 1 0 1
#> TCGA.67.6217.01 1 0 1 1 0
#> TCGA.86.8671.01 1 0 1 1 0
#> TCGA.97.7546.01 1 0 1 1 0
#> TCGA.95.7944.01 2 0 1 0 1
#> TCGA.86.8280.01 1 0 1 1 0
#> TCGA.91.6835.01 1 0 1 1 0
#> TCGA.55.A48Z.01 1 0 1 1 0
#> TCGA.50.5942.01 1 0 1 1 0
#> TCGA.78.7148.01 2 0 1 0 1
#> TCGA.91.6830.01 1 0 1 1 0
#> TCGA.44.6774.01 1 0 1 1 0
#> TCGA.55.8299.01 1 0 1 1 0
#> TCGA.49.AAR2.01 2 0 1 0 1
#> TCGA.44.6146.01 2 0 1 0 1
#> TCGA.62.8397.01 1 0 1 1 0
#> TCGA.91.6848.01 2 0 1 0 1
#> TCGA.97.7552.01 2 0 1 0 1
#> TCGA.50.5936.01 2 0 1 0 1
#> TCGA.55.6979.01 1 0 1 1 0
#> TCGA.50.8459.01 2 0 1 0 1
#> TCGA.78.8648.01 1 0 1 1 0
#> TCGA.49.6743.01 1 0 1 1 0
#> TCGA.97.A4LX.01 2 0 1 0 1
#> TCGA.38.4631.01 1 0 1 1 0
#> TCGA.99.AA5R.01 1 0 1 1 0
#> TCGA.MP.A4T7.01 1 0 1 1 0
#> TCGA.50.8457.01 1 0 1 1 0
#> TCGA.50.5932.01 2 0 1 0 1
#> TCGA.NJ.A55O.01 1 0 1 1 0
#> TCGA.93.A4JO.01 2 0 1 0 1
#> TCGA.44.6145.01 1 0 1 1 0
#> TCGA.86.8075.01 1 0 1 1 0
#> TCGA.55.7724.01 1 0 1 1 0
#> TCGA.55.8510.01 1 0 1 1 0
#> TCGA.49.4514.01 1 0 1 1 0
#> TCGA.55.8204.01 1 0 1 1 0
#> TCGA.86.8076.01 2 0 1 0 1
#> TCGA.97.A4M6.01 1 0 1 1 0
#> TCGA.50.5044.01 1 0 1 1 0
#> TCGA.05.5420.01 2 0 1 0 1
#> TCGA.49.AAR3.01 2 0 1 0 1
#> TCGA.05.4384.01 2 0 1 0 1
#> TCGA.55.6971.01 1 0 1 1 0
#> TCGA.50.5939.01 2 0 1 0 1
#> TCGA.O1.A52J.01 1 0 1 1 0
#> TCGA.91.8497.01 1 0 1 1 0
#> TCGA.MP.A4T2.01 2 0 1 0 1
#> TCGA.86.7714.01 1 0 1 1 0
#> TCGA.86.8585.01 2 0 1 0 1
#> TCGA.99.8028.01 1 0 1 1 0
#> TCGA.49.4487.01 1 0 1 1 0
#> TCGA.55.8206.01 2 0 1 0 1
#> TCGA.97.7553.01 1 0 1 1 0
#> TCGA.50.5944.01 1 0 1 1 0
#> TCGA.55.7728.01 1 0 1 1 0
#> TCGA.78.7537.01 2 0 1 0 1
#> TCGA.55.8097.01 1 0 1 1 0
#> TCGA.05.4424.01 2 0 1 0 1
#> TCGA.44.5645.01 1 0 1 1 0
#> TCGA.49.AAQV.01 1 0 1 1 0
#> TCGA.73.7498.01 1 0 1 1 0
#> TCGA.97.7547.01 1 0 1 1 0
#> TCGA.93.7348.01 1 0 1 1 0
#> TCGA.78.7163.01 2 0 1 0 1
#> TCGA.97.7941.01 1 0 1 1 0
#> TCGA.MP.A4TA.01 1 0 1 1 0
#> TCGA.97.8174.01 2 0 1 0 1
#> TCGA.91.6840.01 1 0 1 1 0
#> TCGA.93.A4JP.01 2 0 1 0 1
#> TCGA.50.5941.01 1 0 1 1 0
#> TCGA.75.7030.01 2 0 1 0 1
#> TCGA.55.7725.01 1 0 1 1 0
#> TCGA.38.A44F.01 2 0 1 0 1
#> TCGA.50.5930.01 2 0 1 0 1
#> TCGA.55.7284.01 2 0 1 0 1
#> TCGA.44.6776.01 1 0 1 1 0
#> TCGA.50.5055.01 1 0 1 1 0
#> TCGA.50.5045.01 1 0 1 1 0
#> TCGA.86.8674.01 2 0 1 0 1
#> TCGA.44.A4SS.01 2 0 1 0 1
#> TCGA.55.A492.01 1 0 1 1 0
#> TCGA.53.7626.01 1 0 1 1 0
#> TCGA.55.6969.01 2 0 1 0 1
#> TCGA.50.6595.01 1 0 1 1 0
#> TCGA.55.6543.01 1 0 1 1 0
#> TCGA.50.5049.01 2 0 1 0 1
#> TCGA.97.A4M2.01 2 0 1 0 1
#> TCGA.L9.A8F4.01 1 0 1 1 0
#> TCGA.50.5068.01 1 0 1 1 0
#> TCGA.MP.A4T4.01 1 0 1 1 0
#> TCGA.53.7813.01 1 0 1 1 0
#> TCGA.NJ.A55A.01 1 0 1 1 0
#> TCGA.55.6987.01 2 0 1 0 1
#> TCGA.64.1681.01 1 0 1 1 0
#> TCGA.95.A4VP.01 1 0 1 1 0
#> TCGA.95.7947.01 2 0 1 0 1
#> TCGA.J2.8192.01 1 0 1 1 0
#> TCGA.50.6593.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.6778.01 3 0.2537 0.833 0.00 0.08 0.92
#> TCGA.55.6975.01 3 0.4291 0.929 0.00 0.18 0.82
#> TCGA.99.8033.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.69.8255.01 3 0.4291 0.929 0.00 0.18 0.82
#> TCGA.69.8453.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.78.7162.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.75.7025.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.55.8096.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.93.A4JQ.01 3 0.5706 0.840 0.00 0.32 0.68
#> TCGA.55.8208.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.49.AAR4.01 2 0.4002 0.799 0.00 0.84 0.16
#> TCGA.64.1679.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.6984.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.AARO.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.75.6206.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.49.6744.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.L9.A743.01 2 0.1529 0.939 0.00 0.96 0.04
#> TCGA.86.7954.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.7910.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.64.5778.01 2 0.0892 0.960 0.00 0.98 0.02
#> TCGA.44.A479.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.8087.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.8091.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.55.8619.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.AAR0.01 2 0.2537 0.912 0.00 0.92 0.08
#> TCGA.44.A4SU.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.50.5072.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.91.6849.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.69.8254.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.53.7624.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.8621.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4T9.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.44.7670.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.97.A4M5.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.86.7711.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.05.5423.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.MP.A4TJ.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.93.7347.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.4490.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.97.8177.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.91.A4BD.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.55.7573.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.7953.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.6970.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.78.7160.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.50.5066.01 2 0.4555 0.748 0.00 0.80 0.20
#> TCGA.97.7938.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.7726.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.MP.A4TH.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.4512.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.L9.A50W.01 2 0.2959 0.869 0.00 0.90 0.10
#> TCGA.50.8460.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.55.8505.01 3 0.4555 0.944 0.00 0.20 0.80
#> TCGA.67.6217.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8671.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.97.7546.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.95.7944.01 3 0.5216 0.917 0.00 0.26 0.74
#> TCGA.86.8280.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.91.6835.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.A48Z.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.50.5942.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.7148.01 2 0.0892 0.960 0.00 0.98 0.02
#> TCGA.91.6830.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.44.6774.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.8299.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.AAR2.01 3 0.0892 0.778 0.00 0.02 0.98
#> TCGA.44.6146.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.62.8397.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.91.6848.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.97.7552.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.50.5936.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.55.6979.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.50.8459.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.78.8648.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.6743.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.97.A4LX.01 2 0.1529 0.938 0.00 0.96 0.04
#> TCGA.38.4631.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.99.AA5R.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4T7.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.8457.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5932.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.NJ.A55O.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.93.A4JO.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.44.6145.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8075.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.7724.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.8510.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.49.4514.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.8204.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8076.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5044.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.05.5420.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.49.AAR3.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.05.4384.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.55.6971.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5939.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.O1.A52J.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.91.8497.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4T2.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.86.7714.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8585.01 3 0.4555 0.944 0.00 0.20 0.80
#> TCGA.99.8028.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.4487.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.8206.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.97.7553.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5944.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.55.7728.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.7537.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.55.8097.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.05.4424.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.44.5645.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.AAQV.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.73.7498.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.97.7547.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.93.7348.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.7163.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.97.7941.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4TA.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.97.8174.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.91.6840.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.93.A4JP.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.50.5941.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.75.7030.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.55.7725.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.38.A44F.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.50.5930.01 3 0.4796 0.950 0.00 0.22 0.78
#> TCGA.55.7284.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.44.6776.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5045.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8674.01 3 0.4555 0.944 0.00 0.20 0.80
#> TCGA.44.A4SS.01 3 0.5216 0.917 0.00 0.26 0.74
#> TCGA.55.A492.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.53.7626.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.6969.01 3 0.4555 0.944 0.00 0.20 0.80
#> TCGA.50.6595.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.6543.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5049.01 3 0.5835 0.804 0.00 0.34 0.66
#> TCGA.97.A4M2.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.L9.A8F4.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.50.5068.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4T4.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.53.7813.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.NJ.A55A.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.6987.01 3 0.5016 0.936 0.00 0.24 0.76
#> TCGA.64.1681.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.95.A4VP.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.95.7947.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.J2.8192.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.50.6593.01 1 0.0000 0.993 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.44.6778.01 3 0.4277 -0.189 0.00 0.00 0.72 0.28
#> TCGA.55.6975.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.99.8033.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.69.8255.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.69.8453.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.78.7162.01 2 0.2011 0.903 0.00 0.92 0.00 0.08
#> TCGA.75.7025.01 2 0.2345 0.897 0.00 0.90 0.00 0.10
#> TCGA.55.8096.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.93.A4JQ.01 3 0.2011 0.832 0.00 0.08 0.92 0.00
#> TCGA.55.8208.01 1 0.4406 0.774 0.70 0.00 0.00 0.30
#> TCGA.49.AAR4.01 2 0.5677 0.668 0.00 0.72 0.14 0.14
#> TCGA.64.1679.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.55.6984.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.49.AARO.01 1 0.3801 0.818 0.78 0.00 0.00 0.22
#> TCGA.75.6206.01 2 0.2345 0.897 0.00 0.90 0.00 0.10
#> TCGA.49.6744.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 2 0.3172 0.829 0.00 0.84 0.00 0.16
#> TCGA.86.7954.01 1 0.4277 0.785 0.72 0.00 0.00 0.28
#> TCGA.55.7910.01 1 0.4277 0.790 0.72 0.00 0.00 0.28
#> TCGA.64.5778.01 2 0.4553 0.755 0.00 0.78 0.18 0.04
#> TCGA.44.A479.01 1 0.4277 0.785 0.72 0.00 0.00 0.28
#> TCGA.55.8087.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.55.8091.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.55.8619.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 2 0.7249 0.455 0.00 0.54 0.20 0.26
#> TCGA.44.A4SU.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.50.5072.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.91.6849.01 1 0.0707 0.873 0.98 0.00 0.00 0.02
#> TCGA.69.8254.01 2 0.1211 0.912 0.00 0.96 0.00 0.04
#> TCGA.53.7624.01 1 0.4713 0.744 0.64 0.00 0.00 0.36
#> TCGA.55.8621.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.S2.AA1A.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.MP.A4T9.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.44.7670.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.97.A4M5.01 2 0.0707 0.909 0.00 0.98 0.02 0.00
#> TCGA.86.7711.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.05.5423.01 2 0.2011 0.903 0.00 0.92 0.00 0.08
#> TCGA.MP.A4TJ.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.4713 0.744 0.64 0.00 0.00 0.36
#> TCGA.93.7347.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.49.4490.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.97.8177.01 1 0.4134 0.795 0.74 0.00 0.00 0.26
#> TCGA.91.A4BD.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.55.7573.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.86.7953.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.55.6970.01 1 0.4406 0.774 0.70 0.00 0.00 0.30
#> TCGA.78.7160.01 2 0.0707 0.909 0.00 0.98 0.02 0.00
#> TCGA.50.5066.01 2 0.6122 0.593 0.00 0.68 0.16 0.16
#> TCGA.97.7938.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.55.7726.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.MP.A4TH.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.49.4512.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 2 0.4642 0.767 0.00 0.74 0.02 0.24
#> TCGA.50.8460.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.55.8505.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.67.6217.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.86.8671.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.97.7546.01 1 0.1637 0.867 0.94 0.00 0.00 0.06
#> TCGA.95.7944.01 3 0.2011 0.832 0.00 0.08 0.92 0.00
#> TCGA.86.8280.01 1 0.4406 0.775 0.70 0.00 0.00 0.30
#> TCGA.91.6835.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.55.A48Z.01 1 0.4406 0.774 0.70 0.00 0.00 0.30
#> TCGA.50.5942.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.78.7148.01 2 0.3821 0.835 0.00 0.84 0.12 0.04
#> TCGA.91.6830.01 1 0.4406 0.774 0.70 0.00 0.00 0.30
#> TCGA.44.6774.01 1 0.3400 0.829 0.82 0.00 0.00 0.18
#> TCGA.55.8299.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.49.AAR2.01 4 0.4994 0.000 0.00 0.00 0.48 0.52
#> TCGA.44.6146.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.62.8397.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.91.6848.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.97.7552.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.50.5936.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.55.6979.01 1 0.2921 0.843 0.86 0.00 0.00 0.14
#> TCGA.50.8459.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.78.8648.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.49.6743.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.97.A4LX.01 2 0.3172 0.792 0.00 0.84 0.16 0.00
#> TCGA.38.4631.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.99.AA5R.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.MP.A4T7.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.50.8457.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.50.5932.01 2 0.2345 0.897 0.00 0.90 0.00 0.10
#> TCGA.NJ.A55O.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.44.6145.01 1 0.1211 0.875 0.96 0.00 0.00 0.04
#> TCGA.86.8075.01 1 0.4277 0.785 0.72 0.00 0.00 0.28
#> TCGA.55.7724.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.55.8510.01 1 0.3400 0.829 0.82 0.00 0.00 0.18
#> TCGA.49.4514.01 1 0.4406 0.774 0.70 0.00 0.00 0.30
#> TCGA.55.8204.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.86.8076.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.50.5044.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.05.5420.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.49.AAR3.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.05.4384.01 2 0.2345 0.897 0.00 0.90 0.00 0.10
#> TCGA.55.6971.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.50.5939.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.O1.A52J.01 1 0.4277 0.785 0.72 0.00 0.00 0.28
#> TCGA.91.8497.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T2.01 2 0.2345 0.897 0.00 0.90 0.00 0.10
#> TCGA.86.7714.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.86.8585.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.99.8028.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.49.4487.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.55.8206.01 2 0.2345 0.897 0.00 0.90 0.00 0.10
#> TCGA.97.7553.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.50.5944.01 1 0.3975 0.806 0.76 0.00 0.00 0.24
#> TCGA.55.7728.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.78.7537.01 2 0.2345 0.897 0.00 0.90 0.00 0.10
#> TCGA.55.8097.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.05.4424.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.44.5645.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.49.AAQV.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.73.7498.01 1 0.1637 0.867 0.94 0.00 0.00 0.06
#> TCGA.97.7547.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.93.7348.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.78.7163.01 2 0.0707 0.913 0.00 0.98 0.00 0.02
#> TCGA.97.7941.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.97.8174.01 2 0.2011 0.902 0.00 0.92 0.00 0.08
#> TCGA.91.6840.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.93.A4JP.01 3 0.1211 0.890 0.00 0.04 0.96 0.00
#> TCGA.50.5941.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.75.7030.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.55.7725.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.38.A44F.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.50.5930.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.55.7284.01 2 0.1211 0.900 0.00 0.96 0.04 0.00
#> TCGA.44.6776.01 1 0.1211 0.872 0.96 0.00 0.00 0.04
#> TCGA.50.5055.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.50.5045.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.86.8674.01 3 0.1411 0.892 0.00 0.02 0.96 0.02
#> TCGA.44.A4SS.01 3 0.2011 0.832 0.00 0.08 0.92 0.00
#> TCGA.55.A492.01 1 0.0707 0.876 0.98 0.00 0.00 0.02
#> TCGA.53.7626.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.55.6969.01 3 0.0707 0.916 0.00 0.02 0.98 0.00
#> TCGA.50.6595.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.55.6543.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.50.5049.01 3 0.3400 0.556 0.00 0.18 0.82 0.00
#> TCGA.97.A4M2.01 2 0.0000 0.915 0.00 1.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.4134 0.799 0.74 0.00 0.00 0.26
#> TCGA.50.5068.01 1 0.1211 0.865 0.96 0.00 0.00 0.04
#> TCGA.MP.A4T4.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.53.7813.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55A.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
#> TCGA.55.6987.01 3 0.1637 0.864 0.00 0.06 0.94 0.00
#> TCGA.64.1681.01 1 0.4277 0.785 0.72 0.00 0.00 0.28
#> TCGA.95.A4VP.01 1 0.0000 0.878 1.00 0.00 0.00 0.00
#> TCGA.95.7947.01 2 0.2706 0.882 0.00 0.90 0.08 0.02
#> TCGA.J2.8192.01 1 0.4522 0.760 0.68 0.00 0.00 0.32
#> TCGA.50.6593.01 1 0.0707 0.874 0.98 0.00 0.00 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.6778.01 3 0.4726 0.1103 0.00 0.00 0.58 0.40 0.02
#> TCGA.55.6975.01 3 0.0000 0.8869 0.00 0.00 1.00 0.00 0.00
#> TCGA.99.8033.01 5 0.4126 0.8852 0.38 0.00 0.00 0.00 0.62
#> TCGA.69.8255.01 3 0.0000 0.8869 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.8453.01 2 0.1043 0.8759 0.00 0.96 0.00 0.04 0.00
#> TCGA.78.7162.01 2 0.2754 0.8640 0.00 0.88 0.00 0.08 0.04
#> TCGA.75.7025.01 2 0.3037 0.8471 0.00 0.86 0.00 0.10 0.04
#> TCGA.55.8096.01 5 0.3983 0.8887 0.34 0.00 0.00 0.00 0.66
#> TCGA.93.A4JQ.01 3 0.3694 0.7839 0.00 0.14 0.82 0.02 0.02
#> TCGA.55.8208.01 1 0.4307 -0.7019 0.50 0.00 0.00 0.00 0.50
#> TCGA.49.AAR4.01 2 0.5440 0.6844 0.00 0.70 0.12 0.16 0.02
#> TCGA.64.1679.01 5 0.3895 0.8824 0.32 0.00 0.00 0.00 0.68
#> TCGA.55.6984.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARO.01 1 0.4540 0.0645 0.64 0.00 0.00 0.02 0.34
#> TCGA.75.6206.01 2 0.3390 0.8375 0.00 0.84 0.00 0.10 0.06
#> TCGA.49.6744.01 1 0.0609 0.8350 0.98 0.00 0.00 0.00 0.02
#> TCGA.L9.A743.01 2 0.2929 0.8081 0.00 0.82 0.00 0.18 0.00
#> TCGA.86.7954.01 5 0.4287 0.7892 0.46 0.00 0.00 0.00 0.54
#> TCGA.55.7910.01 1 0.4613 -0.1492 0.62 0.00 0.00 0.02 0.36
#> TCGA.64.5778.01 2 0.5386 0.7057 0.00 0.70 0.18 0.10 0.02
#> TCGA.44.A479.01 1 0.3895 0.0495 0.68 0.00 0.00 0.00 0.32
#> TCGA.55.8087.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8091.01 2 0.0609 0.8766 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.8619.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 2 0.6623 0.4580 0.00 0.52 0.10 0.34 0.04
#> TCGA.44.A4SU.01 5 0.4126 0.8852 0.38 0.00 0.00 0.00 0.62
#> TCGA.50.5072.01 3 0.0609 0.8790 0.00 0.00 0.98 0.02 0.00
#> TCGA.91.6849.01 1 0.1216 0.8254 0.96 0.00 0.00 0.02 0.02
#> TCGA.69.8254.01 2 0.1732 0.8774 0.00 0.92 0.00 0.08 0.00
#> TCGA.53.7624.01 5 0.3561 0.8190 0.26 0.00 0.00 0.00 0.74
#> TCGA.55.8621.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.1648 0.8129 0.94 0.00 0.00 0.02 0.04
#> TCGA.MP.A4T9.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7670.01 5 0.3983 0.8887 0.34 0.00 0.00 0.00 0.66
#> TCGA.97.A4M5.01 2 0.2331 0.8751 0.00 0.90 0.00 0.08 0.02
#> TCGA.86.7711.01 3 0.0000 0.8869 0.00 0.00 1.00 0.00 0.00
#> TCGA.05.5423.01 2 0.3037 0.8620 0.00 0.86 0.00 0.10 0.04
#> TCGA.MP.A4TJ.01 1 0.0609 0.8350 0.98 0.00 0.00 0.00 0.02
#> TCGA.L9.A5IP.01 5 0.4132 0.8117 0.26 0.00 0.00 0.02 0.72
#> TCGA.93.7347.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4490.01 5 0.3895 0.8824 0.32 0.00 0.00 0.00 0.68
#> TCGA.97.8177.01 1 0.4060 -0.1740 0.64 0.00 0.00 0.00 0.36
#> TCGA.91.A4BD.01 2 0.0609 0.8766 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.7573.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.86.7953.01 5 0.4227 0.8526 0.42 0.00 0.00 0.00 0.58
#> TCGA.55.6970.01 5 0.4287 0.7913 0.46 0.00 0.00 0.00 0.54
#> TCGA.78.7160.01 2 0.1216 0.8742 0.00 0.96 0.00 0.02 0.02
#> TCGA.50.5066.01 2 0.5355 0.6224 0.00 0.66 0.12 0.22 0.00
#> TCGA.97.7938.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7726.01 5 0.4287 0.7930 0.46 0.00 0.00 0.00 0.54
#> TCGA.MP.A4TH.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 2 0.3684 0.7861 0.00 0.72 0.00 0.28 0.00
#> TCGA.50.8460.01 2 0.0609 0.8772 0.00 0.98 0.00 0.02 0.00
#> TCGA.55.8505.01 3 0.0000 0.8869 0.00 0.00 1.00 0.00 0.00
#> TCGA.67.6217.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.86.8671.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7546.01 1 0.1410 0.7892 0.94 0.00 0.00 0.00 0.06
#> TCGA.95.7944.01 3 0.3694 0.7842 0.00 0.14 0.82 0.02 0.02
#> TCGA.86.8280.01 1 0.4302 -0.6443 0.52 0.00 0.00 0.00 0.48
#> TCGA.91.6835.01 1 0.4302 -0.6460 0.52 0.00 0.00 0.00 0.48
#> TCGA.55.A48Z.01 1 0.4227 -0.4364 0.58 0.00 0.00 0.00 0.42
#> TCGA.50.5942.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.78.7148.01 2 0.4653 0.7425 0.00 0.76 0.16 0.06 0.02
#> TCGA.91.6830.01 5 0.4262 0.8244 0.44 0.00 0.00 0.00 0.56
#> TCGA.44.6774.01 1 0.3424 0.3965 0.76 0.00 0.00 0.00 0.24
#> TCGA.55.8299.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR2.01 4 0.4676 0.0000 0.00 0.00 0.12 0.74 0.14
#> TCGA.44.6146.01 2 0.1648 0.8713 0.00 0.94 0.00 0.04 0.02
#> TCGA.62.8397.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.91.6848.01 3 0.1648 0.8857 0.00 0.04 0.94 0.00 0.02
#> TCGA.97.7552.01 2 0.1410 0.8763 0.00 0.94 0.00 0.06 0.00
#> TCGA.50.5936.01 3 0.1648 0.8857 0.00 0.04 0.94 0.00 0.02
#> TCGA.55.6979.01 1 0.3109 0.5130 0.80 0.00 0.00 0.00 0.20
#> TCGA.50.8459.01 2 0.1410 0.8763 0.00 0.94 0.00 0.06 0.00
#> TCGA.78.8648.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6743.01 5 0.3895 0.8824 0.32 0.00 0.00 0.00 0.68
#> TCGA.97.A4LX.01 2 0.4700 0.5973 0.00 0.70 0.26 0.02 0.02
#> TCGA.38.4631.01 5 0.3895 0.8824 0.32 0.00 0.00 0.00 0.68
#> TCGA.99.AA5R.01 1 0.1648 0.8129 0.94 0.00 0.00 0.02 0.04
#> TCGA.MP.A4T7.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.8457.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5932.01 2 0.3390 0.8375 0.00 0.84 0.00 0.10 0.06
#> TCGA.NJ.A55O.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 2 0.1043 0.8759 0.00 0.96 0.00 0.04 0.00
#> TCGA.44.6145.01 1 0.1043 0.8352 0.96 0.00 0.00 0.00 0.04
#> TCGA.86.8075.01 1 0.4287 -0.5875 0.54 0.00 0.00 0.00 0.46
#> TCGA.55.7724.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8510.01 1 0.3684 0.2487 0.72 0.00 0.00 0.00 0.28
#> TCGA.49.4514.01 5 0.4182 0.8747 0.40 0.00 0.00 0.00 0.60
#> TCGA.55.8204.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.86.8076.01 2 0.0000 0.8777 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5044.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.01 3 0.2249 0.8808 0.00 0.04 0.92 0.02 0.02
#> TCGA.49.AAR3.01 2 0.1043 0.8759 0.00 0.96 0.00 0.04 0.00
#> TCGA.05.4384.01 2 0.3697 0.8376 0.00 0.82 0.00 0.10 0.08
#> TCGA.55.6971.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5939.01 3 0.1043 0.8886 0.00 0.04 0.96 0.00 0.00
#> TCGA.O1.A52J.01 1 0.4302 -0.6417 0.52 0.00 0.00 0.00 0.48
#> TCGA.91.8497.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T2.01 2 0.2438 0.8684 0.00 0.90 0.00 0.06 0.04
#> TCGA.86.7714.01 1 0.1648 0.8129 0.94 0.00 0.00 0.02 0.04
#> TCGA.86.8585.01 3 0.0000 0.8869 0.00 0.00 1.00 0.00 0.00
#> TCGA.99.8028.01 1 0.1648 0.8129 0.94 0.00 0.00 0.02 0.04
#> TCGA.49.4487.01 5 0.4182 0.8750 0.40 0.00 0.00 0.00 0.60
#> TCGA.55.8206.01 2 0.2438 0.8695 0.00 0.90 0.00 0.06 0.04
#> TCGA.97.7553.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5944.01 1 0.3684 0.3613 0.72 0.00 0.00 0.00 0.28
#> TCGA.55.7728.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7537.01 2 0.3037 0.8471 0.00 0.86 0.00 0.10 0.04
#> TCGA.55.8097.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4424.01 3 0.2249 0.8784 0.00 0.02 0.92 0.04 0.02
#> TCGA.44.5645.01 1 0.1648 0.8129 0.94 0.00 0.00 0.02 0.04
#> TCGA.49.AAQV.01 1 0.1648 0.8129 0.94 0.00 0.00 0.02 0.04
#> TCGA.73.7498.01 1 0.1410 0.7892 0.94 0.00 0.00 0.00 0.06
#> TCGA.97.7547.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.7348.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.78.7163.01 2 0.2012 0.8663 0.00 0.92 0.00 0.06 0.02
#> TCGA.97.7941.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 5 0.3895 0.8824 0.32 0.00 0.00 0.00 0.68
#> TCGA.97.8174.01 2 0.1648 0.8713 0.00 0.94 0.00 0.04 0.02
#> TCGA.91.6840.01 5 0.3895 0.8824 0.32 0.00 0.00 0.00 0.68
#> TCGA.93.A4JP.01 3 0.1043 0.8886 0.00 0.04 0.96 0.00 0.00
#> TCGA.50.5941.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.7030.01 2 0.1043 0.8759 0.00 0.96 0.00 0.04 0.00
#> TCGA.55.7725.01 1 0.1648 0.8129 0.94 0.00 0.00 0.02 0.04
#> TCGA.38.A44F.01 2 0.1043 0.8759 0.00 0.96 0.00 0.04 0.00
#> TCGA.50.5930.01 3 0.0000 0.8869 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7284.01 2 0.1648 0.8718 0.00 0.94 0.02 0.04 0.00
#> TCGA.44.6776.01 1 0.1043 0.8140 0.96 0.00 0.00 0.00 0.04
#> TCGA.50.5055.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.50.5045.01 1 0.2616 0.7549 0.88 0.00 0.00 0.02 0.10
#> TCGA.86.8674.01 3 0.2438 0.8456 0.00 0.00 0.90 0.06 0.04
#> TCGA.44.A4SS.01 3 0.3694 0.7839 0.00 0.14 0.82 0.02 0.02
#> TCGA.55.A492.01 1 0.0609 0.8350 0.98 0.00 0.00 0.00 0.02
#> TCGA.53.7626.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6969.01 3 0.0000 0.8869 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6595.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.6543.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.50.5049.01 3 0.4225 0.7812 0.00 0.12 0.80 0.06 0.02
#> TCGA.97.A4M2.01 2 0.0609 0.8766 0.00 0.98 0.00 0.00 0.02
#> TCGA.L9.A8F4.01 1 0.4540 -0.0406 0.64 0.00 0.00 0.02 0.34
#> TCGA.50.5068.01 1 0.1410 0.8072 0.94 0.00 0.00 0.00 0.06
#> TCGA.MP.A4T4.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.53.7813.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55A.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.6987.01 3 0.2020 0.8492 0.00 0.10 0.90 0.00 0.00
#> TCGA.64.1681.01 5 0.4302 0.7424 0.48 0.00 0.00 0.00 0.52
#> TCGA.95.A4VP.01 1 0.0000 0.8497 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7947.01 2 0.3852 0.7012 0.00 0.76 0.22 0.00 0.02
#> TCGA.J2.8192.01 5 0.4182 0.8747 0.40 0.00 0.00 0.00 0.60
#> TCGA.50.6593.01 1 0.0609 0.8421 0.98 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.6778.01 6 0.5791 -0.3224 0.00 0.00 0.38 0.18 0.00 0.44
#> TCGA.55.6975.01 3 0.0000 0.8763 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.8033.01 5 0.2631 0.8474 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.69.8255.01 3 0.0000 0.8763 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.8453.01 2 0.2581 0.7353 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.78.7162.01 2 0.2581 0.7222 0.00 0.86 0.00 0.02 0.00 0.12
#> TCGA.75.7025.01 2 0.1556 0.7534 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.55.8096.01 5 0.2790 0.8250 0.14 0.00 0.00 0.00 0.84 0.02
#> TCGA.93.A4JQ.01 3 0.4328 0.6027 0.00 0.18 0.72 0.00 0.00 0.10
#> TCGA.55.8208.01 5 0.3460 0.8337 0.22 0.00 0.00 0.00 0.76 0.02
#> TCGA.49.AAR4.01 2 0.5110 -0.2748 0.00 0.48 0.08 0.00 0.00 0.44
#> TCGA.64.1679.01 5 0.2581 0.8040 0.12 0.00 0.00 0.00 0.86 0.02
#> TCGA.55.6984.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARO.01 1 0.4328 -0.1701 0.52 0.00 0.00 0.00 0.46 0.02
#> TCGA.75.6206.01 2 0.3873 0.6475 0.00 0.78 0.00 0.04 0.02 0.16
#> TCGA.49.6744.01 1 0.2345 0.8901 0.90 0.00 0.00 0.02 0.06 0.02
#> TCGA.L9.A743.01 2 0.4282 0.0393 0.00 0.56 0.02 0.00 0.00 0.42
#> TCGA.86.7954.01 5 0.3156 0.8385 0.18 0.00 0.00 0.02 0.80 0.00
#> TCGA.55.7910.01 5 0.4764 0.3442 0.42 0.00 0.00 0.02 0.54 0.02
#> TCGA.64.5778.01 2 0.5073 0.4331 0.00 0.68 0.16 0.02 0.00 0.14
#> TCGA.44.A479.01 5 0.4199 0.5801 0.38 0.00 0.00 0.02 0.60 0.00
#> TCGA.55.8087.01 1 0.2725 0.8824 0.88 0.00 0.00 0.02 0.06 0.04
#> TCGA.55.8091.01 2 0.0937 0.7732 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.8619.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.49.AAR0.01 6 0.5911 0.1366 0.00 0.42 0.06 0.06 0.00 0.46
#> TCGA.44.A4SU.01 5 0.2790 0.8374 0.14 0.00 0.00 0.02 0.84 0.00
#> TCGA.50.5072.01 3 0.0937 0.8744 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.91.6849.01 1 0.2629 0.8868 0.88 0.00 0.00 0.02 0.08 0.02
#> TCGA.69.8254.01 2 0.2094 0.7748 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.53.7624.01 5 0.2956 0.7449 0.12 0.00 0.00 0.00 0.84 0.04
#> TCGA.55.8621.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.S2.AA1A.01 1 0.0937 0.8821 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.MP.A4T9.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.44.7670.01 5 0.2981 0.8384 0.16 0.00 0.00 0.00 0.82 0.02
#> TCGA.97.A4M5.01 2 0.1092 0.7715 0.00 0.96 0.02 0.02 0.00 0.00
#> TCGA.86.7711.01 3 0.0000 0.8763 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.5423.01 2 0.2350 0.7652 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.MP.A4TJ.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.L9.A5IP.01 5 0.2728 0.7120 0.10 0.00 0.00 0.00 0.86 0.04
#> TCGA.93.7347.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4490.01 5 0.2350 0.7984 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.97.8177.01 5 0.3916 0.7384 0.30 0.00 0.00 0.02 0.68 0.00
#> TCGA.91.A4BD.01 2 0.1480 0.7710 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.55.7573.01 1 0.0547 0.9068 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.86.7953.01 5 0.3156 0.8455 0.18 0.00 0.00 0.00 0.80 0.02
#> TCGA.55.6970.01 5 0.3678 0.8297 0.18 0.00 0.00 0.02 0.78 0.02
#> TCGA.78.7160.01 2 0.2345 0.7547 0.00 0.90 0.06 0.02 0.02 0.00
#> TCGA.50.5066.01 6 0.5110 0.0498 0.00 0.44 0.08 0.00 0.00 0.48
#> TCGA.97.7938.01 1 0.2725 0.8824 0.88 0.00 0.00 0.02 0.06 0.04
#> TCGA.55.7726.01 5 0.3315 0.8451 0.20 0.00 0.00 0.00 0.78 0.02
#> TCGA.MP.A4TH.01 1 0.2020 0.9000 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.91.8496.01 1 0.2725 0.8826 0.88 0.00 0.00 0.02 0.06 0.04
#> TCGA.49.4512.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.L9.A50W.01 2 0.3864 -0.0684 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.50.8460.01 2 0.0547 0.7765 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.8505.01 3 0.0547 0.8760 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.67.6217.01 1 0.2020 0.9032 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.86.8671.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.97.7546.01 1 0.3483 0.8217 0.82 0.00 0.00 0.02 0.12 0.04
#> TCGA.95.7944.01 3 0.4094 0.6206 0.00 0.18 0.74 0.00 0.00 0.08
#> TCGA.86.8280.01 5 0.3198 0.7927 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.91.6835.01 5 0.3711 0.8114 0.26 0.00 0.00 0.00 0.72 0.02
#> TCGA.55.A48Z.01 5 0.3409 0.7670 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.50.5942.01 1 0.0547 0.9068 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.78.7148.01 2 0.4502 0.5712 0.00 0.74 0.14 0.02 0.00 0.10
#> TCGA.91.6830.01 5 0.2981 0.8414 0.16 0.00 0.00 0.02 0.82 0.00
#> TCGA.44.6774.01 5 0.4806 0.2502 0.48 0.00 0.00 0.02 0.48 0.02
#> TCGA.55.8299.01 1 0.0937 0.9096 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.49.AAR2.01 4 0.1814 0.0000 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.44.6146.01 2 0.1480 0.7737 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.62.8397.01 1 0.0937 0.9073 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.91.6848.01 3 0.1480 0.8703 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.97.7552.01 2 0.2581 0.7353 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.50.5936.01 3 0.0937 0.8744 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.6979.01 1 0.4199 0.1852 0.60 0.00 0.00 0.02 0.38 0.00
#> TCGA.50.8459.01 2 0.2581 0.7353 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.78.8648.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.49.6743.01 5 0.2581 0.8040 0.12 0.00 0.00 0.00 0.86 0.02
#> TCGA.97.A4LX.01 2 0.4608 0.3954 0.00 0.68 0.22 0.00 0.00 0.10
#> TCGA.38.4631.01 5 0.2981 0.8378 0.16 0.00 0.00 0.00 0.82 0.02
#> TCGA.99.AA5R.01 1 0.0937 0.8821 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.MP.A4T7.01 1 0.2345 0.8901 0.90 0.00 0.00 0.02 0.06 0.02
#> TCGA.50.8457.01 1 0.1092 0.9102 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.50.5932.01 2 0.3315 0.6389 0.00 0.78 0.00 0.02 0.00 0.20
#> TCGA.NJ.A55O.01 1 0.2020 0.9000 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.93.A4JO.01 2 0.2882 0.7306 0.00 0.86 0.02 0.00 0.02 0.10
#> TCGA.44.6145.01 1 0.0937 0.8898 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.86.8075.01 5 0.3156 0.8384 0.18 0.00 0.00 0.02 0.80 0.00
#> TCGA.55.7724.01 1 0.0937 0.9046 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.55.8510.01 5 0.4787 0.3927 0.44 0.00 0.00 0.02 0.52 0.02
#> TCGA.49.4514.01 5 0.2790 0.8381 0.14 0.00 0.00 0.02 0.84 0.00
#> TCGA.55.8204.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8076.01 2 0.1092 0.7738 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.97.A4M6.01 1 0.2345 0.8901 0.90 0.00 0.00 0.02 0.06 0.02
#> TCGA.50.5044.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.01 3 0.0547 0.8754 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.49.AAR3.01 2 0.2350 0.7416 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.05.4384.01 2 0.4042 0.6207 0.00 0.76 0.00 0.04 0.02 0.18
#> TCGA.55.6971.01 1 0.1092 0.9102 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.50.5939.01 3 0.0547 0.8760 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.O1.A52J.01 5 0.3592 0.7925 0.24 0.00 0.00 0.02 0.74 0.00
#> TCGA.91.8497.01 1 0.2725 0.8824 0.88 0.00 0.00 0.02 0.06 0.04
#> TCGA.MP.A4T2.01 2 0.3007 0.7227 0.00 0.86 0.04 0.02 0.00 0.08
#> TCGA.86.7714.01 1 0.1092 0.9011 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.86.8585.01 3 0.0000 0.8763 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.0937 0.8821 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.49.4487.01 5 0.3156 0.8455 0.18 0.00 0.00 0.00 0.80 0.02
#> TCGA.55.8206.01 2 0.1807 0.7555 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.97.7553.01 1 0.1480 0.9049 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.50.5944.01 1 0.4913 0.2496 0.60 0.00 0.00 0.02 0.34 0.04
#> TCGA.55.7728.01 1 0.0547 0.9104 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.78.7537.01 2 0.2094 0.7466 0.00 0.90 0.00 0.02 0.00 0.08
#> TCGA.55.8097.01 1 0.2725 0.8824 0.88 0.00 0.00 0.02 0.06 0.04
#> TCGA.05.4424.01 3 0.1092 0.8741 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.44.5645.01 1 0.0937 0.8821 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.49.AAQV.01 1 0.1267 0.8701 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.73.7498.01 1 0.3258 0.8451 0.84 0.00 0.00 0.02 0.10 0.04
#> TCGA.97.7547.01 1 0.2345 0.8901 0.90 0.00 0.00 0.02 0.06 0.02
#> TCGA.93.7348.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7163.01 2 0.0937 0.7657 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.97.7941.01 1 0.1092 0.9102 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.MP.A4TA.01 5 0.2790 0.8250 0.14 0.00 0.00 0.00 0.84 0.02
#> TCGA.97.8174.01 2 0.2350 0.7350 0.00 0.88 0.00 0.02 0.00 0.10
#> TCGA.91.6840.01 5 0.2581 0.8040 0.12 0.00 0.00 0.00 0.86 0.02
#> TCGA.93.A4JP.01 3 0.2512 0.8267 0.00 0.06 0.88 0.00 0.00 0.06
#> TCGA.50.5941.01 1 0.1635 0.9068 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.75.7030.01 2 0.3111 0.7220 0.00 0.84 0.02 0.00 0.02 0.12
#> TCGA.55.7725.01 1 0.1092 0.9011 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.38.A44F.01 2 0.2581 0.7353 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.50.5930.01 3 0.0000 0.8763 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7284.01 2 0.3873 0.6732 0.00 0.78 0.02 0.00 0.04 0.16
#> TCGA.44.6776.01 1 0.3688 0.7938 0.80 0.00 0.00 0.02 0.14 0.04
#> TCGA.50.5055.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5045.01 1 0.1814 0.8415 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.86.8674.01 3 0.1480 0.8547 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.44.A4SS.01 3 0.3985 0.6708 0.00 0.14 0.76 0.00 0.00 0.10
#> TCGA.55.A492.01 1 0.3258 0.8451 0.84 0.00 0.00 0.02 0.10 0.04
#> TCGA.53.7626.01 1 0.2020 0.9012 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.55.6969.01 3 0.0547 0.8721 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.6595.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6543.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5049.01 3 0.4711 0.3855 0.00 0.28 0.64 0.00 0.00 0.08
#> TCGA.97.A4M2.01 2 0.1092 0.7738 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.L9.A8F4.01 1 0.4337 -0.1437 0.50 0.00 0.00 0.02 0.48 0.00
#> TCGA.50.5068.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T4.01 1 0.1267 0.8912 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.53.7813.01 1 0.2345 0.8901 0.90 0.00 0.00 0.02 0.06 0.02
#> TCGA.NJ.A55A.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6987.01 3 0.3544 0.7289 0.00 0.12 0.80 0.00 0.00 0.08
#> TCGA.64.1681.01 5 0.3156 0.8385 0.18 0.00 0.00 0.02 0.80 0.00
#> TCGA.95.A4VP.01 1 0.1635 0.9068 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.95.7947.01 2 0.2981 0.6322 0.00 0.82 0.16 0.00 0.00 0.02
#> TCGA.J2.8192.01 5 0.2790 0.8374 0.14 0.00 0.00 0.02 0.84 0.00
#> TCGA.50.6593.01 1 0.0547 0.9068 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.44.6778.01 6 0.6745 -0.1701 0.06 0.00 0.32 0.22 0.02 0.38 0.00
#> TCGA.55.6975.01 3 0.0000 0.8163 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.8033.01 5 0.2832 0.7818 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.69.8255.01 3 0.1860 0.7778 0.04 0.00 0.92 0.02 0.00 0.02 0.00
#> TCGA.69.8453.01 2 0.1671 0.7782 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.78.7162.01 2 0.3199 0.7169 0.14 0.80 0.00 0.00 0.00 0.06 0.00
#> TCGA.75.7025.01 2 0.2512 0.7656 0.10 0.86 0.00 0.00 0.00 0.04 0.00
#> TCGA.55.8096.01 5 0.3680 0.7371 0.06 0.00 0.00 0.00 0.78 0.02 0.14
#> TCGA.93.A4JQ.01 3 0.5240 0.3454 0.02 0.26 0.58 0.00 0.00 0.14 0.00
#> TCGA.55.8208.01 5 0.3841 0.7673 0.04 0.00 0.00 0.00 0.68 0.00 0.28
#> TCGA.49.AAR4.01 2 0.4514 0.1327 0.00 0.48 0.06 0.00 0.00 0.46 0.00
#> TCGA.64.1679.01 5 0.3848 0.7333 0.06 0.00 0.00 0.00 0.76 0.02 0.16
#> TCGA.55.6984.01 7 0.0863 0.7952 0.04 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.49.AARO.01 7 0.4939 0.2201 0.14 0.00 0.00 0.00 0.30 0.00 0.56
#> TCGA.75.6206.01 2 0.4146 0.5995 0.24 0.68 0.00 0.00 0.00 0.08 0.00
#> TCGA.49.6744.01 7 0.3284 0.7662 0.10 0.00 0.00 0.00 0.10 0.00 0.80
#> TCGA.L9.A743.01 2 0.3496 0.3733 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.86.7954.01 5 0.4243 0.7468 0.10 0.00 0.00 0.00 0.68 0.00 0.22
#> TCGA.55.7910.01 5 0.5517 0.1976 0.24 0.00 0.00 0.00 0.42 0.00 0.34
#> TCGA.64.5778.01 2 0.4773 0.5793 0.02 0.66 0.12 0.00 0.00 0.20 0.00
#> TCGA.44.A479.01 5 0.5134 0.3561 0.14 0.00 0.00 0.00 0.46 0.00 0.40
#> TCGA.55.8087.01 7 0.3867 0.7118 0.12 0.00 0.00 0.00 0.14 0.00 0.74
#> TCGA.55.8091.01 2 0.2376 0.7826 0.02 0.86 0.00 0.00 0.00 0.12 0.00
#> TCGA.55.8619.01 7 0.0863 0.8108 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.49.AAR0.01 6 0.6922 0.0361 0.24 0.24 0.04 0.06 0.00 0.42 0.00
#> TCGA.44.A4SU.01 5 0.2906 0.7810 0.02 0.00 0.00 0.00 0.80 0.00 0.18
#> TCGA.50.5072.01 3 0.0000 0.8163 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6849.01 7 0.4742 0.6239 0.22 0.00 0.00 0.00 0.16 0.00 0.62
#> TCGA.69.8254.01 2 0.1433 0.7860 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.53.7624.01 5 0.3879 0.4573 0.10 0.00 0.00 0.00 0.78 0.08 0.04
#> TCGA.55.8621.01 7 0.0863 0.8108 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.S2.AA1A.01 7 0.3199 0.6780 0.14 0.00 0.00 0.00 0.06 0.00 0.80
#> TCGA.MP.A4T9.01 7 0.0504 0.8082 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.44.7670.01 5 0.2745 0.7566 0.02 0.00 0.00 0.00 0.82 0.00 0.16
#> TCGA.97.A4M5.01 2 0.1928 0.7868 0.02 0.90 0.00 0.00 0.00 0.08 0.00
#> TCGA.86.7711.01 3 0.0504 0.8135 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.05.5423.01 2 0.2803 0.7644 0.10 0.84 0.00 0.00 0.00 0.06 0.00
#> TCGA.MP.A4TJ.01 7 0.2313 0.8019 0.06 0.00 0.00 0.00 0.06 0.00 0.88
#> TCGA.L9.A5IP.01 5 0.4635 0.5513 0.16 0.00 0.00 0.00 0.70 0.04 0.10
#> TCGA.93.7347.01 7 0.0000 0.8046 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.4490.01 5 0.3494 0.7107 0.06 0.00 0.00 0.00 0.80 0.02 0.12
#> TCGA.97.8177.01 5 0.4487 0.6366 0.08 0.00 0.00 0.00 0.60 0.00 0.32
#> TCGA.91.A4BD.01 2 0.1363 0.7900 0.02 0.94 0.00 0.00 0.00 0.04 0.00
#> TCGA.55.7573.01 7 0.0504 0.7997 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.86.7953.01 5 0.3519 0.7800 0.04 0.00 0.00 0.00 0.74 0.00 0.22
#> TCGA.55.6970.01 5 0.3307 0.7741 0.02 0.00 0.00 0.00 0.74 0.00 0.24
#> TCGA.78.7160.01 2 0.1664 0.7915 0.00 0.92 0.02 0.00 0.00 0.06 0.00
#> TCGA.50.5066.01 2 0.4923 0.1243 0.00 0.50 0.06 0.02 0.00 0.42 0.00
#> TCGA.97.7938.01 7 0.3687 0.7308 0.12 0.00 0.00 0.00 0.12 0.00 0.76
#> TCGA.55.7726.01 5 0.2832 0.7863 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.MP.A4TH.01 7 0.3058 0.7712 0.10 0.00 0.00 0.00 0.08 0.00 0.82
#> TCGA.91.8496.01 7 0.2278 0.7969 0.04 0.00 0.00 0.00 0.08 0.00 0.88
#> TCGA.49.4512.01 7 0.1363 0.8144 0.04 0.00 0.00 0.00 0.02 0.00 0.94
#> TCGA.L9.A50W.01 2 0.3994 0.2066 0.02 0.50 0.00 0.00 0.00 0.48 0.00
#> TCGA.50.8460.01 2 0.1166 0.7897 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.55.8505.01 3 0.0000 0.8163 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.6217.01 7 0.2572 0.7956 0.08 0.00 0.00 0.00 0.06 0.00 0.86
#> TCGA.86.8671.01 7 0.0863 0.8108 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.97.7546.01 7 0.3985 0.6523 0.10 0.00 0.00 0.00 0.18 0.00 0.72
#> TCGA.95.7944.01 3 0.4993 0.4176 0.02 0.24 0.62 0.00 0.00 0.12 0.00
#> TCGA.86.8280.01 5 0.4547 0.6733 0.08 0.00 0.00 0.00 0.58 0.00 0.34
#> TCGA.91.6835.01 5 0.3459 0.6173 0.00 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.55.A48Z.01 5 0.4681 0.7020 0.10 0.00 0.00 0.00 0.58 0.00 0.32
#> TCGA.50.5942.01 7 0.0863 0.8016 0.04 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.78.7148.01 2 0.4589 0.6005 0.22 0.68 0.04 0.00 0.00 0.06 0.00
#> TCGA.91.6830.01 5 0.3667 0.7759 0.06 0.00 0.00 0.00 0.74 0.00 0.20
#> TCGA.44.6774.01 7 0.4848 -0.0748 0.10 0.00 0.00 0.00 0.40 0.00 0.50
#> TCGA.55.8299.01 7 0.2016 0.8042 0.04 0.00 0.00 0.00 0.06 0.00 0.90
#> TCGA.49.AAR2.01 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6146.01 2 0.2163 0.7824 0.02 0.88 0.00 0.00 0.00 0.10 0.00
#> TCGA.62.8397.01 7 0.2163 0.7811 0.02 0.00 0.00 0.00 0.10 0.00 0.88
#> TCGA.91.6848.01 3 0.1363 0.8021 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.97.7552.01 2 0.1671 0.7782 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.50.5936.01 3 0.0863 0.8096 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.55.6979.01 7 0.4191 0.3602 0.06 0.00 0.00 0.00 0.30 0.00 0.64
#> TCGA.50.8459.01 2 0.1671 0.7782 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.78.8648.01 7 0.1664 0.8073 0.02 0.00 0.00 0.00 0.06 0.00 0.92
#> TCGA.49.6743.01 5 0.3848 0.7333 0.06 0.00 0.00 0.00 0.76 0.02 0.16
#> TCGA.97.A4LX.01 2 0.4939 0.4979 0.02 0.64 0.20 0.00 0.00 0.14 0.00
#> TCGA.38.4631.01 5 0.3680 0.7371 0.06 0.00 0.00 0.00 0.78 0.02 0.14
#> TCGA.99.AA5R.01 7 0.3199 0.6780 0.14 0.00 0.00 0.00 0.06 0.00 0.80
#> TCGA.MP.A4T7.01 7 0.3487 0.7484 0.10 0.00 0.00 0.00 0.12 0.00 0.78
#> TCGA.50.8457.01 7 0.1664 0.8081 0.02 0.00 0.00 0.00 0.06 0.00 0.92
#> TCGA.50.5932.01 2 0.4328 0.4722 0.34 0.60 0.00 0.00 0.00 0.06 0.00
#> TCGA.NJ.A55O.01 7 0.3058 0.7698 0.10 0.00 0.00 0.00 0.08 0.00 0.82
#> TCGA.93.A4JO.01 2 0.1433 0.7834 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.44.6145.01 7 0.1166 0.7981 0.00 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.86.8075.01 5 0.4538 0.6843 0.10 0.00 0.00 0.00 0.62 0.00 0.28
#> TCGA.55.7724.01 7 0.1664 0.8073 0.02 0.00 0.00 0.00 0.06 0.00 0.92
#> TCGA.55.8510.01 7 0.4514 -0.2980 0.06 0.00 0.00 0.00 0.46 0.00 0.48
#> TCGA.49.4514.01 5 0.3052 0.7837 0.02 0.00 0.00 0.00 0.78 0.00 0.20
#> TCGA.55.8204.01 7 0.0863 0.7952 0.04 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.86.8076.01 2 0.0863 0.7885 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.97.A4M6.01 7 0.3284 0.7642 0.10 0.00 0.00 0.00 0.10 0.00 0.80
#> TCGA.50.5044.01 7 0.0000 0.8046 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.05.5420.01 3 0.0504 0.8125 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.49.AAR3.01 2 0.2422 0.7729 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.05.4384.01 2 0.3745 0.6055 0.26 0.70 0.00 0.00 0.00 0.04 0.00
#> TCGA.55.6971.01 7 0.2016 0.8048 0.04 0.00 0.00 0.00 0.06 0.00 0.90
#> TCGA.50.5939.01 3 0.0863 0.8096 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.O1.A52J.01 5 0.4681 0.6145 0.10 0.00 0.00 0.00 0.58 0.00 0.32
#> TCGA.91.8497.01 7 0.3449 0.7511 0.14 0.00 0.00 0.00 0.08 0.00 0.78
#> TCGA.MP.A4T2.01 2 0.1886 0.7750 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.86.7714.01 7 0.3199 0.6898 0.14 0.00 0.00 0.00 0.06 0.00 0.80
#> TCGA.86.8585.01 3 0.0504 0.8135 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 7 0.3199 0.6780 0.14 0.00 0.00 0.00 0.06 0.00 0.80
#> TCGA.49.4487.01 5 0.3661 0.7685 0.02 0.00 0.00 0.00 0.74 0.02 0.22
#> TCGA.55.8206.01 2 0.2829 0.7646 0.08 0.84 0.00 0.00 0.00 0.08 0.00
#> TCGA.97.7553.01 7 0.1664 0.8073 0.02 0.00 0.00 0.00 0.06 0.00 0.92
#> TCGA.50.5944.01 7 0.4514 -0.2496 0.06 0.00 0.00 0.00 0.46 0.00 0.48
#> TCGA.55.7728.01 7 0.0863 0.8108 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.78.7537.01 2 0.2803 0.7491 0.10 0.84 0.00 0.00 0.00 0.06 0.00
#> TCGA.55.8097.01 7 0.3867 0.7115 0.14 0.00 0.00 0.00 0.12 0.00 0.74
#> TCGA.05.4424.01 3 0.1006 0.8061 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.44.5645.01 7 0.3370 0.6726 0.16 0.00 0.00 0.00 0.06 0.00 0.78
#> TCGA.49.AAQV.01 7 0.3199 0.6780 0.14 0.00 0.00 0.00 0.06 0.00 0.80
#> TCGA.73.7498.01 7 0.4177 0.6377 0.12 0.00 0.00 0.00 0.18 0.00 0.70
#> TCGA.97.7547.01 7 0.3867 0.7115 0.14 0.00 0.00 0.00 0.12 0.00 0.74
#> TCGA.93.7348.01 7 0.0504 0.8082 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.78.7163.01 2 0.1664 0.7812 0.06 0.92 0.00 0.00 0.00 0.02 0.00
#> TCGA.97.7941.01 7 0.1363 0.8050 0.04 0.00 0.00 0.00 0.02 0.00 0.94
#> TCGA.MP.A4TA.01 5 0.3848 0.7333 0.06 0.00 0.00 0.00 0.76 0.02 0.16
#> TCGA.97.8174.01 2 0.2569 0.7570 0.14 0.84 0.00 0.00 0.00 0.02 0.00
#> TCGA.91.6840.01 5 0.3833 0.6898 0.06 0.00 0.00 0.00 0.78 0.04 0.12
#> TCGA.93.A4JP.01 3 0.1006 0.8086 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.50.5941.01 7 0.2313 0.8035 0.06 0.00 0.00 0.00 0.06 0.00 0.88
#> TCGA.75.7030.01 2 0.1671 0.7782 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.55.7725.01 7 0.3199 0.6898 0.14 0.00 0.00 0.00 0.06 0.00 0.80
#> TCGA.38.A44F.01 2 0.1671 0.7782 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.50.5930.01 3 0.0863 0.8068 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.55.7284.01 2 0.4044 0.6786 0.02 0.76 0.04 0.00 0.02 0.16 0.00
#> TCGA.44.6776.01 7 0.4348 0.6279 0.14 0.00 0.00 0.00 0.18 0.00 0.68
#> TCGA.50.5055.01 7 0.0504 0.8021 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.50.5045.01 7 0.3670 0.6382 0.14 0.00 0.00 0.00 0.10 0.00 0.76
#> TCGA.86.8674.01 3 0.1718 0.7812 0.04 0.00 0.92 0.04 0.00 0.00 0.00
#> TCGA.44.A4SS.01 3 0.4889 0.4413 0.02 0.22 0.64 0.00 0.00 0.12 0.00
#> TCGA.55.A492.01 7 0.4204 0.6618 0.14 0.00 0.00 0.00 0.16 0.00 0.70
#> TCGA.53.7626.01 7 0.1363 0.8116 0.02 0.00 0.00 0.00 0.04 0.00 0.94
#> TCGA.55.6969.01 3 0.1363 0.8035 0.04 0.00 0.94 0.02 0.00 0.00 0.00
#> TCGA.50.6595.01 7 0.1006 0.8068 0.02 0.00 0.00 0.00 0.02 0.00 0.96
#> TCGA.55.6543.01 7 0.1664 0.7852 0.06 0.00 0.00 0.00 0.02 0.00 0.92
#> TCGA.50.5049.01 3 0.4908 0.3921 0.02 0.26 0.62 0.00 0.00 0.10 0.00
#> TCGA.97.A4M2.01 2 0.0863 0.7885 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.L9.A8F4.01 5 0.5490 0.3070 0.24 0.00 0.00 0.00 0.44 0.00 0.32
#> TCGA.50.5068.01 7 0.2016 0.7599 0.06 0.00 0.00 0.00 0.04 0.00 0.90
#> TCGA.MP.A4T4.01 7 0.1433 0.7977 0.00 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.53.7813.01 7 0.3867 0.7115 0.14 0.00 0.00 0.00 0.12 0.00 0.74
#> TCGA.NJ.A55A.01 7 0.0504 0.8058 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.55.6987.01 3 0.4242 0.5472 0.02 0.18 0.72 0.00 0.00 0.08 0.00
#> TCGA.64.1681.01 5 0.4451 0.7105 0.10 0.00 0.00 0.00 0.64 0.00 0.26
#> TCGA.95.A4VP.01 7 0.2829 0.7868 0.08 0.00 0.00 0.00 0.08 0.00 0.84
#> TCGA.95.7947.01 2 0.4161 0.7235 0.06 0.76 0.08 0.00 0.00 0.10 0.00
#> TCGA.J2.8192.01 5 0.3388 0.7829 0.04 0.00 0.00 0.00 0.76 0.00 0.20
#> TCGA.50.6593.01 7 0.1166 0.8083 0.06 0.00 0.00 0.00 0.00 0.00 0.94
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.44.6778.01 6 0.7419 -0.17960 0.24 0.00 0.20 0.10 0.02 0.36 0.08 0.00
#> TCGA.55.6975.01 1 0.0471 0.83719 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8033.01 5 0.3774 0.72646 0.00 0.00 0.00 0.00 0.70 0.00 0.08 0.22
#> TCGA.69.8255.01 1 0.1275 0.83015 0.94 0.00 0.04 0.00 0.00 0.00 0.02 0.00
#> TCGA.69.8453.01 2 0.1341 0.67988 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.78.7162.01 2 0.3977 0.63586 0.02 0.70 0.02 0.00 0.00 0.24 0.02 0.00
#> TCGA.75.7025.01 2 0.3431 0.68696 0.00 0.74 0.06 0.00 0.00 0.20 0.00 0.00
#> TCGA.55.8096.01 5 0.2132 0.63053 0.00 0.00 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.93.A4JQ.01 1 0.4759 0.48233 0.64 0.22 0.06 0.00 0.00 0.08 0.00 0.00
#> TCGA.55.8208.01 5 0.3293 0.67605 0.00 0.00 0.00 0.00 0.74 0.00 0.04 0.22
#> TCGA.49.AAR4.01 6 0.4834 0.54404 0.06 0.38 0.04 0.00 0.00 0.52 0.00 0.00
#> TCGA.64.1679.01 5 0.2224 0.58759 0.00 0.00 0.00 0.00 0.86 0.00 0.12 0.02
#> TCGA.55.6984.01 8 0.2818 0.74016 0.00 0.00 0.00 0.00 0.06 0.00 0.12 0.82
#> TCGA.49.AARO.01 8 0.4999 0.23691 0.00 0.00 0.00 0.00 0.18 0.00 0.40 0.42
#> TCGA.75.6206.01 2 0.5210 0.43270 0.00 0.52 0.18 0.00 0.00 0.28 0.02 0.00
#> TCGA.49.6744.01 8 0.2025 0.72783 0.00 0.00 0.00 0.00 0.10 0.00 0.02 0.88
#> TCGA.L9.A743.01 6 0.3729 0.37373 0.02 0.46 0.00 0.00 0.00 0.52 0.00 0.00
#> TCGA.86.7954.01 5 0.3198 0.70937 0.00 0.00 0.00 0.00 0.72 0.00 0.02 0.26
#> TCGA.55.7910.01 5 0.5102 0.40885 0.00 0.00 0.00 0.00 0.46 0.00 0.24 0.30
#> TCGA.64.5778.01 2 0.5597 0.14924 0.22 0.52 0.06 0.00 0.00 0.20 0.00 0.00
#> TCGA.44.A479.01 5 0.4199 0.53987 0.00 0.00 0.00 0.00 0.60 0.00 0.08 0.32
#> TCGA.55.8087.01 8 0.2224 0.71194 0.00 0.00 0.00 0.00 0.12 0.00 0.02 0.86
#> TCGA.55.8091.01 2 0.3073 0.71083 0.00 0.80 0.10 0.00 0.00 0.10 0.00 0.00
#> TCGA.55.8619.01 8 0.3054 0.74577 0.00 0.00 0.00 0.00 0.08 0.00 0.12 0.80
#> TCGA.49.AAR0.01 6 0.6242 0.17346 0.08 0.10 0.26 0.00 0.00 0.50 0.06 0.00
#> TCGA.44.A4SU.01 5 0.2404 0.70798 0.00 0.00 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.50.5072.01 1 0.0000 0.83843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6849.01 8 0.3729 0.61990 0.00 0.00 0.00 0.00 0.10 0.00 0.18 0.72
#> TCGA.69.8254.01 2 0.2406 0.68646 0.00 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.53.7624.01 5 0.3941 0.33303 0.00 0.00 0.04 0.00 0.68 0.00 0.26 0.02
#> TCGA.55.8621.01 8 0.1887 0.77896 0.00 0.00 0.00 0.00 0.04 0.00 0.06 0.90
#> TCGA.S2.AA1A.01 8 0.4199 0.44950 0.00 0.00 0.00 0.00 0.06 0.00 0.42 0.52
#> TCGA.MP.A4T9.01 8 0.1804 0.77147 0.00 0.00 0.00 0.00 0.02 0.00 0.08 0.90
#> TCGA.44.7670.01 5 0.2818 0.68335 0.00 0.00 0.00 0.00 0.82 0.00 0.06 0.12
#> TCGA.97.A4M5.01 2 0.2569 0.70992 0.00 0.82 0.02 0.00 0.00 0.16 0.00 0.00
#> TCGA.86.7711.01 1 0.0471 0.83619 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5423.01 2 0.3404 0.67156 0.00 0.72 0.04 0.00 0.00 0.24 0.00 0.00
#> TCGA.MP.A4TJ.01 8 0.2407 0.77574 0.00 0.00 0.00 0.00 0.06 0.00 0.08 0.86
#> TCGA.L9.A5IP.01 5 0.3907 0.27330 0.00 0.00 0.00 0.00 0.58 0.00 0.38 0.04
#> TCGA.93.7347.01 8 0.1804 0.77147 0.00 0.00 0.00 0.00 0.02 0.00 0.08 0.90
#> TCGA.49.4490.01 5 0.2350 0.61480 0.00 0.00 0.00 0.00 0.86 0.00 0.10 0.04
#> TCGA.97.8177.01 5 0.3618 0.54721 0.00 0.00 0.00 0.00 0.60 0.00 0.02 0.38
#> TCGA.91.A4BD.01 2 0.2025 0.72730 0.00 0.88 0.02 0.00 0.00 0.10 0.00 0.00
#> TCGA.55.7573.01 8 0.1341 0.77517 0.00 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.86.7953.01 5 0.2981 0.72024 0.00 0.00 0.00 0.00 0.76 0.00 0.02 0.22
#> TCGA.55.6970.01 5 0.3291 0.69371 0.00 0.00 0.00 0.00 0.70 0.00 0.02 0.28
#> TCGA.78.7160.01 2 0.3102 0.70972 0.02 0.82 0.08 0.00 0.00 0.08 0.00 0.00
#> TCGA.50.5066.01 6 0.4673 0.59553 0.08 0.34 0.00 0.02 0.00 0.56 0.00 0.00
#> TCGA.97.7938.01 8 0.2025 0.72887 0.00 0.00 0.00 0.00 0.10 0.00 0.02 0.88
#> TCGA.55.7726.01 5 0.3404 0.72694 0.00 0.00 0.00 0.00 0.72 0.00 0.04 0.24
#> TCGA.MP.A4TH.01 8 0.0808 0.76996 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.91.8496.01 8 0.1563 0.73900 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.49.4512.01 8 0.1557 0.77969 0.00 0.00 0.00 0.00 0.06 0.00 0.02 0.92
#> TCGA.L9.A50W.01 6 0.3728 0.53026 0.00 0.28 0.02 0.00 0.00 0.68 0.02 0.00
#> TCGA.50.8460.01 2 0.1341 0.72010 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.55.8505.01 1 0.0471 0.83719 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.6217.01 8 0.1275 0.76418 0.00 0.00 0.00 0.00 0.04 0.00 0.02 0.94
#> TCGA.86.8671.01 8 0.2132 0.77573 0.00 0.00 0.00 0.00 0.04 0.00 0.08 0.88
#> TCGA.97.7546.01 8 0.2719 0.64650 0.00 0.00 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.95.7944.01 1 0.4733 0.40880 0.62 0.26 0.06 0.00 0.00 0.06 0.00 0.00
#> TCGA.86.8280.01 5 0.3374 0.64725 0.00 0.00 0.00 0.00 0.68 0.00 0.02 0.30
#> TCGA.91.6835.01 5 0.3971 0.45614 0.00 0.00 0.00 0.00 0.54 0.00 0.04 0.42
#> TCGA.55.A48Z.01 5 0.3845 0.59236 0.00 0.00 0.00 0.00 0.66 0.00 0.06 0.28
#> TCGA.50.5942.01 8 0.0808 0.77652 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.78.7148.01 2 0.6713 0.18669 0.06 0.44 0.26 0.02 0.00 0.18 0.04 0.00
#> TCGA.91.6830.01 5 0.2719 0.72750 0.00 0.00 0.00 0.00 0.80 0.00 0.02 0.18
#> TCGA.44.6774.01 8 0.3690 0.00959 0.00 0.00 0.00 0.00 0.42 0.00 0.02 0.56
#> TCGA.55.8299.01 8 0.2623 0.77380 0.00 0.00 0.00 0.00 0.10 0.00 0.06 0.84
#> TCGA.49.AAR2.01 4 0.0000 0.00000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6146.01 2 0.1557 0.72225 0.00 0.92 0.02 0.00 0.00 0.06 0.00 0.00
#> TCGA.62.8397.01 8 0.0471 0.77702 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.91.6848.01 1 0.1275 0.82784 0.94 0.00 0.04 0.00 0.00 0.02 0.00 0.00
#> TCGA.97.7552.01 2 0.1563 0.67936 0.00 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.50.5936.01 1 0.0471 0.83727 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 8 0.3746 0.51381 0.00 0.00 0.00 0.00 0.32 0.00 0.04 0.64
#> TCGA.50.8459.01 2 0.1341 0.67988 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.78.8648.01 8 0.3263 0.74876 0.00 0.00 0.00 0.00 0.10 0.00 0.12 0.78
#> TCGA.49.6743.01 5 0.2224 0.58759 0.00 0.00 0.00 0.00 0.86 0.00 0.12 0.02
#> TCGA.97.A4LX.01 2 0.4309 0.41903 0.18 0.70 0.06 0.00 0.00 0.06 0.00 0.00
#> TCGA.38.4631.01 5 0.2132 0.63563 0.00 0.00 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.99.AA5R.01 8 0.4199 0.44950 0.00 0.00 0.00 0.00 0.06 0.00 0.42 0.52
#> TCGA.MP.A4T7.01 8 0.2224 0.71259 0.00 0.00 0.00 0.00 0.12 0.00 0.02 0.86
#> TCGA.50.8457.01 8 0.0471 0.77286 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.50.5932.01 2 0.5329 0.34462 0.00 0.50 0.22 0.00 0.00 0.26 0.02 0.00
#> TCGA.NJ.A55O.01 8 0.2404 0.71600 0.00 0.00 0.00 0.00 0.14 0.00 0.02 0.84
#> TCGA.93.A4JO.01 2 0.1947 0.65997 0.00 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.44.6145.01 8 0.2648 0.75411 0.00 0.00 0.00 0.00 0.08 0.00 0.08 0.84
#> TCGA.86.8075.01 5 0.3291 0.70186 0.00 0.00 0.00 0.00 0.70 0.00 0.02 0.28
#> TCGA.55.7724.01 8 0.3450 0.73676 0.00 0.00 0.00 0.00 0.12 0.00 0.12 0.76
#> TCGA.55.8510.01 8 0.3737 -0.27854 0.00 0.00 0.00 0.00 0.48 0.00 0.02 0.50
#> TCGA.49.4514.01 5 0.2267 0.73029 0.00 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.55.8204.01 8 0.2818 0.74016 0.00 0.00 0.00 0.00 0.06 0.00 0.12 0.82
#> TCGA.86.8076.01 2 0.0471 0.72176 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M6.01 8 0.2025 0.73018 0.00 0.00 0.00 0.00 0.10 0.00 0.02 0.88
#> TCGA.50.5044.01 8 0.1804 0.77147 0.00 0.00 0.00 0.00 0.02 0.00 0.08 0.90
#> TCGA.05.5420.01 1 0.0808 0.83679 0.96 0.00 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR3.01 2 0.2350 0.67018 0.00 0.86 0.04 0.00 0.00 0.10 0.00 0.00
#> TCGA.05.4384.01 2 0.5423 0.42807 0.00 0.52 0.18 0.00 0.00 0.26 0.04 0.00
#> TCGA.55.6971.01 8 0.0808 0.76697 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.50.5939.01 1 0.0941 0.83415 0.96 0.02 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.O1.A52J.01 5 0.3374 0.68004 0.00 0.00 0.00 0.00 0.68 0.00 0.02 0.30
#> TCGA.91.8497.01 8 0.2404 0.69444 0.00 0.00 0.00 0.00 0.14 0.00 0.02 0.84
#> TCGA.MP.A4T2.01 2 0.3873 0.67667 0.00 0.72 0.06 0.00 0.00 0.20 0.02 0.00
#> TCGA.86.7714.01 8 0.2938 0.60951 0.00 0.00 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.86.8585.01 1 0.0941 0.83015 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.99.8028.01 8 0.4199 0.44950 0.00 0.00 0.00 0.00 0.06 0.00 0.42 0.52
#> TCGA.49.4487.01 5 0.2818 0.69392 0.00 0.00 0.00 0.00 0.82 0.00 0.06 0.12
#> TCGA.55.8206.01 2 0.3431 0.67676 0.00 0.74 0.06 0.00 0.00 0.20 0.00 0.00
#> TCGA.97.7553.01 8 0.1607 0.77916 0.00 0.00 0.00 0.00 0.04 0.00 0.04 0.92
#> TCGA.50.5944.01 8 0.3618 0.13286 0.00 0.00 0.00 0.00 0.38 0.00 0.02 0.60
#> TCGA.55.7728.01 8 0.1887 0.77671 0.00 0.00 0.00 0.00 0.06 0.00 0.04 0.90
#> TCGA.78.7537.01 2 0.3303 0.68264 0.00 0.76 0.02 0.00 0.00 0.20 0.02 0.00
#> TCGA.55.8097.01 8 0.2404 0.69444 0.00 0.00 0.00 0.00 0.14 0.00 0.02 0.84
#> TCGA.05.4424.01 1 0.2025 0.80496 0.88 0.00 0.10 0.00 0.00 0.02 0.00 0.00
#> TCGA.44.5645.01 8 0.3971 0.46983 0.00 0.00 0.00 0.00 0.04 0.00 0.42 0.54
#> TCGA.49.AAQV.01 8 0.4199 0.44950 0.00 0.00 0.00 0.00 0.06 0.00 0.42 0.52
#> TCGA.73.7498.01 8 0.2981 0.58259 0.00 0.00 0.00 0.00 0.22 0.00 0.02 0.76
#> TCGA.97.7547.01 8 0.2224 0.71369 0.00 0.00 0.00 0.00 0.12 0.00 0.02 0.86
#> TCGA.93.7348.01 8 0.1091 0.77556 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.78.7163.01 2 0.2807 0.71854 0.00 0.84 0.04 0.00 0.00 0.10 0.02 0.00
#> TCGA.97.7941.01 8 0.0000 0.77571 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MP.A4TA.01 5 0.1804 0.61596 0.00 0.00 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.97.8174.01 2 0.3337 0.69643 0.00 0.78 0.04 0.00 0.00 0.16 0.02 0.00
#> TCGA.91.6840.01 5 0.3601 0.59055 0.00 0.00 0.02 0.00 0.76 0.00 0.16 0.06
#> TCGA.93.A4JP.01 1 0.1741 0.81558 0.92 0.02 0.04 0.00 0.00 0.02 0.00 0.00
#> TCGA.50.5941.01 8 0.0808 0.76908 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.75.7030.01 2 0.1563 0.68530 0.00 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.55.7725.01 8 0.2756 0.64207 0.00 0.00 0.00 0.00 0.00 0.00 0.26 0.74
#> TCGA.38.A44F.01 2 0.1563 0.67936 0.00 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.50.5930.01 1 0.0941 0.83015 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.55.7284.01 2 0.5098 0.24431 0.02 0.66 0.14 0.00 0.00 0.10 0.08 0.00
#> TCGA.44.6776.01 8 0.3095 0.54682 0.00 0.00 0.00 0.00 0.24 0.00 0.02 0.74
#> TCGA.50.5055.01 8 0.2818 0.74016 0.00 0.00 0.00 0.00 0.06 0.00 0.12 0.82
#> TCGA.50.5045.01 8 0.4199 0.44950 0.00 0.00 0.00 0.00 0.06 0.00 0.42 0.52
#> TCGA.86.8674.01 1 0.2265 0.78959 0.88 0.00 0.08 0.02 0.00 0.02 0.00 0.00
#> TCGA.44.A4SS.01 1 0.4650 0.51497 0.66 0.20 0.08 0.00 0.00 0.06 0.00 0.00
#> TCGA.55.A492.01 8 0.2569 0.67098 0.00 0.00 0.00 0.00 0.16 0.00 0.02 0.82
#> TCGA.53.7626.01 8 0.0471 0.77286 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.55.6969.01 1 0.0000 0.83843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6595.01 8 0.2818 0.74016 0.00 0.00 0.00 0.00 0.06 0.00 0.12 0.82
#> TCGA.55.6543.01 8 0.2224 0.76266 0.00 0.00 0.00 0.00 0.02 0.00 0.12 0.86
#> TCGA.50.5049.01 1 0.5206 0.02857 0.50 0.32 0.02 0.00 0.00 0.16 0.00 0.00
#> TCGA.97.A4M2.01 2 0.0941 0.72367 0.00 0.96 0.02 0.00 0.00 0.02 0.00 0.00
#> TCGA.L9.A8F4.01 5 0.5259 0.17094 0.00 0.00 0.00 0.00 0.38 0.00 0.32 0.30
#> TCGA.50.5068.01 8 0.2725 0.74224 0.00 0.00 0.00 0.00 0.04 0.00 0.14 0.82
#> TCGA.MP.A4T4.01 8 0.2623 0.76209 0.00 0.00 0.00 0.00 0.10 0.00 0.06 0.84
#> TCGA.53.7813.01 8 0.2404 0.69444 0.00 0.00 0.00 0.00 0.14 0.00 0.02 0.84
#> TCGA.NJ.A55A.01 8 0.1275 0.77756 0.00 0.00 0.00 0.00 0.02 0.00 0.04 0.94
#> TCGA.55.6987.01 1 0.3744 0.61039 0.74 0.18 0.02 0.00 0.00 0.06 0.00 0.00
#> TCGA.64.1681.01 5 0.3198 0.70937 0.00 0.00 0.00 0.00 0.72 0.00 0.02 0.26
#> TCGA.95.A4VP.01 8 0.0808 0.76697 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.95.7947.01 2 0.4503 0.59929 0.10 0.70 0.08 0.00 0.00 0.12 0.00 0.00
#> TCGA.J2.8192.01 5 0.2856 0.71291 0.00 0.00 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.50.6593.01 8 0.1804 0.77147 0.00 0.00 0.00 0.00 0.02 0.00 0.08 0.90
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122 , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221-leaf , Node0222 , Node0223-leaf , Node0231 , Node0232 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0324-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["011"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 95 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.754 0.853 0.937 0.4754 0.548 0.548
#> 3 3 0.942 0.975 0.987 0.4005 0.711 0.507
#> 4 4 0.738 0.615 0.838 0.1141 0.858 0.607
#> 5 5 0.745 0.752 0.740 0.0543 0.854 0.508
#> 6 6 0.748 0.811 0.856 0.0413 0.964 0.826
#> 7 7 0.784 0.753 0.823 0.0254 0.996 0.977
#> 8 8 0.805 0.692 0.815 0.0264 0.929 0.630
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.99.8033.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.8096.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.8208.01 2 0.000 0.997 0.00 1.00
#> TCGA.64.1679.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.6984.01 1 0.000 0.899 1.00 0.00
#> TCGA.49.AARO.01 2 0.000 0.997 0.00 1.00
#> TCGA.49.6744.01 1 0.000 0.899 1.00 0.00
#> TCGA.86.7954.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.7910.01 2 0.000 0.997 0.00 1.00
#> TCGA.44.A479.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.8087.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.8619.01 1 0.000 0.899 1.00 0.00
#> TCGA.44.A4SU.01 2 0.000 0.997 0.00 1.00
#> TCGA.91.6849.01 1 0.000 0.899 1.00 0.00
#> TCGA.53.7624.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.8621.01 1 0.000 0.899 1.00 0.00
#> TCGA.S2.AA1A.01 1 0.000 0.899 1.00 0.00
#> TCGA.MP.A4T9.01 1 0.000 0.899 1.00 0.00
#> TCGA.44.7670.01 2 0.000 0.997 0.00 1.00
#> TCGA.MP.A4TJ.01 1 0.995 0.312 0.54 0.46
#> TCGA.L9.A5IP.01 2 0.000 0.997 0.00 1.00
#> TCGA.93.7347.01 1 0.000 0.899 1.00 0.00
#> TCGA.49.4490.01 2 0.000 0.997 0.00 1.00
#> TCGA.97.8177.01 1 0.680 0.745 0.82 0.18
#> TCGA.55.7573.01 1 0.000 0.899 1.00 0.00
#> TCGA.86.7953.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.6970.01 2 0.000 0.997 0.00 1.00
#> TCGA.97.7938.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.7726.01 2 0.000 0.997 0.00 1.00
#> TCGA.MP.A4TH.01 1 0.000 0.899 1.00 0.00
#> TCGA.91.8496.01 1 0.000 0.899 1.00 0.00
#> TCGA.49.4512.01 1 0.000 0.899 1.00 0.00
#> TCGA.67.6217.01 1 0.000 0.899 1.00 0.00
#> TCGA.86.8671.01 1 0.000 0.899 1.00 0.00
#> TCGA.97.7546.01 1 0.000 0.899 1.00 0.00
#> TCGA.86.8280.01 1 0.995 0.312 0.54 0.46
#> TCGA.91.6835.01 1 0.995 0.312 0.54 0.46
#> TCGA.55.A48Z.01 2 0.000 0.997 0.00 1.00
#> TCGA.50.5942.01 1 0.000 0.899 1.00 0.00
#> TCGA.91.6830.01 2 0.000 0.997 0.00 1.00
#> TCGA.44.6774.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.8299.01 1 0.000 0.899 1.00 0.00
#> TCGA.62.8397.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.6979.01 1 0.990 0.355 0.56 0.44
#> TCGA.78.8648.01 1 0.000 0.899 1.00 0.00
#> TCGA.49.6743.01 2 0.000 0.997 0.00 1.00
#> TCGA.38.4631.01 2 0.000 0.997 0.00 1.00
#> TCGA.99.AA5R.01 1 0.000 0.899 1.00 0.00
#> TCGA.MP.A4T7.01 1 0.722 0.723 0.80 0.20
#> TCGA.50.8457.01 1 0.000 0.899 1.00 0.00
#> TCGA.NJ.A55O.01 1 0.000 0.899 1.00 0.00
#> TCGA.44.6145.01 1 0.995 0.312 0.54 0.46
#> TCGA.86.8075.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.7724.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.8510.01 2 0.000 0.997 0.00 1.00
#> TCGA.49.4514.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.8204.01 1 0.000 0.899 1.00 0.00
#> TCGA.97.A4M6.01 1 0.000 0.899 1.00 0.00
#> TCGA.50.5044.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.6971.01 1 0.995 0.312 0.54 0.46
#> TCGA.O1.A52J.01 2 0.000 0.997 0.00 1.00
#> TCGA.91.8497.01 1 0.000 0.899 1.00 0.00
#> TCGA.86.7714.01 1 0.000 0.899 1.00 0.00
#> TCGA.99.8028.01 1 0.000 0.899 1.00 0.00
#> TCGA.49.4487.01 1 0.995 0.312 0.54 0.46
#> TCGA.97.7553.01 1 0.000 0.899 1.00 0.00
#> TCGA.50.5944.01 2 0.000 0.997 0.00 1.00
#> TCGA.55.7728.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.8097.01 1 0.000 0.899 1.00 0.00
#> TCGA.44.5645.01 1 0.000 0.899 1.00 0.00
#> TCGA.49.AAQV.01 1 0.000 0.899 1.00 0.00
#> TCGA.73.7498.01 2 0.000 0.997 0.00 1.00
#> TCGA.97.7547.01 1 0.000 0.899 1.00 0.00
#> TCGA.93.7348.01 1 0.000 0.899 1.00 0.00
#> TCGA.97.7941.01 1 0.000 0.899 1.00 0.00
#> TCGA.MP.A4TA.01 2 0.000 0.997 0.00 1.00
#> TCGA.91.6840.01 2 0.000 0.997 0.00 1.00
#> TCGA.50.5941.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.7725.01 1 0.000 0.899 1.00 0.00
#> TCGA.44.6776.01 1 0.999 0.255 0.52 0.48
#> TCGA.50.5055.01 1 0.000 0.899 1.00 0.00
#> TCGA.50.5045.01 1 0.990 0.355 0.56 0.44
#> TCGA.55.A492.01 1 0.000 0.899 1.00 0.00
#> TCGA.53.7626.01 1 0.000 0.899 1.00 0.00
#> TCGA.50.6595.01 1 0.000 0.899 1.00 0.00
#> TCGA.55.6543.01 1 0.000 0.899 1.00 0.00
#> TCGA.L9.A8F4.01 2 0.402 0.897 0.08 0.92
#> TCGA.50.5068.01 1 0.000 0.899 1.00 0.00
#> TCGA.MP.A4T4.01 1 0.995 0.312 0.54 0.46
#> TCGA.53.7813.01 1 0.995 0.312 0.54 0.46
#> TCGA.NJ.A55A.01 1 0.000 0.899 1.00 0.00
#> TCGA.64.1681.01 2 0.000 0.997 0.00 1.00
#> TCGA.95.A4VP.01 1 0.995 0.312 0.54 0.46
#> TCGA.J2.8192.01 2 0.000 0.997 0.00 1.00
#> TCGA.50.6593.01 1 0.000 0.899 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.99.8033.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.8096.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.8208.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.64.1679.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.6984.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.49.AARO.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.49.6744.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.86.7954.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.7910.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.44.A479.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.8087.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.55.8619.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.44.A4SU.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.91.6849.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.53.7624.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.8621.01 1 0.334 0.880 0.88 0.00 0.12
#> TCGA.S2.AA1A.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.MP.A4T9.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.44.7670.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.MP.A4TJ.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.L9.A5IP.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.93.7347.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.49.4490.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.97.8177.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.55.7573.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.86.7953.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.6970.01 2 0.455 0.776 0.20 0.80 0.00
#> TCGA.97.7938.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.55.7726.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.MP.A4TH.01 1 0.207 0.937 0.94 0.00 0.06
#> TCGA.91.8496.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.49.4512.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.67.6217.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.86.8671.01 1 0.207 0.937 0.94 0.00 0.06
#> TCGA.97.7546.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.86.8280.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.91.6835.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.55.A48Z.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.50.5942.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.91.6830.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.44.6774.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.8299.01 1 0.334 0.880 0.88 0.00 0.12
#> TCGA.62.8397.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.55.6979.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.78.8648.01 1 0.334 0.880 0.88 0.00 0.12
#> TCGA.49.6743.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.38.4631.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.99.AA5R.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.MP.A4T7.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.50.8457.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.NJ.A55O.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.44.6145.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.86.8075.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.7724.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.55.8510.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.49.4514.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.55.8204.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.97.A4M6.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.50.5044.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.55.6971.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.O1.A52J.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.91.8497.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.86.7714.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.99.8028.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.49.4487.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.97.7553.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.50.5944.01 2 0.429 0.803 0.18 0.82 0.00
#> TCGA.55.7728.01 1 0.334 0.880 0.88 0.00 0.12
#> TCGA.55.8097.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.44.5645.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.49.AAQV.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.73.7498.01 2 0.429 0.803 0.18 0.82 0.00
#> TCGA.97.7547.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.93.7348.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.97.7941.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.MP.A4TA.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.91.6840.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.50.5941.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.55.7725.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.44.6776.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.50.5055.01 1 0.207 0.937 0.94 0.00 0.06
#> TCGA.50.5045.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.55.A492.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.53.7626.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.50.6595.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.55.6543.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.L9.A8F4.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.50.5068.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.MP.A4T4.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.53.7813.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.NJ.A55A.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.64.1681.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.95.A4VP.01 1 0.000 0.981 1.00 0.00 0.00
#> TCGA.J2.8192.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.50.6593.01 1 0.000 0.981 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.99.8033.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.55.8096.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.55.8208.01 1 0.499 -0.23191 0.52 0.00 0.00 0.48
#> TCGA.64.1679.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.55.6984.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.49.AARO.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.49.6744.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.86.7954.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.55.7910.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.44.A479.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.55.8087.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.55.8619.01 3 0.485 0.59264 0.40 0.00 0.60 0.00
#> TCGA.44.A4SU.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.91.6849.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.53.7624.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.55.8621.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 3 0.485 0.59264 0.40 0.00 0.60 0.00
#> TCGA.MP.A4T9.01 3 0.485 0.59264 0.40 0.00 0.60 0.00
#> TCGA.44.7670.01 4 0.000 0.61617 0.00 0.00 0.00 1.00
#> TCGA.MP.A4TJ.01 1 0.499 -0.23191 0.52 0.00 0.00 0.48
#> TCGA.L9.A5IP.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.93.7347.01 3 0.428 0.69049 0.28 0.00 0.72 0.00
#> TCGA.49.4490.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.97.8177.01 4 0.495 0.41385 0.44 0.00 0.00 0.56
#> TCGA.55.7573.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.86.7953.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.55.6970.01 4 0.000 0.61617 0.00 0.00 0.00 1.00
#> TCGA.97.7938.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.55.7726.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.MP.A4TH.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.91.8496.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.49.4512.01 3 0.491 0.56338 0.42 0.00 0.58 0.00
#> TCGA.67.6217.01 4 0.495 0.41385 0.44 0.00 0.00 0.56
#> TCGA.86.8671.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.97.7546.01 3 0.164 0.82738 0.06 0.00 0.94 0.00
#> TCGA.86.8280.01 4 0.398 0.55241 0.24 0.00 0.00 0.76
#> TCGA.91.6835.01 4 0.498 0.35553 0.46 0.00 0.00 0.54
#> TCGA.55.A48Z.01 4 0.000 0.61617 0.00 0.00 0.00 1.00
#> TCGA.50.5942.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.91.6830.01 4 0.000 0.61617 0.00 0.00 0.00 1.00
#> TCGA.44.6774.01 4 0.340 0.49802 0.00 0.18 0.00 0.82
#> TCGA.55.8299.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.62.8397.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.55.6979.01 1 0.485 -0.00223 0.60 0.00 0.00 0.40
#> TCGA.78.8648.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.49.6743.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.38.4631.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.99.AA5R.01 3 0.485 0.59264 0.40 0.00 0.60 0.00
#> TCGA.MP.A4T7.01 4 0.495 0.41385 0.44 0.00 0.00 0.56
#> TCGA.50.8457.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.NJ.A55O.01 4 0.495 0.41385 0.44 0.00 0.00 0.56
#> TCGA.44.6145.01 1 0.499 -0.23191 0.52 0.00 0.00 0.48
#> TCGA.86.8075.01 4 0.479 -0.26139 0.00 0.38 0.00 0.62
#> TCGA.55.7724.01 1 0.317 0.51641 0.84 0.00 0.00 0.16
#> TCGA.55.8510.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.49.4514.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.55.8204.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.97.A4M6.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.50.5044.01 3 0.499 0.45960 0.48 0.00 0.52 0.00
#> TCGA.55.6971.01 4 0.491 0.44145 0.42 0.00 0.00 0.58
#> TCGA.O1.A52J.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.91.8497.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.86.7714.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.99.8028.01 1 0.485 -0.00223 0.60 0.00 0.00 0.40
#> TCGA.49.4487.01 4 0.491 0.44145 0.42 0.00 0.00 0.58
#> TCGA.97.7553.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.50.5944.01 4 0.000 0.61617 0.00 0.00 0.00 1.00
#> TCGA.55.7728.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.55.8097.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.44.5645.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.49.AAQV.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.73.7498.01 4 0.000 0.61617 0.00 0.00 0.00 1.00
#> TCGA.97.7547.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.93.7348.01 3 0.485 0.59264 0.40 0.00 0.60 0.00
#> TCGA.97.7941.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TA.01 2 0.413 0.81485 0.00 0.74 0.00 0.26
#> TCGA.91.6840.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.50.5941.01 1 0.491 -0.26583 0.58 0.00 0.42 0.00
#> TCGA.55.7725.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.44.6776.01 4 0.000 0.61617 0.00 0.00 0.00 1.00
#> TCGA.50.5055.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.50.5045.01 1 0.485 -0.00223 0.60 0.00 0.00 0.40
#> TCGA.55.A492.01 4 0.413 0.53839 0.26 0.00 0.00 0.74
#> TCGA.53.7626.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.50.6595.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
#> TCGA.55.6543.01 3 0.000 0.85659 0.00 0.00 1.00 0.00
#> TCGA.L9.A8F4.01 1 0.499 -0.23191 0.52 0.00 0.00 0.48
#> TCGA.50.5068.01 1 0.479 -0.14231 0.62 0.00 0.38 0.00
#> TCGA.MP.A4T4.01 1 0.499 -0.23191 0.52 0.00 0.00 0.48
#> TCGA.53.7813.01 4 0.491 0.44145 0.42 0.00 0.00 0.58
#> TCGA.NJ.A55A.01 3 0.485 0.59264 0.40 0.00 0.60 0.00
#> TCGA.64.1681.01 2 0.000 0.90166 0.00 1.00 0.00 0.00
#> TCGA.95.A4VP.01 4 0.500 0.23234 0.50 0.00 0.00 0.50
#> TCGA.J2.8192.01 2 0.121 0.89163 0.00 0.96 0.00 0.04
#> TCGA.50.6593.01 1 0.000 0.68729 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.99.8033.01 2 0.3421 0.730 0.00 0.84 0.08 0.08 0.00
#> TCGA.55.8096.01 2 0.6610 0.581 0.00 0.46 0.26 0.28 0.00
#> TCGA.55.8208.01 1 0.0609 0.877 0.98 0.00 0.02 0.00 0.00
#> TCGA.64.1679.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6984.01 3 0.3895 0.968 0.00 0.00 0.68 0.00 0.32
#> TCGA.49.AARO.01 2 0.6610 0.581 0.00 0.46 0.26 0.28 0.00
#> TCGA.49.6744.01 1 0.3424 0.658 0.76 0.00 0.00 0.00 0.24
#> TCGA.86.7954.01 2 0.6610 0.581 0.00 0.46 0.26 0.28 0.00
#> TCGA.55.7910.01 2 0.0609 0.738 0.00 0.98 0.02 0.00 0.00
#> TCGA.44.A479.01 2 0.8107 0.434 0.10 0.36 0.26 0.28 0.00
#> TCGA.55.8087.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.55.8619.01 5 0.1732 0.611 0.00 0.00 0.08 0.00 0.92
#> TCGA.44.A4SU.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.6849.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.53.7624.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8621.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.S2.AA1A.01 5 0.1732 0.611 0.00 0.00 0.08 0.00 0.92
#> TCGA.MP.A4T9.01 5 0.1410 0.628 0.00 0.00 0.06 0.00 0.94
#> TCGA.44.7670.01 4 0.3561 0.742 0.26 0.00 0.00 0.74 0.00
#> TCGA.MP.A4TJ.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A5IP.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.93.7347.01 5 0.2280 0.534 0.00 0.00 0.12 0.00 0.88
#> TCGA.49.4490.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.8177.01 1 0.1732 0.844 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.7573.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.86.7953.01 2 0.2754 0.735 0.00 0.88 0.08 0.04 0.00
#> TCGA.55.6970.01 4 0.4890 0.691 0.14 0.00 0.14 0.72 0.00
#> TCGA.97.7938.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.55.7726.01 2 0.6610 0.581 0.00 0.46 0.26 0.28 0.00
#> TCGA.MP.A4TH.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.91.8496.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.49.4512.01 5 0.1732 0.611 0.00 0.00 0.08 0.00 0.92
#> TCGA.67.6217.01 1 0.1732 0.844 0.92 0.00 0.00 0.08 0.00
#> TCGA.86.8671.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.97.7546.01 3 0.4182 0.853 0.00 0.00 0.60 0.00 0.40
#> TCGA.86.8280.01 4 0.3796 0.686 0.30 0.00 0.00 0.70 0.00
#> TCGA.91.6835.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Z.01 4 0.3561 0.737 0.26 0.00 0.00 0.74 0.00
#> TCGA.50.5942.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.91.6830.01 4 0.5759 0.632 0.20 0.00 0.18 0.62 0.00
#> TCGA.44.6774.01 4 0.8130 -0.402 0.10 0.30 0.26 0.34 0.00
#> TCGA.55.8299.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.62.8397.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.55.6979.01 1 0.0609 0.880 0.98 0.00 0.00 0.00 0.02
#> TCGA.78.8648.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.49.6743.01 2 0.3421 0.730 0.00 0.84 0.08 0.08 0.00
#> TCGA.38.4631.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.AA5R.01 5 0.1732 0.611 0.00 0.00 0.08 0.00 0.92
#> TCGA.MP.A4T7.01 1 0.1043 0.867 0.96 0.00 0.00 0.04 0.00
#> TCGA.50.8457.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.NJ.A55O.01 1 0.1732 0.844 0.92 0.00 0.00 0.08 0.00
#> TCGA.44.6145.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8075.01 4 0.0609 0.631 0.00 0.00 0.02 0.98 0.00
#> TCGA.55.7724.01 1 0.2280 0.813 0.88 0.00 0.00 0.00 0.12
#> TCGA.55.8510.01 2 0.6610 0.581 0.00 0.46 0.26 0.28 0.00
#> TCGA.49.4514.01 2 0.6610 0.581 0.00 0.46 0.26 0.28 0.00
#> TCGA.55.8204.01 1 0.3424 0.658 0.76 0.00 0.00 0.00 0.24
#> TCGA.97.A4M6.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.50.5044.01 5 0.0000 0.666 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.6971.01 1 0.1043 0.867 0.96 0.00 0.00 0.04 0.00
#> TCGA.O1.A52J.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.86.7714.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.99.8028.01 1 0.1043 0.869 0.96 0.00 0.00 0.00 0.04
#> TCGA.49.4487.01 1 0.0609 0.880 0.98 0.00 0.00 0.02 0.00
#> TCGA.97.7553.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.50.5944.01 4 0.2280 0.757 0.12 0.00 0.00 0.88 0.00
#> TCGA.55.7728.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.55.8097.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.44.5645.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.49.AAQV.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.73.7498.01 4 0.2280 0.757 0.12 0.00 0.00 0.88 0.00
#> TCGA.97.7547.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.93.7348.01 5 0.1732 0.611 0.00 0.00 0.08 0.00 0.92
#> TCGA.97.7941.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.MP.A4TA.01 2 0.7455 0.534 0.04 0.42 0.26 0.28 0.00
#> TCGA.91.6840.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5941.01 5 0.1043 0.689 0.04 0.00 0.00 0.00 0.96
#> TCGA.55.7725.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.44.6776.01 4 0.3999 0.739 0.24 0.00 0.02 0.74 0.00
#> TCGA.50.5055.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
#> TCGA.50.5045.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A492.01 4 0.4252 0.694 0.28 0.00 0.02 0.70 0.00
#> TCGA.53.7626.01 1 0.3424 0.658 0.76 0.00 0.00 0.00 0.24
#> TCGA.50.6595.01 1 0.3983 0.422 0.66 0.00 0.00 0.00 0.34
#> TCGA.55.6543.01 3 0.3796 0.991 0.00 0.00 0.70 0.00 0.30
#> TCGA.L9.A8F4.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 5 0.1043 0.689 0.04 0.00 0.00 0.00 0.96
#> TCGA.MP.A4T4.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00
#> TCGA.53.7813.01 1 0.1043 0.867 0.96 0.00 0.00 0.04 0.00
#> TCGA.NJ.A55A.01 5 0.1732 0.611 0.00 0.00 0.08 0.00 0.92
#> TCGA.64.1681.01 2 0.0000 0.742 0.00 1.00 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00
#> TCGA.J2.8192.01 2 0.5382 0.660 0.00 0.64 0.10 0.26 0.00
#> TCGA.50.6593.01 5 0.3796 0.644 0.30 0.00 0.00 0.00 0.70
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.99.8033.01 2 0.2631 0.759 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.55.8096.01 6 0.3309 0.751 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.55.8208.01 1 0.0000 0.884 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.1679.01 2 0.0937 0.877 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.6984.01 3 0.4784 0.707 0.00 0.00 0.74 0.08 0.08 0.10
#> TCGA.49.AARO.01 6 0.3309 0.751 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.49.6744.01 1 0.2941 0.770 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.86.7954.01 6 0.3309 0.751 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.55.7910.01 2 0.2350 0.847 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.44.A479.01 6 0.4393 0.692 0.14 0.14 0.00 0.00 0.00 0.72
#> TCGA.55.8087.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8619.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.44.A4SU.01 2 0.1480 0.881 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.91.6849.01 3 0.0547 0.943 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.53.7624.01 2 0.2190 0.860 0.00 0.90 0.00 0.04 0.06 0.00
#> TCGA.55.8621.01 5 0.3483 0.805 0.12 0.00 0.00 0.04 0.82 0.02
#> TCGA.S2.AA1A.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.MP.A4T9.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.44.7670.01 4 0.4200 0.815 0.14 0.00 0.00 0.74 0.00 0.12
#> TCGA.MP.A4TJ.01 1 0.0547 0.882 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.L9.A5IP.01 2 0.0547 0.884 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.93.7347.01 5 0.5580 0.768 0.00 0.00 0.16 0.08 0.66 0.10
#> TCGA.49.4490.01 2 0.0547 0.884 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.97.8177.01 1 0.2345 0.846 0.90 0.00 0.00 0.02 0.02 0.06
#> TCGA.55.7573.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.7953.01 2 0.2260 0.804 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.55.6970.01 6 0.5265 -0.259 0.10 0.00 0.00 0.40 0.00 0.50
#> TCGA.97.7938.01 3 0.0547 0.943 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.55.7726.01 6 0.3309 0.751 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.MP.A4TH.01 5 0.1814 0.796 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.91.8496.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.4512.01 5 0.5226 0.811 0.00 0.00 0.12 0.08 0.70 0.10
#> TCGA.67.6217.01 1 0.3045 0.814 0.86 0.00 0.00 0.06 0.02 0.06
#> TCGA.86.8671.01 5 0.2048 0.799 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.97.7546.01 3 0.5331 0.595 0.00 0.00 0.66 0.10 0.20 0.04
#> TCGA.86.8280.01 4 0.4631 0.759 0.22 0.00 0.00 0.70 0.02 0.06
#> TCGA.91.6835.01 1 0.0547 0.882 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.A48Z.01 4 0.4328 0.809 0.18 0.00 0.00 0.72 0.00 0.10
#> TCGA.50.5942.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.6830.01 6 0.5039 0.248 0.18 0.00 0.00 0.18 0.00 0.64
#> TCGA.44.6774.01 6 0.3475 0.557 0.14 0.00 0.00 0.06 0.00 0.80
#> TCGA.55.8299.01 5 0.2048 0.799 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.62.8397.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6979.01 1 0.1556 0.860 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.78.8648.01 5 0.2048 0.799 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.49.6743.01 2 0.2631 0.759 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.38.4631.01 2 0.2190 0.860 0.00 0.90 0.00 0.04 0.06 0.00
#> TCGA.99.AA5R.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.MP.A4T7.01 1 0.2345 0.846 0.90 0.00 0.00 0.02 0.02 0.06
#> TCGA.50.8457.01 3 0.0547 0.943 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.3045 0.814 0.86 0.00 0.00 0.06 0.02 0.06
#> TCGA.44.6145.01 1 0.0000 0.884 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8075.01 4 0.3156 0.731 0.00 0.00 0.00 0.80 0.02 0.18
#> TCGA.55.7724.01 1 0.2793 0.787 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.55.8510.01 6 0.3309 0.751 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.49.4514.01 6 0.3309 0.751 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.55.8204.01 1 0.2941 0.770 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.97.A4M6.01 3 0.3321 0.808 0.00 0.00 0.82 0.08 0.00 0.10
#> TCGA.50.5044.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.55.6971.01 1 0.0547 0.882 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.O1.A52J.01 2 0.0547 0.884 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.91.8497.01 3 0.0547 0.943 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.86.7714.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.1814 0.849 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.49.4487.01 1 0.0547 0.882 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.97.7553.01 5 0.2260 0.786 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.50.5944.01 4 0.3163 0.793 0.04 0.00 0.00 0.82 0.00 0.14
#> TCGA.55.7728.01 5 0.2048 0.799 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.55.8097.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.5645.01 3 0.1480 0.917 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.49.AAQV.01 5 0.2260 0.786 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.73.7498.01 4 0.3163 0.793 0.04 0.00 0.00 0.82 0.00 0.14
#> TCGA.97.7547.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.93.7348.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.97.7941.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 6 0.3950 0.742 0.04 0.24 0.00 0.00 0.00 0.72
#> TCGA.91.6840.01 2 0.0547 0.884 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.50.5941.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.55.7725.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6776.01 4 0.4265 0.805 0.14 0.00 0.00 0.76 0.02 0.08
#> TCGA.50.5055.01 5 0.2048 0.799 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.50.5045.01 1 0.1556 0.860 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.55.A492.01 4 0.4265 0.805 0.14 0.00 0.00 0.76 0.02 0.08
#> TCGA.53.7626.01 1 0.2941 0.770 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.50.6595.01 1 0.3409 0.667 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.55.6543.01 3 0.0000 0.948 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.0000 0.884 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 5 0.5269 0.823 0.02 0.00 0.10 0.06 0.72 0.10
#> TCGA.MP.A4T4.01 1 0.0000 0.884 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.7813.01 1 0.0937 0.876 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.NJ.A55A.01 5 0.4967 0.824 0.00 0.00 0.12 0.06 0.72 0.10
#> TCGA.64.1681.01 2 0.0547 0.884 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0547 0.882 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.J2.8192.01 2 0.4326 0.535 0.00 0.68 0.00 0.02 0.02 0.28
#> TCGA.50.6593.01 5 0.2260 0.786 0.14 0.00 0.00 0.00 0.86 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.99.8033.01 2 0.3186 0.727 0.00 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.55.8096.01 6 0.2081 0.889 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.55.8208.01 1 0.0504 0.798 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.64.1679.01 2 0.1363 0.862 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.55.6984.01 3 0.4954 0.411 0.00 0.00 0.52 0.00 0.40 0.04 0.04
#> TCGA.49.AARO.01 6 0.2081 0.889 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.49.6744.01 1 0.4003 0.575 0.64 0.00 0.00 0.00 0.04 0.00 0.32
#> TCGA.86.7954.01 6 0.2081 0.889 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.55.7910.01 2 0.4242 0.710 0.00 0.72 0.00 0.02 0.08 0.00 0.18
#> TCGA.44.A479.01 6 0.2572 0.858 0.08 0.06 0.00 0.00 0.00 0.86 0.00
#> TCGA.55.8087.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8619.01 5 0.2081 0.684 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.44.A4SU.01 2 0.0504 0.864 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.91.6849.01 3 0.2512 0.858 0.00 0.00 0.86 0.00 0.00 0.10 0.04
#> TCGA.53.7624.01 2 0.2163 0.850 0.00 0.88 0.00 0.00 0.00 0.02 0.10
#> TCGA.55.8621.01 5 0.4538 0.689 0.10 0.00 0.00 0.00 0.62 0.00 0.28
#> TCGA.S2.AA1A.01 5 0.2081 0.684 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.MP.A4T9.01 5 0.2081 0.684 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.44.7670.01 4 0.3680 0.770 0.06 0.00 0.00 0.78 0.02 0.00 0.14
#> TCGA.MP.A4TJ.01 1 0.0000 0.804 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A5IP.01 2 0.0863 0.863 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.93.7347.01 5 0.3055 0.653 0.00 0.00 0.14 0.00 0.82 0.02 0.02
#> TCGA.49.4490.01 2 0.0504 0.866 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.97.8177.01 1 0.4092 0.682 0.74 0.00 0.00 0.16 0.00 0.02 0.08
#> TCGA.55.7573.01 3 0.0504 0.887 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.86.7953.01 2 0.2422 0.770 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.55.6970.01 4 0.4328 0.362 0.06 0.00 0.00 0.60 0.00 0.34 0.00
#> TCGA.97.7938.01 3 0.2512 0.858 0.00 0.00 0.86 0.00 0.00 0.10 0.04
#> TCGA.55.7726.01 6 0.2512 0.888 0.04 0.10 0.00 0.00 0.00 0.86 0.00
#> TCGA.MP.A4TH.01 5 0.4669 0.645 0.08 0.00 0.00 0.00 0.52 0.00 0.40
#> TCGA.91.8496.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 5 0.4667 0.567 0.00 0.00 0.14 0.00 0.70 0.12 0.04
#> TCGA.67.6217.01 1 0.4499 0.641 0.70 0.00 0.00 0.16 0.00 0.02 0.12
#> TCGA.86.8671.01 5 0.4681 0.681 0.10 0.00 0.00 0.00 0.58 0.00 0.32
#> TCGA.97.7546.01 3 0.6086 0.544 0.00 0.00 0.54 0.00 0.20 0.12 0.14
#> TCGA.86.8280.01 4 0.3744 0.768 0.08 0.00 0.00 0.78 0.00 0.02 0.12
#> TCGA.91.6835.01 1 0.1166 0.792 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.55.A48Z.01 4 0.1166 0.807 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.50.5942.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6830.01 6 0.4990 0.357 0.20 0.00 0.00 0.22 0.00 0.58 0.00
#> TCGA.44.6774.01 6 0.2769 0.819 0.08 0.02 0.00 0.04 0.00 0.86 0.00
#> TCGA.55.8299.01 5 0.4681 0.681 0.10 0.00 0.00 0.00 0.58 0.00 0.32
#> TCGA.62.8397.01 3 0.1664 0.873 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.55.6979.01 1 0.0863 0.798 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.78.8648.01 5 0.4681 0.681 0.10 0.00 0.00 0.00 0.58 0.00 0.32
#> TCGA.49.6743.01 2 0.3186 0.727 0.00 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.38.4631.01 2 0.2163 0.850 0.00 0.88 0.00 0.00 0.00 0.02 0.10
#> TCGA.99.AA5R.01 5 0.2081 0.684 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.MP.A4T7.01 1 0.3848 0.699 0.76 0.00 0.00 0.16 0.00 0.02 0.06
#> TCGA.50.8457.01 3 0.2512 0.858 0.00 0.00 0.86 0.00 0.00 0.10 0.04
#> TCGA.NJ.A55O.01 1 0.4499 0.641 0.70 0.00 0.00 0.16 0.00 0.02 0.12
#> TCGA.44.6145.01 1 0.0000 0.804 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8075.01 4 0.2829 0.773 0.00 0.00 0.00 0.84 0.00 0.08 0.08
#> TCGA.55.7724.01 1 0.3685 0.598 0.66 0.00 0.00 0.00 0.02 0.00 0.32
#> TCGA.55.8510.01 6 0.2081 0.889 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.49.4514.01 6 0.2081 0.889 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.55.8204.01 1 0.4003 0.575 0.64 0.00 0.00 0.00 0.04 0.00 0.32
#> TCGA.97.A4M6.01 3 0.4772 0.571 0.00 0.00 0.60 0.00 0.32 0.04 0.04
#> TCGA.50.5044.01 5 0.1671 0.703 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.55.6971.01 1 0.1886 0.765 0.88 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.O1.A52J.01 2 0.0504 0.864 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.91.8497.01 3 0.1718 0.875 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.86.7714.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.1671 0.771 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.49.4487.01 1 0.1166 0.792 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.97.7553.01 5 0.5086 0.621 0.14 0.00 0.00 0.00 0.50 0.00 0.36
#> TCGA.50.5944.01 4 0.1928 0.825 0.02 0.00 0.00 0.90 0.00 0.00 0.08
#> TCGA.55.7728.01 5 0.4681 0.681 0.10 0.00 0.00 0.00 0.58 0.00 0.32
#> TCGA.55.8097.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.5645.01 3 0.4079 0.797 0.00 0.00 0.76 0.00 0.08 0.12 0.04
#> TCGA.49.AAQV.01 5 0.4998 0.646 0.14 0.00 0.00 0.00 0.54 0.00 0.32
#> TCGA.73.7498.01 4 0.1928 0.825 0.02 0.00 0.00 0.90 0.00 0.00 0.08
#> TCGA.97.7547.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.7348.01 5 0.2081 0.684 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.97.7941.01 3 0.0504 0.887 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.MP.A4TA.01 6 0.2512 0.888 0.04 0.10 0.00 0.00 0.00 0.86 0.00
#> TCGA.91.6840.01 2 0.1166 0.863 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.50.5941.01 5 0.1928 0.705 0.02 0.00 0.08 0.00 0.90 0.00 0.00
#> TCGA.55.7725.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6776.01 4 0.3661 0.805 0.02 0.00 0.00 0.74 0.00 0.02 0.22
#> TCGA.50.5055.01 5 0.4681 0.681 0.10 0.00 0.00 0.00 0.58 0.00 0.32
#> TCGA.50.5045.01 1 0.0863 0.798 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.55.A492.01 4 0.3887 0.788 0.02 0.00 0.00 0.70 0.00 0.02 0.26
#> TCGA.53.7626.01 1 0.4127 0.549 0.60 0.00 0.00 0.00 0.04 0.00 0.36
#> TCGA.50.6595.01 1 0.4003 0.575 0.64 0.00 0.00 0.00 0.04 0.00 0.32
#> TCGA.55.6543.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.0000 0.804 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 5 0.2016 0.703 0.04 0.00 0.06 0.00 0.90 0.00 0.00
#> TCGA.MP.A4T4.01 1 0.0000 0.804 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.7813.01 1 0.1886 0.765 0.88 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.NJ.A55A.01 5 0.2081 0.684 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.64.1681.01 2 0.0504 0.864 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.95.A4VP.01 1 0.1671 0.778 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.J2.8192.01 2 0.3815 0.460 0.00 0.62 0.00 0.00 0.00 0.36 0.02
#> TCGA.50.6593.01 5 0.5086 0.621 0.14 0.00 0.00 0.00 0.50 0.00 0.36
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.99.8033.01 2 0.2756 0.682 0.00 0.74 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.55.8096.01 6 0.1563 0.891 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.55.8208.01 1 0.1765 0.828 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.64.1679.01 2 0.0808 0.852 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.55.6984.01 5 0.4073 0.330 0.00 0.00 0.24 0.00 0.66 0.00 0.10 0.00
#> TCGA.49.AARO.01 6 0.1563 0.891 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.49.6744.01 8 0.3449 0.406 0.32 0.00 0.00 0.00 0.00 0.02 0.00 0.66
#> TCGA.86.7954.01 6 0.1563 0.891 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.55.7910.01 2 0.4528 0.655 0.00 0.68 0.00 0.00 0.04 0.00 0.14 0.14
#> TCGA.44.A479.01 6 0.1563 0.845 0.10 0.00 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.55.8087.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8619.01 5 0.1557 0.803 0.00 0.00 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.44.A4SU.01 2 0.0941 0.851 0.00 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.91.6849.01 3 0.2852 0.596 0.00 0.00 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.53.7624.01 2 0.1275 0.847 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.55.8621.01 8 0.3318 0.575 0.00 0.00 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.S2.AA1A.01 5 0.1557 0.803 0.00 0.00 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.MP.A4T9.01 5 0.1091 0.798 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.44.7670.01 4 0.5613 0.590 0.12 0.00 0.00 0.60 0.00 0.04 0.18 0.06
#> TCGA.MP.A4TJ.01 1 0.1091 0.832 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.L9.A5IP.01 2 0.0471 0.852 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.93.7347.01 5 0.2407 0.751 0.00 0.00 0.06 0.00 0.86 0.00 0.08 0.00
#> TCGA.49.4490.01 2 0.0941 0.857 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.97.8177.01 1 0.4180 0.621 0.70 0.00 0.00 0.00 0.00 0.04 0.20 0.06
#> TCGA.55.7573.01 3 0.1341 0.826 0.00 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.86.7953.01 2 0.3095 0.704 0.00 0.74 0.00 0.00 0.02 0.24 0.00 0.00
#> TCGA.55.6970.01 4 0.4504 0.506 0.10 0.00 0.00 0.64 0.00 0.24 0.02 0.00
#> TCGA.97.7938.01 3 0.2534 0.675 0.00 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.55.7726.01 6 0.1563 0.891 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.MP.A4TH.01 8 0.4302 0.563 0.00 0.00 0.00 0.00 0.36 0.00 0.08 0.56
#> TCGA.91.8496.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 5 0.4756 0.199 0.00 0.00 0.06 0.00 0.56 0.00 0.34 0.04
#> TCGA.67.6217.01 1 0.5017 0.490 0.58 0.00 0.00 0.00 0.00 0.06 0.28 0.08
#> TCGA.86.8671.01 8 0.3299 0.598 0.00 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.97.7546.01 7 0.5420 0.000 0.00 0.00 0.26 0.00 0.14 0.00 0.54 0.06
#> TCGA.86.8280.01 4 0.6477 0.399 0.24 0.00 0.00 0.42 0.00 0.06 0.24 0.04
#> TCGA.91.6835.01 1 0.0000 0.824 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Z.01 4 0.2224 0.675 0.12 0.00 0.00 0.86 0.00 0.00 0.02 0.00
#> TCGA.50.5942.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6830.01 6 0.5109 0.393 0.24 0.00 0.00 0.14 0.00 0.58 0.04 0.00
#> TCGA.44.6774.01 6 0.1563 0.845 0.10 0.00 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.55.8299.01 8 0.3299 0.598 0.00 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.62.8397.01 3 0.1341 0.821 0.00 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.55.6979.01 1 0.2224 0.824 0.86 0.00 0.00 0.00 0.00 0.02 0.00 0.12
#> TCGA.78.8648.01 8 0.3299 0.598 0.00 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.49.6743.01 2 0.2756 0.682 0.00 0.74 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.38.4631.01 2 0.1275 0.847 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.99.AA5R.01 5 0.1557 0.803 0.00 0.00 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.MP.A4T7.01 1 0.3397 0.720 0.80 0.00 0.00 0.00 0.00 0.04 0.10 0.06
#> TCGA.50.8457.01 3 0.2756 0.646 0.00 0.00 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.NJ.A55O.01 1 0.5017 0.490 0.58 0.00 0.00 0.00 0.00 0.06 0.28 0.08
#> TCGA.44.6145.01 1 0.1765 0.828 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.86.8075.01 4 0.0471 0.695 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.7724.01 8 0.3514 0.360 0.34 0.00 0.00 0.00 0.00 0.02 0.00 0.64
#> TCGA.55.8510.01 6 0.1563 0.891 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.49.4514.01 6 0.1563 0.891 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.55.8204.01 8 0.3449 0.406 0.32 0.00 0.00 0.00 0.00 0.02 0.00 0.66
#> TCGA.97.A4M6.01 5 0.4680 -0.253 0.00 0.00 0.40 0.00 0.48 0.00 0.12 0.00
#> TCGA.50.5044.01 5 0.1091 0.741 0.00 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.55.6971.01 1 0.0471 0.820 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.O1.A52J.01 2 0.0471 0.855 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.1765 0.802 0.00 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.86.7714.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.2981 0.722 0.76 0.00 0.00 0.00 0.00 0.02 0.00 0.22
#> TCGA.49.4487.01 1 0.0000 0.824 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7553.01 8 0.3198 0.646 0.00 0.00 0.00 0.00 0.26 0.00 0.02 0.72
#> TCGA.50.5944.01 4 0.0000 0.696 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7728.01 8 0.3299 0.598 0.00 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.55.8097.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.5645.01 3 0.3746 0.406 0.00 0.00 0.64 0.00 0.04 0.00 0.32 0.00
#> TCGA.49.AAQV.01 8 0.3015 0.642 0.00 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.73.7498.01 4 0.0000 0.696 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.7348.01 5 0.1557 0.794 0.00 0.00 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.97.7941.01 3 0.1341 0.826 0.00 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.MP.A4TA.01 6 0.1563 0.845 0.10 0.00 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.91.6840.01 2 0.0471 0.852 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.50.5941.01 5 0.1341 0.719 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.55.7725.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6776.01 4 0.4887 0.519 0.00 0.00 0.00 0.58 0.02 0.04 0.32 0.04
#> TCGA.50.5055.01 8 0.3299 0.598 0.00 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.50.5045.01 1 0.2224 0.824 0.86 0.00 0.00 0.00 0.00 0.02 0.00 0.12
#> TCGA.55.A492.01 4 0.5590 0.470 0.00 0.00 0.00 0.50 0.02 0.08 0.34 0.06
#> TCGA.53.7626.01 8 0.3941 0.427 0.26 0.00 0.00 0.00 0.00 0.02 0.04 0.68
#> TCGA.50.6595.01 8 0.3015 0.419 0.32 0.00 0.00 0.00 0.00 0.00 0.00 0.68
#> TCGA.55.6543.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.1765 0.828 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.50.5068.01 5 0.1341 0.719 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.MP.A4T4.01 1 0.2224 0.824 0.86 0.00 0.00 0.00 0.00 0.02 0.00 0.12
#> TCGA.53.7813.01 1 0.1275 0.807 0.94 0.00 0.00 0.00 0.00 0.04 0.02 0.00
#> TCGA.NJ.A55A.01 5 0.1557 0.803 0.00 0.00 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.64.1681.01 2 0.0471 0.855 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0471 0.820 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.J2.8192.01 2 0.4105 0.338 0.00 0.54 0.00 0.00 0.02 0.42 0.02 0.00
#> TCGA.50.6593.01 8 0.3941 0.636 0.00 0.00 0.00 0.00 0.26 0.02 0.04 0.68
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01221-leaf , Node01222-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-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["0111"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 38 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 0.997 0.996 0.4187 0.578 0.578
#> 3 3 1.000 1.000 1.000 0.3566 0.718 0.564
#> 4 4 1.000 0.989 0.996 0.2468 0.775 0.527
#> 5 5 0.967 0.957 0.971 0.0675 0.933 0.776
#> 6 6 0.870 0.845 0.926 0.0278 0.990 0.958
#> 7 7 0.811 0.731 0.862 0.0405 0.922 0.671
#> 8 8 0.781 0.726 0.863 0.0154 0.962 0.797
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.55.8208.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.6744.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8621.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.7670.01 2 0.000 0.986 0.00 1.00
#> TCGA.MP.A4TJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8177.01 1 0.000 1.000 1.00 0.00
#> TCGA.MP.A4TH.01 1 0.000 1.000 1.00 0.00
#> TCGA.67.6217.01 2 0.141 0.992 0.02 0.98
#> TCGA.86.8671.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.8280.01 2 0.141 0.992 0.02 0.98
#> TCGA.91.6835.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.A48Z.01 2 0.141 0.992 0.02 0.98
#> TCGA.91.6830.01 2 0.141 0.992 0.02 0.98
#> TCGA.55.8299.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6979.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.8648.01 1 0.000 1.000 1.00 0.00
#> TCGA.MP.A4T7.01 2 0.000 0.986 0.00 1.00
#> TCGA.NJ.A55O.01 2 0.141 0.992 0.02 0.98
#> TCGA.44.6145.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7724.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8204.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6971.01 1 0.000 1.000 1.00 0.00
#> TCGA.99.8028.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.4487.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.7553.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7728.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.AAQV.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.6776.01 2 0.000 0.986 0.00 1.00
#> TCGA.50.5055.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5045.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.A492.01 2 0.000 0.986 0.00 1.00
#> TCGA.53.7626.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.6595.01 1 0.000 1.000 1.00 0.00
#> TCGA.L9.A8F4.01 1 0.000 1.000 1.00 0.00
#> TCGA.MP.A4T4.01 1 0.000 1.000 1.00 0.00
#> TCGA.53.7813.01 2 0.141 0.992 0.02 0.98
#> TCGA.95.A4VP.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.6593.01 2 0.141 0.992 0.02 0.98
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.55.8208.01 1 0 1 1 0 0
#> TCGA.49.6744.01 1 0 1 1 0 0
#> TCGA.55.8621.01 1 0 1 1 0 0
#> TCGA.44.7670.01 3 0 1 0 0 1
#> TCGA.MP.A4TJ.01 1 0 1 1 0 0
#> TCGA.97.8177.01 2 0 1 0 1 0
#> TCGA.MP.A4TH.01 2 0 1 0 1 0
#> TCGA.67.6217.01 2 0 1 0 1 0
#> TCGA.86.8671.01 1 0 1 1 0 0
#> TCGA.86.8280.01 2 0 1 0 1 0
#> TCGA.91.6835.01 1 0 1 1 0 0
#> TCGA.55.A48Z.01 2 0 1 0 1 0
#> TCGA.91.6830.01 2 0 1 0 1 0
#> TCGA.55.8299.01 1 0 1 1 0 0
#> TCGA.55.6979.01 1 0 1 1 0 0
#> TCGA.78.8648.01 1 0 1 1 0 0
#> TCGA.MP.A4T7.01 2 0 1 0 1 0
#> TCGA.NJ.A55O.01 2 0 1 0 1 0
#> TCGA.44.6145.01 1 0 1 1 0 0
#> TCGA.55.7724.01 1 0 1 1 0 0
#> TCGA.55.8204.01 1 0 1 1 0 0
#> TCGA.55.6971.01 1 0 1 1 0 0
#> TCGA.99.8028.01 1 0 1 1 0 0
#> TCGA.49.4487.01 1 0 1 1 0 0
#> TCGA.97.7553.01 2 0 1 0 1 0
#> TCGA.55.7728.01 2 0 1 0 1 0
#> TCGA.49.AAQV.01 1 0 1 1 0 0
#> TCGA.44.6776.01 3 0 1 0 0 1
#> TCGA.50.5055.01 1 0 1 1 0 0
#> TCGA.50.5045.01 1 0 1 1 0 0
#> TCGA.55.A492.01 3 0 1 0 0 1
#> TCGA.53.7626.01 2 0 1 0 1 0
#> TCGA.50.6595.01 1 0 1 1 0 0
#> TCGA.L9.A8F4.01 1 0 1 1 0 0
#> TCGA.MP.A4T4.01 1 0 1 1 0 0
#> TCGA.53.7813.01 2 0 1 0 1 0
#> TCGA.95.A4VP.01 2 0 1 0 1 0
#> TCGA.50.6593.01 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.55.8208.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.49.6744.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.55.8621.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.44.7670.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.MP.A4TJ.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.97.8177.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.MP.A4TH.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.67.6217.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.86.8671.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.86.8280.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.91.6835.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.55.A48Z.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.91.6830.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.55.8299.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.55.6979.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.78.8648.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.MP.A4T7.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.NJ.A55O.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.44.6145.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.55.7724.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.55.8204.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.55.6971.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.99.8028.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.49.4487.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.97.7553.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.55.7728.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.49.AAQV.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.44.6776.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.50.5055.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.50.5045.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.55.A492.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.53.7626.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.50.6595.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.L9.A8F4.01 1 0.317 0.784 0.84 0 0 0.16
#> TCGA.MP.A4T4.01 1 0.000 0.987 1.00 0 0 0.00
#> TCGA.53.7813.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.95.A4VP.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.50.6593.01 2 0.000 1.000 0.00 1 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.55.8208.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.49.6744.01 5 0.4437 0.783 0.14 0.00 0 0.10 0.76
#> TCGA.55.8621.01 5 0.2280 0.838 0.00 0.00 0 0.12 0.88
#> TCGA.44.7670.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.MP.A4TJ.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.97.8177.01 4 0.0000 0.955 0.00 0.00 0 1.00 0.00
#> TCGA.MP.A4TH.01 4 0.0000 0.955 0.00 0.00 0 1.00 0.00
#> TCGA.67.6217.01 2 0.0609 0.971 0.00 0.98 0 0.00 0.02
#> TCGA.86.8671.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.86.8280.01 2 0.0609 0.971 0.00 0.98 0 0.00 0.02
#> TCGA.91.6835.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.55.A48Z.01 2 0.1216 0.970 0.00 0.96 0 0.02 0.02
#> TCGA.91.6830.01 2 0.1216 0.970 0.00 0.96 0 0.02 0.02
#> TCGA.55.8299.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.55.6979.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.78.8648.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.MP.A4T7.01 2 0.0609 0.967 0.00 0.98 0 0.00 0.02
#> TCGA.NJ.A55O.01 2 0.0609 0.973 0.00 0.98 0 0.00 0.02
#> TCGA.44.6145.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.55.7724.01 5 0.1410 0.857 0.00 0.00 0 0.06 0.94
#> TCGA.55.8204.01 5 0.1410 0.857 0.00 0.00 0 0.06 0.94
#> TCGA.55.6971.01 4 0.2280 0.869 0.00 0.00 0 0.88 0.12
#> TCGA.99.8028.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.49.4487.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.97.7553.01 4 0.2280 0.869 0.00 0.00 0 0.88 0.12
#> TCGA.55.7728.01 4 0.0000 0.955 0.00 0.00 0 1.00 0.00
#> TCGA.49.AAQV.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.44.6776.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.50.5055.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.50.5045.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.55.A492.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.53.7626.01 4 0.0000 0.955 0.00 0.00 0 1.00 0.00
#> TCGA.50.6595.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.L9.A8F4.01 5 0.3319 0.756 0.16 0.00 0 0.02 0.82
#> TCGA.MP.A4T4.01 1 0.0000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.53.7813.01 2 0.0609 0.971 0.00 0.98 0 0.00 0.02
#> TCGA.95.A4VP.01 4 0.0000 0.955 0.00 0.00 0 1.00 0.00
#> TCGA.50.6593.01 2 0.1216 0.970 0.00 0.96 0 0.02 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.55.8208.01 1 0.0547 0.941 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.49.6744.01 5 0.6273 0.584 0.18 0.00 0 0.06 0.56 0.20
#> TCGA.55.8621.01 5 0.2350 0.662 0.00 0.00 0 0.10 0.88 0.02
#> TCGA.44.7670.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.MP.A4TJ.01 1 0.3156 0.780 0.80 0.00 0 0.00 0.02 0.18
#> TCGA.97.8177.01 4 0.0000 0.970 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.MP.A4TH.01 4 0.0000 0.970 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.67.6217.01 2 0.1814 0.824 0.00 0.90 0 0.00 0.00 0.10
#> TCGA.86.8671.01 1 0.0547 0.941 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.86.8280.01 2 0.1814 0.824 0.00 0.90 0 0.00 0.00 0.10
#> TCGA.91.6835.01 1 0.0000 0.942 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.55.A48Z.01 2 0.0000 0.844 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.91.6830.01 2 0.1814 0.798 0.00 0.90 0 0.00 0.00 0.10
#> TCGA.55.8299.01 1 0.0547 0.941 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.55.6979.01 1 0.2581 0.843 0.86 0.00 0 0.00 0.02 0.12
#> TCGA.78.8648.01 1 0.0547 0.941 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.MP.A4T7.01 6 0.3409 0.000 0.00 0.30 0 0.00 0.00 0.70
#> TCGA.NJ.A55O.01 2 0.1814 0.798 0.00 0.90 0 0.00 0.00 0.10
#> TCGA.44.6145.01 1 0.3679 0.727 0.76 0.00 0 0.00 0.04 0.20
#> TCGA.55.7724.01 5 0.0547 0.682 0.00 0.00 0 0.02 0.98 0.00
#> TCGA.55.8204.01 5 0.0000 0.673 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.55.6971.01 4 0.1556 0.911 0.00 0.00 0 0.92 0.08 0.00
#> TCGA.99.8028.01 1 0.0547 0.941 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.49.4487.01 1 0.0000 0.942 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.97.7553.01 4 0.1556 0.914 0.00 0.00 0 0.92 0.08 0.00
#> TCGA.55.7728.01 4 0.0000 0.970 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.49.AAQV.01 1 0.0000 0.942 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.44.6776.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0547 0.941 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.50.5045.01 1 0.1267 0.908 0.94 0.00 0 0.00 0.00 0.06
#> TCGA.55.A492.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.53.7626.01 4 0.0000 0.970 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.50.6595.01 1 0.0000 0.942 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 5 0.5520 0.534 0.24 0.00 0 0.00 0.56 0.20
#> TCGA.MP.A4T4.01 1 0.0000 0.942 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.53.7813.01 2 0.2454 0.764 0.00 0.84 0 0.00 0.00 0.16
#> TCGA.95.A4VP.01 4 0.0000 0.970 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.50.6593.01 2 0.0937 0.837 0.00 0.96 0 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.55.8208.01 1 0.0000 0.94318 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6744.01 7 0.3404 0.34900 0.08 0.00 0.00 0.04 0.06 0.00 0.82
#> TCGA.55.8621.01 5 0.4615 0.84639 0.00 0.00 0.00 0.10 0.60 0.00 0.30
#> TCGA.44.7670.01 3 0.0863 0.96961 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.MP.A4TJ.01 7 0.3459 0.63307 0.40 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.97.8177.01 4 0.0000 0.94361 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TH.01 4 0.0000 0.94361 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.6217.01 2 0.3459 0.35383 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.86.8671.01 1 0.0000 0.94318 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8280.01 2 0.3413 0.39075 0.00 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.91.6835.01 1 0.0504 0.93437 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.A48Z.01 2 0.2745 0.60882 0.00 0.82 0.00 0.00 0.02 0.16 0.00
#> TCGA.91.6830.01 2 0.1166 0.61319 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.55.8299.01 1 0.0000 0.94318 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 7 0.3562 0.41028 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.78.8648.01 1 0.0000 0.94318 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T7.01 6 0.6066 0.00852 0.00 0.18 0.00 0.00 0.18 0.54 0.10
#> TCGA.NJ.A55O.01 2 0.1166 0.64240 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.44.6145.01 7 0.3413 0.65146 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.55.7724.01 5 0.3637 0.90573 0.00 0.00 0.00 0.04 0.72 0.00 0.24
#> TCGA.55.8204.01 5 0.2832 0.88562 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.55.6971.01 4 0.3244 0.70095 0.00 0.00 0.00 0.78 0.04 0.00 0.18
#> TCGA.99.8028.01 1 0.0000 0.94318 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.0863 0.91678 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.97.7553.01 4 0.1664 0.88305 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.55.7728.01 4 0.0000 0.94361 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AAQV.01 1 0.0504 0.93437 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.6776.01 3 0.0000 0.98492 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0000 0.94318 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5045.01 1 0.2832 0.52085 0.76 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.55.A492.01 3 0.0000 0.98492 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.53.7626.01 4 0.0000 0.94361 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6595.01 1 0.1671 0.83696 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.L9.A8F4.01 7 0.2163 0.41886 0.10 0.00 0.00 0.00 0.02 0.00 0.88
#> TCGA.MP.A4T4.01 1 0.0000 0.94318 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.7813.01 6 0.3562 -0.59476 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.95.A4VP.01 4 0.0000 0.94361 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6593.01 2 0.0000 0.65330 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.55.8208.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6744.01 7 0.3002 0.496 0.04 0.00 0.00 0.02 0.12 0.00 0.82 0.00
#> TCGA.55.8621.01 5 0.4190 0.727 0.00 0.00 0.00 0.14 0.66 0.00 0.20 0.00
#> TCGA.44.7670.01 3 0.1741 0.928 0.00 0.02 0.92 0.00 0.02 0.00 0.04 0.00
#> TCGA.MP.A4TJ.01 7 0.3193 0.483 0.38 0.00 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.97.8177.01 4 0.0808 0.853 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.MP.A4TH.01 4 0.0000 0.851 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.6217.01 8 0.0000 0.787 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.86.8671.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8280.01 8 0.0000 0.787 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.91.6835.01 1 0.1563 0.823 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.55.A48Z.01 2 0.3329 0.766 0.00 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.91.6830.01 2 0.3942 0.878 0.00 0.62 0.00 0.02 0.00 0.02 0.00 0.34
#> TCGA.55.8299.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 1 0.3329 -0.150 0.52 0.00 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.78.8648.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T7.01 6 0.0941 0.000 0.00 0.02 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.NJ.A55O.01 2 0.3862 0.865 0.00 0.60 0.00 0.00 0.00 0.04 0.00 0.36
#> TCGA.44.6145.01 7 0.3083 0.563 0.34 0.00 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.55.7724.01 5 0.2994 0.791 0.00 0.00 0.00 0.06 0.80 0.00 0.14 0.00
#> TCGA.55.8204.01 5 0.1607 0.667 0.00 0.04 0.00 0.00 0.92 0.00 0.04 0.00
#> TCGA.55.6971.01 4 0.4144 0.547 0.00 0.00 0.00 0.66 0.12 0.00 0.22 0.00
#> TCGA.99.8028.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.2114 0.768 0.84 0.00 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.97.7553.01 4 0.2888 0.757 0.00 0.00 0.00 0.80 0.16 0.00 0.04 0.00
#> TCGA.55.7728.01 4 0.3523 0.741 0.00 0.10 0.00 0.78 0.00 0.02 0.10 0.00
#> TCGA.49.AAQV.01 1 0.1091 0.838 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.44.6776.01 3 0.0000 0.965 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5045.01 1 0.3083 0.421 0.66 0.00 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.55.A492.01 3 0.0000 0.965 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.7626.01 4 0.1557 0.849 0.00 0.00 0.00 0.92 0.06 0.00 0.02 0.00
#> TCGA.50.6595.01 1 0.1947 0.788 0.86 0.00 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.L9.A8F4.01 7 0.2407 0.549 0.06 0.00 0.00 0.00 0.08 0.00 0.86 0.00
#> TCGA.MP.A4T4.01 1 0.1563 0.824 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.53.7813.01 8 0.3426 0.644 0.00 0.22 0.00 0.00 0.02 0.02 0.00 0.74
#> TCGA.95.A4VP.01 4 0.0000 0.851 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6593.01 2 0.3618 0.874 0.00 0.60 0.00 0.02 0.00 0.00 0.00 0.38
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01221-leaf , Node01222-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-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["0113"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 30 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 0.999 0.5177 0.483 0.483
#> 3 3 1.000 0.989 0.994 0.3195 0.752 0.526
#> 4 4 1.000 0.983 0.993 0.0779 0.857 0.605
#> 5 5 0.870 0.843 0.931 0.0320 0.984 0.939
#> 6 6 0.762 0.631 0.840 0.0512 0.984 0.935
#> 7 7 0.767 0.518 0.805 0.0341 0.922 0.691
#> 8 8 0.770 0.535 0.787 0.0230 0.933 0.681
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.55.6984.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.8087.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8619.01 2 0.000 0.999 0.00 1.00
#> TCGA.91.6849.01 1 0.000 1.000 1.00 0.00
#> TCGA.S2.AA1A.01 2 0.000 0.999 0.00 1.00
#> TCGA.MP.A4T9.01 2 0.000 0.999 0.00 1.00
#> TCGA.93.7347.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.7573.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.7938.01 1 0.000 1.000 1.00 0.00
#> TCGA.91.8496.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.4512.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.7546.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5942.01 1 0.000 1.000 1.00 0.00
#> TCGA.62.8397.01 1 0.000 1.000 1.00 0.00
#> TCGA.99.AA5R.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.8457.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.A4M6.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.5044.01 2 0.000 0.999 0.00 1.00
#> TCGA.91.8497.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.7714.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8097.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.5645.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.7547.01 1 0.000 1.000 1.00 0.00
#> TCGA.93.7348.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.7941.01 2 0.141 0.980 0.02 0.98
#> TCGA.50.5941.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.7725.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6543.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5068.01 2 0.000 0.999 0.00 1.00
#> TCGA.NJ.A55A.01 2 0.000 0.999 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.55.6984.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.55.8087.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.55.8619.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.91.6849.01 3 0.207 0.943 0.06 0.00 0.94
#> TCGA.S2.AA1A.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.MP.A4T9.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.93.7347.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.55.7573.01 3 0.000 0.984 0.00 0.00 1.00
#> TCGA.97.7938.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.91.8496.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.49.4512.01 3 0.000 0.984 0.00 0.00 1.00
#> TCGA.97.7546.01 3 0.000 0.984 0.00 0.00 1.00
#> TCGA.50.5942.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.62.8397.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.99.AA5R.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.50.8457.01 3 0.000 0.984 0.00 0.00 1.00
#> TCGA.97.A4M6.01 2 0.207 0.939 0.00 0.94 0.06
#> TCGA.50.5044.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.91.8497.01 3 0.000 0.984 0.00 0.00 1.00
#> TCGA.86.7714.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.55.8097.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.44.5645.01 3 0.000 0.984 0.00 0.00 1.00
#> TCGA.97.7547.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.93.7348.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.97.7941.01 3 0.000 0.984 0.00 0.00 1.00
#> TCGA.50.5941.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.55.7725.01 3 0.207 0.943 0.06 0.00 0.94
#> TCGA.55.6543.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.50.5068.01 2 0.000 0.995 0.00 1.00 0.00
#> TCGA.NJ.A55A.01 2 0.000 0.995 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.55.6984.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.8087.01 4 0.000 0.928 0.00 0.00 0.00 1.00
#> TCGA.55.8619.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.91.6849.01 1 0.000 0.994 1.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T9.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.93.7347.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.7573.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.97.7938.01 1 0.000 0.994 1.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.000 0.994 1.00 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.97.7546.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.50.5942.01 1 0.121 0.955 0.96 0.00 0.00 0.04
#> TCGA.62.8397.01 4 0.000 0.928 0.00 0.00 0.00 1.00
#> TCGA.99.AA5R.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.50.8457.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.97.A4M6.01 3 0.121 0.945 0.00 0.04 0.96 0.00
#> TCGA.50.5044.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.91.8497.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.86.7714.01 1 0.000 0.994 1.00 0.00 0.00 0.00
#> TCGA.55.8097.01 4 0.292 0.835 0.14 0.00 0.00 0.86
#> TCGA.44.5645.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.97.7547.01 1 0.000 0.994 1.00 0.00 0.00 0.00
#> TCGA.93.7348.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.97.7941.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.50.5941.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.7725.01 1 0.000 0.994 1.00 0.00 0.00 0.00
#> TCGA.55.6543.01 1 0.000 0.994 1.00 0.00 0.00 0.00
#> TCGA.50.5068.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.NJ.A55A.01 2 0.000 1.000 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.55.6984.01 2 0.1732 0.935 0.00 0.92 0.00 0.00 0.08
#> TCGA.55.8087.01 4 0.0000 0.740 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8619.01 2 0.1732 0.935 0.00 0.92 0.00 0.00 0.08
#> TCGA.91.6849.01 1 0.2732 0.794 0.84 0.00 0.00 0.00 0.16
#> TCGA.S2.AA1A.01 2 0.1732 0.935 0.00 0.92 0.00 0.00 0.08
#> TCGA.MP.A4T9.01 2 0.1043 0.948 0.00 0.96 0.00 0.00 0.04
#> TCGA.93.7347.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7573.01 3 0.0000 0.895 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.7938.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.1732 0.900 0.00 0.00 0.92 0.00 0.08
#> TCGA.97.7546.01 3 0.2280 0.894 0.00 0.00 0.88 0.00 0.12
#> TCGA.50.5942.01 1 0.1043 0.872 0.96 0.00 0.00 0.04 0.00
#> TCGA.62.8397.01 4 0.0000 0.740 0.00 0.00 0.00 1.00 0.00
#> TCGA.99.AA5R.01 2 0.0609 0.959 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.8457.01 3 0.0000 0.895 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.A4M6.01 3 0.3922 0.645 0.00 0.18 0.78 0.00 0.04
#> TCGA.50.5044.01 2 0.0609 0.959 0.00 0.98 0.00 0.00 0.02
#> TCGA.91.8497.01 3 0.2280 0.894 0.00 0.00 0.88 0.00 0.12
#> TCGA.86.7714.01 1 0.0609 0.905 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.8097.01 4 0.3983 0.342 0.34 0.00 0.00 0.66 0.00
#> TCGA.44.5645.01 3 0.2280 0.894 0.00 0.00 0.88 0.00 0.12
#> TCGA.97.7547.01 1 0.0609 0.902 0.98 0.00 0.00 0.00 0.02
#> TCGA.93.7348.01 2 0.1043 0.948 0.00 0.96 0.00 0.00 0.04
#> TCGA.97.7941.01 3 0.0000 0.895 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5941.01 2 0.1043 0.948 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.7725.01 1 0.2516 0.821 0.86 0.00 0.00 0.00 0.14
#> TCGA.55.6543.01 5 0.3684 0.000 0.28 0.00 0.00 0.00 0.72
#> TCGA.50.5068.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55A.01 2 0.0000 0.961 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.55.6984.01 2 0.4631 0.547 0.00 0.62 0.00 0.00 0.06 0.32
#> TCGA.55.8087.01 4 0.0000 0.631 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8619.01 2 0.4360 0.611 0.00 0.68 0.00 0.00 0.06 0.26
#> TCGA.91.6849.01 1 0.5274 0.578 0.66 0.00 0.22 0.00 0.06 0.06
#> TCGA.S2.AA1A.01 2 0.3982 0.659 0.00 0.74 0.00 0.00 0.06 0.20
#> TCGA.MP.A4T9.01 2 0.2631 0.685 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.93.7347.01 2 0.0000 0.801 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7573.01 3 0.3706 0.521 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.97.7938.01 1 0.0000 0.785 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.785 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.1814 0.729 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.97.7546.01 3 0.0547 0.715 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.50.5942.01 1 0.2794 0.730 0.86 0.00 0.00 0.00 0.06 0.08
#> TCGA.62.8397.01 4 0.0000 0.631 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.99.AA5R.01 2 0.0000 0.801 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.8457.01 3 0.3647 0.557 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.97.A4M6.01 6 0.5628 0.000 0.00 0.24 0.22 0.00 0.00 0.54
#> TCGA.50.5044.01 2 0.0000 0.801 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0000 0.733 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.7714.01 1 0.3270 0.730 0.82 0.00 0.00 0.00 0.06 0.12
#> TCGA.55.8097.01 4 0.3864 0.155 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.44.5645.01 3 0.0000 0.733 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.1480 0.774 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.93.7348.01 2 0.2631 0.685 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.97.7941.01 3 0.3711 0.635 0.00 0.00 0.72 0.00 0.02 0.26
#> TCGA.50.5941.01 2 0.2631 0.685 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.55.7725.01 1 0.5256 0.624 0.68 0.00 0.18 0.00 0.08 0.06
#> TCGA.55.6543.01 5 0.2454 0.000 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.50.5068.01 2 0.0000 0.801 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55A.01 2 0.0547 0.796 0.00 0.98 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.55.6984.01 7 0.3496 0.000 0.00 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.55.8087.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8619.01 2 0.3562 -0.825 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.91.6849.01 1 0.6355 0.316 0.42 0.00 0.34 0.00 0.00 0.10 0.14
#> TCGA.S2.AA1A.01 2 0.3496 -0.608 0.00 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.MP.A4T9.01 2 0.2512 0.668 0.00 0.86 0.00 0.00 0.00 0.10 0.04
#> TCGA.93.7347.01 2 0.0504 0.712 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.55.7573.01 6 0.3294 0.687 0.00 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.97.7938.01 1 0.0000 0.686 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0504 0.686 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.49.4512.01 3 0.2832 0.516 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.97.7546.01 3 0.0000 0.868 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5942.01 1 0.3061 0.650 0.84 0.00 0.00 0.00 0.02 0.06 0.08
#> TCGA.62.8397.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.AA5R.01 2 0.0504 0.699 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.50.8457.01 6 0.3294 0.687 0.00 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.97.A4M6.01 6 0.4193 0.404 0.00 0.20 0.04 0.00 0.00 0.72 0.04
#> TCGA.50.5044.01 2 0.0000 0.712 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0504 0.862 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.86.7714.01 1 0.2804 0.675 0.86 0.00 0.00 0.00 0.02 0.06 0.06
#> TCGA.55.8097.01 1 0.4283 -0.102 0.48 0.00 0.00 0.48 0.00 0.00 0.04
#> TCGA.44.5645.01 3 0.0000 0.868 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.2906 0.643 0.80 0.00 0.00 0.00 0.00 0.02 0.18
#> TCGA.93.7348.01 2 0.2512 0.668 0.00 0.86 0.00 0.00 0.00 0.10 0.04
#> TCGA.97.7941.01 6 0.4127 0.566 0.00 0.00 0.36 0.00 0.00 0.60 0.04
#> TCGA.50.5941.01 2 0.2512 0.668 0.00 0.86 0.00 0.00 0.00 0.10 0.04
#> TCGA.55.7725.01 1 0.6691 0.445 0.50 0.00 0.16 0.00 0.02 0.14 0.18
#> TCGA.55.6543.01 5 0.0504 0.000 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.50.5068.01 2 0.0000 0.712 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55A.01 2 0.0863 0.678 0.00 0.96 0.00 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.55.6984.01 7 0.2938 0.774 0.00 0.30 0.00 0.0 0 0.00 0.70 0.00
#> TCGA.55.8087.01 4 0.0000 1.000 0.00 0.00 0.00 1.0 0 0.00 0.00 0.00
#> TCGA.55.8619.01 7 0.3299 0.727 0.00 0.44 0.00 0.0 0 0.00 0.56 0.00
#> TCGA.91.6849.01 1 0.5838 0.267 0.38 0.00 0.30 0.0 0 0.00 0.04 0.28
#> TCGA.S2.AA1A.01 2 0.3193 -0.290 0.00 0.62 0.00 0.0 0 0.00 0.38 0.00
#> TCGA.MP.A4T9.01 2 0.3178 0.686 0.00 0.80 0.02 0.0 0 0.04 0.14 0.00
#> TCGA.93.7347.01 2 0.0000 0.764 0.00 1.00 0.00 0.0 0 0.00 0.00 0.00
#> TCGA.55.7573.01 6 0.0000 0.565 0.00 0.00 0.00 0.0 0 1.00 0.00 0.00
#> TCGA.97.7938.01 1 0.0000 0.271 1.00 0.00 0.00 0.0 0 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 0.271 1.00 0.00 0.00 0.0 0 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.4391 0.626 0.00 0.00 0.50 0.0 0 0.42 0.00 0.08
#> TCGA.97.7546.01 3 0.3142 0.752 0.00 0.00 0.64 0.0 0 0.36 0.00 0.00
#> TCGA.50.5942.01 8 0.3333 0.803 0.50 0.00 0.00 0.0 0 0.00 0.00 0.50
#> TCGA.62.8397.01 4 0.0000 1.000 0.00 0.00 0.00 1.0 0 0.00 0.00 0.00
#> TCGA.99.AA5R.01 2 0.0471 0.760 0.00 0.98 0.00 0.0 0 0.00 0.02 0.00
#> TCGA.50.8457.01 6 0.0471 0.541 0.00 0.00 0.02 0.0 0 0.98 0.00 0.00
#> TCGA.97.A4M6.01 6 0.5003 0.346 0.00 0.22 0.02 0.0 0 0.62 0.12 0.02
#> TCGA.50.5044.01 2 0.1091 0.726 0.00 0.94 0.00 0.0 0 0.00 0.06 0.00
#> TCGA.91.8497.01 3 0.3142 0.752 0.00 0.00 0.64 0.0 0 0.36 0.00 0.00
#> TCGA.86.7714.01 8 0.3272 0.801 0.42 0.00 0.00 0.0 0 0.00 0.00 0.58
#> TCGA.55.8097.01 1 0.3658 -0.203 0.58 0.00 0.00 0.4 0 0.00 0.00 0.02
#> TCGA.44.5645.01 3 0.3142 0.752 0.00 0.00 0.64 0.0 0 0.36 0.00 0.00
#> TCGA.97.7547.01 1 0.2807 0.323 0.84 0.00 0.04 0.0 0 0.00 0.02 0.10
#> TCGA.93.7348.01 2 0.3178 0.686 0.00 0.80 0.02 0.0 0 0.04 0.14 0.00
#> TCGA.97.7941.01 3 0.5273 -0.091 0.00 0.00 0.44 0.0 0 0.42 0.06 0.08
#> TCGA.50.5941.01 2 0.2404 0.713 0.00 0.84 0.02 0.0 0 0.00 0.14 0.00
#> TCGA.55.7725.01 1 0.5897 0.250 0.38 0.00 0.20 0.0 0 0.00 0.06 0.36
#> TCGA.55.6543.01 5 0.0000 0.000 0.00 0.00 0.00 0.0 1 0.00 0.00 0.00
#> TCGA.50.5068.01 2 0.0471 0.760 0.00 0.98 0.00 0.0 0 0.00 0.02 0.00
#> TCGA.NJ.A55A.01 2 0.1091 0.722 0.00 0.94 0.00 0.0 0 0.00 0.06 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122 , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221-leaf , Node0222 , Node0223-leaf , Node0231 , Node0232 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0324-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["012"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 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 0.5050 0.495 0.495
#> 3 3 1.000 1.000 1.000 0.2673 0.865 0.727
#> 4 4 0.768 0.883 0.858 0.1422 0.904 0.733
#> 5 5 0.743 0.766 0.841 0.0964 0.898 0.628
#> 6 6 0.721 0.682 0.783 0.0367 0.968 0.831
#> 7 7 0.763 0.683 0.699 0.0248 0.965 0.787
#> 8 8 0.803 0.586 0.782 0.0259 0.931 0.578
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.69.8453.01 1 0 1 1 0
#> TCGA.78.7162.01 2 0 1 0 1
#> TCGA.75.7025.01 2 0 1 0 1
#> TCGA.49.AAR4.01 1 0 1 1 0
#> TCGA.75.6206.01 2 0 1 0 1
#> TCGA.L9.A743.01 1 0 1 1 0
#> TCGA.64.5778.01 2 0 1 0 1
#> TCGA.55.8091.01 2 0 1 0 1
#> TCGA.49.AAR0.01 2 0 1 0 1
#> TCGA.69.8254.01 2 0 1 0 1
#> TCGA.97.A4M5.01 1 0 1 1 0
#> TCGA.05.5423.01 2 0 1 0 1
#> TCGA.91.A4BD.01 2 0 1 0 1
#> TCGA.78.7160.01 1 0 1 1 0
#> TCGA.50.5066.01 1 0 1 1 0
#> TCGA.L9.A50W.01 2 0 1 0 1
#> TCGA.50.8460.01 1 0 1 1 0
#> TCGA.78.7148.01 2 0 1 0 1
#> TCGA.44.6146.01 2 0 1 0 1
#> TCGA.97.7552.01 1 0 1 1 0
#> TCGA.50.8459.01 1 0 1 1 0
#> TCGA.97.A4LX.01 1 0 1 1 0
#> TCGA.50.5932.01 2 0 1 0 1
#> TCGA.93.A4JO.01 1 0 1 1 0
#> TCGA.86.8076.01 1 0 1 1 0
#> TCGA.49.AAR3.01 1 0 1 1 0
#> TCGA.05.4384.01 2 0 1 0 1
#> TCGA.MP.A4T2.01 2 0 1 0 1
#> TCGA.55.8206.01 2 0 1 0 1
#> TCGA.78.7537.01 2 0 1 0 1
#> TCGA.78.7163.01 2 0 1 0 1
#> TCGA.97.8174.01 2 0 1 0 1
#> TCGA.75.7030.01 1 0 1 1 0
#> TCGA.38.A44F.01 1 0 1 1 0
#> TCGA.55.7284.01 2 0 1 0 1
#> TCGA.97.A4M2.01 1 0 1 1 0
#> TCGA.95.7947.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.69.8453.01 1 0 1 1 0 0
#> TCGA.78.7162.01 2 0 1 0 1 0
#> TCGA.75.7025.01 2 0 1 0 1 0
#> TCGA.49.AAR4.01 1 0 1 1 0 0
#> TCGA.75.6206.01 3 0 1 0 0 1
#> TCGA.L9.A743.01 1 0 1 1 0 0
#> TCGA.64.5778.01 2 0 1 0 1 0
#> TCGA.55.8091.01 2 0 1 0 1 0
#> TCGA.49.AAR0.01 2 0 1 0 1 0
#> TCGA.69.8254.01 2 0 1 0 1 0
#> TCGA.97.A4M5.01 1 0 1 1 0 0
#> TCGA.05.5423.01 2 0 1 0 1 0
#> TCGA.91.A4BD.01 2 0 1 0 1 0
#> TCGA.78.7160.01 1 0 1 1 0 0
#> TCGA.50.5066.01 1 0 1 1 0 0
#> TCGA.L9.A50W.01 2 0 1 0 1 0
#> TCGA.50.8460.01 1 0 1 1 0 0
#> TCGA.78.7148.01 3 0 1 0 0 1
#> TCGA.44.6146.01 3 0 1 0 0 1
#> TCGA.97.7552.01 1 0 1 1 0 0
#> TCGA.50.8459.01 1 0 1 1 0 0
#> TCGA.97.A4LX.01 1 0 1 1 0 0
#> TCGA.50.5932.01 3 0 1 0 0 1
#> TCGA.93.A4JO.01 1 0 1 1 0 0
#> TCGA.86.8076.01 1 0 1 1 0 0
#> TCGA.49.AAR3.01 1 0 1 1 0 0
#> TCGA.05.4384.01 3 0 1 0 0 1
#> TCGA.MP.A4T2.01 2 0 1 0 1 0
#> TCGA.55.8206.01 2 0 1 0 1 0
#> TCGA.78.7537.01 2 0 1 0 1 0
#> TCGA.78.7163.01 3 0 1 0 0 1
#> TCGA.97.8174.01 2 0 1 0 1 0
#> TCGA.75.7030.01 1 0 1 1 0 0
#> TCGA.38.A44F.01 1 0 1 1 0 0
#> TCGA.55.7284.01 2 0 1 0 1 0
#> TCGA.97.A4M2.01 1 0 1 1 0 0
#> TCGA.95.7947.01 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.69.8453.01 1 0.2706 0.846 0.90 0.02 0.00 0.08
#> TCGA.78.7162.01 2 0.2345 0.861 0.00 0.90 0.00 0.10
#> TCGA.75.7025.01 2 0.2345 0.852 0.10 0.90 0.00 0.00
#> TCGA.49.AAR4.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.75.6206.01 3 0.0000 0.955 0.00 0.00 1.00 0.00
#> TCGA.L9.A743.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.64.5778.01 2 0.2345 0.861 0.00 0.90 0.00 0.10
#> TCGA.55.8091.01 2 0.2647 0.846 0.12 0.88 0.00 0.00
#> TCGA.49.AAR0.01 2 0.3172 0.836 0.00 0.84 0.00 0.16
#> TCGA.69.8254.01 2 0.2647 0.846 0.12 0.88 0.00 0.00
#> TCGA.97.A4M5.01 1 0.4491 0.573 0.80 0.14 0.00 0.06
#> TCGA.05.5423.01 2 0.3853 0.838 0.02 0.82 0.00 0.16
#> TCGA.91.A4BD.01 2 0.2647 0.846 0.12 0.88 0.00 0.00
#> TCGA.78.7160.01 1 0.2921 0.843 0.86 0.00 0.00 0.14
#> TCGA.50.5066.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.L9.A50W.01 2 0.3335 0.841 0.02 0.86 0.00 0.12
#> TCGA.50.8460.01 1 0.0707 0.777 0.98 0.02 0.00 0.00
#> TCGA.78.7148.01 3 0.0000 0.955 0.00 0.00 1.00 0.00
#> TCGA.44.6146.01 3 0.1637 0.932 0.00 0.00 0.94 0.06
#> TCGA.97.7552.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.50.8459.01 1 0.2921 0.843 0.86 0.00 0.00 0.14
#> TCGA.97.A4LX.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.50.5932.01 3 0.0000 0.955 0.00 0.00 1.00 0.00
#> TCGA.93.A4JO.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.86.8076.01 1 0.2921 0.843 0.86 0.00 0.00 0.14
#> TCGA.49.AAR3.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.05.4384.01 3 0.4610 0.821 0.00 0.10 0.80 0.10
#> TCGA.MP.A4T2.01 2 0.2647 0.846 0.12 0.88 0.00 0.00
#> TCGA.55.8206.01 2 0.3335 0.841 0.02 0.86 0.00 0.12
#> TCGA.78.7537.01 2 0.3335 0.841 0.02 0.86 0.00 0.12
#> TCGA.78.7163.01 3 0.0000 0.955 0.00 0.00 1.00 0.00
#> TCGA.97.8174.01 2 0.2345 0.861 0.00 0.90 0.00 0.10
#> TCGA.75.7030.01 1 0.2706 0.846 0.90 0.02 0.00 0.08
#> TCGA.38.A44F.01 4 0.4277 1.000 0.28 0.00 0.00 0.72
#> TCGA.55.7284.01 2 0.3172 0.836 0.00 0.84 0.00 0.16
#> TCGA.97.A4M2.01 1 0.2921 0.843 0.86 0.00 0.00 0.14
#> TCGA.95.7947.01 2 0.4284 0.828 0.02 0.78 0.00 0.20
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.69.8453.01 1 0.3274 0.901 0.78 0.00 0.00 0.22 0.00
#> TCGA.78.7162.01 5 0.4558 0.512 0.08 0.18 0.00 0.00 0.74
#> TCGA.75.7025.01 2 0.6033 0.687 0.22 0.58 0.00 0.00 0.20
#> TCGA.49.AAR4.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.75.6206.01 3 0.0000 0.963 0.00 0.00 1.00 0.00 0.00
#> TCGA.L9.A743.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.64.5778.01 5 0.2616 0.641 0.02 0.10 0.00 0.00 0.88
#> TCGA.55.8091.01 2 0.6033 0.687 0.22 0.58 0.00 0.00 0.20
#> TCGA.49.AAR0.01 5 0.0000 0.675 0.00 0.00 0.00 0.00 1.00
#> TCGA.69.8254.01 2 0.6033 0.687 0.22 0.58 0.00 0.00 0.20
#> TCGA.97.A4M5.01 1 0.2616 0.726 0.88 0.00 0.00 0.02 0.10
#> TCGA.05.5423.01 5 0.4302 0.398 0.00 0.48 0.00 0.00 0.52
#> TCGA.91.A4BD.01 2 0.6033 0.687 0.22 0.58 0.00 0.00 0.20
#> TCGA.78.7160.01 1 0.3424 0.901 0.76 0.00 0.00 0.24 0.00
#> TCGA.50.5066.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.L9.A50W.01 2 0.3513 0.277 0.02 0.80 0.00 0.00 0.18
#> TCGA.50.8460.01 1 0.0609 0.710 0.98 0.00 0.00 0.02 0.00
#> TCGA.78.7148.01 3 0.0000 0.963 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6146.01 3 0.2873 0.864 0.00 0.02 0.86 0.00 0.12
#> TCGA.97.7552.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.8459.01 1 0.3424 0.901 0.76 0.00 0.00 0.24 0.00
#> TCGA.97.A4LX.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5932.01 3 0.0000 0.963 0.00 0.00 1.00 0.00 0.00
#> TCGA.93.A4JO.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8076.01 1 0.3424 0.901 0.76 0.00 0.00 0.24 0.00
#> TCGA.49.AAR3.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.05.4384.01 5 0.4252 0.406 0.00 0.02 0.28 0.00 0.70
#> TCGA.MP.A4T2.01 2 0.6033 0.687 0.22 0.58 0.00 0.00 0.20
#> TCGA.55.8206.01 2 0.2331 0.437 0.02 0.90 0.00 0.00 0.08
#> TCGA.78.7537.01 2 0.3513 0.277 0.02 0.80 0.00 0.00 0.18
#> TCGA.78.7163.01 3 0.0609 0.956 0.00 0.02 0.98 0.00 0.00
#> TCGA.97.8174.01 5 0.4558 0.512 0.08 0.18 0.00 0.00 0.74
#> TCGA.75.7030.01 1 0.3274 0.901 0.78 0.00 0.00 0.22 0.00
#> TCGA.38.A44F.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.7284.01 5 0.0000 0.675 0.00 0.00 0.00 0.00 1.00
#> TCGA.97.A4M2.01 1 0.3424 0.901 0.76 0.00 0.00 0.24 0.00
#> TCGA.95.7947.01 5 0.3895 0.543 0.00 0.32 0.00 0.00 0.68
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.69.8453.01 1 0.3111 0.7074 0.84 0.02 0.00 0.12 0.00 0.02
#> TCGA.78.7162.01 5 0.2981 0.6937 0.00 0.16 0.00 0.00 0.82 0.02
#> TCGA.75.7025.01 2 0.2454 0.8390 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.49.AAR4.01 4 0.0000 0.7920 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.75.6206.01 3 0.0000 0.9352 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 4 0.4503 0.7354 0.00 0.08 0.00 0.68 0.00 0.24
#> TCGA.64.5778.01 5 0.2790 0.7000 0.00 0.14 0.00 0.00 0.84 0.02
#> TCGA.55.8091.01 2 0.2260 0.8569 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.49.AAR0.01 5 0.0000 0.6943 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.69.8254.01 2 0.2260 0.8569 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.97.A4M5.01 1 0.2512 0.6351 0.88 0.06 0.00 0.00 0.06 0.00
#> TCGA.05.5423.01 6 0.4337 0.0451 0.00 0.02 0.00 0.00 0.48 0.50
#> TCGA.91.A4BD.01 2 0.2260 0.8569 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.78.7160.01 1 0.6629 0.6774 0.50 0.10 0.00 0.12 0.00 0.28
#> TCGA.50.5066.01 4 0.0547 0.7877 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.L9.A50W.01 6 0.4929 0.6352 0.00 0.28 0.00 0.00 0.10 0.62
#> TCGA.50.8460.01 1 0.4165 0.6558 0.74 0.16 0.00 0.00 0.00 0.10
#> TCGA.78.7148.01 3 0.0000 0.9352 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6146.01 3 0.4444 0.7334 0.08 0.00 0.74 0.00 0.16 0.02
#> TCGA.97.7552.01 4 0.3982 0.7577 0.00 0.06 0.00 0.74 0.00 0.20
#> TCGA.50.8459.01 1 0.6170 0.6674 0.58 0.08 0.00 0.12 0.00 0.22
#> TCGA.97.A4LX.01 4 0.0000 0.7920 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5932.01 3 0.0000 0.9352 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 4 0.4503 0.7354 0.00 0.08 0.00 0.68 0.00 0.24
#> TCGA.86.8076.01 1 0.6629 0.6774 0.50 0.10 0.00 0.12 0.00 0.28
#> TCGA.49.AAR3.01 4 0.0000 0.7920 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.05.4384.01 5 0.4444 0.4808 0.08 0.00 0.16 0.00 0.74 0.02
#> TCGA.MP.A4T2.01 2 0.2260 0.8569 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.55.8206.01 2 0.5295 -0.3721 0.00 0.46 0.00 0.00 0.10 0.44
#> TCGA.78.7537.01 6 0.4929 0.6352 0.00 0.28 0.00 0.00 0.10 0.62
#> TCGA.78.7163.01 3 0.0547 0.9290 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.97.8174.01 5 0.2981 0.6937 0.00 0.16 0.00 0.00 0.82 0.02
#> TCGA.75.7030.01 1 0.3111 0.7074 0.84 0.02 0.00 0.12 0.00 0.02
#> TCGA.38.A44F.01 4 0.4613 0.7228 0.00 0.08 0.00 0.66 0.00 0.26
#> TCGA.55.7284.01 5 0.1807 0.6639 0.06 0.00 0.00 0.00 0.92 0.02
#> TCGA.97.A4M2.01 1 0.6629 0.6774 0.50 0.10 0.00 0.12 0.00 0.28
#> TCGA.95.7947.01 5 0.4913 0.1204 0.04 0.02 0.00 0.00 0.60 0.34
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.69.8453.01 1 0.1671 0.593 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.78.7162.01 5 0.3061 0.742 0.02 0.08 0.00 0.00 0.84 0.06 0.00
#> TCGA.75.7025.01 2 0.1928 0.846 0.00 0.90 0.00 0.00 0.08 0.02 0.00
#> TCGA.49.AAR4.01 4 0.0000 0.694 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6206.01 3 0.0000 0.885 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 4 0.3525 0.512 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.64.5778.01 5 0.3061 0.740 0.00 0.08 0.00 0.00 0.84 0.06 0.02
#> TCGA.55.8091.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 5 0.0504 0.739 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.69.8254.01 2 0.0504 0.939 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M5.01 1 0.2769 0.563 0.86 0.02 0.00 0.00 0.08 0.00 0.04
#> TCGA.05.5423.01 6 0.3606 0.472 0.00 0.02 0.00 0.00 0.30 0.68 0.00
#> TCGA.91.A4BD.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 7 0.5429 1.000 0.40 0.00 0.00 0.12 0.00 0.02 0.46
#> TCGA.50.5066.01 4 0.0000 0.694 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 6 0.2745 0.778 0.00 0.16 0.00 0.00 0.02 0.82 0.00
#> TCGA.50.8460.01 1 0.4779 0.443 0.68 0.18 0.00 0.00 0.00 0.04 0.10
#> TCGA.78.7148.01 3 0.0000 0.885 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6146.01 3 0.5990 0.617 0.10 0.00 0.60 0.00 0.14 0.02 0.14
#> TCGA.97.7552.01 4 0.4070 0.574 0.00 0.00 0.00 0.62 0.00 0.04 0.34
#> TCGA.50.8459.01 1 0.5535 -0.620 0.54 0.00 0.00 0.12 0.00 0.04 0.30
#> TCGA.97.A4LX.01 4 0.1006 0.687 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.50.5932.01 3 0.0000 0.885 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 4 0.3525 0.512 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.86.8076.01 7 0.5429 1.000 0.40 0.00 0.00 0.12 0.00 0.02 0.46
#> TCGA.49.AAR3.01 4 0.0000 0.694 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.4384.01 5 0.4617 0.586 0.10 0.00 0.02 0.00 0.72 0.02 0.14
#> TCGA.MP.A4T2.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8206.01 6 0.4381 0.580 0.00 0.36 0.00 0.00 0.06 0.58 0.00
#> TCGA.78.7537.01 6 0.2745 0.778 0.00 0.16 0.00 0.00 0.02 0.82 0.00
#> TCGA.78.7163.01 3 0.2421 0.847 0.02 0.00 0.88 0.00 0.00 0.02 0.08
#> TCGA.97.8174.01 5 0.3061 0.742 0.02 0.08 0.00 0.00 0.84 0.06 0.00
#> TCGA.75.7030.01 1 0.1671 0.593 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.38.A44F.01 4 0.4214 0.525 0.00 0.00 0.00 0.56 0.00 0.04 0.40
#> TCGA.55.7284.01 5 0.3061 0.688 0.08 0.02 0.00 0.00 0.84 0.00 0.06
#> TCGA.97.A4M2.01 7 0.5429 1.000 0.40 0.00 0.00 0.12 0.00 0.02 0.46
#> TCGA.95.7947.01 5 0.6153 0.177 0.00 0.04 0.00 0.00 0.38 0.22 0.36
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.69.8453.01 1 0.2938 0.941 0.70 0.00 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.78.7162.01 5 0.3128 0.644 0.00 0.10 0.00 0.00 0.82 0.04 0.00 0.04
#> TCGA.75.7025.01 2 0.2940 0.801 0.02 0.84 0.00 0.02 0.10 0.00 0.00 0.02
#> TCGA.49.AAR4.01 4 0.0471 0.839 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.75.6206.01 3 0.0000 0.893 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 7 0.3658 0.191 0.00 0.00 0.00 0.40 0.00 0.00 0.58 0.02
#> TCGA.64.5778.01 5 0.3262 0.630 0.02 0.10 0.00 0.02 0.82 0.04 0.00 0.00
#> TCGA.55.8091.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 5 0.0471 0.628 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.69.8254.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M5.01 1 0.3942 0.881 0.62 0.00 0.00 0.00 0.02 0.00 0.34 0.02
#> TCGA.05.5423.01 6 0.3426 0.680 0.02 0.00 0.00 0.02 0.22 0.74 0.00 0.00
#> TCGA.91.A4BD.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 7 0.0000 0.473 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5066.01 4 0.2348 0.798 0.00 0.00 0.00 0.88 0.00 0.04 0.02 0.06
#> TCGA.L9.A50W.01 6 0.0941 0.788 0.00 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.50.8460.01 7 0.4995 -0.444 0.36 0.08 0.00 0.00 0.00 0.00 0.52 0.04
#> TCGA.78.7148.01 3 0.0000 0.893 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6146.01 8 0.4958 0.000 0.02 0.00 0.44 0.00 0.10 0.00 0.00 0.44
#> TCGA.97.7552.01 4 0.4100 0.162 0.00 0.00 0.00 0.58 0.00 0.00 0.36 0.06
#> TCGA.50.8459.01 7 0.4050 -0.180 0.34 0.00 0.00 0.00 0.00 0.00 0.60 0.06
#> TCGA.97.A4LX.01 4 0.0941 0.834 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.50.5932.01 3 0.0000 0.893 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 7 0.3658 0.191 0.00 0.00 0.00 0.40 0.00 0.00 0.58 0.02
#> TCGA.86.8076.01 7 0.0000 0.473 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.49.AAR3.01 4 0.0471 0.839 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.05.4384.01 5 0.3272 0.233 0.00 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.MP.A4T2.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8206.01 6 0.5173 0.605 0.02 0.24 0.00 0.02 0.08 0.62 0.00 0.02
#> TCGA.78.7537.01 6 0.0941 0.788 0.00 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.78.7163.01 3 0.2569 0.584 0.02 0.00 0.82 0.00 0.00 0.00 0.00 0.16
#> TCGA.97.8174.01 5 0.3128 0.644 0.00 0.10 0.00 0.00 0.82 0.04 0.00 0.04
#> TCGA.75.7030.01 1 0.2938 0.941 0.70 0.00 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.38.A44F.01 7 0.4174 0.151 0.00 0.00 0.00 0.40 0.00 0.00 0.54 0.06
#> TCGA.55.7284.01 5 0.2938 0.414 0.00 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.97.A4M2.01 7 0.0000 0.473 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.95.7947.01 5 0.6095 0.168 0.22 0.00 0.00 0.00 0.38 0.08 0.00 0.32
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node012. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01221-leaf , Node01222-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-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["0122"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 15 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4767 0.524 0.524
#> 3 3 0.962 0.902 0.985 0.0878 0.962 0.927
#> 4 4 0.790 0.892 0.955 0.2486 0.848 0.686
#> 5 5 0.829 0.867 0.920 0.1624 0.886 0.657
#> 6 6 0.857 0.757 0.891 0.0811 0.971 0.870
#> 7 7 0.781 0.542 0.776 0.0677 0.886 0.478
#> 8 8 0.800 0.555 0.723 0.0373 0.952 0.643
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.78.7162.01 1 0 1 1 0
#> TCGA.75.7025.01 1 0 1 1 0
#> TCGA.64.5778.01 2 0 1 0 1
#> TCGA.55.8091.01 1 0 1 1 0
#> TCGA.49.AAR0.01 2 0 1 0 1
#> TCGA.69.8254.01 1 0 1 1 0
#> TCGA.05.5423.01 2 0 1 0 1
#> TCGA.91.A4BD.01 1 0 1 1 0
#> TCGA.L9.A50W.01 1 0 1 1 0
#> TCGA.MP.A4T2.01 1 0 1 1 0
#> TCGA.55.8206.01 1 0 1 1 0
#> TCGA.78.7537.01 1 0 1 1 0
#> TCGA.97.8174.01 1 0 1 1 0
#> TCGA.55.7284.01 2 0 1 0 1
#> TCGA.95.7947.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.78.7162.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.75.7025.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.64.5778.01 2 0.0892 0.920 0 0.98 0.02
#> TCGA.55.8091.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.49.AAR0.01 2 0.4555 0.764 0 0.80 0.20
#> TCGA.69.8254.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.05.5423.01 3 0.0000 0.000 0 0.00 1.00
#> TCGA.91.A4BD.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.L9.A50W.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.8206.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.78.7537.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.97.8174.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.7284.01 2 0.0000 0.923 0 1.00 0.00
#> TCGA.95.7947.01 2 0.0000 0.923 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.78.7162.01 4 0.340 1.000 0.18 0.00 0.00 0.82
#> TCGA.75.7025.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.64.5778.01 2 0.000 0.890 0.00 1.00 0.00 0.00
#> TCGA.55.8091.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 2 0.292 0.801 0.00 0.86 0.14 0.00
#> TCGA.69.8254.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.05.5423.01 3 0.000 0.000 0.00 0.00 1.00 0.00
#> TCGA.91.A4BD.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.55.8206.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.78.7537.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.97.8174.01 4 0.340 1.000 0.18 0.00 0.00 0.82
#> TCGA.55.7284.01 2 0.000 0.890 0.00 1.00 0.00 0.00
#> TCGA.95.7947.01 2 0.340 0.791 0.00 0.82 0.00 0.18
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.78.7162.01 4 0.000 1.000 0.00 0.00 0.00 1 0.00
#> TCGA.75.7025.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.64.5778.01 2 0.406 0.835 0.00 0.64 0.36 0 0.00
#> TCGA.55.8091.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.49.AAR0.01 2 0.430 0.763 0.00 0.52 0.48 0 0.00
#> TCGA.69.8254.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.05.5423.01 3 0.406 0.000 0.00 0.00 0.64 0 0.36
#> TCGA.91.A4BD.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.L9.A50W.01 5 0.406 1.000 0.36 0.00 0.00 0 0.64
#> TCGA.MP.A4T2.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.55.8206.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.78.7537.01 5 0.406 1.000 0.36 0.00 0.00 0 0.64
#> TCGA.97.8174.01 4 0.000 1.000 0.00 0.00 0.00 1 0.00
#> TCGA.55.7284.01 2 0.406 0.835 0.00 0.64 0.36 0 0.00
#> TCGA.95.7947.01 2 0.000 0.574 0.00 1.00 0.00 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.78.7162.01 4 0.0547 0.897 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.75.7025.01 1 0.0547 0.842 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.64.5778.01 2 0.5037 0.836 0.00 0.54 0.00 0.00 0.08 0.38
#> TCGA.55.8091.01 1 0.0547 0.842 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.49.AAR0.01 2 0.3409 0.814 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.69.8254.01 1 0.0937 0.834 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.05.5423.01 3 0.3076 0.000 0.00 0.24 0.76 0.00 0.00 0.00
#> TCGA.91.A4BD.01 1 0.2941 0.847 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.L9.A50W.01 5 0.1556 1.000 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.MP.A4T2.01 1 0.3460 0.837 0.76 0.02 0.22 0.00 0.00 0.00
#> TCGA.55.8206.01 1 0.2941 0.847 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.78.7537.01 5 0.1556 1.000 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.97.8174.01 4 0.2882 0.897 0.02 0.10 0.02 0.86 0.00 0.00
#> TCGA.55.7284.01 2 0.4199 0.863 0.00 0.60 0.00 0.02 0.00 0.38
#> TCGA.95.7947.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.78.7162.01 4 0.3496 0.601 0.00 0.00 0.00 0.58 0.00 0.42 0.00
#> TCGA.75.7025.01 7 0.6371 0.124 0.36 0.00 0.00 0.10 0.00 0.14 0.40
#> TCGA.64.5778.01 2 0.1886 0.871 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.55.8091.01 7 0.3558 0.143 0.48 0.00 0.00 0.00 0.00 0.00 0.52
#> TCGA.49.AAR0.01 2 0.1166 0.889 0.00 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.69.8254.01 7 0.4820 0.272 0.38 0.00 0.00 0.10 0.00 0.00 0.52
#> TCGA.05.5423.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BD.01 1 0.0863 0.756 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.L9.A50W.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.2081 0.742 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.55.8206.01 1 0.3199 0.637 0.80 0.00 0.00 0.00 0.00 0.14 0.06
#> TCGA.78.7537.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.8174.01 4 0.0000 0.603 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7284.01 2 0.0000 0.911 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7947.01 7 0.5332 -0.422 0.00 0.38 0.00 0.00 0.00 0.18 0.44
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.78.7162.01 4 0.000 0.5083 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.7025.01 6 0.500 0.0000 0.18 0.00 0.00 0.00 0.00 0.42 0.40 0.00
#> TCGA.64.5778.01 2 0.338 0.6693 0.00 0.76 0.00 0.00 0.00 0.08 0.16 0.00
#> TCGA.55.8091.01 7 0.227 0.9520 0.18 0.00 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.49.AAR0.01 2 0.241 0.7456 0.00 0.86 0.08 0.00 0.00 0.06 0.00 0.00
#> TCGA.69.8254.01 7 0.211 0.9514 0.16 0.00 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.05.5423.01 3 0.000 0.0000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BD.01 1 0.128 0.5915 0.94 0.00 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.L9.A50W.01 5 0.000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.241 0.5725 0.86 0.00 0.00 0.00 0.00 0.06 0.00 0.08
#> TCGA.55.8206.01 1 0.330 0.0571 0.56 0.00 0.00 0.00 0.00 0.44 0.00 0.00
#> TCGA.78.7537.01 5 0.000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.8174.01 4 0.487 0.5083 0.00 0.00 0.00 0.48 0.00 0.36 0.00 0.16
#> TCGA.55.7284.01 2 0.000 0.7739 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7947.01 8 0.265 0.0000 0.00 0.24 0.00 0.00 0.00 0.00 0.00 0.76
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node031 , Node032 .
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 220 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.984 0.993 0.4974 0.503 0.503
#> 3 3 1.000 0.972 0.989 0.3277 0.671 0.438
#> 4 4 0.723 0.744 0.843 0.1243 0.863 0.624
#> 5 5 0.723 0.565 0.737 0.0566 0.921 0.707
#> 6 6 0.768 0.729 0.835 0.0418 0.911 0.623
#> 7 7 0.763 0.644 0.780 0.0285 0.936 0.679
#> 8 8 0.787 0.665 0.731 0.0178 0.969 0.814
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.44.4112.01 1 0.000 0.993 1.00 0.00
#> TCGA.NJ.A4YP.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8278.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.AARQ.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6597.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.A46U.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4T8.01 2 0.000 0.992 0.00 1.00
#> TCGA.93.A4JN.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.6851.01 2 0.000 0.992 0.00 1.00
#> TCGA.J2.A4AG.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TK.01 1 0.141 0.977 0.98 0.02
#> TCGA.L9.A443.01 1 0.000 0.993 1.00 0.00
#> TCGA.MN.A4N5.01 1 0.000 0.993 1.00 0.00
#> TCGA.64.5775.01 2 0.000 0.992 0.00 1.00
#> TCGA.62.8394.01 2 0.000 0.992 0.00 1.00
#> TCGA.05.4405.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.5428.01 2 0.000 0.992 0.00 1.00
#> TCGA.MN.A4N1.01 1 0.141 0.977 0.98 0.02
#> TCGA.91.6847.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TC.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.4410.01 2 0.141 0.973 0.02 0.98
#> TCGA.62.A46Y.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6982.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6642.01 2 0.000 0.992 0.00 1.00
#> TCGA.50.6673.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.8207.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.6562.01 2 0.000 0.992 0.00 1.00
#> TCGA.05.4425.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8074.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.7727.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4SW.01 2 0.000 0.992 0.00 1.00
#> TCGA.67.6216.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8203.01 2 0.000 0.992 0.00 1.00
#> TCGA.J2.8194.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.2668.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A57B.01 2 0.000 0.992 0.00 1.00
#> TCGA.NJ.A4YI.01 1 0.141 0.977 0.98 0.02
#> TCGA.L9.A444.01 2 0.000 0.992 0.00 1.00
#> TCGA.86.8668.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.A47G.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6986.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.2665.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.5425.01 2 0.000 0.992 0.00 1.00
#> TCGA.62.A46R.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.A494.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.3917.01 2 0.000 0.992 0.00 1.00
#> TCGA.75.5125.01 2 0.000 0.992 0.00 1.00
#> TCGA.L4.A4E5.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.6775.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7911.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6712.01 2 0.000 0.992 0.00 1.00
#> TCGA.69.7760.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.7948.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A4DG.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.6985.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TF.01 2 0.000 0.992 0.00 1.00
#> TCGA.91.6829.01 2 0.000 0.992 0.00 1.00
#> TCGA.99.7458.01 1 0.000 0.993 1.00 0.00
#> TCGA.38.6178.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.A47B.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7542.01 2 0.000 0.992 0.00 1.00
#> TCGA.05.5429.01 2 0.529 0.863 0.12 0.88
#> TCGA.97.8179.01 2 0.000 0.992 0.00 1.00
#> TCGA.86.A4JF.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8092.01 2 0.000 0.992 0.00 1.00
#> TCGA.75.6207.01 2 0.000 0.992 0.00 1.00
#> TCGA.75.5122.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.AARE.01 2 0.000 0.992 0.00 1.00
#> TCGA.95.7043.01 2 0.000 0.992 0.00 1.00
#> TCGA.86.7701.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.7281.01 2 0.000 0.992 0.00 1.00
#> TCGA.78.7535.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6592.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.7661.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4M0.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5933.01 2 0.000 0.992 0.00 1.00
#> TCGA.78.7153.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.8660.01 1 0.943 0.437 0.64 0.36
#> TCGA.55.7907.01 2 0.000 0.992 0.00 1.00
#> TCGA.49.6767.01 2 0.000 0.992 0.00 1.00
#> TCGA.50.5051.01 2 0.000 0.992 0.00 1.00
#> TCGA.78.7540.01 1 0.141 0.977 0.98 0.02
#> TCGA.95.A4VN.01 1 0.327 0.936 0.94 0.06
#> TCGA.44.A47F.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.8253.01 1 0.000 0.993 1.00 0.00
#> TCGA.J2.A4AE.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6590.01 1 0.000 0.993 1.00 0.00
#> TCGA.80.5608.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.8205.01 2 0.000 0.992 0.00 1.00
#> TCGA.99.8025.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.7283.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7159.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.8120.01 2 0.000 0.992 0.00 1.00
#> TCGA.69.7763.01 1 0.000 0.993 1.00 0.00
#> TCGA.64.5815.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.7761.01 1 0.141 0.977 0.98 0.02
#> TCGA.73.A9RS.01 2 0.000 0.992 0.00 1.00
#> TCGA.69.7978.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.8117.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TD.01 1 0.584 0.838 0.86 0.14
#> TCGA.83.5908.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.7039.01 2 0.000 0.992 0.00 1.00
#> TCGA.71.6725.01 2 0.000 0.992 0.00 1.00
#> TCGA.91.7771.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8359.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.8301.01 1 0.141 0.977 0.98 0.02
#> TCGA.78.7146.01 2 0.141 0.973 0.02 0.98
#> TCGA.44.3918.01 2 0.000 0.992 0.00 1.00
#> TCGA.69.7974.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7161.01 2 0.000 0.992 0.00 1.00
#> TCGA.97.7937.01 2 0.000 0.992 0.00 1.00
#> TCGA.62.A46V.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.6745.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8089.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.7574.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.5644.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.8511.01 2 0.827 0.653 0.26 0.74
#> TCGA.91.A4BC.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.2656.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8673.01 1 0.000 0.993 1.00 0.00
#> TCGA.73.7499.01 2 0.469 0.888 0.10 0.90
#> TCGA.L9.A7SV.01 2 0.000 0.992 0.00 1.00
#> TCGA.05.4390.01 2 0.000 0.992 0.00 1.00
#> TCGA.69.7765.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.8494.01 2 0.000 0.992 0.00 1.00
#> TCGA.69.7979.01 2 0.000 0.992 0.00 1.00
#> TCGA.62.A46P.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7158.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.7980.01 2 0.000 0.992 0.00 1.00
#> TCGA.97.8547.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.4433.01 2 0.827 0.653 0.26 0.74
#> TCGA.97.8175.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.7109.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.A47A.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.6147.01 1 0.000 0.993 1.00 0.00
#> TCGA.75.6211.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.8090.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8073.01 1 0.000 0.993 1.00 0.00
#> TCGA.91.6828.01 2 0.000 0.992 0.00 1.00
#> TCGA.05.4396.01 2 0.000 0.992 0.00 1.00
#> TCGA.MN.A4N4.01 2 0.000 0.992 0.00 1.00
#> TCGA.64.5781.01 2 0.000 0.992 0.00 1.00
#> TCGA.NJ.A4YF.01 2 0.000 0.992 0.00 1.00
#> TCGA.78.7154.01 1 0.141 0.977 0.98 0.02
#> TCGA.78.8662.01 2 0.000 0.992 0.00 1.00
#> TCGA.05.4427.01 2 0.000 0.992 0.00 1.00
#> TCGA.78.7143.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4M3.01 2 0.141 0.973 0.02 0.98
#> TCGA.75.6205.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7903.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A493.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7147.01 2 0.000 0.992 0.00 1.00
#> TCGA.75.5126.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TE.01 2 0.000 0.992 0.00 1.00
#> TCGA.NJ.A4YQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.NJ.A7XG.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A48X.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6594.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8056.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.A4VK.01 2 0.000 0.992 0.00 1.00
#> TCGA.49.4488.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.7994.01 2 0.000 0.992 0.00 1.00
#> TCGA.67.6215.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A5C7.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.7227.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TI.01 1 0.000 0.993 1.00 0.00
#> TCGA.35.5375.01 2 0.000 0.992 0.00 1.00
#> TCGA.38.4632.01 2 0.000 0.992 0.00 1.00
#> TCGA.MP.A4T6.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.6779.01 2 0.000 0.992 0.00 1.00
#> TCGA.86.A4P7.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.6761.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5935.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6981.01 2 0.000 0.992 0.00 1.00
#> TCGA.78.8655.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7914.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.A472.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.4417.01 2 0.000 0.992 0.00 1.00
#> TCGA.67.4679.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.7554.01 2 0.000 0.992 0.00 1.00
#> TCGA.MP.A4SY.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.8039.01 2 0.000 0.992 0.00 1.00
#> TCGA.95.7562.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.7576.01 1 0.000 0.993 1.00 0.00
#> TCGA.80.5607.01 1 0.000 0.993 1.00 0.00
#> TCGA.93.8067.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.8395.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8672.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.2666.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.6777.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6983.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.A59K.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.7567.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.AARN.01 1 0.000 0.993 1.00 0.00
#> TCGA.73.4676.01 2 0.000 0.992 0.00 1.00
#> TCGA.91.6836.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8616.01 2 0.000 0.992 0.00 1.00
#> TCGA.38.7271.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A491.01 1 0.141 0.977 0.98 0.02
#> TCGA.55.6978.01 1 0.141 0.977 0.98 0.02
#> TCGA.NJ.A4YG.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A48Y.01 2 0.000 0.992 0.00 1.00
#> TCGA.MP.A4SV.01 2 0.000 0.992 0.00 1.00
#> TCGA.73.4658.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.7659.01 1 0.000 0.993 1.00 0.00
#> TCGA.NJ.A55R.01 2 0.000 0.992 0.00 1.00
#> TCGA.86.A456.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4M7.01 1 0.141 0.977 0.98 0.02
#> TCGA.44.7662.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.8506.01 2 0.000 0.992 0.00 1.00
#> TCGA.71.8520.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7815.01 2 0.000 0.992 0.00 1.00
#> TCGA.44.7672.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.8172.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.5715.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7152.01 1 0.141 0.977 0.98 0.02
#> TCGA.78.7539.01 2 0.000 0.992 0.00 1.00
#> TCGA.62.A46S.01 2 0.000 0.992 0.00 1.00
#> TCGA.78.7145.01 2 0.000 0.992 0.00 1.00
#> TCGA.55.8302.01 1 0.000 0.993 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.4112.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.NJ.A4YP.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.86.8278.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.AARQ.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.6597.01 3 0.0892 0.963 0.02 0.00 0.98
#> TCGA.62.A46U.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4T8.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.93.A4JN.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.6851.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.J2.A4AG.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.MP.A4TK.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.L9.A443.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MN.A4N5.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.64.5775.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.62.8394.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.05.4405.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.05.5428.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.MN.A4N1.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.91.6847.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.MP.A4TC.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.05.4410.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.62.A46Y.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.6982.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.6642.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.50.6673.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.8207.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.6562.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.05.4425.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8074.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.7727.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.MP.A4SW.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.67.6216.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.8203.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.J2.8194.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.44.2668.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.A57B.01 3 0.0892 0.962 0.00 0.02 0.98
#> TCGA.NJ.A4YI.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.L9.A444.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.86.8668.01 3 0.5016 0.688 0.24 0.00 0.76
#> TCGA.44.A47G.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.6986.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.44.2665.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.05.5425.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.62.A46R.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.A494.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.44.3917.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.75.5125.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.L4.A4E5.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.44.6775.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.7911.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.6712.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.69.7760.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.95.7948.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.A4DG.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.6985.01 3 0.0892 0.963 0.02 0.00 0.98
#> TCGA.MP.A4TF.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.91.6829.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.99.7458.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.38.6178.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.44.A47B.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.7542.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.05.5429.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.97.8179.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.86.A4JF.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.8092.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.75.5122.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.49.AARE.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.95.7043.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.86.7701.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.7281.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.7535.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.50.6592.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.7661.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.97.A4M0.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.5933.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.7153.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.8660.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.7907.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.49.6767.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.50.5051.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.78.7540.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.95.A4VN.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.A47F.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.69.8253.01 3 0.4002 0.806 0.16 0.00 0.84
#> TCGA.J2.A4AE.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.6590.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.80.5608.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.8205.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.99.8025.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.7283.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.7159.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.44.8120.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.69.7763.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.64.5815.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.69.7761.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.73.A9RS.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.69.7978.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.8117.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.MP.A4TD.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.83.5908.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.95.7039.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.71.6725.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.91.7771.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8359.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.8301.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.7146.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.3918.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.69.7974.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.7161.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.97.7937.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.62.A46V.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.6745.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.8089.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.7574.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.44.5644.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.8511.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.91.A4BC.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.2656.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.86.8673.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.73.7499.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.L9.A7SV.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.05.4390.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.69.7765.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.95.8494.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.69.7979.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.62.A46P.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.7158.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.69.7980.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.97.8547.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.05.4433.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.97.8175.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.7109.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.44.A47A.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.44.6147.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.75.6211.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.8090.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8073.01 3 0.6280 0.168 0.46 0.00 0.54
#> TCGA.91.6828.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.05.4396.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.MN.A4N4.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.64.5781.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.NJ.A4YF.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.78.7154.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.8662.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.05.4427.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.78.7143.01 3 0.5216 0.654 0.26 0.00 0.74
#> TCGA.97.A4M3.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.75.6205.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.7903.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.A493.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.7147.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.75.5126.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.NJ.A4YQ.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.NJ.A7XG.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.A48X.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.50.6594.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.86.8056.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.95.A4VK.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.49.4488.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.7994.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.67.6215.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A5C7.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.7227.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.MP.A4TI.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.35.5375.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.38.4632.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.MP.A4T6.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.6779.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.86.A4P7.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.6761.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.50.5935.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.6981.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.8655.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.7914.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.62.A472.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.05.4417.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.67.4679.01 1 0.6126 0.306 0.60 0.00 0.40
#> TCGA.97.7554.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.MP.A4SY.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.95.8039.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.95.7562.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.7576.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.80.5607.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.93.8067.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.62.8395.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.86.8672.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.2666.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.44.6777.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.6983.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.69.A59K.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.95.7567.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.49.AARN.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.73.4676.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.91.6836.01 3 0.6244 0.234 0.44 0.00 0.56
#> TCGA.55.8616.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.38.7271.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.A491.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.55.6978.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.NJ.A4YG.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.A48Y.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.MP.A4SV.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.73.4658.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.44.7659.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.NJ.A55R.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.86.A456.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.97.A4M7.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.44.7662.01 3 0.2066 0.921 0.00 0.06 0.94
#> TCGA.55.8506.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.71.8520.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.55.7815.01 2 0.5706 0.530 0.00 0.68 0.32
#> TCGA.44.7672.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.97.8172.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.05.5715.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.78.7152.01 3 0.0000 0.981 0.00 0.00 1.00
#> TCGA.78.7539.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.62.A46S.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.78.7145.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.55.8302.01 3 0.0000 0.981 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.44.4112.01 4 0.4406 0.781658 0.00 0.00 0.30 0.70
#> TCGA.NJ.A4YP.01 3 0.4994 -0.169165 0.00 0.00 0.52 0.48
#> TCGA.86.8278.01 4 0.3975 0.618801 0.24 0.00 0.00 0.76
#> TCGA.49.AARQ.01 4 0.3801 0.657058 0.22 0.00 0.00 0.78
#> TCGA.50.6597.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.62.A46U.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T8.01 2 0.1211 0.861069 0.00 0.96 0.04 0.00
#> TCGA.93.A4JN.01 1 0.1637 0.910645 0.94 0.00 0.00 0.06
#> TCGA.86.6851.01 2 0.1637 0.850596 0.00 0.94 0.06 0.00
#> TCGA.J2.A4AG.01 3 0.4948 -0.080622 0.00 0.00 0.56 0.44
#> TCGA.MP.A4TK.01 3 0.2647 0.657898 0.00 0.00 0.88 0.12
#> TCGA.L9.A443.01 1 0.3172 0.833582 0.84 0.00 0.00 0.16
#> TCGA.MN.A4N5.01 1 0.4522 0.635041 0.68 0.00 0.00 0.32
#> TCGA.64.5775.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.62.8394.01 3 0.5173 0.454362 0.00 0.32 0.66 0.02
#> TCGA.05.4405.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.MN.A4N1.01 3 0.3400 0.586110 0.00 0.00 0.82 0.18
#> TCGA.91.6847.01 4 0.4522 0.747310 0.00 0.00 0.32 0.68
#> TCGA.MP.A4TC.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.05.4410.01 3 0.1637 0.706064 0.00 0.00 0.94 0.06
#> TCGA.62.A46Y.01 1 0.2921 0.852392 0.86 0.00 0.00 0.14
#> TCGA.55.6982.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.55.6642.01 2 0.2011 0.838454 0.00 0.92 0.08 0.00
#> TCGA.50.6673.01 2 0.3037 0.812382 0.00 0.88 0.10 0.02
#> TCGA.55.8207.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.86.6562.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.05.4425.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.86.8074.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.55.7727.01 3 0.4977 -0.164006 0.00 0.00 0.54 0.46
#> TCGA.MP.A4SW.01 3 0.2647 0.696991 0.00 0.12 0.88 0.00
#> TCGA.67.6216.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.55.8203.01 2 0.4977 0.165293 0.00 0.54 0.46 0.00
#> TCGA.J2.8194.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.44.2668.01 1 0.4713 0.562468 0.64 0.00 0.00 0.36
#> TCGA.55.A57B.01 3 0.4284 0.651080 0.00 0.20 0.78 0.02
#> TCGA.NJ.A4YI.01 3 0.4948 -0.080622 0.00 0.00 0.56 0.44
#> TCGA.L9.A444.01 3 0.0707 0.722585 0.00 0.00 0.98 0.02
#> TCGA.86.8668.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.44.A47G.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.55.6986.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.44.2665.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.05.5425.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.62.A46R.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.55.A494.01 2 0.3037 0.812382 0.00 0.88 0.10 0.02
#> TCGA.44.3917.01 2 0.1211 0.868625 0.00 0.96 0.00 0.04
#> TCGA.75.5125.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.L4.A4E5.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.44.6775.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.55.7911.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.55.6712.01 3 0.0000 0.725765 0.00 0.00 1.00 0.00
#> TCGA.69.7760.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.95.7948.01 1 0.4522 0.635041 0.68 0.00 0.00 0.32
#> TCGA.55.A4DG.01 2 0.2011 0.838454 0.00 0.92 0.08 0.00
#> TCGA.55.6985.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.MP.A4TF.01 3 0.0707 0.723477 0.00 0.00 0.98 0.02
#> TCGA.91.6829.01 2 0.0000 0.870073 0.00 1.00 0.00 0.00
#> TCGA.99.7458.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.38.6178.01 4 0.4284 0.685886 0.20 0.00 0.02 0.78
#> TCGA.44.A47B.01 4 0.4134 0.837574 0.00 0.00 0.26 0.74
#> TCGA.78.7542.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.05.5429.01 3 0.1211 0.715014 0.00 0.00 0.96 0.04
#> TCGA.97.8179.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.86.A4JF.01 3 0.4907 -0.006170 0.00 0.00 0.58 0.42
#> TCGA.55.8092.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.75.6207.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.75.5122.01 4 0.4406 0.807989 0.00 0.00 0.30 0.70
#> TCGA.49.AARE.01 3 0.4079 0.670264 0.00 0.18 0.80 0.02
#> TCGA.95.7043.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.86.7701.01 3 0.1211 0.720765 0.00 0.04 0.96 0.00
#> TCGA.55.7281.01 3 0.4284 0.651080 0.00 0.20 0.78 0.02
#> TCGA.78.7535.01 4 0.4134 0.837409 0.00 0.00 0.26 0.74
#> TCGA.50.6592.01 4 0.4134 0.837574 0.00 0.00 0.26 0.74
#> TCGA.44.7661.01 3 0.5000 -0.322326 0.00 0.00 0.50 0.50
#> TCGA.97.A4M0.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.50.5933.01 3 0.0707 0.722585 0.00 0.00 0.98 0.02
#> TCGA.78.7153.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.78.8660.01 3 0.2011 0.693219 0.00 0.00 0.92 0.08
#> TCGA.55.7907.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.49.6767.01 2 0.2345 0.822947 0.00 0.90 0.10 0.00
#> TCGA.50.5051.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.78.7540.01 3 0.2345 0.677166 0.00 0.00 0.90 0.10
#> TCGA.95.A4VN.01 3 0.2011 0.693219 0.00 0.00 0.92 0.08
#> TCGA.44.A47F.01 1 0.2345 0.884714 0.90 0.00 0.00 0.10
#> TCGA.69.8253.01 4 0.3610 0.832294 0.00 0.00 0.20 0.80
#> TCGA.J2.A4AE.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.50.6590.01 4 0.3975 0.840479 0.00 0.00 0.24 0.76
#> TCGA.80.5608.01 2 0.2011 0.838454 0.00 0.92 0.08 0.00
#> TCGA.55.8205.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.99.8025.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.55.7283.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.78.7159.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.44.8120.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.69.7763.01 1 0.1637 0.910645 0.94 0.00 0.00 0.06
#> TCGA.64.5815.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.69.7761.01 3 0.2011 0.693219 0.00 0.00 0.92 0.08
#> TCGA.73.A9RS.01 2 0.4624 0.473645 0.00 0.66 0.34 0.00
#> TCGA.69.7978.01 3 0.4624 0.258556 0.00 0.00 0.66 0.34
#> TCGA.44.8117.01 4 0.4907 0.582425 0.00 0.00 0.42 0.58
#> TCGA.MP.A4TD.01 3 0.2011 0.693219 0.00 0.00 0.92 0.08
#> TCGA.83.5908.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.95.7039.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.71.6725.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.91.7771.01 4 0.4731 0.719615 0.16 0.00 0.06 0.78
#> TCGA.86.8359.01 2 0.1211 0.861069 0.00 0.96 0.04 0.00
#> TCGA.55.8301.01 3 0.4907 0.000161 0.00 0.00 0.58 0.42
#> TCGA.78.7146.01 3 0.4522 0.361844 0.00 0.00 0.68 0.32
#> TCGA.44.3918.01 3 0.0000 0.725765 0.00 0.00 1.00 0.00
#> TCGA.69.7974.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.78.7161.01 2 0.2647 0.859517 0.00 0.88 0.00 0.12
#> TCGA.97.7937.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.62.A46V.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.49.6745.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.55.8089.01 3 0.0707 0.724449 0.00 0.02 0.98 0.00
#> TCGA.55.7574.01 4 0.4284 0.830846 0.02 0.00 0.20 0.78
#> TCGA.44.5644.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.55.8511.01 3 0.1637 0.706064 0.00 0.00 0.94 0.06
#> TCGA.91.A4BC.01 3 0.0000 0.725765 0.00 0.00 1.00 0.00
#> TCGA.44.2656.01 3 0.3975 0.489390 0.00 0.00 0.76 0.24
#> TCGA.86.8673.01 1 0.4134 0.719919 0.74 0.00 0.00 0.26
#> TCGA.73.7499.01 3 0.4624 0.316834 0.00 0.00 0.66 0.34
#> TCGA.L9.A7SV.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.05.4390.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.69.7765.01 1 0.4624 0.601728 0.66 0.00 0.00 0.34
#> TCGA.95.8494.01 3 0.0000 0.725765 0.00 0.00 1.00 0.00
#> TCGA.69.7979.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.62.A46P.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.78.7158.01 1 0.4522 0.635041 0.68 0.00 0.00 0.32
#> TCGA.69.7980.01 3 0.4079 0.670264 0.00 0.18 0.80 0.02
#> TCGA.97.8547.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.1637 0.706064 0.00 0.00 0.94 0.06
#> TCGA.97.8175.01 4 0.3801 0.657058 0.22 0.00 0.00 0.78
#> TCGA.50.7109.01 2 0.1211 0.861069 0.00 0.96 0.04 0.00
#> TCGA.44.A47A.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.4406 0.807989 0.00 0.00 0.30 0.70
#> TCGA.75.6211.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.55.8090.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.91.6828.01 2 0.1637 0.866961 0.00 0.94 0.00 0.06
#> TCGA.05.4396.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.MN.A4N4.01 2 0.0000 0.870073 0.00 1.00 0.00 0.00
#> TCGA.64.5781.01 3 0.0000 0.725765 0.00 0.00 1.00 0.00
#> TCGA.NJ.A4YF.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.78.7154.01 3 0.4134 0.457586 0.00 0.00 0.74 0.26
#> TCGA.78.8662.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.05.4427.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.78.7143.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.97.A4M3.01 3 0.3610 0.579007 0.00 0.00 0.80 0.20
#> TCGA.75.6205.01 1 0.4624 0.601728 0.66 0.00 0.00 0.34
#> TCGA.55.7903.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.55.A493.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.78.7147.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.75.5126.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.NJ.A4YQ.01 3 0.0707 0.722585 0.00 0.00 0.98 0.02
#> TCGA.NJ.A7XG.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.55.A48X.01 4 0.3801 0.657058 0.22 0.00 0.00 0.78
#> TCGA.50.6594.01 4 0.4907 0.508047 0.00 0.00 0.42 0.58
#> TCGA.86.8056.01 4 0.3801 0.837329 0.00 0.00 0.22 0.78
#> TCGA.95.A4VK.01 3 0.5062 0.488627 0.00 0.30 0.68 0.02
#> TCGA.49.4488.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.55.7994.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.67.6215.01 1 0.1637 0.910645 0.94 0.00 0.00 0.06
#> TCGA.MP.A5C7.01 2 0.5594 0.089307 0.00 0.52 0.46 0.02
#> TCGA.55.7227.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 4 0.3801 0.657058 0.22 0.00 0.00 0.78
#> TCGA.35.5375.01 2 0.2921 0.785061 0.00 0.86 0.14 0.00
#> TCGA.38.4632.01 3 0.0707 0.722585 0.00 0.00 0.98 0.02
#> TCGA.MP.A4T6.01 4 0.4134 0.826891 0.00 0.00 0.26 0.74
#> TCGA.44.6779.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.86.A4P7.01 1 0.1637 0.910645 0.94 0.00 0.00 0.06
#> TCGA.49.6761.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.50.5935.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.55.6981.01 3 0.4284 0.651080 0.00 0.20 0.78 0.02
#> TCGA.78.8655.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.55.7914.01 1 0.1637 0.910645 0.94 0.00 0.00 0.06
#> TCGA.62.A472.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.05.4417.01 3 0.0707 0.722585 0.00 0.00 0.98 0.02
#> TCGA.67.4679.01 4 0.4284 0.830846 0.02 0.00 0.20 0.78
#> TCGA.97.7554.01 3 0.0707 0.724668 0.00 0.02 0.98 0.00
#> TCGA.MP.A4SY.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.95.8039.01 3 0.0707 0.722585 0.00 0.00 0.98 0.02
#> TCGA.95.7562.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.55.7576.01 4 0.4406 0.807989 0.00 0.00 0.30 0.70
#> TCGA.80.5607.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.93.8067.01 1 0.2647 0.869571 0.88 0.00 0.00 0.12
#> TCGA.62.8395.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.86.8672.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.44.2666.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.44.6777.01 4 0.4406 0.807989 0.00 0.00 0.30 0.70
#> TCGA.55.6983.01 1 0.4624 0.601728 0.66 0.00 0.00 0.34
#> TCGA.69.A59K.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.95.7567.01 1 0.1637 0.910645 0.94 0.00 0.00 0.06
#> TCGA.49.AARN.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.73.4676.01 3 0.2335 0.712792 0.00 0.06 0.92 0.02
#> TCGA.91.6836.01 4 0.3801 0.840106 0.00 0.00 0.22 0.78
#> TCGA.55.8616.01 2 0.0000 0.870073 0.00 1.00 0.00 0.00
#> TCGA.38.7271.01 1 0.1637 0.910645 0.94 0.00 0.00 0.06
#> TCGA.55.A491.01 3 0.4948 -0.003770 0.00 0.00 0.56 0.44
#> TCGA.55.6978.01 3 0.2647 0.657898 0.00 0.00 0.88 0.12
#> TCGA.NJ.A4YG.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 3 0.4284 0.651080 0.00 0.20 0.78 0.02
#> TCGA.MP.A4SV.01 2 0.3610 0.846743 0.00 0.80 0.00 0.20
#> TCGA.73.4658.01 4 0.3975 0.618801 0.24 0.00 0.00 0.76
#> TCGA.44.7659.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 2 0.2011 0.838454 0.00 0.92 0.08 0.00
#> TCGA.86.A456.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 3 0.4948 -0.080622 0.00 0.00 0.56 0.44
#> TCGA.44.7662.01 3 0.3610 0.662328 0.00 0.20 0.80 0.00
#> TCGA.55.8506.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.71.8520.01 4 0.4284 0.685886 0.20 0.00 0.02 0.78
#> TCGA.55.7815.01 3 0.3801 0.638469 0.00 0.22 0.78 0.00
#> TCGA.44.7672.01 4 0.4277 0.828936 0.00 0.00 0.28 0.72
#> TCGA.97.8172.01 4 0.4553 0.703187 0.18 0.00 0.04 0.78
#> TCGA.05.5715.01 1 0.0000 0.935550 1.00 0.00 0.00 0.00
#> TCGA.78.7152.01 3 0.4977 -0.085750 0.00 0.00 0.54 0.46
#> TCGA.78.7539.01 2 0.0707 0.868875 0.00 0.98 0.02 0.00
#> TCGA.62.A46S.01 2 0.3975 0.653105 0.00 0.76 0.24 0.00
#> TCGA.78.7145.01 2 0.0000 0.870073 0.00 1.00 0.00 0.00
#> TCGA.55.8302.01 4 0.4406 0.807989 0.00 0.00 0.30 0.70
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.4112.01 4 0.6794 0.3422 0.00 0.00 0.32 0.38 0.30
#> TCGA.NJ.A4YP.01 3 0.6766 -0.1628 0.00 0.00 0.40 0.30 0.30
#> TCGA.86.8278.01 4 0.3697 0.6531 0.08 0.00 0.00 0.82 0.10
#> TCGA.49.AARQ.01 4 0.2012 0.6822 0.06 0.00 0.02 0.92 0.00
#> TCGA.50.6597.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.62.A46U.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T8.01 5 0.4302 0.2393 0.00 0.48 0.00 0.00 0.52
#> TCGA.93.A4JN.01 1 0.2929 0.7901 0.82 0.00 0.00 0.18 0.00
#> TCGA.86.6851.01 5 0.4060 0.4181 0.00 0.36 0.00 0.00 0.64
#> TCGA.J2.A4AG.01 3 0.5961 0.1794 0.00 0.00 0.58 0.26 0.16
#> TCGA.MP.A4TK.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.L9.A443.01 1 0.4182 0.4859 0.60 0.00 0.00 0.40 0.00
#> TCGA.MN.A4N5.01 4 0.4227 -0.0348 0.42 0.00 0.00 0.58 0.00
#> TCGA.64.5775.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.8394.01 5 0.5546 0.4257 0.00 0.10 0.20 0.02 0.68
#> TCGA.05.4405.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.0609 0.7091 0.00 0.98 0.00 0.00 0.02
#> TCGA.MN.A4N1.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.6847.01 4 0.6723 0.4089 0.00 0.00 0.28 0.42 0.30
#> TCGA.MP.A4TC.01 4 0.3983 0.5852 0.00 0.00 0.34 0.66 0.00
#> TCGA.05.4410.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.62.A46Y.01 4 0.4227 -0.0348 0.42 0.00 0.00 0.58 0.00
#> TCGA.55.6982.01 4 0.4921 0.5659 0.00 0.00 0.34 0.62 0.04
#> TCGA.55.6642.01 5 0.4287 0.2853 0.00 0.46 0.00 0.00 0.54
#> TCGA.50.6673.01 5 0.5068 0.4340 0.00 0.30 0.00 0.06 0.64
#> TCGA.55.8207.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.6562.01 5 0.4302 0.2393 0.00 0.48 0.00 0.00 0.52
#> TCGA.05.4425.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8074.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.55.7727.01 3 0.6337 0.0138 0.00 0.00 0.50 0.32 0.18
#> TCGA.MP.A4SW.01 3 0.2732 0.6626 0.00 0.00 0.84 0.00 0.16
#> TCGA.67.6216.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8203.01 5 0.5394 0.2178 0.00 0.06 0.40 0.00 0.54
#> TCGA.J2.8194.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.2668.01 4 0.3796 0.3131 0.30 0.00 0.00 0.70 0.00
#> TCGA.55.A57B.01 3 0.4818 0.2459 0.00 0.00 0.52 0.02 0.46
#> TCGA.NJ.A4YI.01 3 0.6503 0.0105 0.00 0.00 0.48 0.30 0.22
#> TCGA.L9.A444.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8668.01 4 0.4075 0.6465 0.00 0.00 0.06 0.78 0.16
#> TCGA.44.A47G.01 4 0.3983 0.5852 0.00 0.00 0.34 0.66 0.00
#> TCGA.55.6986.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2665.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5425.01 5 0.4302 0.2393 0.00 0.48 0.00 0.00 0.52
#> TCGA.62.A46R.01 3 0.3983 0.4206 0.00 0.00 0.66 0.00 0.34
#> TCGA.55.A494.01 5 0.4854 0.4315 0.00 0.26 0.00 0.06 0.68
#> TCGA.44.3917.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.75.5125.01 3 0.3983 0.4206 0.00 0.00 0.66 0.00 0.34
#> TCGA.L4.A4E5.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.44.6775.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.55.7911.01 4 0.4921 0.5659 0.00 0.00 0.34 0.62 0.04
#> TCGA.55.6712.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7760.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.95.7948.01 1 0.5783 0.4205 0.54 0.00 0.00 0.36 0.10
#> TCGA.55.A4DG.01 5 0.4287 0.2853 0.00 0.46 0.00 0.00 0.54
#> TCGA.55.6985.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.MP.A4TF.01 5 0.5694 -0.3904 0.00 0.00 0.46 0.08 0.46
#> TCGA.91.6829.01 2 0.4726 0.2211 0.00 0.58 0.00 0.02 0.40
#> TCGA.99.7458.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 4 0.2077 0.6874 0.04 0.00 0.04 0.92 0.00
#> TCGA.44.A47B.01 4 0.6610 0.4513 0.00 0.00 0.28 0.46 0.26
#> TCGA.78.7542.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.5429.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.8179.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.A4JF.01 3 0.4527 0.3461 0.00 0.00 0.70 0.26 0.04
#> TCGA.55.8092.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.5122.01 4 0.4921 0.5659 0.00 0.00 0.34 0.62 0.04
#> TCGA.49.AARE.01 3 0.5232 0.4685 0.00 0.00 0.60 0.06 0.34
#> TCGA.95.7043.01 5 0.4302 0.2124 0.00 0.48 0.00 0.00 0.52
#> TCGA.86.7701.01 3 0.2516 0.6789 0.00 0.00 0.86 0.00 0.14
#> TCGA.55.7281.01 3 0.4818 0.2459 0.00 0.00 0.52 0.02 0.46
#> TCGA.78.7535.01 4 0.3796 0.6145 0.00 0.00 0.30 0.70 0.00
#> TCGA.50.6592.01 4 0.5136 0.6169 0.00 0.00 0.26 0.66 0.08
#> TCGA.44.7661.01 3 0.6665 -0.1052 0.00 0.00 0.44 0.30 0.26
#> TCGA.97.A4M0.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7153.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7907.01 3 0.3109 0.6242 0.00 0.00 0.80 0.00 0.20
#> TCGA.49.6767.01 5 0.4302 0.2393 0.00 0.48 0.00 0.00 0.52
#> TCGA.50.5051.01 5 0.4307 0.1537 0.00 0.50 0.00 0.00 0.50
#> TCGA.78.7540.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.A4VN.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A47F.01 1 0.5136 0.6236 0.66 0.00 0.00 0.26 0.08
#> TCGA.69.8253.01 4 0.5068 0.5710 0.00 0.00 0.06 0.64 0.30
#> TCGA.J2.A4AE.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 4 0.3983 0.5852 0.00 0.00 0.34 0.66 0.00
#> TCGA.80.5608.01 5 0.3983 0.4353 0.00 0.34 0.00 0.00 0.66
#> TCGA.55.8205.01 3 0.3109 0.6242 0.00 0.00 0.80 0.00 0.20
#> TCGA.99.8025.01 3 0.3983 0.4206 0.00 0.00 0.66 0.00 0.34
#> TCGA.55.7283.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7159.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.8120.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.69.7763.01 1 0.2732 0.8083 0.84 0.00 0.00 0.16 0.00
#> TCGA.64.5815.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7761.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.A9RS.01 5 0.4728 0.4675 0.00 0.24 0.06 0.00 0.70
#> TCGA.69.7978.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.8117.01 3 0.3796 0.2989 0.00 0.00 0.70 0.30 0.00
#> TCGA.MP.A4TD.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.83.5908.01 4 0.3983 0.5852 0.00 0.00 0.34 0.66 0.00
#> TCGA.95.7039.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.71.6725.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.7771.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.86.8359.01 5 0.4302 0.2393 0.00 0.48 0.00 0.00 0.52
#> TCGA.55.8301.01 3 0.5961 0.1794 0.00 0.00 0.58 0.26 0.16
#> TCGA.78.7146.01 5 0.6503 -0.2805 0.00 0.00 0.30 0.22 0.48
#> TCGA.44.3918.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7974.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7161.01 2 0.3895 0.4103 0.00 0.68 0.00 0.00 0.32
#> TCGA.97.7937.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 3 0.2280 0.6939 0.00 0.00 0.88 0.00 0.12
#> TCGA.55.7574.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.44.5644.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8511.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.A4BC.01 3 0.1410 0.7289 0.00 0.00 0.94 0.00 0.06
#> TCGA.44.2656.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8673.01 4 0.4182 0.0329 0.40 0.00 0.00 0.60 0.00
#> TCGA.73.7499.01 3 0.6691 0.1722 0.00 0.00 0.40 0.24 0.36
#> TCGA.L9.A7SV.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.4390.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7765.01 4 0.4182 0.0329 0.40 0.00 0.00 0.60 0.00
#> TCGA.95.8494.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7979.01 2 0.4227 0.2058 0.00 0.58 0.00 0.00 0.42
#> TCGA.62.A46P.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 1 0.5783 0.4205 0.54 0.00 0.00 0.36 0.10
#> TCGA.69.7980.01 5 0.5351 -0.2481 0.00 0.00 0.38 0.06 0.56
#> TCGA.97.8547.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.8175.01 4 0.1732 0.6719 0.08 0.00 0.00 0.92 0.00
#> TCGA.50.7109.01 5 0.4302 0.2393 0.00 0.48 0.00 0.00 0.52
#> TCGA.44.A47A.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.4990 0.5374 0.00 0.00 0.36 0.60 0.04
#> TCGA.75.6211.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8090.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.91.6828.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.05.4396.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.64.5781.01 3 0.0609 0.7382 0.00 0.00 0.98 0.00 0.02
#> TCGA.NJ.A4YF.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.78.7154.01 3 0.3731 0.5980 0.00 0.00 0.80 0.04 0.16
#> TCGA.78.8662.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.4427.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7143.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.97.A4M3.01 5 0.6555 -0.2872 0.00 0.00 0.32 0.22 0.46
#> TCGA.75.6205.01 4 0.4182 0.0329 0.40 0.00 0.00 0.60 0.00
#> TCGA.55.7903.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 4 0.4921 0.5659 0.00 0.00 0.34 0.62 0.04
#> TCGA.78.7147.01 2 0.4829 -0.0471 0.00 0.50 0.00 0.02 0.48
#> TCGA.75.5126.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.NJ.A7XG.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48X.01 4 0.2331 0.6713 0.08 0.00 0.00 0.90 0.02
#> TCGA.50.6594.01 4 0.6732 0.3125 0.00 0.00 0.26 0.40 0.34
#> TCGA.86.8056.01 4 0.6398 0.4906 0.00 0.00 0.20 0.50 0.30
#> TCGA.95.A4VK.01 5 0.5852 0.4151 0.00 0.08 0.18 0.06 0.68
#> TCGA.49.4488.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7994.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.6215.01 1 0.2929 0.7901 0.82 0.00 0.00 0.18 0.00
#> TCGA.MP.A5C7.01 5 0.4974 0.4155 0.00 0.12 0.06 0.06 0.76
#> TCGA.55.7227.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 4 0.2012 0.6822 0.06 0.00 0.02 0.92 0.00
#> TCGA.35.5375.01 5 0.3796 0.4585 0.00 0.30 0.00 0.00 0.70
#> TCGA.38.4632.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T6.01 4 0.6723 0.4026 0.00 0.00 0.28 0.42 0.30
#> TCGA.44.6779.01 3 0.3983 0.4206 0.00 0.00 0.66 0.00 0.34
#> TCGA.86.A4P7.01 1 0.2732 0.8083 0.84 0.00 0.00 0.16 0.00
#> TCGA.49.6761.01 4 0.4921 0.5659 0.00 0.00 0.34 0.62 0.04
#> TCGA.50.5935.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6981.01 3 0.4252 0.4967 0.00 0.00 0.70 0.02 0.28
#> TCGA.78.8655.01 1 0.0609 0.9059 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.7914.01 1 0.2732 0.8083 0.84 0.00 0.00 0.16 0.00
#> TCGA.62.A472.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4417.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.67.4679.01 4 0.4433 0.6252 0.00 0.00 0.06 0.74 0.20
#> TCGA.97.7554.01 3 0.1043 0.7339 0.00 0.00 0.96 0.00 0.04
#> TCGA.MP.A4SY.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.8039.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.7562.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.55.7576.01 4 0.6455 0.4352 0.00 0.00 0.32 0.48 0.20
#> TCGA.80.5607.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.8067.01 1 0.4060 0.5569 0.64 0.00 0.00 0.36 0.00
#> TCGA.62.8395.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 3 0.3561 0.5500 0.00 0.00 0.74 0.00 0.26
#> TCGA.44.2666.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6777.01 4 0.4990 0.5374 0.00 0.00 0.36 0.60 0.04
#> TCGA.55.6983.01 1 0.5558 0.4515 0.56 0.00 0.00 0.36 0.08
#> TCGA.69.A59K.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 1 0.4227 0.4273 0.58 0.00 0.00 0.42 0.00
#> TCGA.49.AARN.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.01 3 0.4254 0.6192 0.00 0.00 0.74 0.04 0.22
#> TCGA.91.6836.01 4 0.1732 0.6959 0.00 0.00 0.08 0.92 0.00
#> TCGA.55.8616.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.38.7271.01 1 0.2732 0.8083 0.84 0.00 0.00 0.16 0.00
#> TCGA.55.A491.01 3 0.6359 0.0885 0.00 0.00 0.52 0.26 0.22
#> TCGA.55.6978.01 3 0.0000 0.7418 0.00 0.00 1.00 0.00 0.00
#> TCGA.NJ.A4YG.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 3 0.3999 0.5565 0.00 0.00 0.74 0.02 0.24
#> TCGA.MP.A4SV.01 2 0.0000 0.7222 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.4658.01 4 0.1732 0.6719 0.08 0.00 0.00 0.92 0.00
#> TCGA.44.7659.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.4360 0.4546 0.00 0.30 0.00 0.02 0.68
#> TCGA.86.A456.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 3 0.6054 0.1230 0.00 0.00 0.56 0.28 0.16
#> TCGA.44.7662.01 3 0.3983 0.4206 0.00 0.00 0.66 0.00 0.34
#> TCGA.55.8506.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.71.8520.01 4 0.2012 0.6927 0.02 0.00 0.06 0.92 0.00
#> TCGA.55.7815.01 3 0.4126 0.3439 0.00 0.00 0.62 0.00 0.38
#> TCGA.44.7672.01 4 0.3983 0.5852 0.00 0.00 0.34 0.66 0.00
#> TCGA.97.8172.01 4 0.3034 0.6793 0.06 0.00 0.02 0.88 0.04
#> TCGA.05.5715.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7152.01 3 0.6766 -0.1628 0.00 0.00 0.40 0.30 0.30
#> TCGA.78.7539.01 5 0.4126 0.3903 0.00 0.38 0.00 0.00 0.62
#> TCGA.62.A46S.01 5 0.3796 0.4585 0.00 0.30 0.00 0.00 0.70
#> TCGA.78.7145.01 2 0.4182 0.2853 0.00 0.60 0.00 0.00 0.40
#> TCGA.55.8302.01 4 0.4921 0.5659 0.00 0.00 0.34 0.62 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.4112.01 6 0.4247 0.588586 0.00 0.00 0.06 0.24 0.00 0.70
#> TCGA.NJ.A4YP.01 6 0.4566 0.629560 0.00 0.00 0.16 0.14 0.00 0.70
#> TCGA.86.8278.01 4 0.3976 0.442583 0.02 0.02 0.00 0.74 0.00 0.22
#> TCGA.49.AARQ.01 4 0.1635 0.635499 0.02 0.02 0.00 0.94 0.00 0.02
#> TCGA.50.6597.01 4 0.1807 0.631529 0.00 0.00 0.02 0.92 0.00 0.06
#> TCGA.62.A46U.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T8.01 5 0.1480 0.852408 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.93.A4JN.01 1 0.3315 0.749856 0.78 0.00 0.00 0.20 0.00 0.02
#> TCGA.86.6851.01 5 0.1267 0.844627 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.J2.A4AG.01 6 0.6152 0.467095 0.00 0.02 0.40 0.16 0.00 0.42
#> TCGA.MP.A4TK.01 3 0.0937 0.846186 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.L9.A443.01 1 0.4637 0.447340 0.60 0.02 0.00 0.36 0.00 0.02
#> TCGA.MN.A4N5.01 4 0.3592 0.496160 0.24 0.00 0.00 0.74 0.00 0.02
#> TCGA.64.5775.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.62.8394.01 5 0.4678 0.707068 0.00 0.16 0.02 0.00 0.72 0.10
#> TCGA.05.4405.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.4246 0.662093 0.00 0.58 0.00 0.00 0.40 0.02
#> TCGA.MN.A4N1.01 3 0.0937 0.846186 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.91.6847.01 6 0.4631 0.597177 0.00 0.02 0.06 0.22 0.00 0.70
#> TCGA.MP.A4TC.01 4 0.4328 0.509885 0.00 0.00 0.18 0.72 0.00 0.10
#> TCGA.05.4410.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46Y.01 4 0.3309 0.467026 0.28 0.00 0.00 0.72 0.00 0.00
#> TCGA.55.6982.01 4 0.5291 0.256798 0.00 0.02 0.08 0.60 0.00 0.30
#> TCGA.55.6642.01 5 0.2175 0.845051 0.00 0.02 0.02 0.02 0.92 0.02
#> TCGA.50.6673.01 5 0.5027 0.605031 0.00 0.16 0.00 0.00 0.64 0.20
#> TCGA.55.8207.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.6562.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.05.4425.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8074.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.55.7727.01 6 0.5655 0.530636 0.00 0.00 0.36 0.16 0.00 0.48
#> TCGA.MP.A4SW.01 3 0.0937 0.850146 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.67.6216.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8203.01 5 0.3976 0.639027 0.00 0.00 0.22 0.02 0.74 0.02
#> TCGA.J2.8194.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.44.2668.01 4 0.1814 0.611523 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.55.A57B.01 3 0.5652 0.511192 0.00 0.04 0.62 0.00 0.22 0.12
#> TCGA.NJ.A4YI.01 6 0.5618 0.558245 0.00 0.00 0.34 0.16 0.00 0.50
#> TCGA.L9.A444.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8668.01 6 0.4337 0.142304 0.00 0.02 0.00 0.48 0.00 0.50
#> TCGA.44.A47G.01 4 0.4328 0.509885 0.00 0.00 0.18 0.72 0.00 0.10
#> TCGA.55.6986.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2665.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5425.01 5 0.0937 0.854434 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.62.A46R.01 3 0.2350 0.791638 0.00 0.00 0.88 0.00 0.10 0.02
#> TCGA.55.A494.01 5 0.5524 0.633650 0.00 0.16 0.00 0.02 0.62 0.20
#> TCGA.44.3917.01 5 0.1267 0.845036 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.75.5125.01 3 0.2956 0.760446 0.00 0.00 0.84 0.00 0.12 0.04
#> TCGA.L4.A4E5.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.44.6775.01 4 0.1807 0.631529 0.00 0.00 0.02 0.92 0.00 0.06
#> TCGA.55.7911.01 4 0.4566 0.476856 0.00 0.00 0.14 0.70 0.00 0.16
#> TCGA.55.6712.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7760.01 4 0.3111 0.598896 0.00 0.02 0.02 0.84 0.00 0.12
#> TCGA.95.7948.01 4 0.6394 0.070129 0.36 0.02 0.00 0.40 0.00 0.22
#> TCGA.55.A4DG.01 5 0.2020 0.851013 0.00 0.02 0.02 0.00 0.92 0.04
#> TCGA.55.6985.01 4 0.0547 0.648468 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.MP.A4TF.01 6 0.5392 0.540239 0.00 0.18 0.12 0.00 0.04 0.66
#> TCGA.91.6829.01 5 0.1807 0.849616 0.00 0.02 0.00 0.00 0.92 0.06
#> TCGA.99.7458.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 4 0.0547 0.649744 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.44.A47B.01 6 0.3916 0.529062 0.00 0.00 0.02 0.30 0.00 0.68
#> TCGA.78.7542.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.05.5429.01 3 0.1092 0.853319 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.97.8179.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.86.A4JF.01 3 0.4566 0.392193 0.00 0.00 0.70 0.14 0.00 0.16
#> TCGA.55.8092.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.75.6207.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.75.5122.01 4 0.5524 0.375070 0.00 0.02 0.20 0.62 0.00 0.16
#> TCGA.49.AARE.01 3 0.7235 0.171521 0.00 0.18 0.46 0.02 0.08 0.26
#> TCGA.95.7043.01 5 0.1480 0.852408 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.86.7701.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7281.01 3 0.5652 0.511192 0.00 0.04 0.62 0.00 0.22 0.12
#> TCGA.78.7535.01 4 0.4328 0.509885 0.00 0.00 0.18 0.72 0.00 0.10
#> TCGA.50.6592.01 4 0.5020 0.040759 0.00 0.02 0.04 0.56 0.00 0.38
#> TCGA.44.7661.01 6 0.4890 0.608357 0.00 0.00 0.18 0.16 0.00 0.66
#> TCGA.97.A4M0.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7153.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 3 0.0937 0.846186 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.7907.01 3 0.1092 0.849701 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.49.6767.01 5 0.1092 0.854452 0.00 0.02 0.02 0.00 0.96 0.00
#> TCGA.50.5051.01 5 0.1480 0.852408 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.78.7540.01 3 0.1092 0.853319 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.95.A4VN.01 3 0.0547 0.857328 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.44.A47F.01 1 0.6251 0.275677 0.48 0.02 0.00 0.28 0.00 0.22
#> TCGA.69.8253.01 6 0.4002 0.470651 0.00 0.02 0.00 0.32 0.00 0.66
#> TCGA.J2.A4AE.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 4 0.4328 0.509885 0.00 0.00 0.18 0.72 0.00 0.10
#> TCGA.80.5608.01 5 0.1092 0.842859 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.55.8205.01 3 0.1480 0.841409 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.99.8025.01 3 0.1814 0.800748 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.55.7283.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7159.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.44.8120.01 5 0.0937 0.854434 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.69.7763.01 1 0.3156 0.774913 0.80 0.00 0.00 0.18 0.00 0.02
#> TCGA.64.5815.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7761.01 3 0.0547 0.857328 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.73.A9RS.01 5 0.4028 0.729105 0.00 0.16 0.02 0.02 0.78 0.02
#> TCGA.69.7978.01 3 0.0937 0.846186 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.44.8117.01 3 0.4632 -0.001389 0.00 0.00 0.52 0.44 0.00 0.04
#> TCGA.MP.A4TD.01 3 0.0547 0.857328 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.83.5908.01 4 0.4328 0.509885 0.00 0.00 0.18 0.72 0.00 0.10
#> TCGA.95.7039.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.71.6725.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.91.7771.01 4 0.0547 0.649744 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.86.8359.01 5 0.1480 0.852408 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.55.8301.01 6 0.6152 0.467095 0.00 0.02 0.40 0.16 0.00 0.42
#> TCGA.78.7146.01 6 0.5272 0.567699 0.00 0.18 0.04 0.04 0.04 0.70
#> TCGA.44.3918.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7974.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7161.01 5 0.2094 0.815427 0.00 0.08 0.00 0.02 0.90 0.00
#> TCGA.97.7937.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.62.A46V.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 3 0.0937 0.850146 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.7574.01 4 0.0547 0.648468 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.44.5644.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.55.8511.01 3 0.0547 0.857328 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.91.A4BC.01 3 0.0547 0.856291 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.44.2656.01 3 0.0937 0.846186 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.86.8673.01 4 0.2793 0.539836 0.20 0.00 0.00 0.80 0.00 0.00
#> TCGA.73.7499.01 6 0.5469 0.581229 0.00 0.18 0.08 0.04 0.02 0.68
#> TCGA.L9.A7SV.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.05.4390.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.69.7765.01 4 0.2631 0.556197 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.95.8494.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7979.01 5 0.1480 0.852408 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.62.A46P.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 4 0.6400 -0.000073 0.38 0.02 0.00 0.38 0.00 0.22
#> TCGA.69.7980.01 6 0.6628 0.502234 0.00 0.18 0.12 0.02 0.10 0.58
#> TCGA.97.8547.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.1092 0.853319 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.97.8175.01 4 0.0547 0.649744 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.50.7109.01 5 0.1480 0.852408 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.44.A47A.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.5202 0.326941 0.00 0.00 0.26 0.60 0.00 0.14
#> TCGA.75.6211.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.55.8090.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.0547 0.648468 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.91.6828.01 5 0.1267 0.845036 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.05.4396.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.MN.A4N4.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.64.5781.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.78.7154.01 3 0.6209 -0.123013 0.00 0.06 0.50 0.10 0.00 0.34
#> TCGA.78.8662.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.05.4427.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.78.7143.01 4 0.1556 0.623501 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.97.A4M3.01 6 0.6039 0.564799 0.00 0.18 0.10 0.04 0.04 0.64
#> TCGA.75.6205.01 4 0.2631 0.556197 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.55.7903.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 4 0.5390 0.409716 0.00 0.02 0.18 0.64 0.00 0.16
#> TCGA.78.7147.01 5 0.1556 0.837006 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.75.5126.01 1 0.1267 0.898523 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.3076 0.965157 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.NJ.A4YQ.01 3 0.0547 0.857328 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.NJ.A7XG.01 1 0.0547 0.925143 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.A48X.01 4 0.3506 0.522520 0.02 0.02 0.00 0.80 0.00 0.16
#> TCGA.50.6594.01 6 0.4678 0.594856 0.00 0.16 0.02 0.10 0.00 0.72
#> TCGA.86.8056.01 6 0.3309 0.534241 0.00 0.00 0.00 0.28 0.00 0.72
#> TCGA.95.A4VK.01 5 0.6017 0.572932 0.00 0.16 0.02 0.02 0.60 0.20
#> TCGA.49.4488.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.55.7994.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.67.6215.01 1 0.2793 0.768086 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.MP.A5C7.01 5 0.5643 0.566759 0.00 0.16 0.00 0.02 0.60 0.22
#> TCGA.55.7227.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 4 0.0547 0.649744 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.35.5375.01 5 0.3660 0.744120 0.00 0.16 0.00 0.00 0.78 0.06
#> TCGA.38.4632.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T6.01 6 0.4105 0.586338 0.00 0.02 0.02 0.24 0.00 0.72
#> TCGA.44.6779.01 3 0.2956 0.760446 0.00 0.00 0.84 0.00 0.12 0.04
#> TCGA.86.A4P7.01 1 0.2631 0.789936 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.49.6761.01 4 0.4475 0.459474 0.00 0.00 0.10 0.70 0.00 0.20
#> TCGA.50.5935.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6981.01 3 0.2794 0.784489 0.00 0.00 0.86 0.00 0.06 0.08
#> TCGA.78.8655.01 1 0.0937 0.912659 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.55.7914.01 1 0.3156 0.774913 0.80 0.00 0.00 0.18 0.00 0.02
#> TCGA.62.A472.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4417.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.4679.01 6 0.4310 0.250755 0.00 0.02 0.00 0.44 0.00 0.54
#> TCGA.97.7554.01 3 0.0000 0.862107 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4SY.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.8039.01 3 0.0547 0.857297 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.95.7562.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.55.7576.01 6 0.5371 0.412054 0.00 0.00 0.12 0.36 0.00 0.52
#> TCGA.80.5607.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.8067.01 1 0.4689 0.400313 0.58 0.02 0.00 0.38 0.00 0.02
#> TCGA.62.8395.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 3 0.1480 0.841409 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.44.2666.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6777.01 4 0.5524 0.375070 0.00 0.02 0.20 0.62 0.00 0.16
#> TCGA.55.6983.01 4 0.6394 0.070129 0.36 0.02 0.00 0.40 0.00 0.22
#> TCGA.69.A59K.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 4 0.3797 0.175251 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.49.AARN.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.01 3 0.3828 0.166134 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.91.6836.01 4 0.1807 0.631529 0.00 0.00 0.02 0.92 0.00 0.06
#> TCGA.55.8616.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.38.7271.01 1 0.3156 0.774913 0.80 0.00 0.00 0.18 0.00 0.02
#> TCGA.55.A491.01 6 0.5996 0.609360 0.00 0.16 0.12 0.10 0.00 0.62
#> TCGA.55.6978.01 3 0.0937 0.846186 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.NJ.A4YG.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 3 0.2474 0.801473 0.00 0.00 0.88 0.00 0.04 0.08
#> TCGA.MP.A4SV.01 2 0.2941 0.986518 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.73.4658.01 4 0.0547 0.649744 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.44.7659.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.3746 0.728213 0.00 0.14 0.00 0.00 0.78 0.08
#> TCGA.86.A456.01 1 0.0000 0.936731 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 6 0.6119 0.527417 0.00 0.02 0.36 0.16 0.00 0.46
#> TCGA.44.7662.01 3 0.3523 0.688606 0.00 0.00 0.78 0.00 0.18 0.04
#> TCGA.55.8506.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.71.8520.01 4 0.0547 0.649744 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.55.7815.01 3 0.3950 0.615082 0.00 0.00 0.72 0.00 0.24 0.04
#> TCGA.44.7672.01 4 0.4536 0.486270 0.00 0.00 0.18 0.70 0.00 0.12
#> TCGA.97.8172.01 4 0.3678 0.498711 0.02 0.02 0.00 0.78 0.00 0.18
#> TCGA.05.5715.01 1 0.1635 0.903564 0.94 0.02 0.00 0.02 0.00 0.02
#> TCGA.78.7152.01 6 0.4566 0.629560 0.00 0.00 0.16 0.14 0.00 0.70
#> TCGA.78.7539.01 5 0.0547 0.855682 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.62.A46S.01 5 0.3997 0.736008 0.00 0.14 0.00 0.02 0.78 0.06
#> TCGA.78.7145.01 5 0.1865 0.853095 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.55.8302.01 4 0.5524 0.375070 0.00 0.02 0.20 0.62 0.00 0.16
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.44.4112.01 7 0.4828 0.65660 0.00 0.00 0.02 0.06 0.00 0.36 0.56
#> TCGA.NJ.A4YP.01 6 0.5490 -0.23207 0.00 0.00 0.08 0.06 0.00 0.54 0.32
#> TCGA.86.8278.01 4 0.3867 0.35197 0.00 0.00 0.00 0.60 0.00 0.02 0.38
#> TCGA.49.AARQ.01 4 0.0504 0.71276 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.6597.01 4 0.2422 0.52970 0.00 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.62.A46U.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T8.01 5 0.2722 0.84241 0.00 0.12 0.00 0.00 0.84 0.00 0.04
#> TCGA.93.A4JN.01 4 0.3968 0.17813 0.44 0.00 0.00 0.54 0.00 0.00 0.02
#> TCGA.86.6851.01 5 0.2803 0.84810 0.00 0.10 0.00 0.00 0.84 0.00 0.06
#> TCGA.J2.A4AG.01 6 0.5189 0.32528 0.00 0.00 0.24 0.08 0.00 0.62 0.06
#> TCGA.MP.A4TK.01 3 0.3358 0.44843 0.00 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.L9.A443.01 4 0.3637 0.56624 0.24 0.00 0.00 0.72 0.00 0.00 0.04
#> TCGA.MN.A4N5.01 4 0.1928 0.70877 0.08 0.00 0.00 0.90 0.00 0.00 0.02
#> TCGA.64.5775.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8394.01 5 0.1928 0.79473 0.00 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.05.4405.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.4070 0.29206 0.00 0.62 0.00 0.00 0.34 0.00 0.04
#> TCGA.MN.A4N1.01 3 0.3546 0.18511 0.00 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.91.6847.01 7 0.4828 0.65660 0.00 0.00 0.02 0.06 0.00 0.36 0.56
#> TCGA.MP.A4TC.01 6 0.5047 0.45716 0.00 0.00 0.14 0.34 0.00 0.52 0.00
#> TCGA.05.4410.01 3 0.2422 0.68509 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.62.A46Y.01 4 0.1928 0.70877 0.08 0.00 0.00 0.90 0.00 0.00 0.02
#> TCGA.55.6982.01 6 0.5281 0.35734 0.00 0.00 0.08 0.26 0.00 0.60 0.06
#> TCGA.55.6642.01 5 0.3000 0.83787 0.00 0.10 0.02 0.00 0.84 0.00 0.04
#> TCGA.50.6673.01 5 0.5253 0.50231 0.00 0.00 0.04 0.00 0.62 0.14 0.20
#> TCGA.55.8207.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.6562.01 5 0.3263 0.84506 0.00 0.12 0.00 0.00 0.80 0.00 0.08
#> TCGA.05.4425.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8074.01 5 0.3835 0.82718 0.00 0.16 0.00 0.00 0.74 0.00 0.10
#> TCGA.55.7727.01 6 0.5989 0.14709 0.00 0.00 0.18 0.08 0.00 0.54 0.20
#> TCGA.MP.A4SW.01 3 0.0863 0.76870 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.67.6216.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8203.01 5 0.3086 0.73525 0.00 0.00 0.16 0.00 0.80 0.00 0.04
#> TCGA.J2.8194.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2668.01 4 0.0863 0.71874 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.55.A57B.01 3 0.3244 0.65616 0.00 0.00 0.78 0.00 0.18 0.04 0.00
#> TCGA.NJ.A4YI.01 6 0.5989 0.14709 0.00 0.00 0.18 0.08 0.00 0.54 0.20
#> TCGA.L9.A444.01 3 0.0863 0.76563 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.86.8668.01 4 0.5002 -0.06096 0.00 0.00 0.00 0.48 0.00 0.12 0.40
#> TCGA.44.A47G.01 6 0.4998 0.45944 0.00 0.00 0.14 0.32 0.00 0.54 0.00
#> TCGA.55.6986.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2665.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5425.01 5 0.2722 0.84241 0.00 0.12 0.00 0.00 0.84 0.00 0.04
#> TCGA.62.A46R.01 3 0.1433 0.75726 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.55.A494.01 5 0.5055 0.45182 0.00 0.00 0.00 0.00 0.56 0.18 0.26
#> TCGA.44.3917.01 5 0.3244 0.82709 0.00 0.18 0.00 0.00 0.78 0.00 0.04
#> TCGA.75.5125.01 3 0.1671 0.74751 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.L4.A4E5.01 5 0.3835 0.82718 0.00 0.16 0.00 0.00 0.74 0.00 0.10
#> TCGA.44.6775.01 4 0.2572 0.51288 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.55.7911.01 6 0.5429 0.42741 0.00 0.00 0.10 0.32 0.00 0.54 0.04
#> TCGA.55.6712.01 3 0.0504 0.76923 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.69.7760.01 4 0.4597 0.15034 0.00 0.00 0.00 0.56 0.00 0.36 0.08
#> TCGA.95.7948.01 4 0.5223 0.37231 0.10 0.00 0.00 0.52 0.00 0.02 0.36
#> TCGA.55.A4DG.01 5 0.3691 0.82823 0.00 0.06 0.06 0.00 0.80 0.00 0.08
#> TCGA.55.6985.01 4 0.0863 0.70016 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.MP.A4TF.01 6 0.6307 -0.12055 0.00 0.00 0.12 0.00 0.12 0.46 0.30
#> TCGA.91.6829.01 5 0.3867 0.82754 0.00 0.14 0.00 0.00 0.74 0.00 0.12
#> TCGA.99.7458.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 4 0.0000 0.71326 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A47B.01 7 0.5279 0.59066 0.00 0.00 0.02 0.10 0.00 0.40 0.48
#> TCGA.78.7542.01 2 0.1006 0.94567 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.05.5429.01 3 0.3139 0.55577 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.97.8179.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4JF.01 6 0.4638 0.29253 0.00 0.00 0.38 0.08 0.00 0.54 0.00
#> TCGA.55.8092.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5122.01 6 0.4939 0.46616 0.00 0.00 0.14 0.30 0.00 0.56 0.00
#> TCGA.49.AARE.01 6 0.6935 -0.06523 0.00 0.00 0.22 0.00 0.16 0.34 0.28
#> TCGA.95.7043.01 5 0.3449 0.84257 0.00 0.14 0.00 0.00 0.78 0.00 0.08
#> TCGA.86.7701.01 3 0.0863 0.76870 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.55.7281.01 3 0.2912 0.69317 0.00 0.00 0.82 0.00 0.14 0.04 0.00
#> TCGA.78.7535.01 6 0.5047 0.45716 0.00 0.00 0.14 0.34 0.00 0.52 0.00
#> TCGA.50.6592.01 6 0.5281 0.29467 0.00 0.00 0.06 0.26 0.00 0.60 0.08
#> TCGA.44.7661.01 6 0.5751 -0.32474 0.00 0.00 0.10 0.06 0.00 0.48 0.36
#> TCGA.97.A4M0.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 3 0.0863 0.76563 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.78.7153.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 3 0.3294 0.48136 0.00 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.55.7907.01 3 0.1433 0.75808 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.49.6767.01 5 0.2769 0.83889 0.00 0.08 0.04 0.00 0.86 0.00 0.02
#> TCGA.50.5051.01 5 0.2722 0.84241 0.00 0.12 0.00 0.00 0.84 0.00 0.04
#> TCGA.78.7540.01 3 0.3294 0.48912 0.00 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.95.A4VN.01 3 0.3221 0.52476 0.00 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.44.A47F.01 4 0.5207 0.33927 0.16 0.00 0.00 0.48 0.00 0.00 0.36
#> TCGA.69.8253.01 7 0.5083 0.55870 0.00 0.00 0.00 0.24 0.00 0.20 0.56
#> TCGA.J2.A4AE.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 6 0.5047 0.45716 0.00 0.00 0.14 0.34 0.00 0.52 0.00
#> TCGA.80.5608.01 5 0.2016 0.82994 0.00 0.06 0.00 0.00 0.90 0.00 0.04
#> TCGA.55.8205.01 3 0.1433 0.75808 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.99.8025.01 3 0.1433 0.75726 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.55.7283.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7159.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8120.01 5 0.2745 0.83738 0.00 0.16 0.00 0.00 0.82 0.00 0.02
#> TCGA.69.7763.01 1 0.3985 0.07813 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.64.5815.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7761.01 3 0.3139 0.55577 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.73.A9RS.01 5 0.1166 0.78184 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.69.7978.01 6 0.4278 0.05179 0.00 0.00 0.46 0.04 0.00 0.50 0.00
#> TCGA.44.8117.01 6 0.5467 0.42167 0.00 0.00 0.26 0.28 0.00 0.46 0.00
#> TCGA.MP.A4TD.01 3 0.3221 0.52476 0.00 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.83.5908.01 6 0.5047 0.45716 0.00 0.00 0.14 0.34 0.00 0.52 0.00
#> TCGA.95.7039.01 2 0.1006 0.94567 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.71.6725.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.7771.01 4 0.0000 0.71326 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8359.01 5 0.2722 0.84241 0.00 0.12 0.00 0.00 0.84 0.00 0.04
#> TCGA.55.8301.01 6 0.5189 0.32528 0.00 0.00 0.24 0.08 0.00 0.62 0.06
#> TCGA.78.7146.01 6 0.4978 -0.18456 0.00 0.00 0.00 0.00 0.12 0.50 0.38
#> TCGA.44.3918.01 3 0.0863 0.76563 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.69.7974.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7161.01 5 0.3388 0.81607 0.00 0.20 0.00 0.00 0.76 0.00 0.04
#> TCGA.97.7937.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 3 0.1166 0.76450 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.55.7574.01 4 0.0504 0.70543 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.44.5644.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8511.01 3 0.2422 0.68509 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.91.A4BC.01 3 0.0504 0.77038 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.44.2656.01 3 0.4278 0.04093 0.00 0.00 0.50 0.04 0.00 0.46 0.00
#> TCGA.86.8673.01 4 0.1433 0.71301 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.73.7499.01 6 0.5300 -0.10044 0.00 0.00 0.04 0.00 0.10 0.58 0.28
#> TCGA.L9.A7SV.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4390.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7765.01 4 0.1433 0.71301 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.95.8494.01 3 0.0863 0.76563 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.69.7979.01 5 0.3199 0.84649 0.00 0.14 0.00 0.00 0.80 0.00 0.06
#> TCGA.62.A46P.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 4 0.5223 0.37231 0.10 0.00 0.00 0.52 0.00 0.02 0.36
#> TCGA.69.7980.01 6 0.6468 -0.09798 0.00 0.00 0.12 0.00 0.14 0.42 0.32
#> TCGA.97.8547.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.3139 0.55577 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.97.8175.01 4 0.0000 0.71326 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.7109.01 5 0.2722 0.84241 0.00 0.12 0.00 0.00 0.84 0.00 0.04
#> TCGA.44.A47A.01 1 0.0504 0.91641 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.6147.01 6 0.5073 0.46377 0.00 0.00 0.16 0.30 0.00 0.54 0.00
#> TCGA.75.6211.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8090.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.0863 0.69178 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.91.6828.01 5 0.3244 0.82709 0.00 0.18 0.00 0.00 0.78 0.00 0.04
#> TCGA.05.4396.01 2 0.0504 0.95213 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.MN.A4N4.01 5 0.3617 0.83180 0.00 0.16 0.00 0.00 0.76 0.00 0.08
#> TCGA.64.5781.01 3 0.0000 0.76957 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 5 0.3617 0.83422 0.00 0.16 0.00 0.00 0.76 0.00 0.08
#> TCGA.78.7154.01 6 0.4708 0.26573 0.00 0.00 0.26 0.02 0.00 0.64 0.08
#> TCGA.78.8662.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4427.01 2 0.0000 0.96378 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7143.01 4 0.2259 0.55932 0.00 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.97.A4M3.01 6 0.5731 -0.09210 0.00 0.00 0.04 0.00 0.14 0.50 0.32
#> TCGA.75.6205.01 4 0.1433 0.71301 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.55.7903.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 6 0.4939 0.46616 0.00 0.00 0.14 0.30 0.00 0.56 0.00
#> TCGA.78.7147.01 5 0.3867 0.82754 0.00 0.14 0.00 0.00 0.74 0.00 0.12
#> TCGA.75.5126.01 1 0.3047 0.57789 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.1718 0.90137 0.00 0.92 0.00 0.00 0.04 0.00 0.04
#> TCGA.NJ.A4YQ.01 3 0.2708 0.64394 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.NJ.A7XG.01 1 0.1006 0.90166 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.55.A48X.01 4 0.2906 0.62194 0.00 0.00 0.00 0.80 0.00 0.02 0.18
#> TCGA.50.6594.01 6 0.4487 -0.12816 0.00 0.00 0.00 0.00 0.08 0.60 0.32
#> TCGA.86.8056.01 7 0.4902 0.65473 0.00 0.00 0.00 0.12 0.00 0.34 0.54
#> TCGA.95.A4VK.01 5 0.5504 0.42646 0.00 0.00 0.04 0.00 0.58 0.16 0.22
#> TCGA.49.4488.01 2 0.1006 0.94567 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.55.7994.01 2 0.1006 0.94567 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.67.6215.01 4 0.3867 0.35344 0.38 0.00 0.00 0.60 0.00 0.00 0.02
#> TCGA.MP.A5C7.01 5 0.5304 0.45532 0.00 0.00 0.04 0.00 0.60 0.12 0.24
#> TCGA.55.7227.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 4 0.0000 0.71326 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.35.5375.01 5 0.1886 0.78254 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.38.4632.01 3 0.0863 0.76563 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.MP.A4T6.01 6 0.4264 -0.30386 0.00 0.00 0.00 0.06 0.00 0.62 0.32
#> TCGA.44.6779.01 3 0.1671 0.74751 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.86.A4P7.01 1 0.3985 0.07813 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.49.6761.01 6 0.5429 0.42741 0.00 0.00 0.10 0.32 0.00 0.54 0.04
#> TCGA.50.5935.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6981.01 3 0.2278 0.73796 0.00 0.00 0.88 0.00 0.08 0.04 0.00
#> TCGA.78.8655.01 1 0.1928 0.84606 0.90 0.00 0.00 0.08 0.00 0.00 0.02
#> TCGA.55.7914.01 1 0.3985 0.07813 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.62.A472.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4417.01 3 0.1671 0.73863 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.67.4679.01 7 0.4848 0.15143 0.00 0.00 0.00 0.40 0.00 0.10 0.50
#> TCGA.97.7554.01 3 0.0504 0.76923 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.MP.A4SY.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.8039.01 3 0.1166 0.75649 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.95.7562.01 5 0.3835 0.82718 0.00 0.16 0.00 0.00 0.74 0.00 0.10
#> TCGA.55.7576.01 6 0.5989 0.13239 0.00 0.00 0.08 0.18 0.00 0.54 0.20
#> TCGA.80.5607.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.8067.01 4 0.3745 0.54557 0.26 0.00 0.00 0.70 0.00 0.00 0.04
#> TCGA.62.8395.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 3 0.1671 0.74751 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.44.2666.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6777.01 6 0.4939 0.46616 0.00 0.00 0.14 0.30 0.00 0.56 0.00
#> TCGA.55.6983.01 4 0.4908 0.50473 0.10 0.00 0.00 0.62 0.00 0.02 0.26
#> TCGA.69.A59K.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 4 0.2422 0.64485 0.18 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.49.AARN.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.01 3 0.4963 0.41915 0.00 0.00 0.64 0.00 0.02 0.16 0.18
#> TCGA.91.6836.01 4 0.2259 0.55932 0.00 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.55.8616.01 5 0.3617 0.83180 0.00 0.16 0.00 0.00 0.76 0.00 0.08
#> TCGA.38.7271.01 1 0.3994 -0.00101 0.50 0.00 0.00 0.48 0.00 0.00 0.02
#> TCGA.55.A491.01 6 0.3566 -0.05260 0.00 0.00 0.00 0.02 0.04 0.78 0.16
#> TCGA.55.6978.01 3 0.3358 0.45262 0.00 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.NJ.A4YG.01 1 0.0504 0.91641 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.A48Y.01 3 0.1671 0.74751 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.1006 0.94567 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.73.4658.01 4 0.0504 0.70543 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.44.7659.01 1 0.0000 0.92896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.2278 0.76874 0.00 0.00 0.04 0.00 0.88 0.00 0.08
#> TCGA.86.A456.01 1 0.0863 0.89796 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.97.A4M7.01 6 0.5312 0.31292 0.00 0.00 0.22 0.08 0.00 0.62 0.08
#> TCGA.44.7662.01 3 0.2081 0.71208 0.00 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.55.8506.01 5 0.3617 0.83180 0.00 0.16 0.00 0.00 0.76 0.00 0.08
#> TCGA.71.8520.01 4 0.0504 0.70543 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.55.7815.01 3 0.2259 0.69406 0.00 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.44.7672.01 6 0.4998 0.45944 0.00 0.00 0.14 0.32 0.00 0.54 0.00
#> TCGA.97.8172.01 4 0.3052 0.60505 0.00 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.05.5715.01 1 0.1363 0.88833 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.78.7152.01 7 0.5776 0.42095 0.00 0.00 0.10 0.06 0.00 0.38 0.46
#> TCGA.78.7539.01 5 0.3670 0.84503 0.00 0.10 0.00 0.00 0.76 0.00 0.14
#> TCGA.62.A46S.01 5 0.2016 0.76550 0.00 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.78.7145.01 5 0.3835 0.82718 0.00 0.16 0.00 0.00 0.74 0.00 0.10
#> TCGA.55.8302.01 6 0.4939 0.46616 0.00 0.00 0.14 0.30 0.00 0.56 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.44.4112.01 7 0.2623 0.563 0.00 0.00 0.00 0.06 0.00 0.10 0.84 0.00
#> TCGA.NJ.A4YP.01 7 0.4775 0.511 0.00 0.00 0.02 0.06 0.00 0.30 0.60 0.02
#> TCGA.86.8278.01 4 0.5880 0.222 0.00 0.00 0.00 0.44 0.00 0.06 0.26 0.24
#> TCGA.49.AARQ.01 4 0.0471 0.659 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.50.6597.01 4 0.3293 0.473 0.00 0.00 0.00 0.74 0.00 0.22 0.00 0.04
#> TCGA.62.A46U.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T8.01 5 0.2071 0.821 0.00 0.04 0.04 0.00 0.90 0.00 0.00 0.02
#> TCGA.93.A4JN.01 1 0.5366 0.422 0.52 0.00 0.00 0.34 0.00 0.04 0.02 0.08
#> TCGA.86.6851.01 5 0.3369 0.828 0.00 0.04 0.02 0.00 0.82 0.08 0.04 0.00
#> TCGA.J2.A4AG.01 6 0.5257 0.431 0.00 0.00 0.22 0.06 0.00 0.58 0.14 0.00
#> TCGA.MP.A4TK.01 3 0.3714 0.385 0.00 0.00 0.54 0.00 0.00 0.44 0.00 0.02
#> TCGA.L9.A443.01 4 0.5470 0.485 0.18 0.00 0.00 0.60 0.00 0.06 0.02 0.14
#> TCGA.MN.A4N5.01 4 0.2591 0.656 0.08 0.00 0.00 0.86 0.00 0.02 0.00 0.04
#> TCGA.64.5775.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8394.01 5 0.3894 0.778 0.00 0.00 0.00 0.00 0.76 0.10 0.08 0.06
#> TCGA.05.4405.01 1 0.3319 0.805 0.82 0.00 0.00 0.08 0.00 0.02 0.02 0.06
#> TCGA.05.5428.01 2 0.4380 0.328 0.00 0.58 0.00 0.00 0.32 0.10 0.00 0.00
#> TCGA.MN.A4N1.01 6 0.3729 -0.282 0.00 0.00 0.46 0.00 0.00 0.52 0.00 0.02
#> TCGA.91.6847.01 7 0.3078 0.563 0.00 0.00 0.00 0.06 0.00 0.10 0.82 0.02
#> TCGA.MP.A4TC.01 6 0.3943 0.681 0.00 0.00 0.04 0.40 0.00 0.56 0.00 0.00
#> TCGA.05.4410.01 3 0.3374 0.621 0.00 0.00 0.68 0.00 0.00 0.30 0.00 0.02
#> TCGA.62.A46Y.01 4 0.3319 0.636 0.08 0.00 0.00 0.82 0.00 0.02 0.02 0.06
#> TCGA.55.6982.01 6 0.4459 0.647 0.00 0.00 0.02 0.28 0.00 0.64 0.04 0.02
#> TCGA.55.6642.01 5 0.2348 0.814 0.00 0.04 0.06 0.00 0.88 0.00 0.00 0.02
#> TCGA.50.6673.01 5 0.5775 0.396 0.00 0.00 0.08 0.00 0.52 0.06 0.04 0.30
#> TCGA.55.8207.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.6562.01 5 0.3941 0.818 0.00 0.04 0.02 0.00 0.76 0.14 0.04 0.00
#> TCGA.05.4425.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8074.01 5 0.4543 0.784 0.00 0.04 0.00 0.00 0.70 0.18 0.04 0.04
#> TCGA.55.7727.01 7 0.4704 0.516 0.00 0.00 0.04 0.06 0.00 0.32 0.58 0.00
#> TCGA.MP.A4SW.01 3 0.0000 0.747 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.6216.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8203.01 5 0.2025 0.793 0.00 0.00 0.10 0.00 0.88 0.00 0.00 0.02
#> TCGA.J2.8194.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2668.01 4 0.1557 0.661 0.06 0.00 0.00 0.92 0.00 0.00 0.00 0.02
#> TCGA.55.A57B.01 3 0.3131 0.609 0.00 0.00 0.84 0.00 0.04 0.02 0.04 0.06
#> TCGA.NJ.A4YI.01 7 0.4642 0.517 0.00 0.00 0.04 0.06 0.00 0.30 0.60 0.00
#> TCGA.L9.A444.01 3 0.2224 0.751 0.00 0.00 0.86 0.00 0.00 0.12 0.00 0.02
#> TCGA.86.8668.01 7 0.5703 0.364 0.00 0.00 0.00 0.20 0.00 0.08 0.52 0.20
#> TCGA.44.A47G.01 6 0.3862 0.709 0.00 0.00 0.04 0.36 0.00 0.60 0.00 0.00
#> TCGA.55.6986.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2665.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5425.01 5 0.1607 0.825 0.00 0.04 0.04 0.00 0.92 0.00 0.00 0.00
#> TCGA.62.A46R.01 3 0.1557 0.738 0.00 0.00 0.92 0.00 0.02 0.06 0.00 0.00
#> TCGA.55.A494.01 5 0.5405 0.307 0.00 0.00 0.00 0.00 0.46 0.10 0.06 0.38
#> TCGA.44.3917.01 5 0.2348 0.821 0.00 0.06 0.02 0.00 0.88 0.04 0.00 0.00
#> TCGA.75.5125.01 3 0.0941 0.725 0.00 0.00 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.L4.A4E5.01 5 0.4543 0.784 0.00 0.04 0.00 0.00 0.70 0.18 0.04 0.04
#> TCGA.44.6775.01 4 0.3095 0.379 0.00 0.00 0.00 0.74 0.00 0.24 0.00 0.02
#> TCGA.55.7911.01 6 0.3862 0.705 0.00 0.00 0.04 0.36 0.00 0.60 0.00 0.00
#> TCGA.55.6712.01 3 0.1341 0.758 0.00 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.69.7760.01 4 0.4921 0.283 0.00 0.00 0.00 0.52 0.00 0.22 0.00 0.26
#> TCGA.95.7948.01 4 0.7204 0.200 0.14 0.00 0.00 0.30 0.00 0.06 0.26 0.24
#> TCGA.55.A4DG.01 5 0.3913 0.802 0.00 0.00 0.06 0.00 0.74 0.16 0.04 0.00
#> TCGA.55.6985.01 4 0.2114 0.537 0.00 0.00 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.MP.A4TF.01 8 0.5599 0.667 0.00 0.00 0.08 0.00 0.04 0.04 0.32 0.52
#> TCGA.91.6829.01 5 0.4389 0.801 0.00 0.04 0.00 0.00 0.74 0.10 0.08 0.04
#> TCGA.99.7458.01 1 0.2482 0.837 0.88 0.00 0.00 0.02 0.00 0.02 0.02 0.06
#> TCGA.38.6178.01 4 0.1341 0.619 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.44.A47B.01 7 0.3154 0.585 0.00 0.00 0.00 0.06 0.00 0.16 0.78 0.00
#> TCGA.78.7542.01 2 0.1804 0.880 0.00 0.90 0.00 0.00 0.08 0.02 0.00 0.00
#> TCGA.05.5429.01 3 0.3907 0.496 0.00 0.00 0.58 0.00 0.00 0.38 0.00 0.04
#> TCGA.97.8179.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4JF.01 6 0.4642 0.354 0.00 0.00 0.30 0.06 0.00 0.60 0.04 0.00
#> TCGA.55.8092.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0471 0.936 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.75.5122.01 6 0.3746 0.716 0.00 0.00 0.04 0.32 0.00 0.64 0.00 0.00
#> TCGA.49.AARE.01 8 0.4294 0.557 0.00 0.00 0.22 0.00 0.06 0.04 0.00 0.68
#> TCGA.95.7043.01 5 0.1741 0.825 0.00 0.04 0.00 0.00 0.92 0.00 0.02 0.02
#> TCGA.86.7701.01 3 0.1804 0.759 0.00 0.00 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.55.7281.01 3 0.3402 0.587 0.00 0.00 0.82 0.00 0.04 0.02 0.06 0.06
#> TCGA.78.7535.01 6 0.4399 0.598 0.00 0.00 0.04 0.44 0.00 0.50 0.00 0.02
#> TCGA.50.6592.01 6 0.4559 0.606 0.00 0.00 0.00 0.30 0.00 0.60 0.08 0.02
#> TCGA.44.7661.01 7 0.4642 0.532 0.00 0.00 0.04 0.06 0.00 0.30 0.60 0.00
#> TCGA.97.A4M0.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 3 0.1341 0.758 0.00 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.78.7153.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 3 0.3299 0.414 0.00 0.00 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.55.7907.01 3 0.0808 0.747 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.49.6767.01 5 0.2407 0.815 0.00 0.00 0.08 0.00 0.86 0.06 0.00 0.00
#> TCGA.50.5051.01 5 0.2071 0.821 0.00 0.04 0.04 0.00 0.90 0.00 0.00 0.02
#> TCGA.78.7540.01 3 0.3943 0.459 0.00 0.00 0.56 0.00 0.00 0.40 0.00 0.04
#> TCGA.95.A4VN.01 3 0.3237 0.482 0.00 0.00 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.44.A47F.01 4 0.7204 0.200 0.14 0.00 0.00 0.30 0.00 0.06 0.26 0.24
#> TCGA.69.8253.01 7 0.5363 0.413 0.00 0.00 0.00 0.14 0.00 0.08 0.58 0.20
#> TCGA.J2.A4AE.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 6 0.3971 0.655 0.00 0.00 0.04 0.42 0.00 0.54 0.00 0.00
#> TCGA.80.5608.01 5 0.2348 0.814 0.00 0.04 0.06 0.00 0.88 0.00 0.00 0.02
#> TCGA.55.8205.01 3 0.0471 0.739 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.99.8025.01 3 0.1804 0.754 0.00 0.00 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.55.7283.01 1 0.1408 0.855 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.78.7159.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8120.01 5 0.2348 0.826 0.00 0.04 0.02 0.00 0.88 0.06 0.00 0.00
#> TCGA.69.7763.01 1 0.5366 0.422 0.52 0.00 0.00 0.34 0.00 0.04 0.02 0.08
#> TCGA.64.5815.01 1 0.2807 0.828 0.86 0.00 0.00 0.04 0.00 0.02 0.02 0.06
#> TCGA.69.7761.01 3 0.3618 0.506 0.00 0.00 0.60 0.00 0.00 0.38 0.00 0.02
#> TCGA.73.A9RS.01 5 0.2859 0.767 0.00 0.00 0.02 0.00 0.82 0.00 0.02 0.14
#> TCGA.69.7978.01 3 0.3737 0.265 0.00 0.00 0.50 0.00 0.00 0.48 0.00 0.02
#> TCGA.44.8117.01 6 0.5386 0.534 0.00 0.00 0.22 0.28 0.00 0.48 0.00 0.02
#> TCGA.MP.A4TD.01 3 0.3658 0.472 0.00 0.00 0.58 0.00 0.00 0.40 0.00 0.02
#> TCGA.83.5908.01 6 0.3971 0.655 0.00 0.00 0.04 0.42 0.00 0.54 0.00 0.00
#> TCGA.95.7039.01 2 0.1341 0.904 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.71.6725.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.7771.01 4 0.3036 0.574 0.00 0.00 0.00 0.78 0.00 0.18 0.00 0.04
#> TCGA.86.8359.01 5 0.2071 0.821 0.00 0.04 0.04 0.00 0.90 0.00 0.00 0.02
#> TCGA.55.8301.01 6 0.5257 0.432 0.00 0.00 0.22 0.06 0.00 0.58 0.14 0.00
#> TCGA.78.7146.01 8 0.4834 0.607 0.00 0.00 0.00 0.00 0.04 0.06 0.38 0.52
#> TCGA.44.3918.01 3 0.1765 0.755 0.00 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.69.7974.01 1 0.1408 0.855 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.78.7161.01 5 0.1804 0.815 0.00 0.08 0.00 0.00 0.90 0.00 0.00 0.02
#> TCGA.97.7937.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 3 0.0941 0.749 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.55.7574.01 4 0.1341 0.619 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.44.5644.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8511.01 3 0.3449 0.616 0.00 0.00 0.66 0.00 0.00 0.32 0.00 0.02
#> TCGA.91.A4BC.01 3 0.0941 0.749 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.44.2656.01 3 0.3737 0.337 0.00 0.00 0.50 0.00 0.00 0.48 0.00 0.02
#> TCGA.86.8673.01 4 0.1341 0.659 0.08 0.00 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 8 0.5569 0.702 0.00 0.00 0.02 0.00 0.04 0.22 0.16 0.56
#> TCGA.L9.A7SV.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4390.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7765.01 4 0.3319 0.636 0.08 0.00 0.00 0.82 0.00 0.02 0.02 0.06
#> TCGA.95.8494.01 3 0.2224 0.751 0.00 0.00 0.86 0.00 0.00 0.12 0.00 0.02
#> TCGA.69.7979.01 5 0.1887 0.827 0.00 0.04 0.00 0.00 0.90 0.06 0.00 0.00
#> TCGA.62.A46P.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 4 0.7204 0.200 0.14 0.00 0.00 0.30 0.00 0.06 0.26 0.24
#> TCGA.69.7980.01 8 0.4667 0.709 0.00 0.00 0.04 0.00 0.04 0.04 0.20 0.68
#> TCGA.97.8547.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.3907 0.496 0.00 0.00 0.58 0.00 0.00 0.38 0.00 0.04
#> TCGA.97.8175.01 4 0.0941 0.651 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.50.7109.01 5 0.2071 0.821 0.00 0.04 0.04 0.00 0.90 0.00 0.00 0.02
#> TCGA.44.A47A.01 1 0.1804 0.845 0.90 0.00 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.44.6147.01 6 0.4059 0.699 0.00 0.00 0.08 0.28 0.00 0.64 0.00 0.00
#> TCGA.75.6211.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8090.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.1563 0.600 0.00 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.91.6828.01 5 0.2132 0.815 0.00 0.08 0.00 0.00 0.88 0.04 0.00 0.00
#> TCGA.05.4396.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 5 0.3770 0.822 0.00 0.04 0.02 0.00 0.78 0.12 0.04 0.00
#> TCGA.64.5781.01 3 0.1091 0.760 0.00 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.NJ.A4YF.01 5 0.3897 0.811 0.00 0.04 0.00 0.00 0.78 0.10 0.04 0.04
#> TCGA.78.7154.01 6 0.5469 0.266 0.00 0.00 0.16 0.00 0.00 0.54 0.06 0.24
#> TCGA.78.8662.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4427.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7143.01 4 0.2856 0.464 0.00 0.00 0.00 0.78 0.00 0.20 0.00 0.02
#> TCGA.97.A4M3.01 8 0.5077 0.721 0.00 0.00 0.02 0.00 0.04 0.18 0.12 0.64
#> TCGA.75.6205.01 4 0.3319 0.636 0.08 0.00 0.00 0.82 0.00 0.02 0.02 0.06
#> TCGA.55.7903.01 1 0.1408 0.855 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.55.A493.01 6 0.3746 0.716 0.00 0.00 0.04 0.32 0.00 0.64 0.00 0.00
#> TCGA.78.7147.01 5 0.4389 0.801 0.00 0.04 0.00 0.00 0.74 0.10 0.08 0.04
#> TCGA.75.5126.01 1 0.4704 0.581 0.62 0.00 0.00 0.28 0.00 0.02 0.02 0.06
#> TCGA.MP.A4TE.01 2 0.2114 0.805 0.00 0.84 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 3 0.3015 0.593 0.00 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.NJ.A7XG.01 1 0.3871 0.780 0.78 0.00 0.00 0.08 0.00 0.04 0.02 0.08
#> TCGA.55.A48X.01 4 0.5385 0.400 0.00 0.00 0.00 0.56 0.00 0.06 0.16 0.22
#> TCGA.50.6594.01 8 0.5682 0.642 0.00 0.00 0.00 0.02 0.04 0.22 0.18 0.54
#> TCGA.86.8056.01 7 0.4503 0.523 0.00 0.00 0.00 0.10 0.00 0.08 0.70 0.12
#> TCGA.95.A4VK.01 5 0.5128 0.260 0.00 0.00 0.08 0.00 0.52 0.02 0.02 0.36
#> TCGA.49.4488.01 2 0.1341 0.904 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.55.7994.01 2 0.1341 0.904 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.67.6215.01 1 0.5456 0.205 0.44 0.00 0.00 0.42 0.00 0.04 0.02 0.08
#> TCGA.MP.A5C7.01 5 0.5353 0.260 0.00 0.00 0.06 0.00 0.54 0.02 0.06 0.32
#> TCGA.55.7227.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 4 0.1275 0.654 0.00 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.35.5375.01 5 0.4079 0.745 0.00 0.00 0.00 0.00 0.74 0.08 0.06 0.12
#> TCGA.38.4632.01 3 0.2224 0.751 0.00 0.00 0.86 0.00 0.00 0.12 0.00 0.02
#> TCGA.MP.A4T6.01 7 0.5635 -0.164 0.00 0.00 0.00 0.02 0.00 0.30 0.36 0.32
#> TCGA.44.6779.01 3 0.0941 0.725 0.00 0.00 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.86.A4P7.01 1 0.5088 0.452 0.54 0.00 0.00 0.34 0.00 0.02 0.02 0.08
#> TCGA.49.6761.01 6 0.3658 0.671 0.00 0.00 0.02 0.40 0.00 0.58 0.00 0.00
#> TCGA.50.5935.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6981.01 3 0.2071 0.677 0.00 0.00 0.90 0.00 0.04 0.00 0.02 0.04
#> TCGA.78.8655.01 1 0.4645 0.649 0.66 0.00 0.00 0.22 0.00 0.02 0.02 0.08
#> TCGA.55.7914.01 1 0.5366 0.422 0.52 0.00 0.00 0.34 0.00 0.04 0.02 0.08
#> TCGA.62.A472.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4417.01 3 0.3504 0.640 0.00 0.00 0.70 0.00 0.00 0.26 0.00 0.04
#> TCGA.67.4679.01 7 0.5363 0.413 0.00 0.00 0.00 0.14 0.00 0.08 0.58 0.20
#> TCGA.97.7554.01 3 0.2025 0.755 0.00 0.00 0.88 0.00 0.00 0.10 0.00 0.02
#> TCGA.MP.A4SY.01 1 0.2020 0.845 0.90 0.00 0.00 0.00 0.00 0.02 0.02 0.06
#> TCGA.95.8039.01 3 0.2864 0.725 0.00 0.00 0.84 0.00 0.00 0.08 0.02 0.06
#> TCGA.95.7562.01 5 0.4355 0.795 0.00 0.04 0.00 0.00 0.72 0.16 0.06 0.02
#> TCGA.55.7576.01 7 0.4380 0.511 0.00 0.00 0.00 0.10 0.00 0.32 0.58 0.00
#> TCGA.80.5607.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.8067.01 4 0.5009 0.493 0.20 0.00 0.00 0.62 0.00 0.06 0.00 0.12
#> TCGA.62.8395.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 3 0.0471 0.739 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.2666.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6777.01 6 0.4106 0.705 0.00 0.00 0.04 0.30 0.00 0.64 0.02 0.00
#> TCGA.55.6983.01 4 0.7053 0.264 0.12 0.00 0.00 0.36 0.00 0.06 0.24 0.22
#> TCGA.69.A59K.01 1 0.2807 0.828 0.86 0.00 0.00 0.04 0.00 0.02 0.02 0.06
#> TCGA.95.7567.01 4 0.3928 0.567 0.18 0.00 0.00 0.74 0.00 0.02 0.02 0.04
#> TCGA.49.AARN.01 1 0.0471 0.862 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.73.4676.01 7 0.3922 0.149 0.00 0.00 0.30 0.00 0.00 0.06 0.64 0.00
#> TCGA.91.6836.01 4 0.2406 0.476 0.00 0.00 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.55.8616.01 5 0.4096 0.813 0.00 0.04 0.02 0.00 0.74 0.16 0.04 0.00
#> TCGA.38.7271.01 1 0.5366 0.422 0.52 0.00 0.00 0.34 0.00 0.04 0.02 0.08
#> TCGA.55.A491.01 6 0.5591 -0.357 0.00 0.00 0.02 0.02 0.00 0.42 0.14 0.40
#> TCGA.55.6978.01 3 0.3272 0.443 0.00 0.00 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.NJ.A4YG.01 1 0.3319 0.808 0.82 0.00 0.00 0.06 0.00 0.02 0.02 0.08
#> TCGA.55.A48Y.01 3 0.1275 0.707 0.00 0.00 0.94 0.00 0.04 0.00 0.00 0.02
#> TCGA.MP.A4SV.01 2 0.1804 0.880 0.00 0.90 0.00 0.00 0.08 0.02 0.00 0.00
#> TCGA.73.4658.01 4 0.0808 0.640 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.44.7659.01 1 0.0000 0.865 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.4446 0.753 0.00 0.00 0.08 0.00 0.74 0.08 0.04 0.06
#> TCGA.86.A456.01 1 0.3720 0.773 0.78 0.00 0.00 0.12 0.00 0.02 0.02 0.06
#> TCGA.97.A4M7.01 6 0.5406 0.397 0.00 0.00 0.20 0.06 0.00 0.56 0.18 0.00
#> TCGA.44.7662.01 3 0.1275 0.707 0.00 0.00 0.94 0.00 0.04 0.00 0.00 0.02
#> TCGA.55.8506.01 5 0.4096 0.813 0.00 0.04 0.02 0.00 0.74 0.16 0.04 0.00
#> TCGA.71.8520.01 4 0.0808 0.640 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.55.7815.01 3 0.1804 0.674 0.00 0.00 0.90 0.00 0.08 0.00 0.00 0.02
#> TCGA.44.7672.01 6 0.3808 0.715 0.00 0.00 0.04 0.34 0.00 0.62 0.00 0.00
#> TCGA.97.8172.01 4 0.5406 0.391 0.00 0.00 0.00 0.56 0.00 0.06 0.18 0.20
#> TCGA.05.5715.01 1 0.4914 0.662 0.68 0.00 0.00 0.06 0.00 0.06 0.04 0.16
#> TCGA.78.7152.01 7 0.3431 0.576 0.00 0.00 0.00 0.06 0.00 0.20 0.74 0.00
#> TCGA.78.7539.01 5 0.3369 0.828 0.00 0.04 0.00 0.00 0.82 0.08 0.04 0.02
#> TCGA.62.A46S.01 5 0.2591 0.760 0.00 0.00 0.08 0.00 0.86 0.02 0.00 0.04
#> TCGA.78.7145.01 5 0.4543 0.784 0.00 0.04 0.00 0.00 0.70 0.18 0.04 0.04
#> TCGA.55.8302.01 6 0.3746 0.716 0.00 0.00 0.04 0.32 0.00 0.64 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122 , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221-leaf , Node0222 , Node0223-leaf , Node0231 , Node0232 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0324-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["021"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 68 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.996 0.998 0.4873 0.514 0.514
#> 3 3 1.000 0.986 0.994 0.3576 0.824 0.658
#> 4 4 0.799 0.877 0.888 0.0630 1.000 1.000
#> 5 5 0.751 0.533 0.750 0.0499 0.932 0.800
#> 6 6 0.729 0.557 0.748 0.0318 0.873 0.610
#> 7 7 0.728 0.518 0.724 0.0134 0.944 0.792
#> 8 8 0.684 0.481 0.723 0.0182 0.920 0.706
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.86.8278.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.AARQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.62.A46U.01 1 0.000 1.000 1.00 0.00
#> TCGA.93.A4JN.01 2 0.000 0.996 0.00 1.00
#> TCGA.L9.A443.01 1 0.000 1.000 1.00 0.00
#> TCGA.MN.A4N5.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.4405.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A46Y.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8207.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.4425.01 2 0.000 0.996 0.00 1.00
#> TCGA.67.6216.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.2668.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6986.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.2665.01 1 0.000 1.000 1.00 0.00
#> TCGA.95.7948.01 1 0.000 1.000 1.00 0.00
#> TCGA.99.7458.01 1 0.000 1.000 1.00 0.00
#> TCGA.38.6178.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.A4M0.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.7153.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.A47F.01 2 0.000 0.996 0.00 1.00
#> TCGA.J2.A4AE.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7283.01 2 0.000 0.996 0.00 1.00
#> TCGA.69.7763.01 2 0.000 0.996 0.00 1.00
#> TCGA.64.5815.01 2 0.000 0.996 0.00 1.00
#> TCGA.91.7771.01 2 0.000 0.996 0.00 1.00
#> TCGA.69.7974.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A46V.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.6745.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.7574.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.8673.01 2 0.000 0.996 0.00 1.00
#> TCGA.69.7765.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A46P.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7158.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8547.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8175.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.A47A.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8090.01 2 0.000 0.996 0.00 1.00
#> TCGA.75.6205.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.7903.01 2 0.000 0.996 0.00 1.00
#> TCGA.75.5126.01 1 0.000 1.000 1.00 0.00
#> TCGA.NJ.A7XG.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.A48X.01 1 0.000 1.000 1.00 0.00
#> TCGA.67.6215.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7227.01 2 0.000 0.996 0.00 1.00
#> TCGA.MP.A4TI.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.A4P7.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5935.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.8655.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7914.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A472.01 2 0.000 0.996 0.00 1.00
#> TCGA.67.4679.01 2 0.000 0.996 0.00 1.00
#> TCGA.MP.A4SY.01 2 0.000 0.996 0.00 1.00
#> TCGA.80.5607.01 1 0.000 1.000 1.00 0.00
#> TCGA.93.8067.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.8395.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.2666.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6983.01 2 0.000 0.996 0.00 1.00
#> TCGA.69.A59K.01 2 0.000 0.996 0.00 1.00
#> TCGA.95.7567.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.AARN.01 2 0.000 0.996 0.00 1.00
#> TCGA.38.7271.01 2 0.584 0.837 0.14 0.86
#> TCGA.NJ.A4YG.01 2 0.000 0.996 0.00 1.00
#> TCGA.73.4658.01 2 0.000 0.996 0.00 1.00
#> TCGA.44.7659.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.A456.01 2 0.000 0.996 0.00 1.00
#> TCGA.71.8520.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8172.01 1 0.000 1.000 1.00 0.00
#> TCGA.05.5715.01 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.86.8278.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.49.AARQ.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.62.A46U.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.93.A4JN.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.L9.A443.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.MN.A4N5.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.05.4405.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.62.A46Y.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.55.8207.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.05.4425.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.67.6216.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.44.2668.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.55.6986.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.44.2665.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.95.7948.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.99.7458.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.38.6178.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.97.A4M0.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.78.7153.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.44.A47F.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.J2.A4AE.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.55.7283.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.69.7763.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.64.5815.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.91.7771.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.69.7974.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.62.A46V.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.49.6745.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.55.7574.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.86.8673.01 2 0.400 0.806 0.00 0.84 0.16
#> TCGA.69.7765.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.62.A46P.01 3 0.455 0.746 0.00 0.20 0.80
#> TCGA.78.7158.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.97.8547.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.97.8175.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.44.A47A.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.55.8090.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.75.6205.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.55.7903.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.75.5126.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.NJ.A7XG.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.55.A48X.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.67.6215.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.55.7227.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.MP.A4TI.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.86.A4P7.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.50.5935.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.78.8655.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.55.7914.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.62.A472.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.67.4679.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.MP.A4SY.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.80.5607.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.93.8067.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.62.8395.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.44.2666.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.55.6983.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.69.A59K.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.95.7567.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.49.AARN.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.38.7271.01 2 0.207 0.925 0.06 0.94 0.00
#> TCGA.NJ.A4YG.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.73.4658.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.44.7659.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.86.A456.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.71.8520.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.97.8172.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.05.5715.01 1 0.000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.86.8278.01 4 0.0707 0.903 0.02 0.00 0.00 0.98
#> TCGA.49.AARQ.01 4 0.2647 0.882 0.12 0.00 0.00 0.88
#> TCGA.62.A46U.01 4 0.2647 0.884 0.12 0.00 0.00 0.88
#> TCGA.93.A4JN.01 3 0.4713 0.810 0.36 0.00 0.64 0.00
#> TCGA.L9.A443.01 4 0.2345 0.897 0.10 0.00 0.00 0.90
#> TCGA.MN.A4N5.01 3 0.2647 0.868 0.12 0.00 0.88 0.00
#> TCGA.05.4405.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.62.A46Y.01 4 0.2647 0.884 0.12 0.00 0.00 0.88
#> TCGA.55.8207.01 3 0.3853 0.860 0.16 0.02 0.82 0.00
#> TCGA.05.4425.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.67.6216.01 4 0.2921 0.876 0.14 0.00 0.00 0.86
#> TCGA.44.2668.01 3 0.4079 0.852 0.18 0.02 0.80 0.00
#> TCGA.55.6986.01 4 0.1211 0.903 0.04 0.00 0.00 0.96
#> TCGA.44.2665.01 4 0.2921 0.876 0.14 0.00 0.00 0.86
#> TCGA.95.7948.01 4 0.2921 0.876 0.14 0.00 0.00 0.86
#> TCGA.99.7458.01 4 0.2921 0.877 0.14 0.00 0.00 0.86
#> TCGA.38.6178.01 4 0.3610 0.874 0.20 0.00 0.00 0.80
#> TCGA.97.A4M0.01 4 0.3606 0.868 0.14 0.02 0.00 0.84
#> TCGA.78.7153.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.44.A47F.01 3 0.4994 0.770 0.48 0.00 0.52 0.00
#> TCGA.J2.A4AE.01 4 0.2345 0.891 0.10 0.00 0.00 0.90
#> TCGA.55.7283.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.69.7763.01 3 0.1211 0.871 0.04 0.00 0.96 0.00
#> TCGA.64.5815.01 3 0.1211 0.868 0.04 0.00 0.96 0.00
#> TCGA.91.7771.01 3 0.4977 0.779 0.46 0.00 0.54 0.00
#> TCGA.69.7974.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.55.7574.01 4 0.2011 0.895 0.08 0.00 0.00 0.92
#> TCGA.86.8673.01 2 0.5487 0.266 0.02 0.58 0.40 0.00
#> TCGA.69.7765.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.62.A46P.01 3 0.4755 0.705 0.04 0.20 0.76 0.00
#> TCGA.78.7158.01 4 0.2921 0.877 0.14 0.00 0.00 0.86
#> TCGA.97.8547.01 4 0.1637 0.904 0.06 0.00 0.00 0.94
#> TCGA.97.8175.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.44.A47A.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.55.8090.01 2 0.0707 0.940 0.00 0.98 0.02 0.00
#> TCGA.75.6205.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.75.5126.01 4 0.1211 0.901 0.04 0.00 0.00 0.96
#> TCGA.NJ.A7XG.01 3 0.4994 0.770 0.48 0.00 0.52 0.00
#> TCGA.55.A48X.01 4 0.2011 0.894 0.08 0.00 0.00 0.92
#> TCGA.67.6215.01 4 0.2921 0.876 0.14 0.00 0.00 0.86
#> TCGA.55.7227.01 2 0.2647 0.840 0.00 0.88 0.12 0.00
#> TCGA.MP.A4TI.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.86.A4P7.01 4 0.2345 0.890 0.10 0.00 0.00 0.90
#> TCGA.50.5935.01 4 0.2921 0.876 0.14 0.00 0.00 0.86
#> TCGA.78.8655.01 4 0.4277 0.782 0.28 0.00 0.00 0.72
#> TCGA.55.7914.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.62.A472.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.67.4679.01 3 0.2921 0.872 0.14 0.00 0.86 0.00
#> TCGA.MP.A4SY.01 3 0.3606 0.858 0.14 0.02 0.84 0.00
#> TCGA.80.5607.01 4 0.1211 0.901 0.04 0.00 0.00 0.96
#> TCGA.93.8067.01 3 0.1211 0.868 0.04 0.00 0.96 0.00
#> TCGA.62.8395.01 4 0.1637 0.905 0.06 0.00 0.00 0.94
#> TCGA.44.2666.01 3 0.2706 0.863 0.08 0.02 0.90 0.00
#> TCGA.55.6983.01 3 0.4624 0.819 0.34 0.00 0.66 0.00
#> TCGA.69.A59K.01 2 0.0707 0.940 0.02 0.98 0.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.3198 0.844 0.04 0.88 0.00 0.08
#> TCGA.38.7271.01 2 0.6049 0.587 0.12 0.68 0.00 0.20
#> TCGA.NJ.A4YG.01 3 0.0707 0.869 0.02 0.00 0.98 0.00
#> TCGA.73.4658.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.86.A456.01 2 0.0000 0.954 0.00 1.00 0.00 0.00
#> TCGA.71.8520.01 4 0.4277 0.782 0.28 0.00 0.00 0.72
#> TCGA.97.8172.01 4 0.2345 0.898 0.10 0.00 0.00 0.90
#> TCGA.05.5715.01 4 0.2921 0.876 0.14 0.00 0.00 0.86
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.86.8278.01 4 0.2873 0.5947 0.02 0.00 0.00 0.86 0.12
#> TCGA.49.AARQ.01 4 0.2020 0.5728 0.00 0.00 0.00 0.90 0.10
#> TCGA.62.A46U.01 5 0.4307 0.3208 0.00 0.00 0.00 0.50 0.50
#> TCGA.93.A4JN.01 3 0.6619 0.2892 0.36 0.00 0.42 0.00 0.22
#> TCGA.L9.A443.01 4 0.3274 0.5469 0.00 0.00 0.00 0.78 0.22
#> TCGA.MN.A4N5.01 3 0.4433 0.4194 0.20 0.00 0.74 0.00 0.06
#> TCGA.05.4405.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46Y.01 5 0.4307 0.3059 0.00 0.00 0.00 0.50 0.50
#> TCGA.55.8207.01 3 0.5425 0.2019 0.42 0.00 0.52 0.00 0.06
#> TCGA.05.4425.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.6216.01 4 0.0609 0.5899 0.00 0.00 0.00 0.98 0.02
#> TCGA.44.2668.01 3 0.6149 0.3680 0.20 0.02 0.62 0.00 0.16
#> TCGA.55.6986.01 4 0.3513 0.5558 0.02 0.00 0.00 0.80 0.18
#> TCGA.44.2665.01 4 0.1043 0.5777 0.00 0.00 0.00 0.96 0.04
#> TCGA.95.7948.01 4 0.1043 0.5982 0.00 0.00 0.00 0.96 0.04
#> TCGA.99.7458.01 4 0.4302 -0.3614 0.00 0.00 0.00 0.52 0.48
#> TCGA.38.6178.01 4 0.4227 -0.1437 0.00 0.00 0.00 0.58 0.42
#> TCGA.97.A4M0.01 5 0.4990 0.6007 0.00 0.04 0.00 0.36 0.60
#> TCGA.78.7153.01 2 0.0609 0.9243 0.02 0.98 0.00 0.00 0.00
#> TCGA.44.A47F.01 3 0.3106 0.4404 0.14 0.00 0.84 0.00 0.02
#> TCGA.J2.A4AE.01 4 0.4287 -0.2972 0.00 0.00 0.00 0.54 0.46
#> TCGA.55.7283.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7763.01 3 0.4798 0.1852 0.44 0.00 0.54 0.00 0.02
#> TCGA.64.5815.01 3 0.5663 0.0830 0.42 0.04 0.52 0.00 0.02
#> TCGA.91.7771.01 3 0.3274 0.4451 0.22 0.00 0.78 0.00 0.00
#> TCGA.69.7974.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7574.01 4 0.3983 0.2637 0.00 0.00 0.00 0.66 0.34
#> TCGA.86.8673.01 2 0.5050 0.4604 0.18 0.70 0.12 0.00 0.00
#> TCGA.69.7765.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46P.01 1 0.7099 0.0763 0.42 0.34 0.22 0.00 0.02
#> TCGA.78.7158.01 5 0.4126 0.6033 0.00 0.00 0.00 0.38 0.62
#> TCGA.97.8547.01 4 0.4126 0.0952 0.00 0.00 0.00 0.62 0.38
#> TCGA.97.8175.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A47A.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8090.01 2 0.1410 0.8907 0.06 0.94 0.00 0.00 0.00
#> TCGA.75.6205.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.5126.01 4 0.4360 0.3830 0.02 0.00 0.00 0.68 0.30
#> TCGA.NJ.A7XG.01 3 0.2516 0.4564 0.14 0.00 0.86 0.00 0.00
#> TCGA.55.A48X.01 4 0.2020 0.6022 0.00 0.00 0.00 0.90 0.10
#> TCGA.67.6215.01 4 0.1732 0.6046 0.00 0.00 0.00 0.92 0.08
#> TCGA.55.7227.01 2 0.1732 0.8655 0.08 0.92 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 4 0.4227 -0.0893 0.00 0.00 0.00 0.58 0.42
#> TCGA.50.5935.01 4 0.1732 0.5438 0.00 0.00 0.00 0.92 0.08
#> TCGA.78.8655.01 5 0.3852 0.5908 0.02 0.00 0.00 0.22 0.76
#> TCGA.55.7914.01 2 0.1216 0.9071 0.02 0.96 0.00 0.00 0.02
#> TCGA.62.A472.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.4679.01 3 0.4967 0.3661 0.28 0.00 0.66 0.00 0.06
#> TCGA.MP.A4SY.01 3 0.5447 0.1568 0.44 0.00 0.50 0.00 0.06
#> TCGA.80.5607.01 4 0.3106 0.5838 0.02 0.00 0.00 0.84 0.14
#> TCGA.93.8067.01 1 0.4818 -0.4951 0.52 0.00 0.46 0.00 0.02
#> TCGA.62.8395.01 4 0.3999 0.4820 0.02 0.00 0.00 0.74 0.24
#> TCGA.44.2666.01 3 0.5684 0.1264 0.44 0.02 0.50 0.00 0.04
#> TCGA.55.6983.01 3 0.0609 0.4722 0.02 0.00 0.98 0.00 0.00
#> TCGA.69.A59K.01 2 0.1043 0.9104 0.00 0.96 0.00 0.00 0.04
#> TCGA.95.7567.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.3694 0.7377 0.02 0.82 0.00 0.02 0.14
#> TCGA.38.7271.01 2 0.5925 0.1444 0.02 0.52 0.00 0.06 0.40
#> TCGA.NJ.A4YG.01 3 0.4126 0.2239 0.38 0.00 0.62 0.00 0.00
#> TCGA.73.4658.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.A456.01 2 0.0000 0.9373 0.00 1.00 0.00 0.00 0.00
#> TCGA.71.8520.01 5 0.3852 0.5908 0.02 0.00 0.00 0.22 0.76
#> TCGA.97.8172.01 4 0.3684 0.3941 0.00 0.00 0.00 0.72 0.28
#> TCGA.05.5715.01 4 0.1732 0.5438 0.00 0.00 0.00 0.92 0.08
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.86.8278.01 4 0.3819 0.2679 0.28 0.00 0.00 0.70 0.02 0.00
#> TCGA.49.AARQ.01 1 0.4534 0.6549 0.58 0.00 0.00 0.38 0.00 0.04
#> TCGA.62.A46U.01 4 0.2629 0.5426 0.08 0.00 0.00 0.88 0.02 0.02
#> TCGA.93.A4JN.01 6 0.5807 0.0000 0.02 0.00 0.22 0.02 0.12 0.62
#> TCGA.L9.A443.01 4 0.3819 0.2235 0.28 0.00 0.00 0.70 0.00 0.02
#> TCGA.MN.A4N5.01 3 0.5801 0.0524 0.00 0.00 0.50 0.00 0.26 0.24
#> TCGA.05.4405.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46Y.01 4 0.2094 0.5489 0.02 0.00 0.00 0.90 0.00 0.08
#> TCGA.55.8207.01 3 0.3697 0.4430 0.06 0.00 0.82 0.00 0.04 0.08
#> TCGA.05.4425.01 2 0.0547 0.9309 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.67.6216.01 1 0.4534 0.7762 0.58 0.00 0.00 0.38 0.00 0.04
#> TCGA.44.2668.01 3 0.7869 -0.1246 0.02 0.04 0.42 0.08 0.14 0.30
#> TCGA.55.6986.01 4 0.4105 0.3336 0.24 0.00 0.00 0.72 0.02 0.02
#> TCGA.44.2665.01 1 0.4482 0.7919 0.60 0.00 0.00 0.36 0.00 0.04
#> TCGA.95.7948.01 1 0.4246 0.7737 0.58 0.00 0.00 0.40 0.00 0.02
#> TCGA.99.7458.01 4 0.1807 0.5502 0.02 0.00 0.00 0.92 0.00 0.06
#> TCGA.38.6178.01 4 0.4094 0.4306 0.18 0.00 0.00 0.74 0.00 0.08
#> TCGA.97.A4M0.01 4 0.3045 0.5266 0.06 0.00 0.00 0.86 0.02 0.06
#> TCGA.78.7153.01 2 0.0547 0.9311 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.44.A47F.01 5 0.3460 0.5998 0.00 0.00 0.22 0.00 0.76 0.02
#> TCGA.J2.A4AE.01 4 0.2190 0.5419 0.04 0.00 0.00 0.90 0.00 0.06
#> TCGA.55.7283.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7763.01 3 0.4887 0.3654 0.00 0.02 0.70 0.00 0.12 0.16
#> TCGA.64.5815.01 3 0.4430 0.4433 0.00 0.08 0.76 0.00 0.04 0.12
#> TCGA.91.7771.01 5 0.4265 0.6245 0.00 0.00 0.30 0.00 0.66 0.04
#> TCGA.69.7974.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7574.01 4 0.2454 0.4770 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.86.8673.01 2 0.6013 -0.0847 0.02 0.48 0.40 0.00 0.02 0.08
#> TCGA.69.7765.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46P.01 3 0.6758 0.1638 0.06 0.32 0.50 0.00 0.08 0.04
#> TCGA.78.7158.01 4 0.3523 0.5037 0.04 0.00 0.00 0.78 0.00 0.18
#> TCGA.97.8547.01 4 0.3928 0.4553 0.16 0.00 0.00 0.76 0.00 0.08
#> TCGA.97.8175.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47A.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8090.01 2 0.1480 0.8989 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.75.6205.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.5126.01 4 0.4675 0.2752 0.28 0.00 0.00 0.66 0.04 0.02
#> TCGA.NJ.A7XG.01 5 0.4711 0.6662 0.00 0.00 0.28 0.00 0.64 0.08
#> TCGA.55.A48X.01 4 0.3851 -0.4428 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.67.6215.01 1 0.4892 0.6751 0.50 0.00 0.00 0.44 0.00 0.06
#> TCGA.55.7227.01 2 0.2882 0.8079 0.02 0.86 0.10 0.00 0.00 0.02
#> TCGA.MP.A4TI.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 4 0.2048 0.5101 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.50.5935.01 1 0.3309 0.7891 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.78.8655.01 4 0.4246 0.3767 0.02 0.00 0.00 0.58 0.00 0.40
#> TCGA.55.7914.01 2 0.0937 0.9171 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.62.A472.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.4679.01 3 0.7506 0.0994 0.10 0.02 0.42 0.00 0.20 0.26
#> TCGA.MP.A4SY.01 3 0.3324 0.4591 0.06 0.00 0.84 0.00 0.02 0.08
#> TCGA.80.5607.01 4 0.4574 0.2394 0.26 0.00 0.00 0.68 0.02 0.04
#> TCGA.93.8067.01 3 0.3111 0.4736 0.02 0.02 0.84 0.00 0.00 0.12
#> TCGA.62.8395.01 4 0.4834 0.0707 0.26 0.00 0.00 0.64 0.00 0.10
#> TCGA.44.2666.01 3 0.5160 0.4472 0.08 0.04 0.74 0.00 0.06 0.08
#> TCGA.55.6983.01 3 0.4892 -0.4278 0.00 0.00 0.50 0.00 0.44 0.06
#> TCGA.69.A59K.01 2 0.1635 0.9030 0.02 0.94 0.02 0.00 0.00 0.02
#> TCGA.95.7567.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.5603 0.4677 0.06 0.64 0.00 0.24 0.02 0.04
#> TCGA.38.7271.01 4 0.6084 0.0980 0.06 0.38 0.00 0.50 0.02 0.04
#> TCGA.NJ.A4YG.01 3 0.2512 0.4662 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.73.4658.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0547 0.9304 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.86.A456.01 2 0.0000 0.9418 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.71.8520.01 4 0.4348 0.4138 0.04 0.00 0.00 0.64 0.00 0.32
#> TCGA.97.8172.01 4 0.4631 0.1251 0.32 0.00 0.00 0.62 0.00 0.06
#> TCGA.05.5715.01 1 0.3819 0.7841 0.70 0.00 0.00 0.28 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.86.8278.01 1 0.4820 0.4313 0.52 0.00 0.00 0.38 0.10 0.00 0.00
#> TCGA.49.AARQ.01 1 0.5083 0.3418 0.56 0.00 0.00 0.34 0.06 0.04 0.00
#> TCGA.62.A46U.01 4 0.3902 0.4721 0.16 0.00 0.00 0.76 0.04 0.04 0.00
#> TCGA.93.A4JN.01 6 0.8052 -0.0444 0.00 0.00 0.20 0.10 0.20 0.26 0.24
#> TCGA.L9.A443.01 1 0.4657 0.3232 0.54 0.00 0.00 0.40 0.04 0.02 0.00
#> TCGA.MN.A4N5.01 3 0.6526 0.1161 0.00 0.00 0.52 0.02 0.20 0.12 0.14
#> TCGA.05.4405.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46Y.01 4 0.2259 0.5128 0.16 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.55.8207.01 3 0.5983 0.2221 0.00 0.00 0.50 0.00 0.12 0.30 0.08
#> TCGA.05.4425.01 2 0.0504 0.9299 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.67.6216.01 1 0.3307 0.6187 0.74 0.00 0.00 0.24 0.02 0.00 0.00
#> TCGA.44.2668.01 3 0.7863 -0.0849 0.00 0.06 0.46 0.16 0.12 0.12 0.08
#> TCGA.55.6986.01 1 0.4848 0.4052 0.50 0.00 0.00 0.40 0.10 0.00 0.00
#> TCGA.44.2665.01 1 0.3244 0.6271 0.78 0.00 0.00 0.18 0.04 0.00 0.00
#> TCGA.95.7948.01 1 0.3722 0.6230 0.76 0.00 0.00 0.18 0.04 0.02 0.00
#> TCGA.99.7458.01 4 0.2422 0.5029 0.18 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.38.6178.01 4 0.3745 0.4021 0.26 0.00 0.00 0.70 0.04 0.00 0.00
#> TCGA.97.A4M0.01 4 0.3000 0.4760 0.10 0.00 0.00 0.84 0.04 0.02 0.00
#> TCGA.78.7153.01 2 0.1718 0.8917 0.00 0.92 0.00 0.00 0.04 0.04 0.00
#> TCGA.44.A47F.01 7 0.4298 0.4031 0.00 0.00 0.12 0.00 0.04 0.10 0.74
#> TCGA.J2.A4AE.01 4 0.3052 0.4849 0.20 0.00 0.00 0.78 0.02 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7763.01 3 0.2509 0.4079 0.00 0.00 0.88 0.00 0.06 0.02 0.04
#> TCGA.64.5815.01 3 0.2213 0.4330 0.00 0.04 0.90 0.00 0.04 0.00 0.02
#> TCGA.91.7771.01 7 0.4466 0.4406 0.00 0.00 0.20 0.00 0.04 0.06 0.70
#> TCGA.69.7974.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7574.01 4 0.3047 0.3858 0.28 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.86.8673.01 2 0.5132 -0.1361 0.00 0.46 0.44 0.00 0.08 0.00 0.02
#> TCGA.69.7765.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46P.01 3 0.6304 0.1041 0.02 0.32 0.50 0.00 0.04 0.10 0.02
#> TCGA.78.7158.01 4 0.3867 0.4597 0.14 0.00 0.00 0.74 0.12 0.00 0.00
#> TCGA.97.8547.01 4 0.3755 0.2701 0.34 0.00 0.00 0.64 0.02 0.00 0.00
#> TCGA.97.8175.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47A.01 2 0.0504 0.9299 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.8090.01 2 0.1166 0.8982 0.00 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.75.6205.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5126.01 4 0.5723 0.0189 0.30 0.00 0.00 0.48 0.20 0.02 0.00
#> TCGA.NJ.A7XG.01 7 0.4838 0.3990 0.00 0.00 0.14 0.00 0.04 0.14 0.68
#> TCGA.55.A48X.01 4 0.3562 -0.2671 0.50 0.00 0.00 0.50 0.00 0.00 0.00
#> TCGA.67.6215.01 1 0.3417 0.5831 0.72 0.00 0.00 0.26 0.02 0.00 0.00
#> TCGA.55.7227.01 2 0.2745 0.7645 0.00 0.82 0.16 0.00 0.02 0.00 0.00
#> TCGA.MP.A4TI.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 4 0.3637 0.4283 0.24 0.00 0.00 0.72 0.04 0.00 0.00
#> TCGA.50.5935.01 1 0.2376 0.5926 0.86 0.00 0.00 0.12 0.02 0.00 0.00
#> TCGA.78.8655.01 4 0.3228 0.4097 0.02 0.00 0.00 0.80 0.16 0.00 0.02
#> TCGA.55.7914.01 2 0.1363 0.9066 0.00 0.94 0.00 0.04 0.02 0.00 0.00
#> TCGA.62.A472.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.4679.01 6 0.4787 0.0505 0.00 0.00 0.30 0.00 0.00 0.58 0.12
#> TCGA.MP.A4SY.01 3 0.5509 0.2838 0.00 0.00 0.60 0.00 0.10 0.22 0.08
#> TCGA.80.5607.01 1 0.4866 0.3611 0.48 0.00 0.00 0.42 0.10 0.00 0.00
#> TCGA.93.8067.01 3 0.2159 0.4206 0.02 0.00 0.90 0.00 0.06 0.02 0.00
#> TCGA.62.8395.01 1 0.4278 0.2405 0.50 0.00 0.00 0.46 0.04 0.00 0.00
#> TCGA.44.2666.01 3 0.6161 0.3070 0.00 0.04 0.58 0.00 0.10 0.20 0.08
#> TCGA.55.6983.01 3 0.4990 -0.2004 0.00 0.00 0.48 0.00 0.04 0.04 0.44
#> TCGA.69.A59K.01 2 0.1664 0.8922 0.00 0.92 0.00 0.00 0.06 0.00 0.02
#> TCGA.95.7567.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.5232 0.5787 0.02 0.68 0.00 0.12 0.12 0.06 0.00
#> TCGA.38.7271.01 4 0.4669 0.1481 0.00 0.40 0.00 0.52 0.08 0.00 0.00
#> TCGA.NJ.A4YG.01 3 0.2769 0.4003 0.00 0.00 0.86 0.00 0.02 0.04 0.08
#> TCGA.73.4658.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0504 0.9276 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.86.A456.01 2 0.0000 0.9377 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.71.8520.01 4 0.2745 0.4089 0.00 0.00 0.00 0.82 0.16 0.00 0.02
#> TCGA.97.8172.01 4 0.4266 0.0213 0.44 0.00 0.00 0.52 0.04 0.00 0.00
#> TCGA.05.5715.01 1 0.2376 0.5926 0.86 0.00 0.00 0.12 0.02 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.86.8278.01 4 0.4413 0.22006 0.24 0.00 0.02 0.68 0.00 0.02 0.02 0.02
#> TCGA.49.AARQ.01 1 0.5782 0.27492 0.46 0.00 0.10 0.36 0.00 0.02 0.00 0.06
#> TCGA.62.A46U.01 4 0.3913 0.48204 0.04 0.00 0.06 0.74 0.00 0.00 0.00 0.16
#> TCGA.93.A4JN.01 8 0.7097 -0.38323 0.02 0.00 0.14 0.00 0.18 0.12 0.08 0.46
#> TCGA.L9.A443.01 4 0.4924 -0.19259 0.42 0.00 0.02 0.50 0.00 0.02 0.02 0.02
#> TCGA.MN.A4N5.01 5 0.6544 0.13608 0.00 0.00 0.36 0.00 0.38 0.12 0.06 0.08
#> TCGA.05.4405.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46Y.01 4 0.2265 0.51778 0.02 0.00 0.02 0.88 0.00 0.00 0.00 0.08
#> TCGA.55.8207.01 5 0.2807 0.29028 0.02 0.00 0.00 0.00 0.86 0.04 0.02 0.06
#> TCGA.05.4425.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.6216.01 1 0.4137 0.55666 0.50 0.00 0.02 0.46 0.00 0.00 0.02 0.00
#> TCGA.44.2668.01 5 0.8446 0.01106 0.00 0.06 0.24 0.04 0.26 0.14 0.06 0.20
#> TCGA.55.6986.01 4 0.3311 0.40431 0.14 0.00 0.02 0.80 0.00 0.02 0.00 0.02
#> TCGA.44.2665.01 1 0.3299 0.61985 0.56 0.00 0.00 0.44 0.00 0.00 0.00 0.00
#> TCGA.95.7948.01 1 0.3618 0.67570 0.60 0.00 0.00 0.38 0.00 0.00 0.02 0.00
#> TCGA.99.7458.01 4 0.0471 0.52069 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.38.6178.01 4 0.4898 0.30582 0.12 0.00 0.02 0.64 0.00 0.02 0.00 0.20
#> TCGA.97.A4M0.01 4 0.4906 0.23644 0.00 0.10 0.02 0.66 0.00 0.04 0.00 0.18
#> TCGA.78.7153.01 2 0.2859 0.77731 0.00 0.82 0.14 0.00 0.02 0.00 0.00 0.02
#> TCGA.44.A47F.01 7 0.2025 0.28232 0.00 0.00 0.00 0.00 0.10 0.02 0.88 0.00
#> TCGA.J2.A4AE.01 4 0.2407 0.52027 0.06 0.00 0.00 0.86 0.00 0.00 0.00 0.08
#> TCGA.55.7283.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7763.01 5 0.6448 0.17949 0.00 0.02 0.30 0.00 0.44 0.16 0.06 0.02
#> TCGA.64.5815.01 5 0.5823 0.31749 0.00 0.04 0.32 0.00 0.50 0.08 0.06 0.00
#> TCGA.91.7771.01 7 0.6665 0.33913 0.02 0.00 0.14 0.00 0.12 0.24 0.46 0.02
#> TCGA.69.7974.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7574.01 4 0.1607 0.49922 0.04 0.00 0.00 0.92 0.00 0.00 0.00 0.04
#> TCGA.86.8673.01 2 0.4644 0.52060 0.00 0.64 0.16 0.00 0.18 0.02 0.00 0.00
#> TCGA.69.7765.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46P.01 2 0.6933 -0.29533 0.02 0.34 0.26 0.00 0.30 0.04 0.02 0.02
#> TCGA.78.7158.01 4 0.4276 0.27179 0.06 0.00 0.00 0.64 0.00 0.02 0.00 0.28
#> TCGA.97.8547.01 4 0.3675 0.42928 0.14 0.00 0.00 0.76 0.00 0.02 0.00 0.08
#> TCGA.97.8175.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47A.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8090.01 2 0.2265 0.81577 0.00 0.88 0.02 0.00 0.08 0.02 0.00 0.00
#> TCGA.75.6205.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7903.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5126.01 4 0.6411 0.23883 0.12 0.00 0.18 0.54 0.00 0.04 0.02 0.10
#> TCGA.NJ.A7XG.01 7 0.7004 0.30627 0.04 0.00 0.08 0.00 0.24 0.16 0.44 0.04
#> TCGA.55.A48X.01 4 0.3504 0.19570 0.26 0.00 0.00 0.70 0.00 0.00 0.00 0.04
#> TCGA.67.6215.01 1 0.4994 0.57540 0.50 0.00 0.02 0.40 0.00 0.02 0.00 0.06
#> TCGA.55.7227.01 2 0.3303 0.68140 0.00 0.76 0.02 0.00 0.20 0.02 0.00 0.00
#> TCGA.MP.A4TI.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 4 0.3078 0.50502 0.06 0.00 0.02 0.82 0.00 0.00 0.00 0.10
#> TCGA.50.5935.01 1 0.3594 0.67929 0.68 0.00 0.04 0.28 0.00 0.00 0.00 0.00
#> TCGA.78.8655.01 8 0.3658 0.33176 0.02 0.00 0.00 0.40 0.00 0.00 0.00 0.58
#> TCGA.55.7914.01 2 0.3502 0.77738 0.02 0.82 0.04 0.02 0.00 0.02 0.00 0.08
#> TCGA.62.A472.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.4679.01 6 0.4489 0.00000 0.00 0.00 0.00 0.00 0.26 0.64 0.06 0.04
#> TCGA.MP.A4SY.01 5 0.2807 0.30558 0.02 0.00 0.00 0.00 0.86 0.06 0.02 0.04
#> TCGA.80.5607.01 4 0.4534 0.05806 0.30 0.00 0.04 0.62 0.00 0.00 0.02 0.02
#> TCGA.93.8067.01 5 0.5125 0.30146 0.00 0.00 0.26 0.00 0.60 0.02 0.08 0.04
#> TCGA.62.8395.01 4 0.4375 0.23170 0.26 0.00 0.04 0.66 0.00 0.02 0.00 0.02
#> TCGA.44.2666.01 5 0.3903 0.28232 0.02 0.08 0.00 0.00 0.78 0.06 0.06 0.00
#> TCGA.55.6983.01 7 0.6732 0.11506 0.00 0.02 0.12 0.00 0.26 0.26 0.34 0.00
#> TCGA.69.A59K.01 2 0.4434 0.71438 0.00 0.76 0.06 0.04 0.02 0.06 0.00 0.06
#> TCGA.95.7567.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.6150 0.31570 0.00 0.54 0.12 0.22 0.02 0.02 0.00 0.08
#> TCGA.38.7271.01 4 0.5566 0.00749 0.00 0.36 0.08 0.46 0.00 0.00 0.00 0.10
#> TCGA.NJ.A4YG.01 5 0.4575 0.24352 0.00 0.02 0.12 0.00 0.64 0.22 0.00 0.00
#> TCGA.73.4658.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A456.01 2 0.0000 0.89719 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.71.8520.01 8 0.3942 0.42488 0.02 0.00 0.02 0.34 0.00 0.00 0.00 0.62
#> TCGA.97.8172.01 4 0.3941 0.14200 0.26 0.00 0.02 0.68 0.00 0.00 0.00 0.04
#> TCGA.05.5715.01 1 0.3594 0.67929 0.68 0.00 0.04 0.28 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01221-leaf , Node01222-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-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["0212"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 25 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5005 0.500 0.500
#> 3 3 1.000 1.000 1.000 0.3726 0.813 0.627
#> 4 4 1.000 0.997 0.998 0.1158 0.920 0.745
#> 5 5 0.874 0.803 0.877 0.0514 1.000 1.000
#> 6 6 0.866 0.536 0.770 0.0251 0.903 0.613
#> 7 7 0.838 0.617 0.771 0.0248 0.913 0.559
#> 8 8 0.854 0.607 0.834 0.0276 0.957 0.723
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.05.4405.01 2 0 1 0 1
#> TCGA.05.4425.01 2 0 1 0 1
#> TCGA.78.7153.01 2 0 1 0 1
#> TCGA.55.7283.01 2 0 1 0 1
#> TCGA.69.7974.01 2 0 1 0 1
#> TCGA.62.A46V.01 2 0 1 0 1
#> TCGA.49.6745.01 1 0 1 1 0
#> TCGA.86.8673.01 1 0 1 1 0
#> TCGA.69.7765.01 1 0 1 1 0
#> TCGA.97.8175.01 2 0 1 0 1
#> TCGA.44.A47A.01 2 0 1 0 1
#> TCGA.55.8090.01 1 0 1 1 0
#> TCGA.75.6205.01 2 0 1 0 1
#> TCGA.55.7903.01 1 0 1 1 0
#> TCGA.55.7227.01 1 0 1 1 0
#> TCGA.MP.A4TI.01 1 0 1 1 0
#> TCGA.55.7914.01 2 0 1 0 1
#> TCGA.62.A472.01 1 0 1 1 0
#> TCGA.69.A59K.01 2 0 1 0 1
#> TCGA.95.7567.01 1 0 1 1 0
#> TCGA.49.AARN.01 2 0 1 0 1
#> TCGA.38.7271.01 2 0 1 0 1
#> TCGA.73.4658.01 2 0 1 0 1
#> TCGA.44.7659.01 1 0 1 1 0
#> TCGA.86.A456.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.05.4405.01 3 0 1 0 0 1
#> TCGA.05.4425.01 3 0 1 0 0 1
#> TCGA.78.7153.01 3 0 1 0 0 1
#> TCGA.55.7283.01 3 0 1 0 0 1
#> TCGA.69.7974.01 2 0 1 0 1 0
#> TCGA.62.A46V.01 3 0 1 0 0 1
#> TCGA.49.6745.01 1 0 1 1 0 0
#> TCGA.86.8673.01 1 0 1 1 0 0
#> TCGA.69.7765.01 1 0 1 1 0 0
#> TCGA.97.8175.01 2 0 1 0 1 0
#> TCGA.44.A47A.01 3 0 1 0 0 1
#> TCGA.55.8090.01 1 0 1 1 0 0
#> TCGA.75.6205.01 2 0 1 0 1 0
#> TCGA.55.7903.01 1 0 1 1 0 0
#> TCGA.55.7227.01 1 0 1 1 0 0
#> TCGA.MP.A4TI.01 1 0 1 1 0 0
#> TCGA.55.7914.01 3 0 1 0 0 1
#> TCGA.62.A472.01 1 0 1 1 0 0
#> TCGA.69.A59K.01 2 0 1 0 1 0
#> TCGA.95.7567.01 1 0 1 1 0 0
#> TCGA.49.AARN.01 2 0 1 0 1 0
#> TCGA.38.7271.01 2 0 1 0 1 0
#> TCGA.73.4658.01 2 0 1 0 1 0
#> TCGA.44.7659.01 1 0 1 1 0 0
#> TCGA.86.A456.01 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.05.4405.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.05.4425.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.78.7153.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.55.7283.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.69.7974.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.62.A46V.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.49.6745.01 4 0.000 0.987 0.00 0 0 1.00
#> TCGA.86.8673.01 4 0.000 0.987 0.00 0 0 1.00
#> TCGA.69.7765.01 4 0.121 0.958 0.04 0 0 0.96
#> TCGA.97.8175.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.44.A47A.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.55.8090.01 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.75.6205.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.55.7903.01 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.55.7227.01 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.MP.A4TI.01 4 0.000 0.987 0.00 0 0 1.00
#> TCGA.55.7914.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.62.A472.01 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.69.A59K.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.95.7567.01 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.49.AARN.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.38.7271.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.73.4658.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.44.7659.01 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.86.A456.01 2 0.000 1.000 0.00 1 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.05.4405.01 3 0.4726 0.548 0.00 0.40 0.58 0.02 0.0
#> TCGA.05.4425.01 3 0.0000 0.731 0.00 0.00 1.00 0.00 0.0
#> TCGA.78.7153.01 3 0.3983 0.604 0.00 0.00 0.66 0.34 0.0
#> TCGA.55.7283.01 3 0.3983 0.604 0.00 0.00 0.66 0.34 0.0
#> TCGA.69.7974.01 2 0.0000 0.663 0.00 1.00 0.00 0.00 0.0
#> TCGA.62.A46V.01 3 0.4726 0.548 0.00 0.40 0.58 0.02 0.0
#> TCGA.49.6745.01 5 0.0000 0.912 0.00 0.00 0.00 0.00 1.0
#> TCGA.86.8673.01 5 0.0000 0.912 0.00 0.00 0.00 0.00 1.0
#> TCGA.69.7765.01 5 0.2020 0.857 0.10 0.00 0.00 0.00 0.9
#> TCGA.97.8175.01 2 0.4182 0.826 0.00 0.60 0.00 0.40 0.0
#> TCGA.44.A47A.01 3 0.1216 0.726 0.00 0.02 0.96 0.02 0.0
#> TCGA.55.8090.01 1 0.0000 0.993 1.00 0.00 0.00 0.00 0.0
#> TCGA.75.6205.01 2 0.4182 0.826 0.00 0.60 0.00 0.40 0.0
#> TCGA.55.7903.01 1 0.0000 0.993 1.00 0.00 0.00 0.00 0.0
#> TCGA.55.7227.01 1 0.0000 0.993 1.00 0.00 0.00 0.00 0.0
#> TCGA.MP.A4TI.01 5 0.3109 0.831 0.00 0.00 0.00 0.20 0.8
#> TCGA.55.7914.01 3 0.0000 0.731 0.00 0.00 1.00 0.00 0.0
#> TCGA.62.A472.01 1 0.0000 0.993 1.00 0.00 0.00 0.00 0.0
#> TCGA.69.A59K.01 2 0.4182 0.826 0.00 0.60 0.00 0.40 0.0
#> TCGA.95.7567.01 1 0.1043 0.966 0.96 0.00 0.00 0.04 0.0
#> TCGA.49.AARN.01 2 0.0609 0.676 0.00 0.98 0.00 0.02 0.0
#> TCGA.38.7271.01 2 0.4182 0.826 0.00 0.60 0.00 0.40 0.0
#> TCGA.73.4658.01 2 0.4182 0.826 0.00 0.60 0.00 0.40 0.0
#> TCGA.44.7659.01 1 0.0000 0.993 1.00 0.00 0.00 0.00 0.0
#> TCGA.86.A456.01 2 0.0000 0.663 0.00 1.00 0.00 0.00 0.0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.05.4405.01 6 0.4337 -0.2451 0.00 0.00 0.48 0.02 0.00 0.50
#> TCGA.05.4425.01 3 0.3864 0.2899 0.00 0.00 0.52 0.48 0.00 0.00
#> TCGA.78.7153.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7283.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7974.01 2 0.3869 -0.2687 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.62.A46V.01 3 0.4646 -0.3733 0.00 0.00 0.50 0.04 0.00 0.46
#> TCGA.49.6745.01 5 0.0000 0.9747 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8673.01 5 0.0000 0.9747 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.69.7765.01 5 0.0937 0.9491 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.97.8175.01 2 0.1814 0.6883 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.44.A47A.01 3 0.4328 0.3014 0.00 0.00 0.52 0.46 0.00 0.02
#> TCGA.55.8090.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6205.01 2 0.0000 0.7518 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7903.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7227.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 3 0.6059 -0.3325 0.00 0.00 0.38 0.00 0.26 0.36
#> TCGA.55.7914.01 3 0.3864 0.2899 0.00 0.00 0.52 0.48 0.00 0.00
#> TCGA.62.A472.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.0000 0.7518 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 1 0.3746 0.7915 0.78 0.00 0.08 0.00 0.00 0.14
#> TCGA.49.AARN.01 2 0.3828 -0.0449 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.38.7271.01 2 0.0000 0.7518 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.4658.01 2 0.0000 0.7518 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A456.01 6 0.3869 -0.4140 0.00 0.50 0.00 0.00 0.00 0.50
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.05.4405.01 6 0.322 0.407 0.00 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.05.4425.01 3 0.350 0.369 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.78.7153.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7283.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7974.01 6 0.350 0.262 0.00 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.62.A46V.01 6 0.336 0.356 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.49.6745.01 5 0.000 0.920 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8673.01 5 0.000 0.920 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7765.01 5 0.193 0.842 0.08 0.00 0.00 0.00 0.90 0.00 0.02
#> TCGA.97.8175.01 2 0.189 0.744 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.44.A47A.01 3 0.531 0.325 0.00 0.00 0.46 0.36 0.00 0.18 0.00
#> TCGA.55.8090.01 1 0.000 0.964 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6205.01 2 0.000 0.845 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7903.01 1 0.277 0.848 0.86 0.00 0.04 0.00 0.00 0.08 0.02
#> TCGA.55.7227.01 1 0.000 0.964 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 7 0.242 0.000 0.00 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.55.7914.01 3 0.350 0.369 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.62.A472.01 1 0.000 0.964 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.000 0.845 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 3 0.666 -0.284 0.14 0.00 0.40 0.00 0.00 0.30 0.16
#> TCGA.49.AARN.01 2 0.352 -0.106 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.38.7271.01 2 0.000 0.845 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4658.01 2 0.000 0.845 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 1 0.000 0.964 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A456.01 6 0.352 0.213 0.00 0.44 0.00 0.00 0.00 0.56 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.05.4405.01 3 0.3318 -0.122 0.00 0.00 0.54 0.00 0.00 0.46 0.00 0.00
#> TCGA.05.4425.01 3 0.5062 0.368 0.00 0.00 0.48 0.12 0.00 0.38 0.00 0.02
#> TCGA.78.7153.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7283.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7974.01 6 0.4588 1.000 0.00 0.34 0.12 0.00 0.00 0.54 0.00 0.00
#> TCGA.62.A46V.01 3 0.2534 0.380 0.00 0.00 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.49.6745.01 5 0.0000 0.971 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8673.01 5 0.0000 0.971 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7765.01 5 0.0808 0.941 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.97.8175.01 2 0.2756 0.290 0.00 0.74 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.44.A47A.01 3 0.0808 0.449 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.55.8090.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6205.01 2 0.2591 0.610 0.00 0.86 0.00 0.00 0.00 0.08 0.02 0.04
#> TCGA.55.7903.01 1 0.1563 0.881 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.55.7227.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TI.01 7 0.0471 0.000 0.00 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.55.7914.01 3 0.5062 0.368 0.00 0.00 0.48 0.12 0.00 0.38 0.00 0.02
#> TCGA.62.A472.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.2404 0.520 0.00 0.84 0.02 0.00 0.00 0.14 0.00 0.00
#> TCGA.95.7567.01 8 0.1091 0.000 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.94
#> TCGA.49.AARN.01 2 0.3737 -0.579 0.00 0.50 0.02 0.00 0.00 0.48 0.00 0.00
#> TCGA.38.7271.01 2 0.2591 0.610 0.00 0.86 0.00 0.00 0.00 0.08 0.02 0.04
#> TCGA.73.4658.01 2 0.0000 0.617 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A456.01 6 0.4588 1.000 0.00 0.34 0.12 0.00 0.00 0.54 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122 , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221-leaf , Node0222 , Node0223-leaf , Node0231 , Node0232 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0324-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 61 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 0.5076 0.493 0.493
#> 3 3 1.000 0.975 0.971 0.2502 0.874 0.744
#> 4 4 0.716 0.819 0.884 0.1641 0.886 0.690
#> 5 5 0.713 0.741 0.829 0.0626 0.985 0.941
#> 6 6 0.686 0.443 0.753 0.0337 0.934 0.738
#> 7 7 0.668 0.415 0.731 0.0261 0.974 0.866
#> 8 8 0.675 0.412 0.679 0.0124 0.934 0.691
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.MP.A4T8.01 1 0 1 1 0
#> TCGA.86.6851.01 2 0 1 0 1
#> TCGA.64.5775.01 1 0 1 1 0
#> TCGA.62.8394.01 2 0 1 0 1
#> TCGA.05.5428.01 1 0 1 1 0
#> TCGA.55.6642.01 1 0 1 1 0
#> TCGA.50.6673.01 2 0 1 0 1
#> TCGA.86.6562.01 1 0 1 1 0
#> TCGA.86.8074.01 2 0 1 0 1
#> TCGA.55.8203.01 2 0 1 0 1
#> TCGA.J2.8194.01 2 0 1 0 1
#> TCGA.05.5425.01 1 0 1 1 0
#> TCGA.55.A494.01 2 0 1 0 1
#> TCGA.44.3917.01 2 0 1 0 1
#> TCGA.L4.A4E5.01 2 0 1 0 1
#> TCGA.55.A4DG.01 1 0 1 1 0
#> TCGA.91.6829.01 1 0 1 1 0
#> TCGA.78.7542.01 1 0 1 1 0
#> TCGA.97.8179.01 1 0 1 1 0
#> TCGA.55.8092.01 1 0 1 1 0
#> TCGA.75.6207.01 1 0 1 1 0
#> TCGA.95.7043.01 2 0 1 0 1
#> TCGA.49.6767.01 2 0 1 0 1
#> TCGA.50.5051.01 2 0 1 0 1
#> TCGA.80.5608.01 2 0 1 0 1
#> TCGA.78.7159.01 2 0 1 0 1
#> TCGA.44.8120.01 1 0 1 1 0
#> TCGA.73.A9RS.01 1 0 1 1 0
#> TCGA.95.7039.01 2 0 1 0 1
#> TCGA.71.6725.01 2 0 1 0 1
#> TCGA.86.8359.01 1 0 1 1 0
#> TCGA.78.7161.01 2 0 1 0 1
#> TCGA.97.7937.01 1 0 1 1 0
#> TCGA.44.5644.01 2 0 1 0 1
#> TCGA.L9.A7SV.01 1 0 1 1 0
#> TCGA.05.4390.01 2 0 1 0 1
#> TCGA.69.7979.01 2 0 1 0 1
#> TCGA.50.7109.01 1 0 1 1 0
#> TCGA.75.6211.01 2 0 1 0 1
#> TCGA.91.6828.01 1 0 1 1 0
#> TCGA.05.4396.01 1 0 1 1 0
#> TCGA.MN.A4N4.01 1 0 1 1 0
#> TCGA.NJ.A4YF.01 2 0 1 0 1
#> TCGA.78.8662.01 2 0 1 0 1
#> TCGA.05.4427.01 2 0 1 0 1
#> TCGA.78.7147.01 2 0 1 0 1
#> TCGA.MP.A4TE.01 1 0 1 1 0
#> TCGA.95.A4VK.01 2 0 1 0 1
#> TCGA.49.4488.01 2 0 1 0 1
#> TCGA.55.7994.01 1 0 1 1 0
#> TCGA.MP.A5C7.01 2 0 1 0 1
#> TCGA.35.5375.01 1 0 1 1 0
#> TCGA.95.7562.01 1 0 1 1 0
#> TCGA.55.8616.01 2 0 1 0 1
#> TCGA.MP.A4SV.01 1 0 1 1 0
#> TCGA.NJ.A55R.01 1 0 1 1 0
#> TCGA.55.8506.01 2 0 1 0 1
#> TCGA.55.7815.01 1 0 1 1 0
#> TCGA.78.7539.01 2 0 1 0 1
#> TCGA.62.A46S.01 1 0 1 1 0
#> TCGA.78.7145.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.MP.A4T8.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.86.6851.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.64.5775.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.62.8394.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.05.5428.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.55.6642.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.50.6673.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.86.6562.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.86.8074.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.55.8203.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.J2.8194.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.05.5425.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.55.A494.01 2 0.4796 0.704 0.00 0.78 0.22
#> TCGA.44.3917.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.L4.A4E5.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.55.A4DG.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.91.6829.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.78.7542.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.97.8179.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.55.8092.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.75.6207.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.95.7043.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.49.6767.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.50.5051.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.80.5608.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.78.7159.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.44.8120.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.73.A9RS.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.95.7039.01 2 0.0892 0.962 0.00 0.98 0.02
#> TCGA.71.6725.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.86.8359.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.78.7161.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.97.7937.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.44.5644.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.L9.A7SV.01 1 0.0892 0.977 0.98 0.00 0.02
#> TCGA.05.4390.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.69.7979.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.50.7109.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.75.6211.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.91.6828.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.05.4396.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.MN.A4N4.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.NJ.A4YF.01 2 0.2066 0.929 0.00 0.94 0.06
#> TCGA.78.8662.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.05.4427.01 2 0.0892 0.962 0.00 0.98 0.02
#> TCGA.78.7147.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.MP.A4TE.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.95.A4VK.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.49.4488.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.55.7994.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.MP.A5C7.01 3 0.2066 1.000 0.00 0.06 0.94
#> TCGA.35.5375.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.95.7562.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.55.8616.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.MP.A4SV.01 1 0.1529 0.975 0.96 0.00 0.04
#> TCGA.NJ.A55R.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.55.8506.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.55.7815.01 1 0.0000 0.978 1.00 0.00 0.00
#> TCGA.78.7539.01 2 0.1529 0.949 0.00 0.96 0.04
#> TCGA.62.A46S.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.78.7145.01 2 0.0000 0.980 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.MP.A4T8.01 1 0.4406 0.495 0.70 0.00 0.00 0.30
#> TCGA.86.6851.01 2 0.0707 0.917 0.00 0.98 0.00 0.02
#> TCGA.64.5775.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.62.8394.01 2 0.0707 0.913 0.00 0.98 0.00 0.02
#> TCGA.05.5428.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.55.6642.01 4 0.2921 0.883 0.14 0.00 0.00 0.86
#> TCGA.50.6673.01 2 0.1211 0.914 0.00 0.96 0.00 0.04
#> TCGA.86.6562.01 4 0.4134 0.798 0.26 0.00 0.00 0.74
#> TCGA.86.8074.01 2 0.0707 0.913 0.00 0.98 0.00 0.02
#> TCGA.55.8203.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.J2.8194.01 3 0.3853 0.804 0.00 0.16 0.82 0.02
#> TCGA.05.5425.01 4 0.2921 0.883 0.14 0.00 0.00 0.86
#> TCGA.55.A494.01 2 0.4284 0.713 0.00 0.78 0.20 0.02
#> TCGA.44.3917.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.L4.A4E5.01 2 0.0000 0.916 0.00 1.00 0.00 0.00
#> TCGA.55.A4DG.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.91.6829.01 1 0.4977 -0.201 0.54 0.00 0.00 0.46
#> TCGA.78.7542.01 1 0.3610 0.655 0.80 0.00 0.00 0.20
#> TCGA.97.8179.01 4 0.4855 0.596 0.40 0.00 0.00 0.60
#> TCGA.55.8092.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.75.6207.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.95.7043.01 2 0.0000 0.916 0.00 1.00 0.00 0.00
#> TCGA.49.6767.01 2 0.0000 0.916 0.00 1.00 0.00 0.00
#> TCGA.50.5051.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.80.5608.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.78.7159.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.44.8120.01 1 0.3801 0.606 0.78 0.00 0.00 0.22
#> TCGA.73.A9RS.01 4 0.3172 0.881 0.16 0.00 0.00 0.84
#> TCGA.95.7039.01 2 0.4692 0.871 0.04 0.82 0.04 0.10
#> TCGA.71.6725.01 2 0.4502 0.876 0.04 0.82 0.02 0.12
#> TCGA.86.8359.01 4 0.2921 0.883 0.14 0.00 0.00 0.86
#> TCGA.78.7161.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.97.7937.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.44.5644.01 3 0.0707 0.945 0.00 0.00 0.98 0.02
#> TCGA.L9.A7SV.01 1 0.3610 0.659 0.80 0.00 0.00 0.20
#> TCGA.05.4390.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.69.7979.01 2 0.0707 0.917 0.00 0.98 0.00 0.02
#> TCGA.50.7109.01 4 0.2921 0.883 0.14 0.00 0.00 0.86
#> TCGA.75.6211.01 3 0.0000 0.956 0.00 0.00 1.00 0.00
#> TCGA.91.6828.01 1 0.4134 0.571 0.74 0.00 0.00 0.26
#> TCGA.05.4396.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 4 0.3610 0.862 0.20 0.00 0.00 0.80
#> TCGA.NJ.A4YF.01 2 0.3606 0.804 0.00 0.84 0.14 0.02
#> TCGA.78.8662.01 2 0.4692 0.871 0.04 0.82 0.04 0.10
#> TCGA.05.4427.01 2 0.4692 0.871 0.04 0.82 0.04 0.10
#> TCGA.78.7147.01 2 0.0707 0.917 0.00 0.98 0.00 0.02
#> TCGA.MP.A4TE.01 1 0.6216 0.518 0.66 0.00 0.12 0.22
#> TCGA.95.A4VK.01 2 0.0707 0.912 0.00 0.98 0.02 0.00
#> TCGA.49.4488.01 2 0.0707 0.917 0.00 0.98 0.00 0.02
#> TCGA.55.7994.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 3 0.4284 0.747 0.00 0.20 0.78 0.02
#> TCGA.35.5375.01 4 0.3610 0.868 0.20 0.00 0.00 0.80
#> TCGA.95.7562.01 4 0.4907 0.541 0.42 0.00 0.00 0.58
#> TCGA.55.8616.01 2 0.4692 0.871 0.04 0.82 0.04 0.10
#> TCGA.MP.A4SV.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 4 0.3172 0.878 0.16 0.00 0.00 0.84
#> TCGA.55.8506.01 2 0.4692 0.871 0.04 0.82 0.04 0.10
#> TCGA.55.7815.01 4 0.4522 0.697 0.32 0.00 0.00 0.68
#> TCGA.78.7539.01 2 0.4731 0.792 0.00 0.78 0.16 0.06
#> TCGA.62.A46S.01 4 0.2921 0.883 0.14 0.00 0.00 0.86
#> TCGA.78.7145.01 2 0.0000 0.916 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.MP.A4T8.01 1 0.5498 0.390 0.58 0.00 0.00 0.08 0.34
#> TCGA.86.6851.01 2 0.1410 0.846 0.00 0.94 0.00 0.06 0.00
#> TCGA.64.5775.01 1 0.0609 0.788 0.98 0.00 0.00 0.02 0.00
#> TCGA.62.8394.01 2 0.1043 0.831 0.00 0.96 0.00 0.04 0.00
#> TCGA.05.5428.01 1 0.1043 0.788 0.96 0.00 0.00 0.04 0.00
#> TCGA.55.6642.01 5 0.0000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.6673.01 2 0.3291 0.832 0.00 0.84 0.04 0.12 0.00
#> TCGA.86.6562.01 5 0.5659 0.666 0.10 0.00 0.00 0.32 0.58
#> TCGA.86.8074.01 2 0.1043 0.831 0.00 0.96 0.00 0.04 0.00
#> TCGA.55.8203.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.J2.8194.01 3 0.4075 0.755 0.00 0.16 0.78 0.06 0.00
#> TCGA.05.5425.01 5 0.3109 0.765 0.00 0.00 0.00 0.20 0.80
#> TCGA.55.A494.01 2 0.4254 0.633 0.00 0.74 0.22 0.04 0.00
#> TCGA.44.3917.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.L4.A4E5.01 2 0.1732 0.847 0.00 0.92 0.00 0.08 0.00
#> TCGA.55.A4DG.01 1 0.1043 0.788 0.96 0.00 0.00 0.04 0.00
#> TCGA.91.6829.01 5 0.6816 0.278 0.32 0.00 0.00 0.32 0.36
#> TCGA.78.7542.01 1 0.6327 0.254 0.52 0.00 0.00 0.28 0.20
#> TCGA.97.8179.01 5 0.5759 0.652 0.18 0.00 0.00 0.20 0.62
#> TCGA.55.8092.01 1 0.0609 0.788 0.98 0.00 0.00 0.02 0.00
#> TCGA.75.6207.01 1 0.0000 0.793 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 2 0.1043 0.845 0.00 0.96 0.00 0.04 0.00
#> TCGA.49.6767.01 2 0.1043 0.831 0.00 0.96 0.00 0.04 0.00
#> TCGA.50.5051.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.80.5608.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7159.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.8120.01 1 0.6244 0.273 0.54 0.00 0.00 0.26 0.20
#> TCGA.73.A9RS.01 5 0.4398 0.756 0.04 0.00 0.00 0.24 0.72
#> TCGA.95.7039.01 2 0.5838 0.708 0.06 0.56 0.02 0.36 0.00
#> TCGA.71.6725.01 2 0.4360 0.785 0.00 0.68 0.02 0.30 0.00
#> TCGA.86.8359.01 5 0.1732 0.772 0.00 0.00 0.00 0.08 0.92
#> TCGA.78.7161.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.7937.01 1 0.1410 0.787 0.94 0.00 0.00 0.06 0.00
#> TCGA.44.5644.01 3 0.3106 0.830 0.00 0.00 0.84 0.14 0.02
#> TCGA.L9.A7SV.01 1 0.6455 0.205 0.48 0.00 0.00 0.32 0.20
#> TCGA.05.4390.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7979.01 2 0.0609 0.842 0.00 0.98 0.00 0.02 0.00
#> TCGA.50.7109.01 5 0.0000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.75.6211.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.6828.01 1 0.4527 0.549 0.70 0.00 0.00 0.04 0.26
#> TCGA.05.4396.01 1 0.0000 0.793 1.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 5 0.4921 0.719 0.04 0.00 0.00 0.34 0.62
#> TCGA.NJ.A4YF.01 2 0.4170 0.716 0.00 0.78 0.14 0.08 0.00
#> TCGA.78.8662.01 2 0.5093 0.750 0.02 0.62 0.02 0.34 0.00
#> TCGA.05.4427.01 2 0.6038 0.708 0.08 0.56 0.02 0.34 0.00
#> TCGA.78.7147.01 2 0.1732 0.846 0.00 0.92 0.00 0.08 0.00
#> TCGA.MP.A4TE.01 1 0.5778 0.572 0.68 0.00 0.04 0.10 0.18
#> TCGA.95.A4VK.01 2 0.2077 0.842 0.00 0.92 0.04 0.04 0.00
#> TCGA.49.4488.01 2 0.2020 0.842 0.00 0.90 0.00 0.10 0.00
#> TCGA.55.7994.01 1 0.0609 0.790 0.98 0.00 0.00 0.02 0.00
#> TCGA.MP.A5C7.01 3 0.4982 0.661 0.00 0.20 0.70 0.10 0.00
#> TCGA.35.5375.01 5 0.3971 0.761 0.10 0.00 0.00 0.10 0.80
#> TCGA.95.7562.01 5 0.5130 0.630 0.22 0.00 0.00 0.10 0.68
#> TCGA.55.8616.01 2 0.5162 0.737 0.02 0.60 0.02 0.36 0.00
#> TCGA.MP.A4SV.01 1 0.0000 0.793 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.3110 0.757 0.06 0.00 0.00 0.08 0.86
#> TCGA.55.8506.01 2 0.5162 0.737 0.02 0.60 0.02 0.36 0.00
#> TCGA.55.7815.01 5 0.4644 0.531 0.28 0.00 0.00 0.04 0.68
#> TCGA.78.7539.01 2 0.4725 0.692 0.00 0.72 0.20 0.08 0.00
#> TCGA.62.A46S.01 5 0.0000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.78.7145.01 2 0.0609 0.835 0.00 0.98 0.00 0.02 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.MP.A4T8.01 1 0.5007 0.42457 0.66 0.00 0.00 0.08 0.24 0.02
#> TCGA.86.6851.01 2 0.3647 0.00625 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.64.5775.01 1 0.0000 0.72290 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8394.01 6 0.4144 0.65366 0.00 0.36 0.00 0.02 0.00 0.62
#> TCGA.05.5428.01 1 0.0000 0.72290 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6642.01 5 0.1092 0.55513 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.50.6673.01 2 0.4873 -0.08083 0.00 0.60 0.08 0.00 0.00 0.32
#> TCGA.86.6562.01 5 0.6376 -0.31310 0.12 0.00 0.00 0.34 0.48 0.06
#> TCGA.86.8074.01 6 0.4482 0.65018 0.00 0.36 0.00 0.04 0.00 0.60
#> TCGA.55.8203.01 3 0.0547 0.88319 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.J2.8194.01 3 0.4851 0.69397 0.00 0.06 0.70 0.04 0.00 0.20
#> TCGA.05.5425.01 5 0.3076 0.48922 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.55.A494.01 6 0.6046 0.38827 0.00 0.28 0.18 0.02 0.00 0.52
#> TCGA.44.3917.01 3 0.0547 0.88288 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.L4.A4E5.01 2 0.4576 -0.30027 0.00 0.56 0.00 0.04 0.00 0.40
#> TCGA.55.A4DG.01 1 0.1267 0.68408 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.91.6829.01 4 0.6540 0.00000 0.30 0.00 0.00 0.36 0.32 0.02
#> TCGA.78.7542.01 1 0.5609 0.12765 0.58 0.00 0.00 0.28 0.12 0.02
#> TCGA.97.8179.01 5 0.6365 -0.12346 0.28 0.00 0.00 0.14 0.52 0.06
#> TCGA.55.8092.01 1 0.0547 0.71840 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.75.6207.01 1 0.0000 0.72290 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 6 0.4609 0.53736 0.00 0.42 0.00 0.04 0.00 0.54
#> TCGA.49.6767.01 6 0.4576 0.62945 0.00 0.40 0.00 0.04 0.00 0.56
#> TCGA.50.5051.01 3 0.0000 0.88608 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.80.5608.01 3 0.0937 0.88453 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.78.7159.01 3 0.0547 0.88712 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.44.8120.01 1 0.6331 -0.64198 0.46 0.00 0.00 0.24 0.28 0.02
#> TCGA.73.A9RS.01 5 0.3315 0.47291 0.02 0.00 0.00 0.20 0.78 0.00
#> TCGA.95.7039.01 2 0.0937 0.55229 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.71.6725.01 2 0.2260 0.45852 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.86.8359.01 5 0.3315 0.52306 0.00 0.00 0.00 0.20 0.78 0.02
#> TCGA.78.7161.01 3 0.0937 0.88434 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.97.7937.01 1 0.1480 0.69499 0.94 0.04 0.00 0.02 0.00 0.00
#> TCGA.44.5644.01 3 0.6846 0.54041 0.02 0.10 0.58 0.20 0.02 0.08
#> TCGA.L9.A7SV.01 1 0.6226 -0.20229 0.52 0.02 0.00 0.32 0.12 0.02
#> TCGA.05.4390.01 3 0.0000 0.88608 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7979.01 6 0.4534 0.62527 0.00 0.38 0.00 0.04 0.00 0.58
#> TCGA.50.7109.01 5 0.1480 0.54964 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.75.6211.01 3 0.0937 0.88280 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.91.6828.01 1 0.5113 0.39790 0.64 0.00 0.00 0.08 0.26 0.02
#> TCGA.05.4396.01 1 0.0547 0.71840 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.MN.A4N4.01 5 0.4246 0.28605 0.02 0.00 0.00 0.40 0.58 0.00
#> TCGA.NJ.A4YF.01 6 0.5977 0.43777 0.00 0.22 0.16 0.04 0.00 0.58
#> TCGA.78.8662.01 2 0.3420 0.47723 0.04 0.84 0.00 0.06 0.00 0.06
#> TCGA.05.4427.01 2 0.0937 0.55229 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.78.7147.01 2 0.3797 -0.28334 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.MP.A4TE.01 1 0.6487 0.34216 0.56 0.00 0.02 0.20 0.18 0.04
#> TCGA.95.A4VK.01 6 0.6053 0.41285 0.00 0.42 0.10 0.04 0.00 0.44
#> TCGA.49.4488.01 2 0.3819 0.15674 0.00 0.70 0.00 0.02 0.00 0.28
#> TCGA.55.7994.01 1 0.0000 0.72290 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 3 0.5103 0.63854 0.00 0.06 0.66 0.04 0.00 0.24
#> TCGA.35.5375.01 5 0.3544 0.40676 0.12 0.00 0.00 0.08 0.80 0.00
#> TCGA.95.7562.01 5 0.5524 0.05025 0.20 0.00 0.00 0.16 0.62 0.02
#> TCGA.55.8616.01 2 0.0937 0.55229 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 1 0.0000 0.72290 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.4444 0.39027 0.16 0.00 0.00 0.08 0.74 0.02
#> TCGA.55.8506.01 2 0.0937 0.55229 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 5 0.4845 -0.00361 0.40 0.00 0.00 0.06 0.54 0.00
#> TCGA.78.7539.01 2 0.5564 -0.17091 0.00 0.48 0.08 0.02 0.00 0.42
#> TCGA.62.A46S.01 5 0.1814 0.54192 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.78.7145.01 6 0.4632 0.57289 0.00 0.44 0.00 0.04 0.00 0.52
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.MP.A4T8.01 1 0.5431 0.28538 0.56 0.00 0.00 0.06 0.30 0.00 0.08
#> TCGA.86.6851.01 2 0.4266 -0.30045 0.00 0.52 0.00 0.00 0.00 0.44 0.04
#> TCGA.64.5775.01 1 0.1006 0.64708 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.62.8394.01 6 0.3386 0.68132 0.00 0.18 0.00 0.02 0.00 0.78 0.02
#> TCGA.05.5428.01 1 0.1664 0.63197 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.55.6642.01 5 0.0504 0.59740 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.50.6673.01 2 0.6147 -0.20104 0.00 0.40 0.06 0.00 0.00 0.38 0.16
#> TCGA.86.6562.01 5 0.5931 -0.03861 0.12 0.00 0.00 0.40 0.42 0.00 0.06
#> TCGA.86.8074.01 6 0.3667 0.65403 0.00 0.20 0.00 0.00 0.00 0.74 0.06
#> TCGA.55.8203.01 3 0.1006 0.71724 0.00 0.02 0.96 0.00 0.00 0.00 0.02
#> TCGA.J2.8194.01 3 0.5205 0.48578 0.00 0.04 0.70 0.08 0.00 0.10 0.08
#> TCGA.05.5425.01 5 0.3722 0.54659 0.00 0.00 0.00 0.18 0.76 0.04 0.02
#> TCGA.55.A494.01 6 0.5276 0.39219 0.00 0.10 0.08 0.00 0.00 0.64 0.18
#> TCGA.44.3917.01 3 0.4110 0.47436 0.00 0.06 0.78 0.04 0.00 0.02 0.10
#> TCGA.L4.A4E5.01 6 0.3221 0.62395 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.55.A4DG.01 1 0.3228 0.51435 0.80 0.02 0.00 0.16 0.00 0.00 0.02
#> TCGA.91.6829.01 4 0.5875 0.00000 0.30 0.00 0.00 0.44 0.24 0.00 0.02
#> TCGA.78.7542.01 1 0.5070 0.22384 0.64 0.00 0.00 0.24 0.08 0.02 0.02
#> TCGA.97.8179.01 5 0.6146 -0.03552 0.18 0.00 0.00 0.30 0.46 0.00 0.06
#> TCGA.55.8092.01 1 0.1006 0.64708 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.75.6207.01 1 0.0504 0.64865 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.95.7043.01 6 0.4821 0.60988 0.00 0.22 0.00 0.04 0.00 0.66 0.08
#> TCGA.49.6767.01 6 0.4773 0.63869 0.00 0.20 0.00 0.02 0.00 0.66 0.12
#> TCGA.50.5051.01 3 0.1006 0.74506 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.80.5608.01 3 0.1363 0.73728 0.00 0.00 0.94 0.02 0.00 0.04 0.00
#> TCGA.78.7159.01 3 0.0504 0.74627 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.44.8120.01 1 0.5798 -0.71690 0.44 0.00 0.00 0.34 0.20 0.00 0.02
#> TCGA.73.A9RS.01 5 0.4623 0.47834 0.04 0.00 0.00 0.28 0.64 0.00 0.04
#> TCGA.95.7039.01 2 0.1166 0.60788 0.06 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.71.6725.01 2 0.4770 0.49731 0.02 0.72 0.00 0.04 0.00 0.12 0.10
#> TCGA.86.8359.01 5 0.2769 0.58283 0.00 0.00 0.00 0.08 0.86 0.02 0.04
#> TCGA.78.7161.01 3 0.1860 0.71653 0.00 0.00 0.92 0.02 0.00 0.04 0.02
#> TCGA.97.7937.01 1 0.2804 0.61348 0.86 0.02 0.00 0.06 0.00 0.00 0.06
#> TCGA.44.5644.01 7 0.5776 0.00000 0.00 0.10 0.38 0.06 0.00 0.00 0.46
#> TCGA.L9.A7SV.01 1 0.6987 -0.66888 0.36 0.04 0.00 0.36 0.16 0.00 0.08
#> TCGA.05.4390.01 3 0.0000 0.73942 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7979.01 6 0.3307 0.66695 0.00 0.24 0.00 0.02 0.00 0.74 0.00
#> TCGA.50.7109.01 5 0.1363 0.59181 0.00 0.00 0.00 0.04 0.94 0.00 0.02
#> TCGA.75.6211.01 3 0.3343 0.60341 0.00 0.04 0.82 0.04 0.00 0.00 0.10
#> TCGA.91.6828.01 1 0.5300 0.28628 0.58 0.00 0.00 0.10 0.28 0.00 0.04
#> TCGA.05.4396.01 1 0.1363 0.64355 0.94 0.00 0.00 0.04 0.02 0.00 0.00
#> TCGA.MN.A4N4.01 5 0.5625 0.23951 0.06 0.00 0.00 0.40 0.48 0.04 0.02
#> TCGA.NJ.A4YF.01 6 0.6512 0.39093 0.00 0.24 0.10 0.00 0.00 0.44 0.22
#> TCGA.78.8662.01 2 0.3439 0.55496 0.00 0.82 0.00 0.06 0.00 0.06 0.06
#> TCGA.05.4427.01 2 0.1664 0.60225 0.06 0.92 0.00 0.00 0.00 0.00 0.02
#> TCGA.78.7147.01 6 0.3968 0.43067 0.00 0.44 0.00 0.00 0.00 0.54 0.02
#> TCGA.MP.A4TE.01 1 0.7003 0.26975 0.50 0.00 0.14 0.10 0.18 0.00 0.08
#> TCGA.95.A4VK.01 6 0.6087 0.42579 0.00 0.26 0.06 0.02 0.00 0.54 0.12
#> TCGA.49.4488.01 2 0.4266 -0.25353 0.00 0.52 0.00 0.00 0.00 0.44 0.04
#> TCGA.55.7994.01 1 0.0000 0.64918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 3 0.6863 0.10256 0.00 0.12 0.52 0.10 0.00 0.18 0.08
#> TCGA.35.5375.01 5 0.3835 0.51323 0.10 0.00 0.00 0.16 0.74 0.00 0.00
#> TCGA.95.7562.01 5 0.5526 0.23519 0.18 0.00 0.00 0.20 0.58 0.00 0.04
#> TCGA.55.8616.01 2 0.0504 0.60170 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 1 0.0000 0.64918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 5 0.4514 0.47541 0.14 0.00 0.00 0.14 0.70 0.00 0.02
#> TCGA.55.8506.01 2 0.1166 0.60788 0.06 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 5 0.5023 0.23014 0.26 0.00 0.00 0.08 0.62 0.00 0.04
#> TCGA.78.7539.01 2 0.6502 0.00368 0.00 0.44 0.16 0.00 0.00 0.28 0.12
#> TCGA.62.A46S.01 5 0.2163 0.57521 0.00 0.00 0.00 0.10 0.88 0.00 0.02
#> TCGA.78.7145.01 6 0.3637 0.66786 0.00 0.24 0.00 0.00 0.00 0.72 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.MP.A4T8.01 1 0.6881 0.1697 0.44 0.06 0.00 0.30 0.08 0.00 0.06 0.06
#> TCGA.86.6851.01 6 0.3808 -0.0273 0.00 0.30 0.00 0.00 0.02 0.66 0.00 0.02
#> TCGA.64.5775.01 1 0.2020 0.6183 0.90 0.02 0.00 0.02 0.00 0.00 0.06 0.00
#> TCGA.62.8394.01 6 0.3128 0.5326 0.00 0.04 0.00 0.00 0.10 0.82 0.04 0.00
#> TCGA.05.5428.01 1 0.2914 0.5712 0.84 0.00 0.00 0.00 0.04 0.00 0.04 0.08
#> TCGA.55.6642.01 4 0.1408 0.5049 0.00 0.00 0.00 0.94 0.02 0.00 0.02 0.02
#> TCGA.50.6673.01 6 0.5717 0.1034 0.00 0.22 0.04 0.00 0.12 0.58 0.02 0.02
#> TCGA.86.6562.01 4 0.6804 -0.0844 0.18 0.06 0.00 0.46 0.06 0.00 0.02 0.22
#> TCGA.86.8074.01 6 0.3002 0.5345 0.00 0.02 0.00 0.00 0.12 0.82 0.04 0.00
#> TCGA.55.8203.01 3 0.1741 0.7161 0.00 0.02 0.92 0.00 0.04 0.00 0.00 0.02
#> TCGA.J2.8194.01 3 0.4808 0.4190 0.00 0.08 0.66 0.00 0.16 0.10 0.00 0.00
#> TCGA.05.5425.01 4 0.5040 0.3038 0.02 0.00 0.00 0.62 0.04 0.00 0.08 0.24
#> TCGA.55.A494.01 6 0.5298 0.4526 0.00 0.06 0.06 0.00 0.30 0.56 0.02 0.00
#> TCGA.44.3917.01 3 0.3185 0.5653 0.00 0.08 0.82 0.00 0.04 0.00 0.06 0.00
#> TCGA.L4.A4E5.01 6 0.3503 0.4376 0.00 0.12 0.00 0.00 0.08 0.78 0.02 0.00
#> TCGA.55.A4DG.01 1 0.2482 0.6008 0.88 0.02 0.00 0.00 0.02 0.00 0.06 0.02
#> TCGA.91.6829.01 1 0.6559 -0.3551 0.34 0.00 0.00 0.20 0.02 0.00 0.10 0.34
#> TCGA.78.7542.01 1 0.7089 -0.1795 0.46 0.06 0.00 0.18 0.08 0.00 0.04 0.18
#> TCGA.97.8179.01 8 0.6877 0.0968 0.16 0.08 0.00 0.30 0.04 0.00 0.02 0.40
#> TCGA.55.8092.01 1 0.1275 0.6301 0.94 0.04 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.75.6207.01 1 0.0471 0.6339 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 6 0.4826 0.4648 0.00 0.02 0.00 0.00 0.30 0.60 0.04 0.04
#> TCGA.49.6767.01 6 0.2680 0.5379 0.00 0.02 0.00 0.00 0.12 0.84 0.02 0.00
#> TCGA.50.5051.01 3 0.1557 0.7267 0.00 0.02 0.92 0.00 0.06 0.00 0.00 0.00
#> TCGA.80.5608.01 3 0.0471 0.7470 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.78.7159.01 3 0.0000 0.7430 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8120.01 1 0.5048 -0.0199 0.48 0.04 0.00 0.08 0.00 0.00 0.00 0.40
#> TCGA.73.A9RS.01 4 0.5908 0.1545 0.06 0.04 0.00 0.44 0.00 0.00 0.08 0.38
#> TCGA.95.7039.01 2 0.4233 0.8402 0.04 0.60 0.00 0.00 0.02 0.34 0.00 0.00
#> TCGA.71.6725.01 2 0.3658 0.8087 0.00 0.58 0.00 0.00 0.00 0.40 0.00 0.02
#> TCGA.86.8359.01 4 0.3586 0.4510 0.00 0.04 0.00 0.78 0.06 0.00 0.00 0.12
#> TCGA.78.7161.01 3 0.2025 0.6941 0.00 0.00 0.88 0.00 0.10 0.00 0.02 0.00
#> TCGA.97.7937.01 1 0.2204 0.6084 0.90 0.04 0.00 0.00 0.02 0.00 0.02 0.02
#> TCGA.44.5644.01 7 0.4888 0.0000 0.00 0.10 0.36 0.00 0.02 0.00 0.52 0.00
#> TCGA.L9.A7SV.01 8 0.5839 0.0582 0.36 0.02 0.00 0.06 0.02 0.00 0.06 0.48
#> TCGA.05.4390.01 3 0.0471 0.7391 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.69.7979.01 6 0.3847 0.5228 0.00 0.04 0.00 0.00 0.10 0.78 0.06 0.02
#> TCGA.50.7109.01 4 0.1741 0.5062 0.00 0.00 0.00 0.92 0.02 0.00 0.02 0.04
#> TCGA.75.6211.01 3 0.2348 0.6881 0.00 0.06 0.88 0.00 0.02 0.00 0.04 0.00
#> TCGA.91.6828.01 1 0.6285 0.1381 0.44 0.06 0.00 0.36 0.02 0.00 0.08 0.04
#> TCGA.05.4396.01 1 0.2858 0.6030 0.86 0.04 0.00 0.04 0.00 0.00 0.04 0.02
#> TCGA.MN.A4N4.01 8 0.6533 -0.1077 0.08 0.00 0.00 0.30 0.02 0.00 0.26 0.34
#> TCGA.NJ.A4YF.01 6 0.7699 0.3060 0.00 0.14 0.14 0.02 0.12 0.42 0.14 0.02
#> TCGA.78.8662.01 2 0.5242 0.7209 0.00 0.50 0.00 0.00 0.02 0.38 0.06 0.04
#> TCGA.05.4427.01 2 0.4415 0.8067 0.06 0.60 0.00 0.00 0.00 0.32 0.00 0.02
#> TCGA.78.7147.01 6 0.3291 0.2461 0.00 0.28 0.00 0.00 0.00 0.70 0.00 0.02
#> TCGA.MP.A4TE.01 1 0.7061 0.2424 0.50 0.02 0.08 0.14 0.04 0.00 0.18 0.04
#> TCGA.95.A4VK.01 6 0.6129 0.3536 0.00 0.12 0.16 0.00 0.18 0.52 0.00 0.02
#> TCGA.49.4488.01 6 0.4059 0.0973 0.00 0.28 0.00 0.00 0.08 0.64 0.00 0.00
#> TCGA.55.7994.01 1 0.0000 0.6321 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 3 0.5966 0.1082 0.00 0.08 0.50 0.00 0.30 0.08 0.04 0.00
#> TCGA.35.5375.01 4 0.5039 0.3338 0.08 0.00 0.00 0.56 0.02 0.00 0.02 0.32
#> TCGA.95.7562.01 4 0.6885 0.0195 0.22 0.06 0.00 0.40 0.00 0.00 0.10 0.22
#> TCGA.55.8616.01 2 0.3193 0.8500 0.00 0.62 0.00 0.00 0.00 0.38 0.00 0.00
#> TCGA.MP.A4SV.01 1 0.0808 0.6338 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 4 0.5239 0.3773 0.16 0.02 0.00 0.64 0.00 0.00 0.10 0.08
#> TCGA.55.8506.01 2 0.3570 0.8581 0.02 0.62 0.00 0.00 0.00 0.36 0.00 0.00
#> TCGA.55.7815.01 4 0.4887 0.1869 0.32 0.02 0.00 0.58 0.00 0.00 0.04 0.04
#> TCGA.78.7539.01 6 0.6051 0.1533 0.00 0.26 0.06 0.00 0.18 0.48 0.00 0.02
#> TCGA.62.A46S.01 4 0.0808 0.5020 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.78.7145.01 6 0.2862 0.5351 0.00 0.08 0.00 0.00 0.10 0.82 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01221-leaf , Node01222-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-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 21 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4672 0.533 0.533
#> 3 3 1.000 0.973 0.978 0.1157 0.952 0.911
#> 4 4 0.732 0.676 0.867 0.1871 0.886 0.765
#> 5 5 0.805 0.721 0.922 0.1434 0.857 0.639
#> 6 6 0.752 0.679 0.908 0.0232 0.995 0.983
#> 7 7 0.781 0.606 0.899 0.0572 0.929 0.750
#> 8 8 0.843 0.588 0.912 0.0403 0.986 0.938
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.86.6851.01 1 0 1 1 0
#> TCGA.62.8394.01 1 0 1 1 0
#> TCGA.50.6673.01 1 0 1 1 0
#> TCGA.86.8074.01 1 0 1 1 0
#> TCGA.55.A494.01 1 0 1 1 0
#> TCGA.L4.A4E5.01 1 0 1 1 0
#> TCGA.95.7043.01 1 0 1 1 0
#> TCGA.49.6767.01 1 0 1 1 0
#> TCGA.95.7039.01 2 0 1 0 1
#> TCGA.71.6725.01 2 0 1 0 1
#> TCGA.69.7979.01 1 0 1 1 0
#> TCGA.NJ.A4YF.01 1 0 1 1 0
#> TCGA.78.8662.01 2 0 1 0 1
#> TCGA.05.4427.01 2 0 1 0 1
#> TCGA.78.7147.01 1 0 1 1 0
#> TCGA.95.A4VK.01 1 0 1 1 0
#> TCGA.49.4488.01 2 0 1 0 1
#> TCGA.55.8616.01 2 0 1 0 1
#> TCGA.55.8506.01 2 0 1 0 1
#> TCGA.78.7539.01 1 0 1 1 0
#> TCGA.78.7145.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.86.6851.01 1 0.2066 0.958 0.94 0.00 0.06
#> TCGA.62.8394.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.50.6673.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.86.8074.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.55.A494.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.L4.A4E5.01 1 0.2066 0.958 0.94 0.00 0.06
#> TCGA.95.7043.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.49.6767.01 1 0.2066 0.958 0.94 0.00 0.06
#> TCGA.95.7039.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.71.6725.01 3 0.4002 0.881 0.00 0.16 0.84
#> TCGA.69.7979.01 1 0.1529 0.967 0.96 0.00 0.04
#> TCGA.NJ.A4YF.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.78.8662.01 3 0.2066 0.891 0.00 0.06 0.94
#> TCGA.05.4427.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.78.7147.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.95.A4VK.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.49.4488.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.55.8616.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.55.8506.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.78.7539.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.78.7145.01 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.86.6851.01 4 0.495 1.0000 0.44 0.00 0.00 0.56
#> TCGA.62.8394.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
#> TCGA.50.6673.01 1 0.380 0.3715 0.78 0.00 0.00 0.22
#> TCGA.86.8074.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
#> TCGA.55.A494.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
#> TCGA.L4.A4E5.01 1 0.498 -0.7461 0.54 0.00 0.00 0.46
#> TCGA.95.7043.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
#> TCGA.49.6767.01 4 0.495 1.0000 0.44 0.00 0.00 0.56
#> TCGA.95.7039.01 2 0.000 0.9193 0.00 1.00 0.00 0.00
#> TCGA.71.6725.01 3 0.317 0.4428 0.00 0.16 0.84 0.00
#> TCGA.69.7979.01 1 0.441 -0.0794 0.70 0.00 0.00 0.30
#> TCGA.NJ.A4YF.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
#> TCGA.78.8662.01 3 0.557 0.5469 0.00 0.02 0.54 0.44
#> TCGA.05.4427.01 2 0.000 0.9193 0.00 1.00 0.00 0.00
#> TCGA.78.7147.01 1 0.121 0.7795 0.96 0.00 0.00 0.04
#> TCGA.95.A4VK.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
#> TCGA.49.4488.01 2 0.428 0.5981 0.00 0.72 0.28 0.00
#> TCGA.55.8616.01 2 0.000 0.9193 0.00 1.00 0.00 0.00
#> TCGA.55.8506.01 2 0.000 0.9193 0.00 1.00 0.00 0.00
#> TCGA.78.7539.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
#> TCGA.78.7145.01 1 0.000 0.8268 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.86.6851.01 4 0.1410 0.7339 0.06 0.0 0.00 0.94 0.00
#> TCGA.62.8394.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
#> TCGA.50.6673.01 4 0.4060 0.5183 0.36 0.0 0.00 0.64 0.00
#> TCGA.86.8074.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
#> TCGA.55.A494.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
#> TCGA.L4.A4E5.01 4 0.2929 0.7304 0.18 0.0 0.00 0.82 0.00
#> TCGA.95.7043.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
#> TCGA.49.6767.01 4 0.0609 0.6788 0.02 0.0 0.00 0.98 0.00
#> TCGA.95.7039.01 2 0.0000 1.0000 0.00 1.0 0.00 0.00 0.00
#> TCGA.71.6725.01 3 0.0609 0.1536 0.00 0.0 0.98 0.00 0.02
#> TCGA.69.7979.01 1 0.4227 0.0382 0.58 0.0 0.00 0.42 0.00
#> TCGA.NJ.A4YF.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
#> TCGA.78.8662.01 5 0.0000 0.0000 0.00 0.0 0.00 0.00 1.00
#> TCGA.05.4427.01 2 0.0000 1.0000 0.00 1.0 0.00 0.00 0.00
#> TCGA.78.7147.01 1 0.1732 0.8525 0.92 0.0 0.00 0.08 0.00
#> TCGA.95.A4VK.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
#> TCGA.49.4488.01 3 0.4307 -0.0199 0.00 0.5 0.50 0.00 0.00
#> TCGA.55.8616.01 2 0.0000 1.0000 0.00 1.0 0.00 0.00 0.00
#> TCGA.55.8506.01 2 0.0000 1.0000 0.00 1.0 0.00 0.00 0.00
#> TCGA.78.7539.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
#> TCGA.78.7145.01 1 0.0000 0.9310 1.00 0.0 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.86.6851.01 4 0.1480 0.577 0.04 0.00 0.00 0.94 0 0.02
#> TCGA.62.8394.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.50.6673.01 4 0.4806 0.397 0.38 0.00 0.00 0.56 0 0.06
#> TCGA.86.8074.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.55.A494.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.L4.A4E5.01 4 0.4247 0.572 0.24 0.00 0.00 0.70 0 0.06
#> TCGA.95.7043.01 1 0.0937 0.886 0.96 0.00 0.00 0.00 0 0.04
#> TCGA.49.6767.01 4 0.2260 0.471 0.00 0.00 0.00 0.86 0 0.14
#> TCGA.95.7039.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.71.6725.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.69.7979.01 1 0.5354 0.236 0.58 0.00 0.00 0.26 0 0.16
#> TCGA.NJ.A4YF.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.78.8662.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.05.4427.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.78.7147.01 1 0.3270 0.714 0.82 0.00 0.00 0.12 0 0.06
#> TCGA.95.A4VK.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.49.4488.01 6 0.4926 0.000 0.00 0.24 0.12 0.00 0 0.64
#> TCGA.55.8616.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.55.8506.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.78.7539.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.78.7145.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.86.6851.01 4 0.464 0.0721 0.00 0.00 0.0 0.54 0 0.08 0.38
#> TCGA.62.8394.01 1 0.000 0.9387 1.00 0.00 0.0 0.00 0 0.00 0.00
#> TCGA.50.6673.01 4 0.630 0.2899 0.34 0.00 0.0 0.42 0 0.08 0.16
#> TCGA.86.8074.01 1 0.000 0.9387 1.00 0.00 0.0 0.00 0 0.00 0.00
#> TCGA.55.A494.01 1 0.000 0.9387 1.00 0.00 0.0 0.00 0 0.00 0.00
#> TCGA.L4.A4E5.01 4 0.435 0.3060 0.10 0.00 0.0 0.66 0 0.00 0.24
#> TCGA.95.7043.01 1 0.101 0.9035 0.96 0.00 0.0 0.02 0 0.02 0.00
#> TCGA.49.6767.01 7 0.000 0.0000 0.00 0.00 0.0 0.00 0 0.00 1.00
#> TCGA.95.7039.01 2 0.000 1.0000 0.00 1.00 0.0 0.00 0 0.00 0.00
#> TCGA.71.6725.01 3 0.000 0.0000 0.00 0.00 1.0 0.00 0 0.00 0.00
#> TCGA.69.7979.01 4 0.474 0.2599 0.20 0.00 0.0 0.68 0 0.06 0.06
#> TCGA.NJ.A4YF.01 1 0.000 0.9387 1.00 0.00 0.0 0.00 0 0.00 0.00
#> TCGA.78.8662.01 5 0.000 0.0000 0.00 0.00 0.0 0.00 1 0.00 0.00
#> TCGA.05.4427.01 2 0.000 1.0000 0.00 1.00 0.0 0.00 0 0.00 0.00
#> TCGA.78.7147.01 1 0.415 0.3306 0.64 0.00 0.0 0.32 0 0.02 0.02
#> TCGA.95.A4VK.01 1 0.000 0.9387 1.00 0.00 0.0 0.00 0 0.00 0.00
#> TCGA.49.4488.01 6 0.280 0.0000 0.00 0.06 0.1 0.00 0 0.84 0.00
#> TCGA.55.8616.01 2 0.000 1.0000 0.00 1.00 0.0 0.00 0 0.00 0.00
#> TCGA.55.8506.01 2 0.000 1.0000 0.00 1.00 0.0 0.00 0 0.00 0.00
#> TCGA.78.7539.01 1 0.000 0.9387 1.00 0.00 0.0 0.00 0 0.00 0.00
#> TCGA.78.7145.01 1 0.000 0.9387 1.00 0.00 0.0 0.00 0 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.86.6851.01 4 0.2981 0.377 0.00 0 0 0.76 0 0 0.22 0.02
#> TCGA.62.8394.01 1 0.0000 0.912 1.00 0 0 0.00 0 0 0.00 0.00
#> TCGA.50.6673.01 4 0.4764 0.359 0.16 0 0 0.66 0 0 0.06 0.12
#> TCGA.86.8074.01 1 0.0471 0.898 0.98 0 0 0.02 0 0 0.00 0.00
#> TCGA.55.A494.01 1 0.0000 0.912 1.00 0 0 0.00 0 0 0.00 0.00
#> TCGA.L4.A4E5.01 4 0.4138 0.254 0.04 0 0 0.72 0 0 0.08 0.16
#> TCGA.95.7043.01 1 0.2719 0.723 0.80 0 0 0.02 0 0 0.00 0.18
#> TCGA.49.6767.01 7 0.0000 0.000 0.00 0 0 0.00 0 0 1.00 0.00
#> TCGA.95.7039.01 2 0.0000 1.000 0.00 1 0 0.00 0 0 0.00 0.00
#> TCGA.71.6725.01 3 0.0000 0.000 0.00 0 1 0.00 0 0 0.00 0.00
#> TCGA.69.7979.01 8 0.3922 0.000 0.06 0 0 0.30 0 0 0.00 0.64
#> TCGA.NJ.A4YF.01 1 0.0000 0.912 1.00 0 0 0.00 0 0 0.00 0.00
#> TCGA.78.8662.01 5 0.0000 0.000 0.00 0 0 0.00 1 0 0.00 0.00
#> TCGA.05.4427.01 2 0.0000 1.000 0.00 1 0 0.00 0 0 0.00 0.00
#> TCGA.78.7147.01 1 0.4255 0.258 0.58 0 0 0.34 0 0 0.00 0.08
#> TCGA.95.A4VK.01 1 0.0000 0.912 1.00 0 0 0.00 0 0 0.00 0.00
#> TCGA.49.4488.01 6 0.0000 0.000 0.00 0 0 0.00 0 1 0.00 0.00
#> TCGA.55.8616.01 2 0.0000 1.000 0.00 1 0 0.00 0 0 0.00 0.00
#> TCGA.55.8506.01 2 0.0000 1.000 0.00 1 0 0.00 0 0 0.00 0.00
#> TCGA.78.7539.01 1 0.0000 0.912 1.00 0 0 0.00 0 0 0.00 0.00
#> TCGA.78.7145.01 1 0.0000 0.912 1.00 0 0 0.00 0 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122 , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221-leaf , Node0222 , Node0223-leaf , Node0231 , Node0232 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0324-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["023"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 91 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5011 0.499 0.499
#> 3 3 0.741 0.827 0.856 0.2324 0.895 0.790
#> 4 4 0.616 0.692 0.745 0.1241 0.863 0.661
#> 5 5 0.630 0.625 0.685 0.0910 0.915 0.707
#> 6 6 0.669 0.655 0.738 0.0542 0.911 0.651
#> 7 7 0.696 0.572 0.755 0.0376 0.963 0.823
#> 8 8 0.701 0.596 0.752 0.0186 0.914 0.589
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.44.4112.01 1 0 1 1 0
#> TCGA.NJ.A4YP.01 2 0 1 0 1
#> TCGA.50.6597.01 1 0 1 1 0
#> TCGA.J2.A4AG.01 1 0 1 1 0
#> TCGA.MP.A4TK.01 1 0 1 1 0
#> TCGA.MN.A4N1.01 2 0 1 0 1
#> TCGA.91.6847.01 2 0 1 0 1
#> TCGA.MP.A4TC.01 2 0 1 0 1
#> TCGA.05.4410.01 2 0 1 0 1
#> TCGA.55.6982.01 1 0 1 1 0
#> TCGA.55.7727.01 2 0 1 0 1
#> TCGA.MP.A4SW.01 2 0 1 0 1
#> TCGA.55.A57B.01 1 0 1 1 0
#> TCGA.NJ.A4YI.01 1 0 1 1 0
#> TCGA.L9.A444.01 1 0 1 1 0
#> TCGA.86.8668.01 1 0 1 1 0
#> TCGA.44.A47G.01 1 0 1 1 0
#> TCGA.62.A46R.01 1 0 1 1 0
#> TCGA.75.5125.01 2 0 1 0 1
#> TCGA.44.6775.01 1 0 1 1 0
#> TCGA.55.7911.01 1 0 1 1 0
#> TCGA.55.6712.01 2 0 1 0 1
#> TCGA.69.7760.01 2 0 1 0 1
#> TCGA.55.6985.01 1 0 1 1 0
#> TCGA.MP.A4TF.01 1 0 1 1 0
#> TCGA.44.A47B.01 2 0 1 0 1
#> TCGA.05.5429.01 2 0 1 0 1
#> TCGA.86.A4JF.01 2 0 1 0 1
#> TCGA.75.5122.01 2 0 1 0 1
#> TCGA.49.AARE.01 1 0 1 1 0
#> TCGA.86.7701.01 2 0 1 0 1
#> TCGA.55.7281.01 1 0 1 1 0
#> TCGA.78.7535.01 2 0 1 0 1
#> TCGA.50.6592.01 1 0 1 1 0
#> TCGA.44.7661.01 1 0 1 1 0
#> TCGA.50.5933.01 2 0 1 0 1
#> TCGA.78.8660.01 2 0 1 0 1
#> TCGA.55.7907.01 2 0 1 0 1
#> TCGA.78.7540.01 1 0 1 1 0
#> TCGA.95.A4VN.01 1 0 1 1 0
#> TCGA.69.8253.01 1 0 1 1 0
#> TCGA.50.6590.01 1 0 1 1 0
#> TCGA.55.8205.01 1 0 1 1 0
#> TCGA.99.8025.01 1 0 1 1 0
#> TCGA.69.7761.01 2 0 1 0 1
#> TCGA.69.7978.01 2 0 1 0 1
#> TCGA.44.8117.01 1 0 1 1 0
#> TCGA.MP.A4TD.01 2 0 1 0 1
#> TCGA.83.5908.01 1 0 1 1 0
#> TCGA.55.8301.01 2 0 1 0 1
#> TCGA.78.7146.01 1 0 1 1 0
#> TCGA.44.3918.01 1 0 1 1 0
#> TCGA.55.8089.01 2 0 1 0 1
#> TCGA.55.8511.01 1 0 1 1 0
#> TCGA.91.A4BC.01 2 0 1 0 1
#> TCGA.44.2656.01 2 0 1 0 1
#> TCGA.73.7499.01 1 0 1 1 0
#> TCGA.95.8494.01 2 0 1 0 1
#> TCGA.69.7980.01 1 0 1 1 0
#> TCGA.05.4433.01 2 0 1 0 1
#> TCGA.44.6147.01 1 0 1 1 0
#> TCGA.86.8073.01 2 0 1 0 1
#> TCGA.64.5781.01 1 0 1 1 0
#> TCGA.78.7154.01 2 0 1 0 1
#> TCGA.78.7143.01 1 0 1 1 0
#> TCGA.97.A4M3.01 1 0 1 1 0
#> TCGA.55.A493.01 1 0 1 1 0
#> TCGA.NJ.A4YQ.01 1 0 1 1 0
#> TCGA.50.6594.01 1 0 1 1 0
#> TCGA.86.8056.01 1 0 1 1 0
#> TCGA.38.4632.01 2 0 1 0 1
#> TCGA.MP.A4T6.01 1 0 1 1 0
#> TCGA.44.6779.01 1 0 1 1 0
#> TCGA.49.6761.01 1 0 1 1 0
#> TCGA.55.6981.01 1 0 1 1 0
#> TCGA.05.4417.01 1 0 1 1 0
#> TCGA.97.7554.01 1 0 1 1 0
#> TCGA.95.8039.01 2 0 1 0 1
#> TCGA.55.7576.01 2 0 1 0 1
#> TCGA.86.8672.01 2 0 1 0 1
#> TCGA.44.6777.01 1 0 1 1 0
#> TCGA.73.4676.01 2 0 1 0 1
#> TCGA.91.6836.01 1 0 1 1 0
#> TCGA.55.A491.01 1 0 1 1 0
#> TCGA.55.6978.01 2 0 1 0 1
#> TCGA.55.A48Y.01 2 0 1 0 1
#> TCGA.97.A4M7.01 2 0 1 0 1
#> TCGA.44.7662.01 2 0 1 0 1
#> TCGA.44.7672.01 1 0 1 1 0
#> TCGA.78.7152.01 2 0 1 0 1
#> TCGA.55.8302.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.4112.01 1 0.5016 0.523 0.76 0.00 0.24
#> TCGA.NJ.A4YP.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.50.6597.01 1 0.0892 0.881 0.98 0.00 0.02
#> TCGA.J2.A4AG.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.MP.A4TK.01 1 0.4002 0.710 0.84 0.00 0.16
#> TCGA.MN.A4N1.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.91.6847.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.MP.A4TC.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.05.4410.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.55.6982.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.55.7727.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.MP.A4SW.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.55.A57B.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.NJ.A4YI.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.L9.A444.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.86.8668.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.44.A47G.01 1 0.6126 -0.204 0.60 0.00 0.40
#> TCGA.62.A46R.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.75.5125.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.44.6775.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.55.7911.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.55.6712.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.69.7760.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.55.6985.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.MP.A4TF.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.44.A47B.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.05.5429.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.86.A4JF.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.75.5122.01 2 0.5560 0.847 0.00 0.70 0.30
#> TCGA.49.AARE.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.86.7701.01 2 0.0892 0.845 0.00 0.98 0.02
#> TCGA.55.7281.01 1 0.2066 0.846 0.94 0.00 0.06
#> TCGA.78.7535.01 2 0.5560 0.847 0.00 0.70 0.30
#> TCGA.50.6592.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.44.7661.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.50.5933.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.78.8660.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.55.7907.01 2 0.0892 0.845 0.00 0.98 0.02
#> TCGA.78.7540.01 1 0.2537 0.825 0.92 0.00 0.08
#> TCGA.95.A4VN.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.69.8253.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.50.6590.01 1 0.1529 0.864 0.96 0.00 0.04
#> TCGA.55.8205.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.99.8025.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.69.7761.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.69.7978.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.44.8117.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.MP.A4TD.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.83.5908.01 1 0.2959 0.801 0.90 0.00 0.10
#> TCGA.55.8301.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.78.7146.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.44.3918.01 1 0.6302 -0.541 0.52 0.00 0.48
#> TCGA.55.8089.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.55.8511.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.91.A4BC.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.44.2656.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.73.7499.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.95.8494.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.69.7980.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.05.4433.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.44.6147.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.86.8073.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.64.5781.01 1 0.2066 0.846 0.94 0.00 0.06
#> TCGA.78.7154.01 2 0.3686 0.849 0.00 0.86 0.14
#> TCGA.78.7143.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.97.A4M3.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.55.A493.01 1 0.4002 0.710 0.84 0.00 0.16
#> TCGA.NJ.A4YQ.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.50.6594.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.86.8056.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.38.4632.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.MP.A4T6.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.44.6779.01 1 0.4002 0.710 0.84 0.00 0.16
#> TCGA.49.6761.01 1 0.6192 -0.300 0.58 0.00 0.42
#> TCGA.55.6981.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.05.4417.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.97.7554.01 3 0.5835 1.000 0.34 0.00 0.66
#> TCGA.95.8039.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.55.7576.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.86.8672.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.44.6777.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.73.4676.01 2 0.5835 0.845 0.00 0.66 0.34
#> TCGA.91.6836.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.55.A491.01 1 0.0000 0.895 1.00 0.00 0.00
#> TCGA.55.6978.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.55.A48Y.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.97.A4M7.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.44.7662.01 2 0.0000 0.843 0.00 1.00 0.00
#> TCGA.44.7672.01 1 0.4555 0.627 0.80 0.00 0.20
#> TCGA.78.7152.01 2 0.3340 0.848 0.00 0.88 0.12
#> TCGA.55.8302.01 2 0.0000 0.843 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.44.4112.01 1 0.6510 0.2574 0.54 0.00 0.38 0.08
#> TCGA.NJ.A4YP.01 2 0.0707 0.8657 0.00 0.98 0.02 0.00
#> TCGA.50.6597.01 1 0.4713 0.6390 0.64 0.00 0.36 0.00
#> TCGA.J2.A4AG.01 1 0.4522 0.6682 0.68 0.00 0.32 0.00
#> TCGA.MP.A4TK.01 1 0.4406 0.4437 0.70 0.00 0.30 0.00
#> TCGA.MN.A4N1.01 2 0.2921 0.7876 0.00 0.86 0.14 0.00
#> TCGA.91.6847.01 4 0.6453 0.9033 0.00 0.36 0.08 0.56
#> TCGA.MP.A4TC.01 4 0.6941 0.8511 0.00 0.36 0.12 0.52
#> TCGA.05.4410.01 2 0.2921 0.7876 0.00 0.86 0.14 0.00
#> TCGA.55.6982.01 1 0.0000 0.7078 1.00 0.00 0.00 0.00
#> TCGA.55.7727.01 2 0.0707 0.8657 0.00 0.98 0.02 0.00
#> TCGA.MP.A4SW.01 4 0.6453 0.9010 0.00 0.36 0.08 0.56
#> TCGA.55.A57B.01 3 0.7274 0.7114 0.24 0.00 0.54 0.22
#> TCGA.NJ.A4YI.01 3 0.7684 0.7761 0.22 0.00 0.42 0.36
#> TCGA.L9.A444.01 3 0.7610 0.7644 0.22 0.00 0.46 0.32
#> TCGA.86.8668.01 1 0.4406 0.6786 0.70 0.00 0.30 0.00
#> TCGA.44.A47G.01 3 0.5594 -0.2794 0.46 0.00 0.52 0.02
#> TCGA.62.A46R.01 3 0.7684 0.7761 0.22 0.00 0.42 0.36
#> TCGA.75.5125.01 4 0.5355 0.9375 0.00 0.36 0.02 0.62
#> TCGA.44.6775.01 1 0.4406 0.6786 0.70 0.00 0.30 0.00
#> TCGA.55.7911.01 3 0.7684 0.7761 0.22 0.00 0.42 0.36
#> TCGA.55.6712.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.69.7760.01 4 0.4713 0.9430 0.00 0.36 0.00 0.64
#> TCGA.55.6985.01 1 0.3975 0.6975 0.76 0.00 0.24 0.00
#> TCGA.MP.A4TF.01 1 0.0707 0.7033 0.98 0.00 0.02 0.00
#> TCGA.44.A47B.01 2 0.1211 0.8608 0.00 0.96 0.04 0.00
#> TCGA.05.5429.01 4 0.5793 0.9266 0.00 0.36 0.04 0.60
#> TCGA.86.A4JF.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.75.5122.01 2 0.2011 0.7965 0.00 0.92 0.00 0.08
#> TCGA.49.AARE.01 1 0.0707 0.7036 0.98 0.00 0.02 0.00
#> TCGA.86.7701.01 4 0.5355 0.9381 0.00 0.36 0.02 0.62
#> TCGA.55.7281.01 1 0.4855 0.5861 0.60 0.00 0.40 0.00
#> TCGA.78.7535.01 2 0.4491 0.7085 0.00 0.80 0.14 0.06
#> TCGA.50.6592.01 1 0.0000 0.7078 1.00 0.00 0.00 0.00
#> TCGA.44.7661.01 1 0.4624 0.6520 0.66 0.00 0.34 0.00
#> TCGA.50.5933.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.55.7907.01 4 0.6453 0.9049 0.00 0.36 0.08 0.56
#> TCGA.78.7540.01 1 0.4948 0.5050 0.56 0.00 0.44 0.00
#> TCGA.95.A4VN.01 3 0.7274 0.7289 0.22 0.00 0.54 0.24
#> TCGA.69.8253.01 1 0.3801 0.7033 0.78 0.00 0.22 0.00
#> TCGA.50.6590.01 1 0.2011 0.6696 0.92 0.00 0.08 0.00
#> TCGA.55.8205.01 3 0.7274 0.7289 0.22 0.00 0.54 0.24
#> TCGA.99.8025.01 3 0.7684 0.7761 0.22 0.00 0.42 0.36
#> TCGA.69.7761.01 4 0.4713 0.9430 0.00 0.36 0.00 0.64
#> TCGA.69.7978.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.44.8117.01 3 0.7684 0.7761 0.22 0.00 0.42 0.36
#> TCGA.MP.A4TD.01 2 0.3606 0.6879 0.00 0.84 0.02 0.14
#> TCGA.83.5908.01 1 0.4977 0.4646 0.54 0.00 0.46 0.00
#> TCGA.55.8301.01 4 0.4713 0.9430 0.00 0.36 0.00 0.64
#> TCGA.78.7146.01 1 0.0000 0.7078 1.00 0.00 0.00 0.00
#> TCGA.44.3918.01 1 0.7206 -0.1986 0.46 0.00 0.40 0.14
#> TCGA.55.8089.01 4 0.5355 0.9374 0.00 0.36 0.02 0.62
#> TCGA.55.8511.01 3 0.7684 0.7761 0.22 0.00 0.42 0.36
#> TCGA.91.A4BC.01 4 0.4713 0.9430 0.00 0.36 0.00 0.64
#> TCGA.44.2656.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.73.7499.01 1 0.0000 0.7078 1.00 0.00 0.00 0.00
#> TCGA.95.8494.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.69.7980.01 1 0.0000 0.7078 1.00 0.00 0.00 0.00
#> TCGA.05.4433.01 4 0.5793 0.9266 0.00 0.36 0.04 0.60
#> TCGA.44.6147.01 1 0.0000 0.7078 1.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.6941 0.8511 0.00 0.36 0.12 0.52
#> TCGA.64.5781.01 1 0.2647 0.6400 0.88 0.00 0.12 0.00
#> TCGA.78.7154.01 2 0.5883 -0.0928 0.00 0.64 0.06 0.30
#> TCGA.78.7143.01 1 0.3975 0.6975 0.76 0.00 0.24 0.00
#> TCGA.97.A4M3.01 1 0.3801 0.7033 0.78 0.00 0.22 0.00
#> TCGA.55.A493.01 1 0.5606 0.3300 0.50 0.00 0.48 0.02
#> TCGA.NJ.A4YQ.01 1 0.1637 0.6864 0.94 0.00 0.06 0.00
#> TCGA.50.6594.01 1 0.0707 0.7036 0.98 0.00 0.02 0.00
#> TCGA.86.8056.01 1 0.4522 0.6682 0.68 0.00 0.32 0.00
#> TCGA.38.4632.01 2 0.2921 0.7876 0.00 0.86 0.14 0.00
#> TCGA.MP.A4T6.01 1 0.0000 0.7078 1.00 0.00 0.00 0.00
#> TCGA.44.6779.01 1 0.4797 0.4577 0.72 0.00 0.26 0.02
#> TCGA.49.6761.01 3 0.5594 -0.2794 0.46 0.00 0.52 0.02
#> TCGA.55.6981.01 1 0.4406 0.6786 0.70 0.00 0.30 0.00
#> TCGA.05.4417.01 1 0.0707 0.7137 0.98 0.00 0.02 0.00
#> TCGA.97.7554.01 3 0.7684 0.7761 0.22 0.00 0.42 0.36
#> TCGA.95.8039.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.55.7576.01 2 0.0707 0.8674 0.00 0.98 0.02 0.00
#> TCGA.86.8672.01 2 0.1411 0.8516 0.00 0.96 0.02 0.02
#> TCGA.44.6777.01 1 0.4624 0.6520 0.66 0.00 0.34 0.00
#> TCGA.73.4676.01 2 0.0000 0.8727 0.00 1.00 0.00 0.00
#> TCGA.91.6836.01 1 0.1211 0.6930 0.96 0.00 0.04 0.00
#> TCGA.55.A491.01 1 0.3801 0.7033 0.78 0.00 0.22 0.00
#> TCGA.55.6978.01 4 0.4713 0.9430 0.00 0.36 0.00 0.64
#> TCGA.55.A48Y.01 4 0.5355 0.9375 0.00 0.36 0.02 0.62
#> TCGA.97.A4M7.01 4 0.4713 0.9430 0.00 0.36 0.00 0.64
#> TCGA.44.7662.01 4 0.6941 0.8511 0.00 0.36 0.12 0.52
#> TCGA.44.7672.01 3 0.5000 -0.4224 0.50 0.00 0.50 0.00
#> TCGA.78.7152.01 2 0.6586 -0.6055 0.00 0.50 0.08 0.42
#> TCGA.55.8302.01 4 0.5355 0.9374 0.00 0.36 0.02 0.62
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.4112.01 1 0.6047 -0.3897 0.48 0.00 0.12 0.00 0.40
#> TCGA.NJ.A4YP.01 2 0.3731 0.8976 0.00 0.80 0.00 0.16 0.04
#> TCGA.50.6597.01 1 0.6039 -0.5097 0.46 0.04 0.04 0.00 0.46
#> TCGA.J2.A4AG.01 1 0.5095 -0.1398 0.56 0.04 0.00 0.00 0.40
#> TCGA.MP.A4TK.01 1 0.5927 -0.2152 0.54 0.00 0.12 0.00 0.34
#> TCGA.MN.A4N1.01 2 0.5818 0.7858 0.00 0.66 0.02 0.14 0.18
#> TCGA.91.6847.01 4 0.4855 0.7472 0.00 0.06 0.04 0.76 0.14
#> TCGA.MP.A4TC.01 4 0.3999 0.7478 0.00 0.02 0.00 0.74 0.24
#> TCGA.05.4410.01 2 0.5971 0.7694 0.00 0.64 0.02 0.14 0.20
#> TCGA.55.6982.01 1 0.1410 0.5715 0.94 0.00 0.00 0.00 0.06
#> TCGA.55.7727.01 2 0.3319 0.9039 0.00 0.82 0.00 0.16 0.02
#> TCGA.MP.A4SW.01 4 0.2280 0.8417 0.00 0.00 0.00 0.88 0.12
#> TCGA.55.A57B.01 3 0.5680 0.6245 0.14 0.00 0.62 0.00 0.24
#> TCGA.NJ.A4YI.01 3 0.2754 0.8285 0.08 0.04 0.88 0.00 0.00
#> TCGA.L9.A444.01 3 0.3697 0.7938 0.08 0.00 0.82 0.00 0.10
#> TCGA.86.8668.01 1 0.4990 0.0271 0.60 0.04 0.00 0.00 0.36
#> TCGA.44.A47G.01 5 0.5961 0.7448 0.26 0.00 0.16 0.00 0.58
#> TCGA.62.A46R.01 3 0.1732 0.8328 0.08 0.00 0.92 0.00 0.00
#> TCGA.75.5125.01 4 0.0000 0.8747 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6775.01 1 0.4990 0.0271 0.60 0.04 0.00 0.00 0.36
#> TCGA.55.7911.01 3 0.1732 0.8328 0.08 0.00 0.92 0.00 0.00
#> TCGA.55.6712.01 2 0.3319 0.9039 0.00 0.82 0.00 0.16 0.02
#> TCGA.69.7760.01 4 0.1216 0.8677 0.00 0.02 0.00 0.96 0.02
#> TCGA.55.6985.01 1 0.4527 0.3016 0.70 0.04 0.00 0.00 0.26
#> TCGA.MP.A4TF.01 1 0.2280 0.5234 0.88 0.00 0.00 0.00 0.12
#> TCGA.44.A47B.01 2 0.4637 0.8743 0.00 0.74 0.00 0.16 0.10
#> TCGA.05.5429.01 4 0.2012 0.8554 0.00 0.00 0.02 0.92 0.06
#> TCGA.86.A4JF.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.75.5122.01 2 0.4613 0.6886 0.00 0.62 0.00 0.36 0.02
#> TCGA.49.AARE.01 1 0.1216 0.5803 0.96 0.02 0.00 0.00 0.02
#> TCGA.86.7701.01 4 0.2927 0.8390 0.00 0.02 0.02 0.88 0.08
#> TCGA.55.7281.01 5 0.6033 0.5079 0.44 0.04 0.04 0.00 0.48
#> TCGA.78.7535.01 2 0.6146 0.6634 0.00 0.56 0.00 0.20 0.24
#> TCGA.50.6592.01 1 0.1732 0.5592 0.92 0.00 0.00 0.00 0.08
#> TCGA.44.7661.01 5 0.4675 0.7445 0.38 0.00 0.02 0.00 0.60
#> TCGA.50.5933.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.78.8660.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.55.7907.01 4 0.4500 0.7944 0.00 0.02 0.04 0.76 0.18
#> TCGA.78.7540.01 5 0.4990 0.7763 0.36 0.00 0.04 0.00 0.60
#> TCGA.95.A4VN.01 3 0.5013 0.6870 0.08 0.00 0.68 0.00 0.24
#> TCGA.69.8253.01 1 0.4254 0.3751 0.74 0.04 0.00 0.00 0.22
#> TCGA.50.6590.01 1 0.3521 0.4492 0.82 0.00 0.04 0.00 0.14
#> TCGA.55.8205.01 3 0.5013 0.6870 0.08 0.00 0.68 0.00 0.24
#> TCGA.99.8025.01 3 0.2754 0.8285 0.08 0.04 0.88 0.00 0.00
#> TCGA.69.7761.01 4 0.0000 0.8747 0.00 0.00 0.00 1.00 0.00
#> TCGA.69.7978.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.44.8117.01 3 0.2754 0.8285 0.08 0.04 0.88 0.00 0.00
#> TCGA.MP.A4TD.01 2 0.4920 0.7700 0.00 0.66 0.02 0.30 0.02
#> TCGA.83.5908.01 5 0.5232 0.7902 0.34 0.00 0.06 0.00 0.60
#> TCGA.55.8301.01 4 0.1043 0.8740 0.00 0.00 0.00 0.96 0.04
#> TCGA.78.7146.01 1 0.1410 0.5666 0.94 0.00 0.00 0.00 0.06
#> TCGA.44.3918.01 3 0.6794 -0.1115 0.32 0.00 0.38 0.00 0.30
#> TCGA.55.8089.01 4 0.0609 0.8734 0.00 0.00 0.00 0.98 0.02
#> TCGA.55.8511.01 3 0.1732 0.8328 0.08 0.00 0.92 0.00 0.00
#> TCGA.91.A4BC.01 4 0.0609 0.8734 0.00 0.00 0.00 0.98 0.02
#> TCGA.44.2656.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.73.7499.01 1 0.0000 0.5831 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.8494.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.69.7980.01 1 0.0000 0.5831 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 4 0.0609 0.8723 0.00 0.00 0.00 0.98 0.02
#> TCGA.44.6147.01 1 0.0000 0.5831 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.3999 0.7478 0.00 0.02 0.00 0.74 0.24
#> TCGA.64.5781.01 1 0.4096 0.3431 0.76 0.00 0.04 0.00 0.20
#> TCGA.78.7154.01 4 0.6954 -0.0998 0.00 0.36 0.06 0.48 0.10
#> TCGA.78.7143.01 1 0.4644 0.2575 0.68 0.04 0.00 0.00 0.28
#> TCGA.97.A4M3.01 1 0.4254 0.3751 0.74 0.04 0.00 0.00 0.22
#> TCGA.55.A493.01 5 0.5788 0.7927 0.30 0.00 0.12 0.00 0.58
#> TCGA.NJ.A4YQ.01 1 0.2516 0.5007 0.86 0.00 0.00 0.00 0.14
#> TCGA.50.6594.01 1 0.0609 0.5788 0.98 0.02 0.00 0.00 0.00
#> TCGA.86.8056.01 1 0.5131 -0.2252 0.54 0.04 0.00 0.00 0.42
#> TCGA.38.4632.01 2 0.5971 0.7694 0.00 0.64 0.02 0.14 0.20
#> TCGA.MP.A4T6.01 1 0.0000 0.5831 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6779.01 1 0.5599 0.0338 0.62 0.00 0.12 0.00 0.26
#> TCGA.49.6761.01 5 0.6009 0.7089 0.24 0.00 0.18 0.00 0.58
#> TCGA.55.6981.01 1 0.5048 -0.0550 0.58 0.04 0.00 0.00 0.38
#> TCGA.05.4417.01 1 0.0609 0.5812 0.98 0.00 0.00 0.00 0.02
#> TCGA.97.7554.01 3 0.2754 0.8285 0.08 0.04 0.88 0.00 0.00
#> TCGA.95.8039.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.55.7576.01 2 0.3319 0.9045 0.00 0.82 0.02 0.16 0.00
#> TCGA.86.8672.01 2 0.4312 0.8909 0.00 0.78 0.02 0.16 0.04
#> TCGA.44.6777.01 5 0.4182 0.6921 0.40 0.00 0.00 0.00 0.60
#> TCGA.73.4676.01 2 0.2732 0.9095 0.00 0.84 0.00 0.16 0.00
#> TCGA.91.6836.01 1 0.3641 0.4844 0.82 0.06 0.00 0.00 0.12
#> TCGA.55.A491.01 1 0.4254 0.3751 0.74 0.04 0.00 0.00 0.22
#> TCGA.55.6978.01 4 0.0000 0.8747 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.A48Y.01 4 0.0609 0.8734 0.00 0.00 0.00 0.98 0.02
#> TCGA.97.A4M7.01 4 0.0000 0.8747 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.7662.01 4 0.3999 0.7478 0.00 0.02 0.00 0.74 0.24
#> TCGA.44.7672.01 5 0.5788 0.7927 0.30 0.00 0.12 0.00 0.58
#> TCGA.78.7152.01 4 0.5083 0.6161 0.00 0.16 0.00 0.70 0.14
#> TCGA.55.8302.01 4 0.1043 0.8740 0.00 0.00 0.00 0.96 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.4112.01 5 0.6968 0.2649 0.18 0.00 0.12 0.00 0.48 0.22
#> TCGA.NJ.A4YP.01 2 0.2581 0.7995 0.12 0.86 0.02 0.00 0.00 0.00
#> TCGA.50.6597.01 5 0.0547 0.5918 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.J2.A4AG.01 5 0.1556 0.5660 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.MP.A4TK.01 5 0.7230 0.0398 0.32 0.00 0.12 0.00 0.38 0.18
#> TCGA.MN.A4N1.01 2 0.4144 0.6521 0.00 0.62 0.36 0.02 0.00 0.00
#> TCGA.91.6847.01 4 0.5887 0.6716 0.06 0.06 0.24 0.62 0.00 0.02
#> TCGA.MP.A4TC.01 4 0.4873 0.6547 0.00 0.08 0.32 0.60 0.00 0.00
#> TCGA.05.4410.01 2 0.4845 0.5926 0.00 0.54 0.40 0.06 0.00 0.00
#> TCGA.55.6982.01 1 0.3409 0.7777 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.55.7727.01 2 0.3475 0.7832 0.14 0.80 0.06 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 4 0.5996 0.7258 0.16 0.10 0.12 0.62 0.00 0.00
#> TCGA.55.A57B.01 6 0.6138 0.5646 0.12 0.00 0.10 0.00 0.18 0.60
#> TCGA.NJ.A4YI.01 6 0.2725 0.7902 0.00 0.00 0.06 0.04 0.02 0.88
#> TCGA.L9.A444.01 6 0.2094 0.7766 0.00 0.00 0.02 0.00 0.08 0.90
#> TCGA.86.8668.01 5 0.2094 0.5618 0.08 0.00 0.02 0.00 0.90 0.00
#> TCGA.44.A47G.01 5 0.6129 0.3460 0.06 0.00 0.12 0.00 0.56 0.26
#> TCGA.62.A46R.01 6 0.0547 0.8015 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.75.5125.01 4 0.3258 0.8300 0.04 0.10 0.02 0.84 0.00 0.00
#> TCGA.44.6775.01 5 0.1556 0.5660 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.55.7911.01 6 0.0547 0.8015 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.55.6712.01 2 0.1092 0.8140 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.69.7760.01 4 0.1267 0.8399 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.55.6985.01 5 0.3523 0.3855 0.18 0.00 0.04 0.00 0.78 0.00
#> TCGA.MP.A4TF.01 1 0.3711 0.7806 0.72 0.00 0.02 0.00 0.26 0.00
#> TCGA.44.A47B.01 2 0.3985 0.7694 0.14 0.76 0.10 0.00 0.00 0.00
#> TCGA.05.5429.01 4 0.3631 0.8236 0.04 0.10 0.04 0.82 0.00 0.00
#> TCGA.86.A4JF.01 2 0.0547 0.8175 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.75.5122.01 2 0.3976 0.6398 0.02 0.74 0.02 0.22 0.00 0.00
#> TCGA.49.AARE.01 1 0.5291 0.7475 0.60 0.00 0.08 0.02 0.30 0.00
#> TCGA.86.7701.01 4 0.4664 0.7872 0.06 0.14 0.06 0.74 0.00 0.00
#> TCGA.55.7281.01 5 0.0547 0.5918 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.78.7535.01 2 0.5265 0.5438 0.00 0.50 0.40 0.10 0.00 0.00
#> TCGA.50.6592.01 1 0.3819 0.7835 0.70 0.00 0.02 0.00 0.28 0.00
#> TCGA.44.7661.01 5 0.3795 0.5569 0.06 0.00 0.12 0.00 0.80 0.02
#> TCGA.50.5933.01 2 0.0000 0.8174 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.8174 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7907.01 4 0.6508 0.5714 0.04 0.24 0.24 0.48 0.00 0.00
#> TCGA.78.7540.01 5 0.4664 0.5540 0.06 0.00 0.14 0.00 0.74 0.06
#> TCGA.95.A4VN.01 6 0.5190 0.6303 0.04 0.00 0.10 0.00 0.18 0.68
#> TCGA.69.8253.01 5 0.4195 0.3425 0.20 0.00 0.04 0.02 0.74 0.00
#> TCGA.50.6590.01 1 0.5304 0.5931 0.62 0.00 0.04 0.00 0.28 0.06
#> TCGA.55.8205.01 6 0.5392 0.6176 0.04 0.00 0.12 0.00 0.18 0.66
#> TCGA.99.8025.01 6 0.2725 0.7902 0.00 0.00 0.06 0.04 0.02 0.88
#> TCGA.69.7761.01 4 0.1556 0.8448 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.69.7978.01 2 0.1092 0.8140 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.44.8117.01 6 0.2725 0.7902 0.00 0.00 0.06 0.04 0.02 0.88
#> TCGA.MP.A4TD.01 2 0.5274 0.5900 0.06 0.66 0.06 0.22 0.00 0.00
#> TCGA.83.5908.01 5 0.4733 0.5440 0.06 0.00 0.12 0.00 0.74 0.08
#> TCGA.55.8301.01 4 0.2882 0.8356 0.02 0.10 0.02 0.86 0.00 0.00
#> TCGA.78.7146.01 1 0.3819 0.7835 0.70 0.00 0.02 0.00 0.28 0.00
#> TCGA.44.3918.01 6 0.7165 0.1846 0.18 0.00 0.12 0.00 0.28 0.42
#> TCGA.55.8089.01 4 0.2094 0.8432 0.00 0.08 0.02 0.90 0.00 0.00
#> TCGA.55.8511.01 6 0.1092 0.8006 0.00 0.00 0.02 0.00 0.02 0.96
#> TCGA.91.A4BC.01 4 0.1556 0.8448 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.44.2656.01 2 0.0000 0.8174 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 1 0.5289 0.7634 0.58 0.00 0.14 0.00 0.28 0.00
#> TCGA.95.8494.01 2 0.1480 0.8164 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.69.7980.01 1 0.5289 0.7634 0.58 0.00 0.14 0.00 0.28 0.00
#> TCGA.05.4433.01 4 0.2094 0.8421 0.00 0.08 0.02 0.90 0.00 0.00
#> TCGA.44.6147.01 1 0.4798 0.7733 0.62 0.00 0.08 0.00 0.30 0.00
#> TCGA.86.8073.01 4 0.4873 0.6547 0.00 0.08 0.32 0.60 0.00 0.00
#> TCGA.64.5781.01 1 0.4765 0.6243 0.64 0.00 0.02 0.00 0.30 0.04
#> TCGA.78.7154.01 2 0.6579 0.1991 0.04 0.52 0.14 0.28 0.00 0.02
#> TCGA.78.7143.01 5 0.4094 0.3545 0.18 0.00 0.08 0.00 0.74 0.00
#> TCGA.97.A4M3.01 5 0.4195 0.3425 0.20 0.00 0.04 0.02 0.74 0.00
#> TCGA.55.A493.01 5 0.6326 0.4322 0.12 0.00 0.12 0.00 0.58 0.18
#> TCGA.NJ.A4YQ.01 1 0.3499 0.7238 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.50.6594.01 1 0.6119 0.6675 0.46 0.00 0.16 0.02 0.36 0.00
#> TCGA.86.8056.01 5 0.1807 0.5740 0.06 0.00 0.02 0.00 0.92 0.00
#> TCGA.38.4632.01 2 0.4845 0.5926 0.00 0.54 0.40 0.06 0.00 0.00
#> TCGA.MP.A4T6.01 1 0.5324 0.7322 0.54 0.00 0.12 0.00 0.34 0.00
#> TCGA.44.6779.01 1 0.7169 0.0186 0.38 0.00 0.10 0.00 0.32 0.20
#> TCGA.49.6761.01 5 0.6129 0.3584 0.06 0.00 0.12 0.00 0.56 0.26
#> TCGA.55.6981.01 5 0.1556 0.5660 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.05.4417.01 1 0.4199 0.7043 0.60 0.00 0.02 0.00 0.38 0.00
#> TCGA.97.7554.01 6 0.2725 0.7902 0.00 0.00 0.06 0.04 0.02 0.88
#> TCGA.95.8039.01 2 0.2190 0.8110 0.06 0.90 0.04 0.00 0.00 0.00
#> TCGA.55.7576.01 2 0.1807 0.8123 0.00 0.92 0.06 0.02 0.00 0.00
#> TCGA.86.8672.01 2 0.3258 0.7677 0.04 0.84 0.10 0.02 0.00 0.00
#> TCGA.44.6777.01 5 0.3270 0.5625 0.06 0.00 0.12 0.00 0.82 0.00
#> TCGA.73.4676.01 2 0.0547 0.8174 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.91.6836.01 1 0.4890 0.6598 0.66 0.00 0.16 0.00 0.18 0.00
#> TCGA.55.A491.01 5 0.3315 0.3727 0.20 0.00 0.02 0.00 0.78 0.00
#> TCGA.55.6978.01 4 0.1556 0.8448 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.55.A48Y.01 4 0.2094 0.8432 0.00 0.08 0.02 0.90 0.00 0.00
#> TCGA.97.A4M7.01 4 0.1556 0.8448 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.44.7662.01 4 0.4873 0.6547 0.00 0.08 0.32 0.60 0.00 0.00
#> TCGA.44.7672.01 5 0.5529 0.5060 0.06 0.00 0.12 0.00 0.66 0.16
#> TCGA.78.7152.01 4 0.6903 0.5508 0.16 0.20 0.14 0.50 0.00 0.00
#> TCGA.55.8302.01 4 0.3846 0.8245 0.02 0.10 0.08 0.80 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.44.4112.01 5 0.5756 0.1118 0.22 0.00 0.02 0.00 0.48 0.28 0.00
#> TCGA.NJ.A4YP.01 2 0.4838 0.6225 0.00 0.68 0.14 0.04 0.00 0.00 0.14
#> TCGA.50.6597.01 5 0.4361 0.7078 0.16 0.00 0.16 0.00 0.68 0.00 0.00
#> TCGA.J2.A4AG.01 5 0.4990 0.6934 0.20 0.00 0.22 0.00 0.58 0.00 0.00
#> TCGA.MP.A4TK.01 1 0.5669 0.2500 0.50 0.00 0.02 0.00 0.28 0.20 0.00
#> TCGA.MN.A4N1.01 2 0.4701 -0.1417 0.00 0.50 0.00 0.04 0.02 0.00 0.44
#> TCGA.91.6847.01 4 0.6163 0.2733 0.00 0.02 0.32 0.48 0.04 0.00 0.14
#> TCGA.MP.A4TC.01 4 0.3562 -0.1493 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.05.4410.01 7 0.4936 0.0857 0.00 0.44 0.00 0.06 0.02 0.00 0.48
#> TCGA.55.6982.01 1 0.1006 0.8007 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.55.7727.01 2 0.4667 0.6255 0.00 0.70 0.14 0.04 0.00 0.00 0.12
#> TCGA.MP.A4SW.01 4 0.5086 0.0853 0.00 0.00 0.14 0.50 0.00 0.00 0.36
#> TCGA.55.A57B.01 6 0.4731 0.6914 0.06 0.00 0.02 0.00 0.22 0.68 0.02
#> TCGA.NJ.A4YI.01 6 0.3199 0.7270 0.00 0.00 0.06 0.00 0.00 0.80 0.14
#> TCGA.L9.A444.01 6 0.2569 0.7706 0.00 0.00 0.02 0.00 0.14 0.84 0.00
#> TCGA.86.8668.01 5 0.5182 0.6756 0.22 0.00 0.24 0.00 0.54 0.00 0.00
#> TCGA.44.A47G.01 5 0.3370 0.5073 0.06 0.00 0.00 0.00 0.78 0.16 0.00
#> TCGA.62.A46R.01 6 0.0863 0.7819 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.75.5125.01 4 0.3058 0.5931 0.00 0.00 0.10 0.82 0.00 0.00 0.08
#> TCGA.44.6775.01 5 0.5092 0.6824 0.22 0.00 0.22 0.00 0.56 0.00 0.00
#> TCGA.55.7911.01 6 0.1166 0.7835 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.55.6712.01 2 0.2804 0.7225 0.00 0.86 0.02 0.06 0.00 0.00 0.06
#> TCGA.69.7760.01 4 0.0863 0.7005 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.6985.01 5 0.5467 0.6125 0.28 0.00 0.26 0.00 0.46 0.00 0.00
#> TCGA.MP.A4TF.01 1 0.1505 0.7959 0.94 0.00 0.02 0.00 0.02 0.00 0.02
#> TCGA.44.A47B.01 2 0.5618 0.3802 0.00 0.54 0.14 0.04 0.00 0.00 0.28
#> TCGA.05.5429.01 4 0.4022 0.6238 0.00 0.02 0.08 0.78 0.02 0.00 0.10
#> TCGA.86.A4JF.01 2 0.1860 0.7466 0.00 0.92 0.02 0.04 0.00 0.00 0.02
#> TCGA.75.5122.01 2 0.4610 0.4805 0.00 0.66 0.02 0.24 0.00 0.00 0.08
#> TCGA.49.AARE.01 1 0.3538 0.7143 0.80 0.02 0.14 0.00 0.02 0.00 0.02
#> TCGA.86.7701.01 4 0.4022 0.6160 0.00 0.02 0.10 0.78 0.02 0.00 0.08
#> TCGA.55.7281.01 5 0.4514 0.7081 0.14 0.00 0.14 0.00 0.70 0.02 0.00
#> TCGA.78.7535.01 7 0.4426 0.2276 0.00 0.38 0.00 0.06 0.00 0.00 0.56
#> TCGA.50.6592.01 1 0.0504 0.8036 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.7661.01 5 0.2081 0.6802 0.14 0.00 0.00 0.00 0.86 0.00 0.00
#> TCGA.50.5933.01 2 0.0863 0.7503 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0863 0.7503 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.55.7907.01 4 0.7151 0.0354 0.00 0.14 0.16 0.44 0.04 0.00 0.22
#> TCGA.78.7540.01 5 0.3011 0.6671 0.12 0.00 0.00 0.00 0.82 0.06 0.00
#> TCGA.95.A4VN.01 6 0.3417 0.7061 0.00 0.00 0.02 0.00 0.26 0.72 0.00
#> TCGA.69.8253.01 5 0.5619 0.5350 0.30 0.00 0.32 0.00 0.38 0.00 0.00
#> TCGA.50.6590.01 1 0.1363 0.7955 0.94 0.00 0.02 0.00 0.04 0.00 0.00
#> TCGA.55.8205.01 6 0.3685 0.6690 0.00 0.00 0.02 0.00 0.32 0.66 0.00
#> TCGA.99.8025.01 6 0.3199 0.7270 0.00 0.00 0.06 0.00 0.00 0.80 0.14
#> TCGA.69.7761.01 4 0.0000 0.7138 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.7978.01 2 0.0863 0.7503 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.44.8117.01 6 0.3199 0.7270 0.00 0.00 0.06 0.00 0.00 0.80 0.14
#> TCGA.MP.A4TD.01 2 0.6585 0.1543 0.00 0.46 0.10 0.30 0.02 0.00 0.12
#> TCGA.83.5908.01 5 0.3011 0.6671 0.12 0.00 0.00 0.00 0.82 0.06 0.00
#> TCGA.55.8301.01 4 0.0504 0.7103 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.78.7146.01 1 0.0000 0.8049 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.3918.01 6 0.5517 0.4231 0.14 0.00 0.02 0.00 0.36 0.48 0.00
#> TCGA.55.8089.01 4 0.0000 0.7138 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8511.01 6 0.0863 0.7819 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.91.A4BC.01 4 0.0000 0.7138 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.2656.01 2 0.0863 0.7503 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.73.7499.01 1 0.2016 0.7895 0.90 0.00 0.06 0.00 0.00 0.00 0.04
#> TCGA.95.8494.01 2 0.1363 0.7483 0.00 0.94 0.02 0.04 0.00 0.00 0.00
#> TCGA.69.7980.01 1 0.1363 0.7993 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.05.4433.01 4 0.1363 0.7010 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.44.6147.01 1 0.1363 0.7993 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.86.8073.01 4 0.3562 -0.1493 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.64.5781.01 1 0.3292 0.7234 0.84 0.00 0.02 0.00 0.06 0.06 0.02
#> TCGA.78.7154.01 4 0.7445 0.0184 0.00 0.26 0.16 0.36 0.04 0.00 0.18
#> TCGA.78.7143.01 5 0.5467 0.6125 0.28 0.00 0.26 0.00 0.46 0.00 0.00
#> TCGA.97.A4M3.01 5 0.5619 0.5350 0.30 0.00 0.32 0.00 0.38 0.00 0.00
#> TCGA.55.A493.01 5 0.4092 0.4677 0.08 0.00 0.02 0.00 0.74 0.16 0.00
#> TCGA.NJ.A4YQ.01 1 0.1006 0.8018 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.50.6594.01 1 0.4354 0.5834 0.68 0.02 0.26 0.00 0.02 0.00 0.02
#> TCGA.86.8056.01 5 0.4763 0.7019 0.18 0.00 0.20 0.00 0.62 0.00 0.00
#> TCGA.38.4632.01 2 0.4936 -0.2143 0.00 0.48 0.00 0.06 0.02 0.00 0.44
#> TCGA.MP.A4T6.01 1 0.2512 0.7700 0.86 0.00 0.10 0.00 0.00 0.00 0.04
#> TCGA.44.6779.01 1 0.6039 0.2312 0.50 0.00 0.02 0.00 0.20 0.26 0.02
#> TCGA.49.6761.01 5 0.3199 0.5341 0.06 0.00 0.00 0.00 0.80 0.14 0.00
#> TCGA.55.6981.01 5 0.4990 0.6869 0.22 0.00 0.20 0.00 0.58 0.00 0.00
#> TCGA.05.4417.01 1 0.3011 0.6565 0.82 0.00 0.06 0.00 0.12 0.00 0.00
#> TCGA.97.7554.01 6 0.3199 0.7270 0.00 0.00 0.06 0.00 0.00 0.80 0.14
#> TCGA.95.8039.01 2 0.3114 0.7153 0.00 0.84 0.04 0.04 0.00 0.00 0.08
#> TCGA.55.7576.01 2 0.2509 0.7171 0.00 0.88 0.00 0.04 0.02 0.00 0.06
#> TCGA.86.8672.01 2 0.4225 0.6655 0.00 0.78 0.08 0.04 0.04 0.00 0.06
#> TCGA.44.6777.01 5 0.2259 0.6832 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.73.4676.01 2 0.0863 0.7503 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.91.6836.01 1 0.5254 0.5820 0.62 0.02 0.26 0.00 0.06 0.00 0.04
#> TCGA.55.A491.01 5 0.5619 0.5350 0.30 0.00 0.32 0.00 0.38 0.00 0.00
#> TCGA.55.6978.01 4 0.0000 0.7138 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 4 0.0000 0.7138 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 4 0.0504 0.7074 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.44.7662.01 7 0.3562 -0.1647 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.44.7672.01 5 0.3058 0.6070 0.08 0.00 0.00 0.00 0.82 0.10 0.00
#> TCGA.78.7152.01 7 0.6470 0.0706 0.00 0.10 0.16 0.36 0.00 0.00 0.38
#> TCGA.55.8302.01 4 0.2509 0.6767 0.00 0.00 0.06 0.88 0.02 0.00 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.44.4112.01 8 0.3314 0.7155 0.08 0.00 0.02 0.00 0.10 0.00 0.00 0.80
#> TCGA.NJ.A4YP.01 2 0.2650 0.6892 0.00 0.76 0.24 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6597.01 5 0.4096 0.6218 0.00 0.00 0.02 0.00 0.68 0.00 0.06 0.24
#> TCGA.J2.A4AG.01 5 0.1947 0.7487 0.00 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.MP.A4TK.01 8 0.3986 0.6227 0.14 0.00 0.04 0.00 0.08 0.00 0.00 0.74
#> TCGA.MN.A4N1.01 2 0.5061 0.2055 0.02 0.48 0.04 0.00 0.00 0.00 0.42 0.04
#> TCGA.91.6847.01 3 0.6827 0.0000 0.06 0.00 0.38 0.38 0.02 0.02 0.10 0.04
#> TCGA.MP.A4TC.01 7 0.4040 0.6866 0.00 0.02 0.02 0.38 0.00 0.00 0.58 0.00
#> TCGA.05.4410.01 2 0.4624 0.1558 0.00 0.46 0.02 0.00 0.00 0.00 0.46 0.06
#> TCGA.55.6982.01 1 0.3431 0.7906 0.74 0.00 0.00 0.00 0.20 0.00 0.00 0.06
#> TCGA.55.7727.01 2 0.3637 0.6447 0.00 0.70 0.26 0.02 0.00 0.00 0.02 0.00
#> TCGA.MP.A4SW.01 4 0.5101 0.2058 0.00 0.02 0.28 0.54 0.00 0.00 0.16 0.00
#> TCGA.55.A57B.01 8 0.4529 0.4664 0.06 0.00 0.08 0.00 0.00 0.18 0.00 0.68
#> TCGA.NJ.A4YI.01 6 0.0941 0.7621 0.00 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.L9.A444.01 6 0.4698 0.2184 0.00 0.00 0.12 0.00 0.00 0.44 0.00 0.44
#> TCGA.86.8668.01 5 0.1341 0.7652 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.44.A47G.01 8 0.2569 0.7235 0.00 0.00 0.00 0.00 0.16 0.02 0.00 0.82
#> TCGA.62.A46R.01 6 0.3589 0.7551 0.00 0.00 0.10 0.00 0.00 0.74 0.00 0.16
#> TCGA.75.5125.01 4 0.3169 0.6058 0.00 0.02 0.18 0.78 0.00 0.00 0.02 0.00
#> TCGA.44.6775.01 5 0.1947 0.7522 0.00 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.55.7911.01 6 0.3970 0.7125 0.00 0.00 0.10 0.00 0.00 0.68 0.00 0.22
#> TCGA.55.6712.01 2 0.1275 0.7485 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.69.7760.01 4 0.0941 0.7147 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.55.6985.01 5 0.0941 0.7434 0.02 0.00 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.MP.A4TF.01 1 0.3934 0.7819 0.70 0.00 0.00 0.00 0.16 0.00 0.00 0.14
#> TCGA.44.A47B.01 2 0.4487 0.5787 0.00 0.62 0.28 0.02 0.00 0.00 0.08 0.00
#> TCGA.05.5429.01 4 0.3637 0.6399 0.02 0.04 0.08 0.80 0.00 0.00 0.06 0.00
#> TCGA.86.A4JF.01 2 0.0471 0.7557 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5122.01 2 0.4284 0.2816 0.00 0.58 0.04 0.36 0.00 0.00 0.00 0.02
#> TCGA.49.AARE.01 1 0.6534 0.3486 0.40 0.00 0.08 0.00 0.34 0.00 0.12 0.06
#> TCGA.86.7701.01 4 0.3131 0.6406 0.04 0.06 0.04 0.84 0.00 0.00 0.00 0.02
#> TCGA.55.7281.01 5 0.4191 0.5390 0.00 0.00 0.02 0.00 0.66 0.00 0.06 0.26
#> TCGA.78.7535.01 7 0.4255 0.1135 0.00 0.34 0.00 0.08 0.00 0.00 0.58 0.00
#> TCGA.50.6592.01 1 0.3589 0.7918 0.74 0.00 0.00 0.00 0.16 0.00 0.00 0.10
#> TCGA.44.7661.01 8 0.2938 0.6099 0.00 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.50.5933.01 2 0.1275 0.7475 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.78.8660.01 2 0.0471 0.7563 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.7907.01 4 0.7718 -0.0482 0.04 0.18 0.14 0.42 0.02 0.02 0.16 0.02
#> TCGA.78.7540.01 8 0.4673 0.3973 0.00 0.00 0.02 0.00 0.34 0.00 0.08 0.56
#> TCGA.95.A4VN.01 8 0.3856 0.4638 0.00 0.00 0.10 0.00 0.00 0.20 0.00 0.70
#> TCGA.69.8253.01 5 0.3185 0.6753 0.06 0.00 0.04 0.00 0.82 0.00 0.08 0.00
#> TCGA.50.6590.01 1 0.4169 0.7475 0.70 0.00 0.02 0.00 0.10 0.00 0.00 0.18
#> TCGA.55.8205.01 8 0.3551 0.4685 0.00 0.00 0.06 0.00 0.00 0.22 0.00 0.72
#> TCGA.99.8025.01 6 0.0941 0.7621 0.00 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.69.7761.01 4 0.1275 0.7114 0.00 0.02 0.04 0.94 0.00 0.00 0.00 0.00
#> TCGA.69.7978.01 2 0.0471 0.7539 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.8117.01 6 0.0471 0.7668 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.MP.A4TD.01 2 0.4968 0.2179 0.02 0.52 0.06 0.38 0.00 0.00 0.00 0.02
#> TCGA.83.5908.01 8 0.3015 0.5935 0.00 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.55.8301.01 4 0.1275 0.7011 0.00 0.04 0.00 0.94 0.00 0.00 0.00 0.02
#> TCGA.78.7146.01 1 0.3589 0.7918 0.74 0.00 0.00 0.00 0.16 0.00 0.00 0.10
#> TCGA.44.3918.01 8 0.4185 0.6447 0.04 0.00 0.08 0.00 0.04 0.08 0.00 0.76
#> TCGA.55.8089.01 4 0.0471 0.7093 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.55.8511.01 6 0.3434 0.7609 0.00 0.00 0.10 0.00 0.00 0.76 0.00 0.14
#> TCGA.91.A4BC.01 4 0.0941 0.7147 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.44.2656.01 2 0.0000 0.7556 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 1 0.4191 0.7572 0.66 0.00 0.00 0.00 0.26 0.00 0.06 0.02
#> TCGA.95.8494.01 2 0.1557 0.7490 0.00 0.92 0.06 0.00 0.00 0.00 0.00 0.02
#> TCGA.69.7980.01 1 0.4147 0.7766 0.68 0.00 0.00 0.00 0.24 0.00 0.04 0.04
#> TCGA.05.4433.01 4 0.2348 0.6802 0.00 0.02 0.04 0.88 0.00 0.00 0.06 0.00
#> TCGA.44.6147.01 1 0.3941 0.7635 0.68 0.00 0.00 0.00 0.26 0.00 0.04 0.02
#> TCGA.86.8073.01 7 0.4040 0.6866 0.00 0.02 0.02 0.38 0.00 0.00 0.58 0.00
#> TCGA.64.5781.01 1 0.4247 0.6295 0.62 0.00 0.00 0.00 0.10 0.00 0.00 0.28
#> TCGA.78.7154.01 4 0.7224 -0.4202 0.04 0.24 0.26 0.38 0.02 0.02 0.02 0.02
#> TCGA.78.7143.01 5 0.0941 0.7434 0.02 0.00 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.97.A4M3.01 5 0.3185 0.6753 0.06 0.00 0.04 0.00 0.82 0.00 0.08 0.00
#> TCGA.55.A493.01 8 0.2114 0.7212 0.00 0.00 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.NJ.A4YQ.01 1 0.3729 0.7523 0.72 0.00 0.00 0.00 0.10 0.00 0.00 0.18
#> TCGA.50.6594.01 5 0.5872 -0.2250 0.32 0.00 0.08 0.00 0.44 0.00 0.16 0.00
#> TCGA.86.8056.01 5 0.3744 0.6820 0.00 0.00 0.02 0.00 0.74 0.00 0.06 0.18
#> TCGA.38.4632.01 2 0.5277 0.1937 0.02 0.46 0.04 0.00 0.00 0.00 0.42 0.06
#> TCGA.MP.A4T6.01 1 0.4050 0.6743 0.60 0.00 0.00 0.00 0.34 0.00 0.06 0.00
#> TCGA.44.6779.01 8 0.4529 0.5603 0.18 0.00 0.06 0.00 0.08 0.00 0.00 0.68
#> TCGA.49.6761.01 8 0.3794 0.7048 0.00 0.00 0.04 0.00 0.18 0.04 0.00 0.74
#> TCGA.55.6981.01 5 0.2114 0.7364 0.00 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.05.4417.01 1 0.4174 0.6786 0.62 0.00 0.00 0.00 0.32 0.00 0.04 0.02
#> TCGA.97.7554.01 6 0.0471 0.7668 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.95.8039.01 2 0.2267 0.7128 0.00 0.82 0.18 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7576.01 2 0.2532 0.7343 0.02 0.88 0.04 0.00 0.00 0.00 0.02 0.04
#> TCGA.86.8672.01 2 0.3181 0.7044 0.02 0.84 0.08 0.02 0.00 0.02 0.00 0.02
#> TCGA.44.6777.01 8 0.3193 0.5021 0.00 0.00 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.73.4676.01 2 0.0471 0.7563 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.91.6836.01 1 0.5241 0.4649 0.66 0.00 0.10 0.00 0.08 0.00 0.12 0.04
#> TCGA.55.A491.01 5 0.1887 0.7233 0.06 0.00 0.00 0.00 0.90 0.00 0.04 0.00
#> TCGA.55.6978.01 4 0.1408 0.7152 0.00 0.02 0.02 0.94 0.00 0.00 0.02 0.00
#> TCGA.55.A48Y.01 4 0.0941 0.7147 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.97.A4M7.01 4 0.1741 0.7118 0.00 0.02 0.04 0.92 0.00 0.00 0.02 0.00
#> TCGA.44.7662.01 7 0.4077 0.6693 0.00 0.02 0.02 0.40 0.00 0.00 0.56 0.00
#> TCGA.44.7672.01 8 0.2756 0.6660 0.00 0.00 0.00 0.00 0.26 0.00 0.00 0.74
#> TCGA.78.7152.01 4 0.5837 0.0286 0.00 0.08 0.30 0.46 0.00 0.00 0.16 0.00
#> TCGA.55.8302.01 4 0.2807 0.6583 0.04 0.06 0.00 0.86 0.00 0.02 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node023. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01221-leaf , Node01222-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-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 50 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.998 0.999 0.5036 0.497 0.497
#> 3 3 1.000 0.974 0.990 0.2761 0.733 0.524
#> 4 4 1.000 0.959 0.983 0.1687 0.833 0.569
#> 5 5 0.862 0.830 0.928 0.0213 0.973 0.895
#> 6 6 0.774 0.701 0.872 0.0300 0.992 0.966
#> 7 7 0.745 0.706 0.862 0.0120 1.000 1.000
#> 8 8 0.765 0.528 0.772 0.0298 0.966 0.853
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.44.4112.01 1 0.000 0.998 1.00 0.00
#> TCGA.50.6597.01 1 0.000 0.998 1.00 0.00
#> TCGA.J2.A4AG.01 1 0.000 0.998 1.00 0.00
#> TCGA.MP.A4TK.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.6982.01 1 0.000 0.998 1.00 0.00
#> TCGA.55.A57B.01 1 0.327 0.936 0.94 0.06
#> TCGA.NJ.A4YI.01 2 0.000 1.000 0.00 1.00
#> TCGA.L9.A444.01 2 0.000 1.000 0.00 1.00
#> TCGA.86.8668.01 1 0.000 0.998 1.00 0.00
#> TCGA.44.A47G.01 2 0.000 1.000 0.00 1.00
#> TCGA.62.A46R.01 2 0.000 1.000 0.00 1.00
#> TCGA.44.6775.01 1 0.000 0.998 1.00 0.00
#> TCGA.55.7911.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.6985.01 1 0.000 0.998 1.00 0.00
#> TCGA.MP.A4TF.01 1 0.000 0.998 1.00 0.00
#> TCGA.49.AARE.01 1 0.000 0.998 1.00 0.00
#> TCGA.55.7281.01 1 0.000 0.998 1.00 0.00
#> TCGA.50.6592.01 1 0.000 0.998 1.00 0.00
#> TCGA.44.7661.01 1 0.000 0.998 1.00 0.00
#> TCGA.78.7540.01 2 0.000 1.000 0.00 1.00
#> TCGA.95.A4VN.01 2 0.000 1.000 0.00 1.00
#> TCGA.69.8253.01 1 0.000 0.998 1.00 0.00
#> TCGA.50.6590.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.8205.01 2 0.000 1.000 0.00 1.00
#> TCGA.99.8025.01 2 0.000 1.000 0.00 1.00
#> TCGA.44.8117.01 2 0.000 1.000 0.00 1.00
#> TCGA.83.5908.01 2 0.000 1.000 0.00 1.00
#> TCGA.78.7146.01 1 0.000 0.998 1.00 0.00
#> TCGA.44.3918.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.8511.01 2 0.000 1.000 0.00 1.00
#> TCGA.73.7499.01 1 0.000 0.998 1.00 0.00
#> TCGA.69.7980.01 1 0.000 0.998 1.00 0.00
#> TCGA.44.6147.01 1 0.000 0.998 1.00 0.00
#> TCGA.64.5781.01 2 0.000 1.000 0.00 1.00
#> TCGA.78.7143.01 1 0.000 0.998 1.00 0.00
#> TCGA.97.A4M3.01 1 0.000 0.998 1.00 0.00
#> TCGA.55.A493.01 2 0.000 1.000 0.00 1.00
#> TCGA.NJ.A4YQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.50.6594.01 1 0.000 0.998 1.00 0.00
#> TCGA.86.8056.01 1 0.000 0.998 1.00 0.00
#> TCGA.MP.A4T6.01 1 0.000 0.998 1.00 0.00
#> TCGA.44.6779.01 2 0.000 1.000 0.00 1.00
#> TCGA.49.6761.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.6981.01 1 0.000 0.998 1.00 0.00
#> TCGA.05.4417.01 1 0.000 0.998 1.00 0.00
#> TCGA.97.7554.01 2 0.000 1.000 0.00 1.00
#> TCGA.44.6777.01 1 0.000 0.998 1.00 0.00
#> TCGA.91.6836.01 1 0.000 0.998 1.00 0.00
#> TCGA.55.A491.01 1 0.000 0.998 1.00 0.00
#> TCGA.44.7672.01 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.44.4112.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.50.6597.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.J2.A4AG.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.MP.A4TK.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.55.6982.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.55.A57B.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.NJ.A4YI.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.L9.A444.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.86.8668.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.44.A47G.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.62.A46R.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.44.6775.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.55.7911.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.55.6985.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.MP.A4TF.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.49.AARE.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.55.7281.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.50.6592.01 2 0.4291 0.762 0.18 0.82 0
#> TCGA.44.7661.01 2 0.0892 0.966 0.02 0.98 0
#> TCGA.78.7540.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.95.A4VN.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.69.8253.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.50.6590.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.55.8205.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.99.8025.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.44.8117.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.83.5908.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.78.7146.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.44.3918.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.55.8511.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.73.7499.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.69.7980.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.44.6147.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.64.5781.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.78.7143.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.97.A4M3.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.55.A493.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.NJ.A4YQ.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.50.6594.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.86.8056.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.MP.A4T6.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.44.6779.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.49.6761.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.55.6981.01 1 0.5560 0.560 0.70 0.30 0
#> TCGA.05.4417.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.97.7554.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.44.6777.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.91.6836.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.55.A491.01 1 0.0000 0.983 1.00 0.00 0
#> TCGA.44.7672.01 2 0.0000 0.987 0.00 1.00 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.44.4112.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.50.6597.01 1 0.1211 0.963 0.96 0.00 0.00 0.04
#> TCGA.J2.A4AG.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.MP.A4TK.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.6982.01 1 0.0707 0.979 0.98 0.00 0.00 0.02
#> TCGA.55.A57B.01 4 0.0707 0.929 0.00 0.02 0.00 0.98
#> TCGA.NJ.A4YI.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.L9.A444.01 3 0.3172 0.809 0.00 0.16 0.84 0.00
#> TCGA.86.8668.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.62.A46R.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.44.6775.01 1 0.0707 0.979 0.98 0.00 0.00 0.02
#> TCGA.55.7911.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.55.6985.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TF.01 1 0.1637 0.943 0.94 0.00 0.00 0.06
#> TCGA.49.AARE.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.55.7281.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.50.6592.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.44.7661.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.78.7540.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.95.A4VN.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.69.8253.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.50.6590.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.8205.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.99.8025.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.44.8117.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.83.5908.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.78.7146.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.44.3918.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.8511.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.73.7499.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.69.7980.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.64.5781.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.78.7143.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.50.6594.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.86.8056.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T6.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.44.6779.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.49.6761.01 4 0.4907 0.281 0.00 0.42 0.00 0.58
#> TCGA.55.6981.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.05.4417.01 4 0.2345 0.843 0.10 0.00 0.00 0.90
#> TCGA.97.7554.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.44.6777.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.91.6836.01 4 0.0000 0.945 0.00 0.00 0.00 1.00
#> TCGA.55.A491.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.44.7672.01 2 0.0000 1.000 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.44.4112.01 4 0.0609 0.858 0.00 0.00 0.00 0.98 0.02
#> TCGA.50.6597.01 1 0.3946 0.818 0.80 0.00 0.00 0.12 0.08
#> TCGA.J2.A4AG.01 4 0.0000 0.864 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TK.01 2 0.0000 0.854 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6982.01 1 0.2616 0.889 0.88 0.00 0.00 0.10 0.02
#> TCGA.55.A57B.01 4 0.3037 0.769 0.00 0.10 0.00 0.86 0.04
#> TCGA.NJ.A4YI.01 3 0.0609 0.955 0.00 0.00 0.98 0.00 0.02
#> TCGA.L9.A444.01 3 0.4263 0.659 0.00 0.18 0.76 0.00 0.06
#> TCGA.86.8668.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 2 0.0000 0.854 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.A46R.01 3 0.0000 0.959 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6775.01 1 0.2616 0.889 0.88 0.00 0.00 0.10 0.02
#> TCGA.55.7911.01 3 0.0609 0.955 0.00 0.00 0.98 0.00 0.02
#> TCGA.55.6985.01 1 0.1043 0.937 0.96 0.00 0.00 0.04 0.00
#> TCGA.MP.A4TF.01 1 0.3513 0.803 0.80 0.00 0.00 0.18 0.02
#> TCGA.49.AARE.01 1 0.1648 0.928 0.94 0.00 0.00 0.04 0.02
#> TCGA.55.7281.01 4 0.1410 0.857 0.00 0.00 0.00 0.94 0.06
#> TCGA.50.6592.01 4 0.1648 0.848 0.00 0.02 0.00 0.94 0.04
#> TCGA.44.7661.01 4 0.0609 0.863 0.00 0.00 0.00 0.98 0.02
#> TCGA.78.7540.01 5 0.4287 0.000 0.00 0.46 0.00 0.00 0.54
#> TCGA.95.A4VN.01 2 0.1410 0.798 0.00 0.94 0.00 0.00 0.06
#> TCGA.69.8253.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 2 0.0000 0.854 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8205.01 3 0.0609 0.955 0.00 0.00 0.98 0.00 0.02
#> TCGA.99.8025.01 3 0.0000 0.959 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.8117.01 3 0.0000 0.959 0.00 0.00 1.00 0.00 0.00
#> TCGA.83.5908.01 2 0.1410 0.794 0.00 0.94 0.00 0.00 0.06
#> TCGA.78.7146.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.3918.01 2 0.1732 0.778 0.00 0.92 0.00 0.00 0.08
#> TCGA.55.8511.01 3 0.0000 0.959 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.7499.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7980.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.2438 0.819 0.00 0.06 0.00 0.90 0.04
#> TCGA.64.5781.01 2 0.0609 0.843 0.00 0.98 0.00 0.00 0.02
#> TCGA.78.7143.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.2077 0.759 0.00 0.92 0.00 0.04 0.04
#> TCGA.NJ.A4YQ.01 2 0.0609 0.843 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.6594.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8056.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T6.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6779.01 2 0.0000 0.854 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.6761.01 2 0.6398 -0.239 0.00 0.50 0.00 0.20 0.30
#> TCGA.55.6981.01 4 0.0000 0.864 0.00 0.00 0.00 1.00 0.00
#> TCGA.05.4417.01 4 0.5355 0.545 0.22 0.00 0.00 0.66 0.12
#> TCGA.97.7554.01 3 0.0000 0.959 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6777.01 4 0.1043 0.859 0.00 0.00 0.00 0.96 0.04
#> TCGA.91.6836.01 4 0.6019 0.442 0.12 0.00 0.00 0.50 0.38
#> TCGA.55.A491.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7672.01 2 0.0000 0.854 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.44.4112.01 4 0.226 0.6414 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.50.6597.01 1 0.580 0.2881 0.50 0.00 0.00 0.24 0.00 0.26
#> TCGA.J2.A4AG.01 4 0.226 0.6470 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.MP.A4TK.01 2 0.148 0.8278 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.55.6982.01 1 0.438 0.6662 0.72 0.00 0.00 0.12 0.00 0.16
#> TCGA.55.A57B.01 4 0.484 0.4491 0.00 0.16 0.00 0.72 0.06 0.06
#> TCGA.NJ.A4YI.01 3 0.109 0.9122 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.L9.A444.01 3 0.518 0.6761 0.00 0.12 0.70 0.00 0.12 0.06
#> TCGA.86.8668.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 2 0.202 0.8365 0.00 0.92 0.00 0.02 0.04 0.02
#> TCGA.62.A46R.01 3 0.000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6775.01 1 0.489 0.5925 0.66 0.00 0.00 0.18 0.00 0.16
#> TCGA.55.7911.01 3 0.327 0.8362 0.00 0.00 0.82 0.00 0.12 0.06
#> TCGA.55.6985.01 1 0.366 0.7190 0.78 0.00 0.00 0.06 0.00 0.16
#> TCGA.MP.A4TF.01 1 0.544 0.4223 0.56 0.00 0.00 0.28 0.00 0.16
#> TCGA.49.AARE.01 1 0.409 0.6913 0.74 0.00 0.00 0.08 0.00 0.18
#> TCGA.55.7281.01 4 0.332 0.6138 0.00 0.00 0.00 0.82 0.10 0.08
#> TCGA.50.6592.01 4 0.368 0.5775 0.00 0.00 0.00 0.76 0.04 0.20
#> TCGA.44.7661.01 4 0.000 0.6930 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7540.01 5 0.359 0.0000 0.00 0.24 0.00 0.00 0.74 0.02
#> TCGA.95.A4VN.01 2 0.296 0.7349 0.00 0.84 0.00 0.00 0.12 0.04
#> TCGA.69.8253.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 2 0.181 0.8250 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.55.8205.01 3 0.251 0.8773 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.99.8025.01 3 0.000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.8117.01 3 0.000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.83.5908.01 2 0.127 0.8167 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.78.7146.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.3918.01 2 0.127 0.8392 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.55.8511.01 3 0.000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.7499.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7980.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.338 0.6185 0.00 0.08 0.00 0.84 0.04 0.04
#> TCGA.64.5781.01 2 0.163 0.8379 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.78.7143.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.202 0.8323 0.00 0.92 0.00 0.02 0.04 0.02
#> TCGA.NJ.A4YQ.01 2 0.163 0.8434 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.50.6594.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8056.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T6.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6779.01 2 0.148 0.8310 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.49.6761.01 2 0.714 -0.2074 0.00 0.40 0.00 0.20 0.10 0.30
#> TCGA.55.6981.01 4 0.181 0.6869 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.05.4417.01 4 0.596 -0.0614 0.24 0.00 0.00 0.44 0.00 0.32
#> TCGA.97.7554.01 3 0.000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6777.01 4 0.234 0.6660 0.00 0.02 0.00 0.90 0.06 0.02
#> TCGA.91.6836.01 6 0.351 0.0000 0.02 0.00 0.00 0.16 0.02 0.80
#> TCGA.55.A491.01 1 0.000 0.8514 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7672.01 2 0.109 0.8456 0.00 0.96 0.00 0.02 0.02 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.44.4112.01 4 0.2376 0.686 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.50.6597.01 1 0.5286 0.545 0.62 0.00 0.00 0.22 0.00 0.06 0.10
#> TCGA.J2.A4AG.01 4 0.0504 0.738 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.MP.A4TK.01 2 0.1505 0.813 0.00 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.55.6982.01 1 0.4388 0.594 0.64 0.00 0.00 0.30 0.00 0.04 0.02
#> TCGA.55.A57B.01 4 0.5681 0.345 0.00 0.22 0.00 0.58 0.00 0.12 0.08
#> TCGA.NJ.A4YI.01 3 0.1166 0.865 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.L9.A444.01 3 0.4669 0.451 0.00 0.08 0.52 0.00 0.00 0.40 0.00
#> TCGA.86.8668.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 2 0.1433 0.806 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.62.A46R.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6775.01 1 0.3991 0.692 0.72 0.00 0.00 0.22 0.00 0.04 0.02
#> TCGA.55.7911.01 3 0.2832 0.768 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.55.6985.01 1 0.2912 0.778 0.82 0.00 0.00 0.14 0.00 0.04 0.00
#> TCGA.MP.A4TF.01 1 0.4684 0.346 0.52 0.00 0.00 0.42 0.00 0.04 0.02
#> TCGA.49.AARE.01 1 0.3086 0.764 0.80 0.00 0.00 0.16 0.00 0.04 0.00
#> TCGA.55.7281.01 4 0.4145 0.598 0.00 0.00 0.00 0.74 0.02 0.14 0.10
#> TCGA.50.6592.01 4 0.1718 0.728 0.00 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.44.7661.01 4 0.0863 0.739 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.78.7540.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.A4VN.01 2 0.3139 0.682 0.00 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.69.8253.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 2 0.1363 0.806 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.55.8205.01 3 0.2422 0.804 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.99.8025.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.8117.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.83.5908.01 2 0.2278 0.795 0.00 0.88 0.00 0.00 0.04 0.08 0.00
#> TCGA.78.7146.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.3918.01 2 0.3517 0.691 0.00 0.70 0.00 0.00 0.00 0.28 0.02
#> TCGA.55.8511.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7980.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.4260 0.571 0.00 0.14 0.00 0.74 0.00 0.08 0.04
#> TCGA.64.5781.01 2 0.2864 0.772 0.00 0.84 0.00 0.00 0.02 0.12 0.02
#> TCGA.78.7143.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.2016 0.804 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.NJ.A4YQ.01 2 0.2163 0.782 0.00 0.88 0.00 0.00 0.02 0.10 0.00
#> TCGA.50.6594.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8056.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T6.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6779.01 2 0.3780 0.660 0.00 0.72 0.00 0.00 0.02 0.24 0.02
#> TCGA.49.6761.01 2 0.6371 0.226 0.00 0.42 0.00 0.08 0.00 0.32 0.18
#> TCGA.55.6981.01 4 0.0000 0.742 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.4417.01 4 0.4992 0.233 0.28 0.00 0.00 0.60 0.00 0.02 0.10
#> TCGA.97.7554.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6777.01 4 0.2509 0.712 0.00 0.02 0.00 0.88 0.00 0.06 0.04
#> TCGA.91.6836.01 7 0.1433 0.000 0.00 0.00 0.00 0.08 0.00 0.00 0.92
#> TCGA.55.A491.01 1 0.0504 0.861 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.44.7672.01 2 0.1433 0.806 0.00 0.92 0.00 0.00 0.00 0.08 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.44.4112.01 4 0.4530 0.4285 0.02 0.00 0.00 0.66 0.00 0.24 0.06 0.02
#> TCGA.50.6597.01 1 0.6908 -0.2264 0.38 0.00 0.00 0.14 0.00 0.30 0.10 0.08
#> TCGA.J2.A4AG.01 4 0.3015 0.4024 0.00 0.00 0.00 0.68 0.00 0.32 0.00 0.00
#> TCGA.MP.A4TK.01 2 0.2807 0.7371 0.00 0.86 0.00 0.04 0.02 0.00 0.02 0.06
#> TCGA.55.6982.01 1 0.5062 -0.1795 0.48 0.00 0.00 0.12 0.00 0.38 0.00 0.02
#> TCGA.55.A57B.01 4 0.5269 0.4648 0.00 0.14 0.00 0.64 0.02 0.12 0.00 0.08
#> TCGA.NJ.A4YI.01 3 0.1947 0.7051 0.00 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.L9.A444.01 8 0.5366 0.0000 0.00 0.18 0.36 0.00 0.00 0.02 0.00 0.44
#> TCGA.86.8668.01 1 0.1341 0.7388 0.92 0.00 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.44.A47G.01 2 0.2020 0.7308 0.00 0.90 0.00 0.02 0.02 0.00 0.00 0.06
#> TCGA.62.A46R.01 3 0.0000 0.8219 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6775.01 1 0.4554 -0.1620 0.48 0.00 0.00 0.10 0.00 0.42 0.00 0.00
#> TCGA.55.7911.01 3 0.3514 0.2751 0.00 0.02 0.64 0.00 0.00 0.00 0.00 0.34
#> TCGA.55.6985.01 1 0.4050 0.2551 0.60 0.00 0.00 0.06 0.00 0.34 0.00 0.00
#> TCGA.MP.A4TF.01 6 0.4786 0.1947 0.38 0.00 0.00 0.14 0.00 0.48 0.00 0.00
#> TCGA.49.AARE.01 1 0.4040 0.2626 0.58 0.00 0.00 0.02 0.00 0.38 0.00 0.02
#> TCGA.55.7281.01 4 0.3185 0.6158 0.00 0.00 0.00 0.82 0.00 0.04 0.06 0.08
#> TCGA.50.6592.01 6 0.3922 0.0871 0.00 0.06 0.00 0.30 0.00 0.64 0.00 0.00
#> TCGA.44.7661.01 4 0.3868 0.5824 0.00 0.02 0.00 0.72 0.02 0.22 0.00 0.02
#> TCGA.78.7540.01 5 0.0941 0.0000 0.00 0.02 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.95.A4VN.01 2 0.3570 0.4230 0.00 0.62 0.00 0.02 0.00 0.00 0.00 0.36
#> TCGA.69.8253.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6590.01 2 0.2265 0.7257 0.00 0.88 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.55.8205.01 3 0.3291 0.4360 0.00 0.02 0.70 0.00 0.00 0.00 0.00 0.28
#> TCGA.99.8025.01 3 0.0000 0.8219 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8117.01 3 0.0000 0.8219 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.83.5908.01 2 0.3135 0.7222 0.00 0.82 0.00 0.02 0.02 0.00 0.02 0.12
#> TCGA.78.7146.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.3918.01 2 0.4363 0.6484 0.00 0.70 0.00 0.04 0.04 0.02 0.00 0.20
#> TCGA.55.8511.01 3 0.0000 0.8219 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7980.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.01 4 0.2025 0.6106 0.00 0.10 0.00 0.88 0.02 0.00 0.00 0.00
#> TCGA.64.5781.01 2 0.3421 0.6700 0.00 0.80 0.00 0.08 0.00 0.08 0.00 0.04
#> TCGA.78.7143.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.3850 0.6760 0.00 0.76 0.00 0.12 0.00 0.06 0.00 0.06
#> TCGA.NJ.A4YQ.01 2 0.2348 0.7326 0.00 0.88 0.00 0.00 0.00 0.06 0.02 0.04
#> TCGA.50.6594.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8056.01 1 0.0000 0.7780 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T6.01 1 0.0471 0.7700 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.6779.01 2 0.4211 0.5799 0.00 0.70 0.00 0.00 0.00 0.16 0.02 0.12
#> TCGA.49.6761.01 2 0.6873 0.1963 0.00 0.36 0.00 0.20 0.04 0.00 0.12 0.28
#> TCGA.55.6981.01 4 0.2981 0.5202 0.00 0.00 0.00 0.76 0.00 0.22 0.00 0.02
#> TCGA.05.4417.01 6 0.6188 0.3261 0.14 0.00 0.00 0.34 0.00 0.42 0.08 0.02
#> TCGA.97.7554.01 3 0.0000 0.8219 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6777.01 4 0.0000 0.6549 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6836.01 7 0.1275 0.0000 0.00 0.00 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.55.A491.01 1 0.1341 0.7377 0.92 0.00 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.44.7672.01 2 0.2591 0.7292 0.00 0.86 0.00 0.04 0.02 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: Node023. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01221-leaf , Node01222-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-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 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.765 0.933 0.967 0.5064 0.488 0.488
#> 3 3 0.999 0.960 0.985 0.2142 0.788 0.609
#> 4 4 0.640 0.738 0.869 0.0891 0.906 0.767
#> 5 5 0.630 0.708 0.856 0.0674 0.935 0.815
#> 6 6 0.594 0.585 0.769 0.0501 0.940 0.820
#> 7 7 0.641 0.574 0.781 0.0525 0.861 0.570
#> 8 8 0.648 0.548 0.786 0.0285 0.934 0.711
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.NJ.A4YP.01 1 0.000 0.984 1.00 0.00
#> TCGA.MN.A4N1.01 1 0.000 0.984 1.00 0.00
#> TCGA.91.6847.01 2 0.000 0.944 0.00 1.00
#> TCGA.MP.A4TC.01 2 0.242 0.925 0.04 0.96
#> TCGA.05.4410.01 1 0.000 0.984 1.00 0.00
#> TCGA.55.7727.01 1 0.000 0.984 1.00 0.00
#> TCGA.MP.A4SW.01 1 0.469 0.883 0.90 0.10
#> TCGA.75.5125.01 1 0.000 0.984 1.00 0.00
#> TCGA.55.6712.01 1 0.634 0.806 0.84 0.16
#> TCGA.69.7760.01 2 0.680 0.800 0.18 0.82
#> TCGA.44.A47B.01 1 0.000 0.984 1.00 0.00
#> TCGA.05.5429.01 2 0.000 0.944 0.00 1.00
#> TCGA.86.A4JF.01 1 0.000 0.984 1.00 0.00
#> TCGA.75.5122.01 2 0.141 0.937 0.02 0.98
#> TCGA.86.7701.01 2 0.000 0.944 0.00 1.00
#> TCGA.78.7535.01 1 0.000 0.984 1.00 0.00
#> TCGA.50.5933.01 1 0.000 0.984 1.00 0.00
#> TCGA.78.8660.01 1 0.000 0.984 1.00 0.00
#> TCGA.55.7907.01 1 0.000 0.984 1.00 0.00
#> TCGA.69.7761.01 2 0.000 0.944 0.00 1.00
#> TCGA.69.7978.01 1 0.242 0.949 0.96 0.04
#> TCGA.MP.A4TD.01 2 0.722 0.779 0.20 0.80
#> TCGA.55.8301.01 2 0.141 0.937 0.02 0.98
#> TCGA.55.8089.01 2 0.000 0.944 0.00 1.00
#> TCGA.91.A4BC.01 2 0.000 0.944 0.00 1.00
#> TCGA.44.2656.01 1 0.000 0.984 1.00 0.00
#> TCGA.95.8494.01 1 0.000 0.984 1.00 0.00
#> TCGA.05.4433.01 2 0.000 0.944 0.00 1.00
#> TCGA.86.8073.01 2 0.722 0.779 0.20 0.80
#> TCGA.78.7154.01 2 0.000 0.944 0.00 1.00
#> TCGA.38.4632.01 1 0.000 0.984 1.00 0.00
#> TCGA.95.8039.01 1 0.000 0.984 1.00 0.00
#> TCGA.55.7576.01 1 0.000 0.984 1.00 0.00
#> TCGA.86.8672.01 2 0.000 0.944 0.00 1.00
#> TCGA.73.4676.01 1 0.000 0.984 1.00 0.00
#> TCGA.55.6978.01 2 0.000 0.944 0.00 1.00
#> TCGA.55.A48Y.01 2 0.000 0.944 0.00 1.00
#> TCGA.97.A4M7.01 2 0.000 0.944 0.00 1.00
#> TCGA.44.7662.01 2 0.141 0.937 0.02 0.98
#> TCGA.78.7152.01 1 0.000 0.984 1.00 0.00
#> TCGA.55.8302.01 2 0.943 0.498 0.36 0.64
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.NJ.A4YP.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.MN.A4N1.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.91.6847.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.MP.A4TC.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.05.4410.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.55.7727.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.254 0.901 0.08 0.92 0.00
#> TCGA.75.5125.01 1 0.613 0.316 0.60 0.40 0.00
#> TCGA.55.6712.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.69.7760.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.44.A47B.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.05.5429.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.86.A4JF.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.75.5122.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.86.7701.01 2 0.153 0.953 0.00 0.96 0.04
#> TCGA.78.7535.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.50.5933.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.78.8660.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.55.7907.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.69.7761.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.69.7978.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.MP.A4TD.01 2 0.254 0.901 0.08 0.92 0.00
#> TCGA.55.8301.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.55.8089.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.91.A4BC.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.44.2656.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.95.8494.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.05.4433.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.86.8073.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.78.7154.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.38.4632.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.95.8039.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.55.7576.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.86.8672.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.73.4676.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.55.6978.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.55.A48Y.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.97.A4M7.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.44.7662.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.78.7152.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.55.8302.01 2 0.000 0.986 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.NJ.A4YP.01 1 0.201 0.9068 0.92 0.08 0.00 0.00
#> TCGA.MN.A4N1.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.91.6847.01 3 0.000 0.8087 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TC.01 2 0.000 0.7156 0.00 1.00 0.00 0.00
#> TCGA.05.4410.01 1 0.340 0.8447 0.82 0.18 0.00 0.00
#> TCGA.55.7727.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.353 0.6625 0.10 0.86 0.00 0.04
#> TCGA.75.5125.01 2 0.526 0.4166 0.26 0.70 0.00 0.04
#> TCGA.55.6712.01 2 0.000 0.7156 0.00 1.00 0.00 0.00
#> TCGA.69.7760.01 3 0.586 0.6159 0.04 0.00 0.58 0.38
#> TCGA.44.A47B.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.05.5429.01 3 0.201 0.7927 0.00 0.00 0.92 0.08
#> TCGA.86.A4JF.01 1 0.317 0.8657 0.84 0.16 0.00 0.00
#> TCGA.75.5122.01 2 0.201 0.6714 0.00 0.92 0.00 0.08
#> TCGA.86.7701.01 2 0.461 0.6181 0.00 0.80 0.10 0.10
#> TCGA.78.7535.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.50.5933.01 1 0.317 0.8657 0.84 0.16 0.00 0.00
#> TCGA.78.8660.01 1 0.317 0.8657 0.84 0.16 0.00 0.00
#> TCGA.55.7907.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.69.7761.01 4 0.479 0.9589 0.00 0.38 0.00 0.62
#> TCGA.69.7978.01 2 0.000 0.7156 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TD.01 2 0.353 0.6625 0.10 0.86 0.00 0.04
#> TCGA.55.8301.01 2 0.201 0.6714 0.00 0.92 0.00 0.08
#> TCGA.55.8089.01 4 0.485 0.9790 0.00 0.40 0.00 0.60
#> TCGA.91.A4BC.01 4 0.485 0.9790 0.00 0.40 0.00 0.60
#> TCGA.44.2656.01 1 0.317 0.8657 0.84 0.16 0.00 0.00
#> TCGA.95.8494.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.491 0.4725 0.00 0.00 0.58 0.42
#> TCGA.86.8073.01 2 0.320 0.6811 0.08 0.88 0.00 0.04
#> TCGA.78.7154.01 3 0.000 0.8087 0.00 0.00 1.00 0.00
#> TCGA.38.4632.01 1 0.201 0.9071 0.92 0.08 0.00 0.00
#> TCGA.95.8039.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.55.7576.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.292 0.5896 0.00 0.86 0.00 0.14
#> TCGA.73.4676.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.55.6978.01 2 0.452 -0.0215 0.00 0.68 0.00 0.32
#> TCGA.55.A48Y.01 2 0.498 -0.6212 0.00 0.54 0.00 0.46
#> TCGA.97.A4M7.01 2 0.361 0.5767 0.00 0.80 0.00 0.20
#> TCGA.44.7662.01 2 0.164 0.6881 0.00 0.94 0.00 0.06
#> TCGA.78.7152.01 1 0.000 0.9287 1.00 0.00 0.00 0.00
#> TCGA.55.8302.01 2 0.283 0.6935 0.06 0.90 0.00 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.NJ.A4YP.01 1 0.3319 0.784 0.82 0.16 0.00 0.00 0.02
#> TCGA.MN.A4N1.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6847.01 3 0.1410 0.720 0.00 0.00 0.94 0.00 0.06
#> TCGA.MP.A4TC.01 2 0.2732 0.759 0.00 0.84 0.00 0.16 0.00
#> TCGA.05.4410.01 2 0.5925 -0.153 0.40 0.52 0.00 0.02 0.06
#> TCGA.55.7727.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.2077 0.770 0.00 0.92 0.00 0.04 0.04
#> TCGA.75.5125.01 2 0.2077 0.723 0.04 0.92 0.00 0.00 0.04
#> TCGA.55.6712.01 2 0.2331 0.760 0.00 0.90 0.00 0.08 0.02
#> TCGA.69.7760.01 5 0.1410 0.000 0.00 0.00 0.06 0.00 0.94
#> TCGA.44.A47B.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 3 0.1043 0.705 0.00 0.00 0.96 0.04 0.00
#> TCGA.86.A4JF.01 1 0.5621 0.634 0.62 0.30 0.00 0.02 0.06
#> TCGA.75.5122.01 2 0.3109 0.731 0.00 0.80 0.00 0.20 0.00
#> TCGA.86.7701.01 2 0.6047 0.624 0.00 0.68 0.12 0.12 0.08
#> TCGA.78.7535.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 1 0.5621 0.634 0.62 0.30 0.00 0.02 0.06
#> TCGA.78.8660.01 1 0.5621 0.634 0.62 0.30 0.00 0.02 0.06
#> TCGA.55.7907.01 1 0.1648 0.833 0.94 0.04 0.00 0.00 0.02
#> TCGA.69.7761.01 4 0.0609 0.940 0.00 0.02 0.00 0.98 0.00
#> TCGA.69.7978.01 2 0.2438 0.727 0.00 0.90 0.00 0.04 0.06
#> TCGA.MP.A4TD.01 2 0.1648 0.764 0.00 0.94 0.00 0.02 0.04
#> TCGA.55.8301.01 2 0.3109 0.738 0.00 0.80 0.00 0.20 0.00
#> TCGA.55.8089.01 4 0.1043 0.963 0.00 0.04 0.00 0.96 0.00
#> TCGA.91.A4BC.01 4 0.1043 0.963 0.00 0.04 0.00 0.96 0.00
#> TCGA.44.2656.01 1 0.5621 0.634 0.62 0.30 0.00 0.02 0.06
#> TCGA.95.8494.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.4287 0.258 0.00 0.00 0.54 0.46 0.00
#> TCGA.86.8073.01 2 0.1648 0.773 0.00 0.94 0.00 0.04 0.02
#> TCGA.78.7154.01 3 0.1410 0.720 0.00 0.00 0.94 0.00 0.06
#> TCGA.38.4632.01 1 0.3291 0.793 0.84 0.12 0.00 0.00 0.04
#> TCGA.95.8039.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7576.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.3109 0.745 0.00 0.80 0.00 0.20 0.00
#> TCGA.73.4676.01 1 0.0000 0.847 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 2 0.4302 0.246 0.00 0.52 0.00 0.48 0.00
#> TCGA.55.A48Y.01 4 0.1732 0.917 0.00 0.08 0.00 0.92 0.00
#> TCGA.97.A4M7.01 2 0.4840 0.560 0.00 0.64 0.00 0.32 0.04
#> TCGA.44.7662.01 2 0.2929 0.751 0.00 0.82 0.00 0.18 0.00
#> TCGA.78.7152.01 1 0.0609 0.844 0.98 0.02 0.00 0.00 0.00
#> TCGA.55.8302.01 2 0.2077 0.770 0.00 0.92 0.00 0.04 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.NJ.A4YP.01 1 0.4566 0.648 0.70 0.16 0.00 0.00 0.00 0.14
#> TCGA.MN.A4N1.01 1 0.0000 0.737 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6847.01 3 0.4646 0.479 0.00 0.00 0.50 0.00 0.04 0.46
#> TCGA.MP.A4TC.01 2 0.2956 0.697 0.00 0.84 0.00 0.12 0.00 0.04
#> TCGA.05.4410.01 1 0.6103 0.386 0.38 0.30 0.00 0.00 0.00 0.32
#> TCGA.55.7727.01 1 0.0000 0.737 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.1480 0.722 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.75.5125.01 2 0.2631 0.677 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.55.6712.01 2 0.2981 0.683 0.00 0.82 0.00 0.02 0.00 0.16
#> TCGA.69.7760.01 5 0.0547 0.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.44.A47B.01 1 0.0000 0.737 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 3 0.0547 0.425 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.86.A4JF.01 1 0.5987 0.486 0.44 0.26 0.00 0.00 0.00 0.30
#> TCGA.75.5122.01 2 0.4475 0.640 0.00 0.70 0.00 0.20 0.00 0.10
#> TCGA.86.7701.01 2 0.6631 0.483 0.00 0.52 0.00 0.14 0.10 0.24
#> TCGA.78.7535.01 1 0.0000 0.737 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 1 0.5987 0.486 0.44 0.26 0.00 0.00 0.00 0.30
#> TCGA.78.8660.01 1 0.5987 0.486 0.44 0.26 0.00 0.00 0.00 0.30
#> TCGA.55.7907.01 1 0.2512 0.716 0.88 0.06 0.00 0.00 0.00 0.06
#> TCGA.69.7761.01 4 0.1092 0.685 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.69.7978.01 2 0.2941 0.629 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.MP.A4TD.01 2 0.4165 0.624 0.00 0.74 0.00 0.00 0.10 0.16
#> TCGA.55.8301.01 2 0.2260 0.694 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.55.8089.01 4 0.0000 0.731 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.A4BC.01 4 0.0000 0.731 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.2656.01 1 0.5987 0.486 0.44 0.26 0.00 0.00 0.00 0.30
#> TCGA.95.8494.01 1 0.0000 0.737 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 3 0.4282 0.198 0.00 0.00 0.56 0.42 0.00 0.02
#> TCGA.86.8073.01 2 0.4008 0.702 0.00 0.80 0.00 0.06 0.06 0.08
#> TCGA.78.7154.01 3 0.4646 0.476 0.00 0.00 0.50 0.00 0.04 0.46
#> TCGA.38.4632.01 1 0.4723 0.640 0.68 0.14 0.00 0.00 0.00 0.18
#> TCGA.95.8039.01 1 0.0547 0.736 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.7576.01 1 0.0000 0.737 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.5265 0.219 0.00 0.50 0.00 0.40 0.00 0.10
#> TCGA.73.4676.01 1 0.0000 0.737 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 4 0.4282 0.125 0.00 0.42 0.00 0.56 0.00 0.02
#> TCGA.55.A48Y.01 4 0.3688 0.657 0.00 0.14 0.00 0.80 0.04 0.02
#> TCGA.97.A4M7.01 2 0.5459 0.369 0.00 0.58 0.00 0.32 0.04 0.06
#> TCGA.44.7662.01 2 0.3475 0.677 0.00 0.80 0.00 0.14 0.00 0.06
#> TCGA.78.7152.01 1 0.1092 0.733 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.55.8302.01 2 0.1556 0.716 0.00 0.92 0.00 0.00 0.00 0.08
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.NJ.A4YP.01 1 0.5085 0.3807 0.60 0.02 0.12 0.00 0.00 0.00 0.26
#> TCGA.MN.A4N1.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6847.01 3 0.3139 0.6796 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.MP.A4TC.01 2 0.3548 0.6572 0.00 0.80 0.04 0.04 0.00 0.00 0.12
#> TCGA.05.4410.01 7 0.2745 0.7593 0.16 0.02 0.00 0.00 0.00 0.00 0.82
#> TCGA.55.7727.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.3637 0.5632 0.00 0.72 0.04 0.00 0.00 0.00 0.24
#> TCGA.75.5125.01 2 0.5516 0.3360 0.04 0.50 0.10 0.00 0.00 0.00 0.36
#> TCGA.55.6712.01 2 0.3985 0.3348 0.00 0.52 0.00 0.02 0.00 0.00 0.46
#> TCGA.69.7760.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A47B.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 6 0.0000 0.1030 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.A4JF.01 7 0.2906 0.7630 0.18 0.00 0.02 0.00 0.00 0.00 0.80
#> TCGA.75.5122.01 2 0.3911 0.5906 0.00 0.70 0.00 0.06 0.00 0.00 0.24
#> TCGA.86.7701.01 2 0.6864 0.3878 0.00 0.50 0.20 0.02 0.02 0.08 0.18
#> TCGA.78.7535.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 7 0.2422 0.7721 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.78.8660.01 7 0.2422 0.7721 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.55.7907.01 1 0.3086 0.6901 0.80 0.00 0.04 0.00 0.00 0.00 0.16
#> TCGA.69.7761.01 4 0.2016 0.7446 0.00 0.06 0.00 0.90 0.00 0.04 0.00
#> TCGA.69.7978.01 7 0.3221 0.1831 0.00 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.MP.A4TD.01 7 0.6163 -0.3578 0.00 0.38 0.18 0.02 0.02 0.00 0.40
#> TCGA.55.8301.01 2 0.2313 0.6425 0.00 0.88 0.00 0.06 0.00 0.00 0.06
#> TCGA.55.8089.01 4 0.1166 0.7673 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.91.A4BC.01 4 0.0863 0.7645 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.44.2656.01 7 0.2422 0.7721 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.95.8494.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 6 0.4317 0.3607 0.00 0.00 0.02 0.38 0.00 0.58 0.02
#> TCGA.86.8073.01 2 0.5166 0.4977 0.00 0.62 0.08 0.02 0.02 0.00 0.26
#> TCGA.78.7154.01 3 0.4386 0.6525 0.00 0.00 0.54 0.02 0.00 0.42 0.02
#> TCGA.38.4632.01 1 0.4505 -0.0273 0.50 0.00 0.06 0.00 0.00 0.00 0.44
#> TCGA.95.8039.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7576.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.5204 0.4818 0.00 0.62 0.04 0.22 0.00 0.00 0.12
#> TCGA.73.4676.01 1 0.0000 0.8788 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 2 0.3755 0.3080 0.00 0.64 0.00 0.34 0.00 0.00 0.02
#> TCGA.55.A48Y.01 4 0.4778 0.3918 0.00 0.34 0.06 0.58 0.00 0.00 0.02
#> TCGA.97.A4M7.01 2 0.4022 0.5719 0.00 0.78 0.10 0.08 0.02 0.00 0.02
#> TCGA.44.7662.01 2 0.3914 0.6251 0.00 0.78 0.06 0.06 0.00 0.00 0.10
#> TCGA.78.7152.01 1 0.1363 0.8467 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.55.8302.01 2 0.4487 0.4901 0.00 0.60 0.08 0.00 0.00 0.00 0.32
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.NJ.A4YP.01 1 0.6891 -0.0390 0.38 0.12 0.02 0.00 0.00 0.02 0.30 0.16
#> TCGA.MN.A4N1.01 1 0.0000 0.8917 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6847.01 3 0.1804 0.4334 0.00 0.00 0.90 0.00 0.02 0.08 0.00 0.00
#> TCGA.MP.A4TC.01 2 0.2859 0.6039 0.00 0.82 0.00 0.02 0.00 0.00 0.14 0.02
#> TCGA.05.4410.01 7 0.2265 0.7124 0.08 0.02 0.00 0.00 0.00 0.00 0.88 0.02
#> TCGA.55.7727.01 1 0.0000 0.8917 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SW.01 2 0.4760 0.3882 0.00 0.62 0.00 0.00 0.02 0.00 0.20 0.16
#> TCGA.75.5125.01 7 0.4554 -0.0758 0.00 0.42 0.00 0.00 0.00 0.00 0.48 0.10
#> TCGA.55.6712.01 2 0.3374 0.5047 0.00 0.68 0.00 0.00 0.00 0.00 0.30 0.02
#> TCGA.69.7760.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A47B.01 1 0.0000 0.8917 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5429.01 6 0.0808 0.3228 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.86.A4JF.01 7 0.2025 0.7494 0.10 0.02 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.75.5122.01 2 0.3895 0.6157 0.00 0.74 0.00 0.12 0.00 0.00 0.12 0.02
#> TCGA.86.7701.01 8 0.4828 0.5256 0.00 0.24 0.04 0.06 0.00 0.02 0.00 0.64
#> TCGA.78.7535.01 1 0.0000 0.8917 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 7 0.2025 0.7494 0.10 0.02 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.78.8660.01 7 0.2025 0.7494 0.10 0.02 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.55.7907.01 1 0.3913 0.6376 0.74 0.04 0.00 0.00 0.00 0.00 0.16 0.06
#> TCGA.69.7761.01 4 0.0941 0.7031 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.69.7978.01 7 0.3142 0.2724 0.00 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.MP.A4TD.01 8 0.5329 0.5407 0.00 0.26 0.02 0.00 0.00 0.00 0.22 0.50
#> TCGA.55.8301.01 2 0.2914 0.6069 0.00 0.84 0.00 0.04 0.00 0.00 0.08 0.04
#> TCGA.55.8089.01 4 0.0471 0.7370 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 4 0.0471 0.7370 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.44.2656.01 7 0.2025 0.7494 0.10 0.02 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.95.8494.01 1 0.0471 0.8829 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.05.4433.01 6 0.4284 0.4164 0.00 0.00 0.04 0.36 0.00 0.58 0.02 0.00
#> TCGA.86.8073.01 2 0.5128 -0.3365 0.00 0.52 0.00 0.02 0.00 0.02 0.08 0.36
#> TCGA.78.7154.01 3 0.5566 0.4215 0.00 0.02 0.50 0.00 0.00 0.16 0.02 0.30
#> TCGA.38.4632.01 7 0.3618 0.3228 0.38 0.00 0.00 0.00 0.00 0.00 0.60 0.02
#> TCGA.95.8039.01 1 0.0471 0.8829 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.55.7576.01 1 0.0000 0.8917 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8672.01 2 0.4350 0.5135 0.00 0.62 0.00 0.30 0.00 0.00 0.06 0.02
#> TCGA.73.4676.01 1 0.0000 0.8917 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 2 0.3514 0.4505 0.00 0.64 0.00 0.34 0.00 0.00 0.00 0.02
#> TCGA.55.A48Y.01 4 0.5259 0.1716 0.00 0.34 0.02 0.52 0.00 0.00 0.02 0.10
#> TCGA.97.A4M7.01 2 0.5152 0.2131 0.00 0.60 0.00 0.14 0.02 0.02 0.00 0.22
#> TCGA.44.7662.01 2 0.2725 0.6024 0.00 0.82 0.00 0.14 0.00 0.00 0.04 0.00
#> TCGA.78.7152.01 1 0.2204 0.8265 0.90 0.02 0.00 0.00 0.00 0.02 0.04 0.02
#> TCGA.55.8302.01 2 0.3729 0.5167 0.00 0.72 0.00 0.00 0.00 0.00 0.18 0.10
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node031 , Node032 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 44 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5121 0.488 0.488
#> 3 3 0.666 0.849 0.848 0.2015 1.000 1.000
#> 4 4 0.566 0.376 0.713 0.1016 0.902 0.799
#> 5 5 0.543 0.601 0.760 0.0976 0.875 0.686
#> 6 6 0.543 0.332 0.720 0.0426 0.948 0.824
#> 7 7 0.617 0.622 0.740 0.0594 0.897 0.615
#> 8 8 0.648 0.464 0.699 0.0186 0.963 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.97.A4M1.01 2 0 1 0 1
#> TCGA.97.8552.01 2 0 1 0 1
#> TCGA.44.2659.11 2 0 1 0 1
#> TCGA.44.5645.11 2 0 1 0 1
#> TCGA.44.2662.11 1 0 1 1 0
#> TCGA.50.5930.11 1 0 1 1 0
#> TCGA.55.8512.01 1 0 1 1 0
#> TCGA.44.6146.11 1 0 1 1 0
#> TCGA.44.6148.01 1 0 1 1 0
#> TCGA.49.6745.11 1 0 1 1 0
#> TCGA.55.7816.01 2 0 1 0 1
#> TCGA.50.6593.11 2 0 1 0 1
#> TCGA.44.2656.11 1 0 1 1 0
#> TCGA.44.6778.11 1 0 1 1 0
#> TCGA.38.4631.11 2 0 1 0 1
#> TCGA.44.2665.11 2 0 1 0 1
#> TCGA.86.A4P8.01 2 0 1 0 1
#> TCGA.38.4632.11 1 0 1 1 0
#> TCGA.44.2655.11 2 0 1 0 1
#> TCGA.50.5939.11 1 0 1 1 0
#> TCGA.44.6145.11 2 0 1 0 1
#> TCGA.75.6203.01 2 0 1 0 1
#> TCGA.50.6594.11 2 0 1 0 1
#> TCGA.44.2668.11 1 0 1 1 0
#> TCGA.49.4488.11 2 0 1 0 1
#> TCGA.55.6980.01 1 0 1 1 0
#> TCGA.50.5935.11 2 0 1 0 1
#> TCGA.49.AARR.01 1 0 1 1 0
#> TCGA.73.4676.11 1 0 1 1 0
#> TCGA.L4.A4E6.01 1 0 1 1 0
#> TCGA.73.4658.11 2 0 1 0 1
#> TCGA.44.6148.11 1 0 1 1 0
#> TCGA.50.5933.11 1 0 1 1 0
#> TCGA.50.5936.11 1 0 1 1 0
#> TCGA.50.5931.11 2 0 1 0 1
#> TCGA.44.6144.11 1 0 1 1 0
#> TCGA.75.6212.01 2 0 1 0 1
#> TCGA.50.5932.11 1 0 1 1 0
#> TCGA.44.6147.11 2 0 1 0 1
#> TCGA.44.5643.11 1 0 1 1 0
#> TCGA.50.6592.11 2 0 1 0 1
#> TCGA.55.8513.01 2 0 1 0 1
#> TCGA.05.5420.11 1 0 1 1 0
#> TCGA.50.6591.11 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.97.A4M1.01 2 0.4002 0.864 0.16 0.84 0.00
#> TCGA.97.8552.01 2 0.5706 0.812 0.32 0.68 0.00
#> TCGA.44.2659.11 2 0.6045 0.799 0.38 0.62 0.00
#> TCGA.44.5645.11 2 0.2066 0.864 0.06 0.94 0.00
#> TCGA.44.2662.11 3 0.2959 0.882 0.10 0.00 0.90
#> TCGA.50.5930.11 3 0.1529 0.896 0.04 0.00 0.96
#> TCGA.55.8512.01 3 0.2537 0.880 0.08 0.00 0.92
#> TCGA.44.6146.11 3 0.1529 0.889 0.04 0.00 0.96
#> TCGA.44.6148.01 3 0.4002 0.873 0.16 0.00 0.84
#> TCGA.49.6745.11 3 0.1529 0.896 0.04 0.00 0.96
#> TCGA.55.7816.01 2 0.3340 0.849 0.12 0.88 0.00
#> TCGA.50.6593.11 2 0.0892 0.876 0.02 0.98 0.00
#> TCGA.44.2656.11 3 0.2066 0.884 0.06 0.00 0.94
#> TCGA.44.6778.11 3 0.6280 0.701 0.46 0.00 0.54
#> TCGA.38.4631.11 2 0.2066 0.864 0.06 0.94 0.00
#> TCGA.44.2665.11 2 0.6126 0.797 0.40 0.60 0.00
#> TCGA.86.A4P8.01 2 0.5706 0.812 0.32 0.68 0.00
#> TCGA.38.4632.11 3 0.6280 0.701 0.46 0.00 0.54
#> TCGA.44.2655.11 2 0.5706 0.812 0.32 0.68 0.00
#> TCGA.50.5939.11 3 0.1529 0.896 0.04 0.00 0.96
#> TCGA.44.6145.11 2 0.1529 0.876 0.04 0.96 0.00
#> TCGA.75.6203.01 2 0.1529 0.866 0.04 0.96 0.00
#> TCGA.50.6594.11 2 0.3340 0.849 0.12 0.88 0.00
#> TCGA.44.2668.11 3 0.0892 0.895 0.02 0.00 0.98
#> TCGA.49.4488.11 2 0.5706 0.812 0.32 0.68 0.00
#> TCGA.55.6980.01 3 0.5016 0.840 0.24 0.00 0.76
#> TCGA.50.5935.11 2 0.0892 0.876 0.02 0.98 0.00
#> TCGA.49.AARR.01 3 0.6280 0.701 0.46 0.00 0.54
#> TCGA.73.4676.11 3 0.0892 0.896 0.02 0.00 0.98
#> TCGA.L4.A4E6.01 3 0.3340 0.881 0.12 0.00 0.88
#> TCGA.73.4658.11 2 0.0000 0.874 0.00 1.00 0.00
#> TCGA.44.6148.11 3 0.4002 0.873 0.16 0.00 0.84
#> TCGA.50.5933.11 3 0.2537 0.893 0.08 0.00 0.92
#> TCGA.50.5936.11 3 0.0892 0.895 0.02 0.00 0.98
#> TCGA.50.5931.11 2 0.5560 0.818 0.30 0.70 0.00
#> TCGA.44.6144.11 3 0.2066 0.893 0.06 0.00 0.94
#> TCGA.75.6212.01 2 0.0000 0.874 0.00 1.00 0.00
#> TCGA.50.5932.11 3 0.2959 0.887 0.10 0.00 0.90
#> TCGA.44.6147.11 2 0.0000 0.874 0.00 1.00 0.00
#> TCGA.44.5643.11 3 0.6280 0.701 0.46 0.00 0.54
#> TCGA.50.6592.11 2 0.2537 0.862 0.08 0.92 0.00
#> TCGA.55.8513.01 2 0.5706 0.812 0.32 0.68 0.00
#> TCGA.05.5420.11 3 0.1529 0.896 0.04 0.00 0.96
#> TCGA.50.6591.11 2 0.2537 0.862 0.08 0.92 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.97.A4M1.01 2 0.5657 0.349 0.16 0.72 0.00 0.12
#> TCGA.97.8552.01 2 0.4994 -0.741 0.48 0.52 0.00 0.00
#> TCGA.44.2659.11 2 0.5606 -0.823 0.48 0.50 0.00 0.02
#> TCGA.44.5645.11 2 0.4949 0.455 0.06 0.76 0.00 0.18
#> TCGA.44.2662.11 3 0.6500 0.403 0.26 0.00 0.62 0.12
#> TCGA.50.5930.11 3 0.0000 0.701 0.00 0.00 1.00 0.00
#> TCGA.55.8512.01 3 0.5147 0.631 0.20 0.00 0.74 0.06
#> TCGA.44.6146.11 3 0.2335 0.714 0.06 0.00 0.92 0.02
#> TCGA.44.6148.01 3 0.6104 0.369 0.18 0.00 0.68 0.14
#> TCGA.49.6745.11 3 0.0000 0.701 0.00 0.00 1.00 0.00
#> TCGA.55.7816.01 2 0.3525 0.491 0.04 0.86 0.00 0.10
#> TCGA.50.6593.11 2 0.1913 0.504 0.02 0.94 0.00 0.04
#> TCGA.44.2656.11 3 0.3198 0.686 0.08 0.00 0.88 0.04
#> TCGA.44.6778.11 4 0.4907 1.000 0.00 0.00 0.42 0.58
#> TCGA.38.4631.11 2 0.2335 0.523 0.02 0.92 0.00 0.06
#> TCGA.44.2665.11 1 0.6005 0.000 0.50 0.46 0.00 0.04
#> TCGA.86.A4P8.01 2 0.5535 -0.666 0.42 0.56 0.00 0.02
#> TCGA.38.4632.11 4 0.4907 1.000 0.00 0.00 0.42 0.58
#> TCGA.44.2655.11 2 0.4994 -0.741 0.48 0.52 0.00 0.00
#> TCGA.50.5939.11 3 0.0707 0.701 0.00 0.00 0.98 0.02
#> TCGA.44.6145.11 2 0.3972 0.466 0.08 0.84 0.00 0.08
#> TCGA.75.6203.01 2 0.2830 0.501 0.06 0.90 0.00 0.04
#> TCGA.50.6594.11 2 0.5784 0.389 0.10 0.70 0.00 0.20
#> TCGA.44.2668.11 3 0.2335 0.698 0.06 0.00 0.92 0.02
#> TCGA.49.4488.11 2 0.5487 -0.574 0.40 0.58 0.00 0.02
#> TCGA.55.6980.01 3 0.7135 0.255 0.20 0.00 0.56 0.24
#> TCGA.50.5935.11 2 0.3247 0.508 0.06 0.88 0.00 0.06
#> TCGA.49.AARR.01 4 0.4907 1.000 0.00 0.00 0.42 0.58
#> TCGA.73.4676.11 3 0.3198 0.701 0.08 0.00 0.88 0.04
#> TCGA.L4.A4E6.01 3 0.6366 0.568 0.24 0.00 0.64 0.12
#> TCGA.73.4658.11 2 0.1411 0.514 0.02 0.96 0.00 0.02
#> TCGA.44.6148.11 3 0.6104 0.369 0.18 0.00 0.68 0.14
#> TCGA.50.5933.11 3 0.5486 0.597 0.20 0.00 0.72 0.08
#> TCGA.50.5936.11 3 0.3821 0.689 0.12 0.00 0.84 0.04
#> TCGA.50.5931.11 2 0.5428 -0.580 0.38 0.60 0.00 0.02
#> TCGA.44.6144.11 3 0.3611 0.658 0.08 0.00 0.86 0.06
#> TCGA.75.6212.01 2 0.1211 0.519 0.00 0.96 0.00 0.04
#> TCGA.50.5932.11 3 0.5902 0.560 0.16 0.00 0.70 0.14
#> TCGA.44.6147.11 2 0.1411 0.514 0.02 0.96 0.00 0.02
#> TCGA.44.5643.11 4 0.4907 1.000 0.00 0.00 0.42 0.58
#> TCGA.50.6592.11 2 0.3247 0.487 0.06 0.88 0.00 0.06
#> TCGA.55.8513.01 2 0.4994 -0.741 0.48 0.52 0.00 0.00
#> TCGA.05.5420.11 3 0.0000 0.701 0.00 0.00 1.00 0.00
#> TCGA.50.6591.11 2 0.4292 0.481 0.08 0.82 0.00 0.10
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.97.A4M1.01 2 0.6315 0.346 0.10 0.52 0.00 0.02 0.36
#> TCGA.97.8552.01 1 0.3561 0.858 0.74 0.26 0.00 0.00 0.00
#> TCGA.44.2659.11 1 0.5440 0.786 0.70 0.16 0.00 0.02 0.12
#> TCGA.44.5645.11 2 0.6184 -0.810 0.00 0.48 0.00 0.14 0.38
#> TCGA.44.2662.11 3 0.6003 0.601 0.04 0.00 0.66 0.12 0.18
#> TCGA.50.5930.11 3 0.1216 0.759 0.00 0.00 0.96 0.02 0.02
#> TCGA.55.8512.01 3 0.6003 0.652 0.12 0.00 0.66 0.04 0.18
#> TCGA.44.6146.11 3 0.1648 0.772 0.00 0.00 0.94 0.04 0.02
#> TCGA.44.6148.01 3 0.6484 0.452 0.04 0.00 0.60 0.22 0.14
#> TCGA.49.6745.11 3 0.1648 0.756 0.00 0.00 0.94 0.02 0.04
#> TCGA.55.7816.01 2 0.5173 0.277 0.04 0.50 0.00 0.00 0.46
#> TCGA.50.6593.11 2 0.0609 0.467 0.02 0.98 0.00 0.00 0.00
#> TCGA.44.2656.11 3 0.2616 0.755 0.00 0.00 0.88 0.02 0.10
#> TCGA.44.6778.11 4 0.3561 0.988 0.00 0.00 0.26 0.74 0.00
#> TCGA.38.4631.11 2 0.4096 0.209 0.00 0.76 0.00 0.04 0.20
#> TCGA.44.2665.11 1 0.4106 0.818 0.80 0.14 0.00 0.02 0.04
#> TCGA.86.A4P8.01 1 0.5245 0.813 0.64 0.28 0.00 0.00 0.08
#> TCGA.38.4632.11 4 0.3561 0.988 0.00 0.00 0.26 0.74 0.00
#> TCGA.44.2655.11 1 0.3274 0.853 0.78 0.22 0.00 0.00 0.00
#> TCGA.50.5939.11 3 0.1216 0.759 0.00 0.00 0.96 0.02 0.02
#> TCGA.44.6145.11 2 0.5382 0.429 0.10 0.64 0.00 0.00 0.26
#> TCGA.75.6203.01 2 0.3946 0.323 0.00 0.80 0.00 0.08 0.12
#> TCGA.50.6594.11 5 0.6207 0.000 0.00 0.40 0.00 0.14 0.46
#> TCGA.44.2668.11 3 0.1216 0.770 0.02 0.00 0.96 0.00 0.02
#> TCGA.49.4488.11 1 0.4675 0.757 0.60 0.38 0.00 0.00 0.02
#> TCGA.55.6980.01 3 0.6975 0.432 0.10 0.00 0.58 0.20 0.12
#> TCGA.50.5935.11 2 0.1820 0.428 0.02 0.94 0.00 0.02 0.02
#> TCGA.49.AARR.01 4 0.3561 0.988 0.00 0.00 0.26 0.74 0.00
#> TCGA.73.4676.11 3 0.2927 0.758 0.02 0.00 0.88 0.02 0.08
#> TCGA.L4.A4E6.01 3 0.6356 0.642 0.14 0.00 0.64 0.06 0.16
#> TCGA.73.4658.11 2 0.2616 0.397 0.00 0.88 0.00 0.02 0.10
#> TCGA.44.6148.11 3 0.6484 0.452 0.04 0.00 0.60 0.22 0.14
#> TCGA.50.5933.11 3 0.4855 0.715 0.04 0.00 0.76 0.06 0.14
#> TCGA.50.5936.11 3 0.1648 0.767 0.02 0.00 0.94 0.00 0.04
#> TCGA.50.5931.11 1 0.4613 0.796 0.62 0.36 0.00 0.00 0.02
#> TCGA.44.6144.11 3 0.3390 0.739 0.02 0.00 0.86 0.06 0.06
#> TCGA.75.6212.01 2 0.3690 0.499 0.02 0.78 0.00 0.00 0.20
#> TCGA.50.5932.11 3 0.5818 0.659 0.12 0.00 0.70 0.08 0.10
#> TCGA.44.6147.11 2 0.1043 0.481 0.00 0.96 0.00 0.00 0.04
#> TCGA.44.5643.11 4 0.3684 0.963 0.00 0.00 0.28 0.72 0.00
#> TCGA.50.6592.11 2 0.5524 0.369 0.06 0.64 0.00 0.02 0.28
#> TCGA.55.8513.01 1 0.3109 0.855 0.80 0.20 0.00 0.00 0.00
#> TCGA.05.5420.11 3 0.2249 0.760 0.02 0.00 0.92 0.02 0.04
#> TCGA.50.6591.11 2 0.5095 0.375 0.04 0.56 0.00 0.00 0.40
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.97.A4M1.01 2 0.7734 0.1126 0.10 0.44 0.00 0.06 0.14 0.26
#> TCGA.97.8552.01 1 0.3688 0.7494 0.80 0.14 0.00 0.04 0.00 0.02
#> TCGA.44.2659.11 1 0.4430 0.7098 0.76 0.12 0.00 0.00 0.04 0.08
#> TCGA.44.5645.11 5 0.5115 0.4970 0.02 0.46 0.00 0.00 0.48 0.04
#> TCGA.44.2662.11 3 0.6296 -0.2794 0.00 0.00 0.44 0.02 0.20 0.34
#> TCGA.50.5930.11 3 0.1635 0.4591 0.02 0.00 0.94 0.02 0.00 0.02
#> TCGA.55.8512.01 3 0.4328 -0.6604 0.00 0.00 0.52 0.00 0.02 0.46
#> TCGA.44.6146.11 3 0.2260 0.3081 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.44.6148.01 3 0.6812 -0.0868 0.00 0.00 0.48 0.08 0.22 0.22
#> TCGA.49.6745.11 3 0.1635 0.4591 0.02 0.00 0.94 0.02 0.00 0.02
#> TCGA.55.7816.01 2 0.5783 0.0374 0.00 0.50 0.00 0.00 0.22 0.28
#> TCGA.50.6593.11 2 0.3258 0.4258 0.06 0.86 0.00 0.02 0.04 0.02
#> TCGA.44.2656.11 3 0.3318 0.3140 0.02 0.00 0.82 0.00 0.02 0.14
#> TCGA.44.6778.11 4 0.2793 1.0000 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.38.4631.11 2 0.4345 0.1330 0.02 0.74 0.00 0.00 0.18 0.06
#> TCGA.44.2665.11 1 0.4895 0.6914 0.76 0.08 0.00 0.06 0.06 0.04
#> TCGA.86.A4P8.01 1 0.7261 0.3869 0.44 0.34 0.00 0.08 0.06 0.08
#> TCGA.38.4632.11 4 0.2793 1.0000 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.44.2655.11 1 0.2581 0.7535 0.86 0.12 0.00 0.02 0.00 0.00
#> TCGA.50.5939.11 3 0.1635 0.4591 0.02 0.00 0.94 0.02 0.00 0.02
#> TCGA.44.6145.11 2 0.5858 0.3732 0.08 0.68 0.00 0.04 0.08 0.12
#> TCGA.75.6203.01 2 0.3111 0.3783 0.00 0.84 0.00 0.02 0.12 0.02
#> TCGA.50.6594.11 5 0.4844 0.5547 0.02 0.32 0.00 0.04 0.62 0.00
#> TCGA.44.2668.11 3 0.0937 0.4260 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.49.4488.11 1 0.4310 0.4102 0.54 0.44 0.00 0.02 0.00 0.00
#> TCGA.55.6980.01 3 0.6800 -0.5204 0.06 0.00 0.48 0.12 0.02 0.32
#> TCGA.50.5935.11 2 0.2938 0.4213 0.04 0.88 0.00 0.02 0.04 0.02
#> TCGA.49.AARR.01 4 0.2793 1.0000 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.73.4676.11 3 0.2454 0.3134 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.L4.A4E6.01 6 0.4337 0.0000 0.00 0.00 0.48 0.02 0.00 0.50
#> TCGA.73.4658.11 2 0.3697 0.3180 0.04 0.82 0.00 0.00 0.06 0.08
#> TCGA.44.6148.11 3 0.6812 -0.0868 0.00 0.00 0.48 0.08 0.22 0.22
#> TCGA.50.5933.11 3 0.3592 0.0526 0.00 0.00 0.74 0.02 0.00 0.24
#> TCGA.50.5936.11 3 0.2260 0.3367 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.50.5931.11 2 0.5874 -0.3945 0.42 0.48 0.00 0.04 0.02 0.04
#> TCGA.44.6144.11 3 0.2956 0.3452 0.00 0.00 0.84 0.04 0.00 0.12
#> TCGA.75.6212.01 2 0.5351 0.4143 0.02 0.70 0.00 0.06 0.06 0.16
#> TCGA.50.5932.11 3 0.5706 -0.2950 0.06 0.00 0.62 0.04 0.02 0.26
#> TCGA.44.6147.11 2 0.2020 0.4367 0.02 0.92 0.00 0.00 0.02 0.04
#> TCGA.44.5643.11 4 0.2793 1.0000 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.50.6592.11 2 0.6176 0.2242 0.04 0.64 0.00 0.06 0.16 0.10
#> TCGA.55.8513.01 1 0.2048 0.7515 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.05.5420.11 3 0.2020 0.4552 0.02 0.00 0.92 0.02 0.00 0.04
#> TCGA.50.6591.11 2 0.6322 0.2322 0.02 0.54 0.00 0.02 0.16 0.26
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.97.A4M1.01 2 0.6223 0.3521 0.14 0.62 0.00 0.02 0.08 0.04 0.10
#> TCGA.97.8552.01 1 0.3289 0.7733 0.82 0.10 0.00 0.00 0.02 0.00 0.06
#> TCGA.44.2659.11 1 0.4045 0.7346 0.72 0.14 0.00 0.00 0.00 0.00 0.14
#> TCGA.44.5645.11 5 0.2708 0.7173 0.00 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.44.2662.11 7 0.5204 0.6248 0.00 0.00 0.22 0.00 0.04 0.12 0.62
#> TCGA.50.5930.11 3 0.0504 0.7443 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.8512.01 6 0.5837 0.5457 0.02 0.00 0.24 0.00 0.06 0.58 0.10
#> TCGA.44.6146.11 3 0.3086 0.6728 0.00 0.00 0.80 0.00 0.00 0.16 0.04
#> TCGA.44.6148.01 7 0.5717 0.8325 0.00 0.00 0.28 0.12 0.00 0.06 0.54
#> TCGA.49.6745.11 3 0.1006 0.7386 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.55.7816.01 2 0.4335 0.3907 0.04 0.72 0.00 0.00 0.20 0.02 0.02
#> TCGA.50.6593.11 2 0.5429 0.5056 0.12 0.68 0.00 0.00 0.08 0.06 0.06
#> TCGA.44.2656.11 3 0.3991 0.5164 0.02 0.00 0.72 0.00 0.00 0.22 0.04
#> TCGA.44.6778.11 4 0.2003 0.9594 0.02 0.00 0.02 0.92 0.02 0.00 0.02
#> TCGA.38.4631.11 2 0.3413 0.3094 0.00 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.44.2665.11 1 0.4838 0.6616 0.68 0.14 0.00 0.00 0.04 0.00 0.14
#> TCGA.86.A4P8.01 1 0.5165 0.6551 0.58 0.28 0.00 0.00 0.02 0.00 0.12
#> TCGA.38.4632.11 4 0.1505 0.9641 0.02 0.00 0.02 0.94 0.02 0.00 0.00
#> TCGA.44.2655.11 1 0.2376 0.7716 0.86 0.12 0.00 0.00 0.00 0.00 0.02
#> TCGA.50.5939.11 3 0.1006 0.7431 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.44.6145.11 2 0.5046 0.4971 0.10 0.66 0.00 0.00 0.18 0.00 0.06
#> TCGA.75.6203.01 2 0.5411 0.3343 0.02 0.58 0.00 0.00 0.30 0.06 0.04
#> TCGA.50.6594.11 5 0.4969 0.7363 0.00 0.20 0.00 0.00 0.66 0.08 0.06
#> TCGA.44.2668.11 3 0.1363 0.7449 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.49.4488.11 1 0.5215 0.5787 0.58 0.30 0.00 0.00 0.06 0.00 0.06
#> TCGA.55.6980.01 6 0.4966 0.5745 0.02 0.00 0.12 0.16 0.00 0.68 0.02
#> TCGA.50.5935.11 2 0.5630 0.4535 0.10 0.62 0.00 0.00 0.20 0.06 0.02
#> TCGA.49.AARR.01 4 0.0504 0.9639 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.73.4676.11 3 0.3307 0.6001 0.00 0.00 0.74 0.02 0.00 0.24 0.00
#> TCGA.L4.A4E6.01 6 0.5740 0.6382 0.00 0.00 0.22 0.02 0.10 0.60 0.06
#> TCGA.73.4658.11 2 0.4461 0.3984 0.04 0.62 0.00 0.00 0.32 0.02 0.00
#> TCGA.44.6148.11 7 0.5717 0.8325 0.00 0.00 0.28 0.12 0.00 0.06 0.54
#> TCGA.50.5933.11 3 0.5133 -0.0658 0.00 0.00 0.48 0.02 0.02 0.44 0.04
#> TCGA.50.5936.11 3 0.3485 0.6900 0.02 0.00 0.82 0.02 0.00 0.10 0.04
#> TCGA.50.5931.11 1 0.4993 0.6604 0.64 0.26 0.00 0.00 0.02 0.04 0.04
#> TCGA.44.6144.11 3 0.3991 0.5559 0.00 0.00 0.72 0.04 0.02 0.22 0.00
#> TCGA.75.6212.01 2 0.2911 0.5367 0.08 0.86 0.00 0.00 0.02 0.02 0.02
#> TCGA.50.5932.11 6 0.5322 0.5102 0.02 0.00 0.30 0.08 0.00 0.58 0.02
#> TCGA.44.6147.11 2 0.4801 0.5286 0.06 0.70 0.00 0.00 0.18 0.04 0.02
#> TCGA.44.5643.11 4 0.0863 0.9588 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.50.6592.11 2 0.3566 0.4566 0.02 0.78 0.00 0.00 0.04 0.00 0.16
#> TCGA.55.8513.01 1 0.1433 0.7722 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.11 3 0.1166 0.7389 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.50.6591.11 2 0.4418 0.4657 0.06 0.76 0.00 0.00 0.08 0.02 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.97.A4M1.01 2 0.6742 -0.0168 0.08 0.44 0.00 0.02 0.28 0.00 0.14 0.04
#> TCGA.97.8552.01 1 0.2569 0.7898 0.82 0.16 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.44.2659.11 1 0.4034 0.7852 0.76 0.12 0.00 0.00 0.04 0.06 0.02 0.00
#> TCGA.44.5645.11 5 0.5203 0.1920 0.00 0.28 0.00 0.00 0.42 0.00 0.00 0.30
#> TCGA.44.2662.11 7 0.5330 0.6158 0.02 0.00 0.12 0.00 0.02 0.12 0.66 0.06
#> TCGA.50.5930.11 3 0.1275 0.7386 0.02 0.00 0.94 0.00 0.04 0.00 0.00 0.00
#> TCGA.55.8512.01 6 0.2856 0.5529 0.00 0.00 0.20 0.00 0.00 0.78 0.02 0.00
#> TCGA.44.6146.11 3 0.1557 0.7340 0.00 0.00 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.44.6148.01 7 0.3299 0.8341 0.00 0.00 0.18 0.06 0.00 0.00 0.76 0.00
#> TCGA.49.6745.11 3 0.2071 0.7260 0.02 0.00 0.90 0.00 0.04 0.04 0.00 0.00
#> TCGA.55.7816.01 5 0.3808 0.0119 0.00 0.34 0.00 0.00 0.62 0.00 0.04 0.00
#> TCGA.50.6593.11 2 0.2224 0.4125 0.02 0.86 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.44.2656.11 3 0.4655 0.3102 0.02 0.00 0.58 0.00 0.04 0.34 0.02 0.00
#> TCGA.44.6778.11 4 0.2204 0.9536 0.02 0.00 0.02 0.90 0.02 0.00 0.00 0.04
#> TCGA.38.4631.11 2 0.3299 -0.0507 0.00 0.56 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.44.2665.11 1 0.5208 0.6900 0.66 0.10 0.00 0.00 0.02 0.16 0.04 0.02
#> TCGA.86.A4P8.01 1 0.4756 0.6024 0.56 0.34 0.00 0.00 0.04 0.06 0.00 0.00
#> TCGA.38.4632.11 4 0.1741 0.9609 0.02 0.00 0.02 0.92 0.00 0.00 0.00 0.04
#> TCGA.44.2655.11 1 0.1765 0.8050 0.88 0.12 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5939.11 3 0.0471 0.7475 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.6145.11 2 0.4903 0.3553 0.10 0.70 0.00 0.00 0.12 0.04 0.02 0.02
#> TCGA.75.6203.01 2 0.2407 0.3510 0.00 0.86 0.00 0.00 0.08 0.00 0.00 0.06
#> TCGA.50.6594.11 8 0.5158 -0.6500 0.00 0.26 0.00 0.00 0.30 0.00 0.00 0.44
#> TCGA.44.2668.11 3 0.0471 0.7438 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.49.4488.11 1 0.4050 0.6076 0.60 0.34 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.55.6980.01 6 0.7359 0.4145 0.02 0.00 0.14 0.08 0.08 0.44 0.02 0.22
#> TCGA.50.5935.11 2 0.0000 0.4392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARR.01 4 0.0471 0.9635 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.73.4676.11 3 0.2404 0.7168 0.00 0.00 0.84 0.00 0.00 0.02 0.00 0.14
#> TCGA.L4.A4E6.01 6 0.5498 0.5335 0.00 0.00 0.18 0.00 0.00 0.54 0.06 0.22
#> TCGA.73.4658.11 2 0.3193 0.1205 0.00 0.62 0.00 0.00 0.38 0.00 0.00 0.00
#> TCGA.44.6148.11 7 0.3299 0.8341 0.00 0.00 0.18 0.06 0.00 0.00 0.76 0.00
#> TCGA.50.5933.11 3 0.5158 0.0813 0.00 0.00 0.44 0.00 0.00 0.26 0.00 0.30
#> TCGA.50.5936.11 3 0.4896 0.5614 0.00 0.00 0.68 0.00 0.06 0.12 0.02 0.12
#> TCGA.50.5931.11 2 0.4125 -0.4221 0.44 0.52 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.44.6144.11 3 0.3660 0.5991 0.00 0.00 0.70 0.00 0.00 0.06 0.00 0.24
#> TCGA.75.6212.01 2 0.3021 0.3722 0.00 0.80 0.00 0.00 0.16 0.00 0.02 0.02
#> TCGA.50.5932.11 8 0.7129 -0.6350 0.02 0.00 0.30 0.02 0.06 0.28 0.02 0.30
#> TCGA.44.6147.11 2 0.2406 0.3673 0.00 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.44.5643.11 4 0.0471 0.9635 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.50.6592.11 2 0.5984 0.1705 0.02 0.54 0.00 0.00 0.22 0.16 0.04 0.02
#> TCGA.55.8513.01 1 0.1563 0.7981 0.90 0.10 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.11 3 0.3903 0.7173 0.02 0.00 0.78 0.00 0.06 0.06 0.00 0.08
#> TCGA.50.6591.11 2 0.5213 0.0328 0.00 0.54 0.00 0.00 0.32 0.02 0.10 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: Node03. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122 , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221-leaf , Node0222 , Node0223-leaf , Node0231 , Node0232 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0324-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["031"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 22 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 7.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.2475 0.753 0.753
#> 3 3 1.000 1.000 1.000 1.0134 0.714 0.629
#> 4 4 0.853 0.929 0.950 0.4547 0.758 0.517
#> 5 5 0.818 0.818 0.865 0.0864 0.935 0.750
#> 6 6 0.905 0.763 0.849 0.0522 0.892 0.537
#> 7 7 0.932 0.843 0.922 0.0358 0.965 0.789
#> 8 8 0.832 0.713 0.878 0.0285 0.965 0.742
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 7
#> attr(,"optional")
#> [1] 2 3 6
There is also optional best \(k\) = 2 3 6 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.44.2662.11 1 0 1 1 0
#> TCGA.50.5930.11 1 0 1 1 0
#> TCGA.55.8512.01 2 0 1 0 1
#> TCGA.44.6146.11 1 0 1 1 0
#> TCGA.44.6148.01 2 0 1 0 1
#> TCGA.49.6745.11 1 0 1 1 0
#> TCGA.44.2656.11 1 0 1 1 0
#> TCGA.44.6778.11 1 0 1 1 0
#> TCGA.38.4632.11 1 0 1 1 0
#> TCGA.50.5939.11 1 0 1 1 0
#> TCGA.44.2668.11 1 0 1 1 0
#> TCGA.55.6980.01 2 0 1 0 1
#> TCGA.49.AARR.01 1 0 1 1 0
#> TCGA.73.4676.11 1 0 1 1 0
#> TCGA.L4.A4E6.01 1 0 1 1 0
#> TCGA.44.6148.11 1 0 1 1 0
#> TCGA.50.5933.11 1 0 1 1 0
#> TCGA.50.5936.11 1 0 1 1 0
#> TCGA.44.6144.11 1 0 1 1 0
#> TCGA.50.5932.11 1 0 1 1 0
#> TCGA.44.5643.11 1 0 1 1 0
#> TCGA.05.5420.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.2662.11 1 0 1 1 0 0
#> TCGA.50.5930.11 1 0 1 1 0 0
#> TCGA.55.8512.01 2 0 1 0 1 0
#> TCGA.44.6146.11 1 0 1 1 0 0
#> TCGA.44.6148.01 2 0 1 0 1 0
#> TCGA.49.6745.11 3 0 1 0 0 1
#> TCGA.44.2656.11 1 0 1 1 0 0
#> TCGA.44.6778.11 1 0 1 1 0 0
#> TCGA.38.4632.11 1 0 1 1 0 0
#> TCGA.50.5939.11 1 0 1 1 0 0
#> TCGA.44.2668.11 1 0 1 1 0 0
#> TCGA.55.6980.01 3 0 1 0 0 1
#> TCGA.49.AARR.01 3 0 1 0 0 1
#> TCGA.73.4676.11 1 0 1 1 0 0
#> TCGA.L4.A4E6.01 1 0 1 1 0 0
#> TCGA.44.6148.11 3 0 1 0 0 1
#> TCGA.50.5933.11 3 0 1 0 0 1
#> TCGA.50.5936.11 1 0 1 1 0 0
#> TCGA.44.6144.11 1 0 1 1 0 0
#> TCGA.50.5932.11 1 0 1 1 0 0
#> TCGA.44.5643.11 1 0 1 1 0 0
#> TCGA.05.5420.11 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.44.2662.11 4 0.121 1.000 0.04 0 0.00 0.96
#> TCGA.50.5930.11 4 0.121 1.000 0.04 0 0.00 0.96
#> TCGA.55.8512.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.44.6146.11 1 0.000 0.912 1.00 0 0.00 0.00
#> TCGA.44.6148.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.49.6745.11 3 0.317 0.845 0.16 0 0.84 0.00
#> TCGA.44.2656.11 4 0.121 1.000 0.04 0 0.00 0.96
#> TCGA.44.6778.11 4 0.121 1.000 0.04 0 0.00 0.96
#> TCGA.38.4632.11 4 0.121 1.000 0.04 0 0.00 0.96
#> TCGA.50.5939.11 4 0.121 1.000 0.04 0 0.00 0.96
#> TCGA.44.2668.11 4 0.121 1.000 0.04 0 0.00 0.96
#> TCGA.55.6980.01 3 0.121 0.876 0.00 0 0.96 0.04
#> TCGA.49.AARR.01 3 0.000 0.891 0.00 0 1.00 0.00
#> TCGA.73.4676.11 1 0.317 0.839 0.84 0 0.00 0.16
#> TCGA.L4.A4E6.01 1 0.292 0.853 0.86 0 0.00 0.14
#> TCGA.44.6148.11 3 0.000 0.891 0.00 0 1.00 0.00
#> TCGA.50.5933.11 3 0.317 0.845 0.16 0 0.84 0.00
#> TCGA.50.5936.11 1 0.000 0.912 1.00 0 0.00 0.00
#> TCGA.44.6144.11 1 0.317 0.839 0.84 0 0.00 0.16
#> TCGA.50.5932.11 1 0.000 0.912 1.00 0 0.00 0.00
#> TCGA.44.5643.11 1 0.000 0.912 1.00 0 0.00 0.00
#> TCGA.05.5420.11 1 0.000 0.912 1.00 0 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.2662.11 4 0.0000 0.723 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5930.11 4 0.0000 0.723 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8512.01 2 0.0000 0.953 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6146.11 1 0.1216 0.979 0.96 0.00 0.00 0.02 0.02
#> TCGA.44.6148.01 2 0.2012 0.953 0.02 0.92 0.00 0.00 0.06
#> TCGA.49.6745.11 3 0.1410 0.902 0.06 0.00 0.94 0.00 0.00
#> TCGA.44.2656.11 4 0.0000 0.723 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6778.11 4 0.4262 0.444 0.00 0.00 0.00 0.56 0.44
#> TCGA.38.4632.11 4 0.4262 0.444 0.00 0.00 0.00 0.56 0.44
#> TCGA.50.5939.11 4 0.4262 0.444 0.00 0.00 0.00 0.56 0.44
#> TCGA.44.2668.11 4 0.0000 0.723 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.6980.01 3 0.3424 0.747 0.00 0.00 0.76 0.00 0.24
#> TCGA.49.AARR.01 3 0.0000 0.908 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.4676.11 5 0.4854 0.903 0.26 0.00 0.00 0.06 0.68
#> TCGA.L4.A4E6.01 5 0.4854 0.903 0.26 0.00 0.00 0.06 0.68
#> TCGA.44.6148.11 3 0.0000 0.908 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5933.11 3 0.1410 0.902 0.06 0.00 0.94 0.00 0.00
#> TCGA.50.5936.11 1 0.0609 0.986 0.98 0.00 0.00 0.02 0.00
#> TCGA.44.6144.11 5 0.5351 0.776 0.38 0.00 0.00 0.06 0.56
#> TCGA.50.5932.11 1 0.0609 0.986 0.98 0.00 0.00 0.02 0.00
#> TCGA.44.5643.11 1 0.0609 0.986 0.98 0.00 0.00 0.02 0.00
#> TCGA.05.5420.11 1 0.1216 0.979 0.96 0.00 0.00 0.02 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.2662.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5930.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8512.01 2 0.1092 0.969 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.44.6146.11 1 0.0937 0.966 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.44.6148.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.11 3 0.0547 0.972 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.44.2656.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6778.11 5 0.4310 0.367 0.00 0.00 0.00 0.44 0.54 0.02
#> TCGA.38.4632.11 5 0.4310 0.367 0.00 0.00 0.00 0.44 0.54 0.02
#> TCGA.50.5939.11 5 0.4310 0.367 0.00 0.00 0.00 0.44 0.54 0.02
#> TCGA.44.2668.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6980.01 6 0.3499 0.000 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.49.AARR.01 3 0.0000 0.972 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.4676.11 5 0.4121 0.359 0.06 0.00 0.00 0.00 0.72 0.22
#> TCGA.L4.A4E6.01 5 0.4462 0.351 0.06 0.00 0.00 0.00 0.66 0.28
#> TCGA.44.6148.11 3 0.0000 0.972 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5933.11 3 0.0547 0.972 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.50.5936.11 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6144.11 5 0.3409 0.288 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.50.5932.11 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.5643.11 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.11 1 0.0937 0.966 0.96 0.00 0.00 0.00 0.04 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.44.2662.11 4 0.0863 0.9639 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.50.5930.11 4 0.0000 0.9882 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8512.01 2 0.0000 0.8644 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6146.11 1 0.1166 0.9547 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.44.6148.01 2 0.3149 0.8644 0.00 0.84 0.00 0.00 0.06 0.04 0.06
#> TCGA.49.6745.11 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2656.11 4 0.0000 0.9882 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6778.11 5 0.2259 0.7553 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.38.4632.11 5 0.2259 0.7553 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.50.5939.11 5 0.2259 0.7553 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.44.2668.11 4 0.0000 0.9882 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6980.01 6 0.2081 0.0000 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.49.AARR.01 3 0.1006 0.9572 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.73.4676.11 7 0.1671 0.9199 0.00 0.00 0.00 0.00 0.10 0.00 0.90
#> TCGA.L4.A4E6.01 7 0.2572 0.9195 0.00 0.00 0.00 0.00 0.08 0.06 0.86
#> TCGA.44.6148.11 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.11 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5936.11 1 0.0000 0.9700 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6144.11 5 0.4978 0.0561 0.38 0.00 0.00 0.00 0.50 0.00 0.12
#> TCGA.50.5932.11 1 0.0000 0.9700 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.5643.11 1 0.0000 0.9700 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.11 1 0.1166 0.9547 0.94 0.00 0.00 0.00 0.06 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.44.2662.11 4 0.1275 0.9226 0.00 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.50.5930.11 4 0.0808 0.9482 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.8512.01 2 0.3369 0.8445 0.00 0.82 0.00 0.00 0.04 0.02 0.04 0.08
#> TCGA.44.6146.11 1 0.3299 -0.4219 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.44.6148.01 2 0.0000 0.8445 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6745.11 3 0.0000 0.9553 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2656.11 4 0.1091 0.9474 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.44.6778.11 5 0.2114 1.0000 0.00 0.00 0.00 0.16 0.84 0.00 0.00 0.00
#> TCGA.38.4632.11 5 0.2114 1.0000 0.00 0.00 0.00 0.16 0.84 0.00 0.00 0.00
#> TCGA.50.5939.11 5 0.2114 1.0000 0.00 0.00 0.00 0.16 0.84 0.00 0.00 0.00
#> TCGA.44.2668.11 4 0.0808 0.9437 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.6980.01 6 0.0808 0.0000 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.49.AARR.01 3 0.2624 0.8575 0.00 0.00 0.86 0.00 0.06 0.00 0.02 0.06
#> TCGA.73.4676.11 7 0.1091 0.7621 0.00 0.00 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.L4.A4E6.01 7 0.3551 0.7597 0.00 0.00 0.00 0.00 0.06 0.00 0.72 0.22
#> TCGA.44.6148.11 3 0.0000 0.9553 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.11 3 0.0000 0.9553 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5936.11 1 0.1563 0.6228 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.44.6144.11 8 0.5649 0.4028 0.12 0.00 0.00 0.00 0.12 0.00 0.22 0.54
#> TCGA.50.5932.11 1 0.0471 0.6772 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.44.5643.11 1 0.0471 0.6800 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.05.5420.11 8 0.3318 0.0252 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122 , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221-leaf , Node0222 , Node0223-leaf , Node0231 , Node0232 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0324-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["032"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 22 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 0.2475 0.753 0.753
#> 3 3 1.000 1.000 1.000 1.0484 0.740 0.655
#> 4 4 0.981 0.970 0.945 0.0273 0.983 0.965
#> 5 5 0.989 0.931 0.978 0.0390 0.991 0.982
#> 6 6 0.827 0.803 0.943 0.0572 0.996 0.991
#> 7 7 0.810 0.753 0.959 0.0909 0.939 0.869
#> 8 8 0.684 0.629 0.910 0.0708 0.996 0.989
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.97.A4M1.01 1 0 1 1 0
#> TCGA.97.8552.01 1 0 1 1 0
#> TCGA.44.2659.11 2 0 1 0 1
#> TCGA.44.5645.11 2 0 1 0 1
#> TCGA.55.7816.01 2 0 1 0 1
#> TCGA.50.6593.11 2 0 1 0 1
#> TCGA.38.4631.11 2 0 1 0 1
#> TCGA.44.2665.11 2 0 1 0 1
#> TCGA.86.A4P8.01 2 0 1 0 1
#> TCGA.44.2655.11 2 0 1 0 1
#> TCGA.44.6145.11 2 0 1 0 1
#> TCGA.75.6203.01 2 0 1 0 1
#> TCGA.50.6594.11 2 0 1 0 1
#> TCGA.49.4488.11 2 0 1 0 1
#> TCGA.50.5935.11 2 0 1 0 1
#> TCGA.73.4658.11 2 0 1 0 1
#> TCGA.50.5931.11 2 0 1 0 1
#> TCGA.75.6212.01 1 0 1 1 0
#> TCGA.44.6147.11 2 0 1 0 1
#> TCGA.50.6592.11 2 0 1 0 1
#> TCGA.55.8513.01 2 0 1 0 1
#> TCGA.50.6591.11 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.97.A4M1.01 1 0 1 1 0 0
#> TCGA.97.8552.01 1 0 1 1 0 0
#> TCGA.44.2659.11 3 0 1 0 0 1
#> TCGA.44.5645.11 2 0 1 0 1 0
#> TCGA.55.7816.01 2 0 1 0 1 0
#> TCGA.50.6593.11 2 0 1 0 1 0
#> TCGA.38.4631.11 2 0 1 0 1 0
#> TCGA.44.2665.11 3 0 1 0 0 1
#> TCGA.86.A4P8.01 2 0 1 0 1 0
#> TCGA.44.2655.11 2 0 1 0 1 0
#> TCGA.44.6145.11 2 0 1 0 1 0
#> TCGA.75.6203.01 3 0 1 0 0 1
#> TCGA.50.6594.11 2 0 1 0 1 0
#> TCGA.49.4488.11 2 0 1 0 1 0
#> TCGA.50.5935.11 2 0 1 0 1 0
#> TCGA.73.4658.11 2 0 1 0 1 0
#> TCGA.50.5931.11 2 0 1 0 1 0
#> TCGA.75.6212.01 1 0 1 1 0 0
#> TCGA.44.6147.11 2 0 1 0 1 0
#> TCGA.50.6592.11 2 0 1 0 1 0
#> TCGA.55.8513.01 3 0 1 0 0 1
#> TCGA.50.6591.11 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.97.A4M1.01 1 0.000 0.840 1.0 0 0.0 0.0
#> TCGA.97.8552.01 1 0.000 0.840 1.0 0 0.0 0.0
#> TCGA.44.2659.11 4 0.000 1.000 0.0 0 0.0 1.0
#> TCGA.44.5645.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.55.7816.01 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.50.6593.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.38.4631.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.44.2665.11 4 0.000 1.000 0.0 0 0.0 1.0
#> TCGA.86.A4P8.01 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.44.2655.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.44.6145.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.75.6203.01 3 0.485 1.000 0.0 0 0.6 0.4
#> TCGA.50.6594.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.49.4488.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.50.5935.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.73.4658.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.50.5931.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.75.6212.01 1 0.485 0.655 0.6 0 0.4 0.0
#> TCGA.44.6147.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.50.6592.11 2 0.000 1.000 0.0 1 0.0 0.0
#> TCGA.55.8513.01 3 0.485 1.000 0.0 0 0.6 0.4
#> TCGA.50.6591.11 2 0.000 1.000 0.0 1 0.0 0.0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.97.A4M1.01 1 0.104 0.966 0.96 0.00 0.04 0.00 0.00
#> TCGA.97.8552.01 1 0.000 0.966 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2659.11 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.5645.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7816.01 2 0.165 0.956 0.00 0.94 0.02 0.00 0.04
#> TCGA.50.6593.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.38.4631.11 2 0.122 0.970 0.00 0.96 0.02 0.00 0.02
#> TCGA.44.2665.11 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.A4P8.01 2 0.122 0.970 0.00 0.96 0.02 0.00 0.02
#> TCGA.44.2655.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6145.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6203.01 3 0.141 0.929 0.00 0.00 0.94 0.06 0.00
#> TCGA.50.6594.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.4488.11 2 0.122 0.970 0.00 0.96 0.02 0.00 0.02
#> TCGA.50.5935.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.4658.11 2 0.122 0.970 0.00 0.96 0.02 0.00 0.02
#> TCGA.50.5931.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6212.01 5 0.104 0.000 0.04 0.00 0.00 0.00 0.96
#> TCGA.44.6147.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6592.11 2 0.000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8513.01 3 0.228 0.930 0.00 0.00 0.88 0.12 0.00
#> TCGA.50.6591.11 2 0.000 0.985 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.97.A4M1.01 1 0.0000 0.000 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.97.8552.01 6 0.3578 0.000 0.34 0.00 0.00 0.00 0 0.66
#> TCGA.44.2659.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.44.5645.11 2 0.0547 0.948 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.55.7816.01 2 0.3309 0.718 0.00 0.72 0.00 0.00 0 0.28
#> TCGA.50.6593.11 2 0.0547 0.945 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.38.4631.11 2 0.1556 0.922 0.00 0.92 0.00 0.00 0 0.08
#> TCGA.44.2665.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.86.A4P8.01 2 0.1814 0.926 0.00 0.90 0.00 0.00 0 0.10
#> TCGA.44.2655.11 2 0.0547 0.948 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.44.6145.11 2 0.0547 0.948 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.75.6203.01 3 0.0937 0.902 0.00 0.00 0.96 0.00 0 0.04
#> TCGA.50.6594.11 2 0.0000 0.947 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.49.4488.11 2 0.1814 0.912 0.00 0.90 0.00 0.00 0 0.10
#> TCGA.50.5935.11 2 0.0547 0.945 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.73.4658.11 2 0.1814 0.912 0.00 0.90 0.00 0.00 0 0.10
#> TCGA.50.5931.11 2 0.0000 0.947 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.75.6212.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.44.6147.11 2 0.0547 0.948 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.50.6592.11 2 0.0547 0.948 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.55.8513.01 3 0.1267 0.902 0.00 0.00 0.94 0.06 0 0.00
#> TCGA.50.6591.11 2 0.0547 0.948 0.00 0.98 0.00 0.00 0 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.97.A4M1.01 1 0.0000 0.000 1 0.00 0.00 0.00 0 0 0.00
#> TCGA.97.8552.01 6 0.0000 0.000 0 0.00 0.00 0.00 0 1 0.00
#> TCGA.44.2659.11 4 0.0000 1.000 0 0.00 0.00 1.00 0 0 0.00
#> TCGA.44.5645.11 2 0.0504 0.936 0 0.98 0.00 0.00 0 0 0.02
#> TCGA.55.7816.01 7 0.1166 0.000 0 0.06 0.00 0.00 0 0 0.94
#> TCGA.50.6593.11 2 0.0000 0.937 0 1.00 0.00 0.00 0 0 0.00
#> TCGA.38.4631.11 2 0.2259 0.839 0 0.84 0.00 0.00 0 0 0.16
#> TCGA.44.2665.11 4 0.0000 1.000 0 0.00 0.00 1.00 0 0 0.00
#> TCGA.86.A4P8.01 2 0.1886 0.870 0 0.88 0.00 0.00 0 0 0.12
#> TCGA.44.2655.11 2 0.0504 0.936 0 0.98 0.00 0.00 0 0 0.02
#> TCGA.44.6145.11 2 0.0863 0.933 0 0.96 0.00 0.00 0 0 0.04
#> TCGA.75.6203.01 3 0.0863 0.925 0 0.00 0.96 0.00 0 0 0.04
#> TCGA.50.6594.11 2 0.0000 0.937 0 1.00 0.00 0.00 0 0 0.00
#> TCGA.49.4488.11 2 0.2422 0.817 0 0.82 0.00 0.00 0 0 0.18
#> TCGA.50.5935.11 2 0.0000 0.937 0 1.00 0.00 0.00 0 0 0.00
#> TCGA.73.4658.11 2 0.2259 0.839 0 0.84 0.00 0.00 0 0 0.16
#> TCGA.50.5931.11 2 0.0000 0.937 0 1.00 0.00 0.00 0 0 0.00
#> TCGA.75.6212.01 5 0.0000 0.000 0 0.00 0.00 0.00 1 0 0.00
#> TCGA.44.6147.11 2 0.0504 0.936 0 0.98 0.00 0.00 0 0 0.02
#> TCGA.50.6592.11 2 0.0504 0.936 0 0.98 0.00 0.00 0 0 0.02
#> TCGA.55.8513.01 3 0.0863 0.925 0 0.00 0.96 0.04 0 0 0.00
#> TCGA.50.6591.11 2 0.0504 0.936 0 0.98 0.00 0.00 0 0 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.97.A4M1.01 1 0.0000 0.000 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.97.8552.01 6 0.0471 0.000 0.02 0.00 0.00 0 0 0.98 0.00 0.00
#> TCGA.44.2659.11 4 0.0000 1.000 0.00 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.44.5645.11 2 0.1563 0.869 0.00 0.90 0.00 0 0 0.00 0.00 0.10
#> TCGA.55.7816.01 7 0.0000 0.000 0.00 0.00 0.00 0 0 0.00 1.00 0.00
#> TCGA.50.6593.11 2 0.0941 0.877 0.00 0.96 0.00 0 0 0.00 0.02 0.02
#> TCGA.38.4631.11 2 0.3503 0.794 0.00 0.78 0.00 0 0 0.02 0.08 0.12
#> TCGA.44.2665.11 4 0.0000 1.000 0.00 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.86.A4P8.01 2 0.3078 0.819 0.00 0.82 0.00 0 0 0.02 0.06 0.10
#> TCGA.44.2655.11 2 0.1563 0.869 0.00 0.90 0.00 0 0 0.00 0.00 0.10
#> TCGA.44.6145.11 2 0.2224 0.863 0.00 0.86 0.00 0 0 0.00 0.02 0.12
#> TCGA.75.6203.01 3 0.0000 0.000 0.00 0.00 1.00 0 0 0.00 0.00 0.00
#> TCGA.50.6594.11 2 0.0471 0.881 0.00 0.98 0.00 0 0 0.00 0.00 0.02
#> TCGA.49.4488.11 2 0.4061 0.749 0.00 0.72 0.00 0 0 0.02 0.12 0.14
#> TCGA.50.5935.11 2 0.0000 0.881 0.00 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.73.4658.11 2 0.3879 0.763 0.00 0.74 0.00 0 0 0.02 0.14 0.10
#> TCGA.50.5931.11 2 0.1804 0.870 0.00 0.90 0.00 0 0 0.00 0.02 0.08
#> TCGA.75.6212.01 5 0.0000 0.000 0.00 0.00 0.00 0 1 0.00 0.00 0.00
#> TCGA.44.6147.11 2 0.1563 0.869 0.00 0.90 0.00 0 0 0.00 0.00 0.10
#> TCGA.50.6592.11 2 0.1557 0.874 0.00 0.92 0.00 0 0 0.00 0.02 0.06
#> TCGA.55.8513.01 8 0.2650 0.000 0.00 0.00 0.24 0 0 0.00 0.00 0.76
#> TCGA.50.6591.11 2 0.1563 0.869 0.00 0.90 0.00 0 0 0.00 0.00 0.10
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