Date: 2021-07-22 18:42:55 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 376133 rows and 434 columns.
#> Performed in total 95200 partitions.
#> There are 45 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, 434 cols
#> |-- 01, 140 cols, 16943 signatures
#> | |-- 011, 49 cols, 18153 signatures
#> | | |-- 0111, 17 cols, 1443 signatures
#> | | | |-- 01111, 5 cols (b)
#> | | | `-- 01112, 12 cols, 644 signatures (c)
#> | | |-- 0112, 21 cols, 2615 signatures
#> | | | |-- 01121, 8 cols (b)
#> | | | |-- 01122, 6 cols (b)
#> | | | |-- 01123, 4 cols (b)
#> | | | `-- 01124, 3 cols (b)
#> | | `-- 0113, 11 cols (b)
#> | |-- 012, 49 cols, 11356 signatures
#> | | |-- 0121, 23 cols, 12451 signatures
#> | | | |-- 01211, 12 cols, 90 signatures (c)
#> | | | |-- 01212, 7 cols (b)
#> | | | `-- 01213, 4 cols (b)
#> | | |-- 0122, 15 cols, 311 signatures (c)
#> | | `-- 0123, 11 cols (b)
#> | `-- 013, 42 cols, 21477 signatures
#> | |-- 0131, 12 cols, 35 signatures (c)
#> | |-- 0132, 12 cols, 2447 signatures
#> | | |-- 01321, 2 cols (b)
#> | | |-- 01322, 4 cols (b)
#> | | |-- 01323, 3 cols (b)
#> | | `-- 01324, 3 cols (b)
#> | |-- 0133, 11 cols (b)
#> | `-- 0134, 7 cols (b)
#> |-- 02, 118 cols, 10747 signatures
#> | |-- 021, 34 cols, 54159 signatures
#> | | |-- 0211, 2 cols (b)
#> | | |-- 0212, 9 cols (b)
#> | | |-- 0213, 15 cols, 3167 signatures
#> | | | |-- 02131, 6 cols (b)
#> | | | `-- 02132, 9 cols (b)
#> | | `-- 0214, 8 cols (b)
#> | |-- 022, 59 cols, 2929 signatures
#> | | |-- 0221, 16 cols, 1210 signatures
#> | | | |-- 02211, 10 cols (b)
#> | | | `-- 02212, 6 cols (b)
#> | | `-- 0222, 43 cols, 2275 signatures
#> | | |-- 02221, 14 cols, 834 signatures (c)
#> | | |-- 02222, 14 cols, 1601 signatures
#> | | | |-- 022221, 11 cols (b)
#> | | | `-- 022222, 3 cols (b)
#> | | `-- 02223, 15 cols, 15 signatures (c)
#> | `-- 023, 25 cols, 7299 signatures
#> | |-- 0231, 15 cols, 3632 signatures
#> | | |-- 02311, 2 cols (b)
#> | | `-- 02312, 13 cols, 618 signatures (c)
#> | |-- 0232, 7 cols (b)
#> | `-- 0233, 3 cols (b)
#> `-- 03, 176 cols, 12363 signatures
#> |-- 031, 60 cols, 582 signatures (c)
#> |-- 032, 50 cols, 7050 signatures
#> | |-- 0321, 22 cols, 521 signatures (c)
#> | |-- 0322, 17 cols, 954 signatures (c)
#> | `-- 0323, 11 cols (b)
#> `-- 033, 66 cols, 9518 signatures
#> |-- 0331, 24 cols, 4378 signatures
#> | |-- 03311, 9 cols (b)
#> | |-- 03312, 9 cols (b)
#> | `-- 03313, 6 cols (b)
#> |-- 0332, 31 cols, 3264 signatures
#> | |-- 03321, 14 cols, 110 signatures (c)
#> | |-- 03322, 6 cols (b)
#> | `-- 03323, 11 cols (b)
#> `-- 0333, 11 cols (b)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 376133 434
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "01111" "01112" "0112" "01121" "01122" "01123"
#> [11] "01124" "0113" "012" "0121" "01211" "01212" "01213" "0122" "0123" "013"
#> [21] "0131" "0132" "01321" "01322" "01323" "01324" "0133" "0134" "02" "021"
#> [31] "0211" "0212" "0213" "02131" "02132" "0214" "022" "0221" "02211" "02212"
#> [41] "0222" "02221" "02222" "022221" "022222" "02223" "023" "0231" "02311" "02312"
#> [51] "0232" "0233" "03" "031" "032" "0321" "0322" "0323" "033" "0331"
#> [61] "03311" "03312" "03313" "0332" "03321" "03322" "03323" "0333"
all_leaves(res_rh)
#> [1] "01111" "01112" "01121" "01122" "01123" "01124" "0113" "01211" "01212" "01213"
#> [11] "0122" "0123" "0131" "01321" "01322" "01323" "01324" "0133" "0134" "0211"
#> [21] "0212" "02131" "02132" "0214" "02211" "02212" "02221" "022221" "022222" "02223"
#> [31] "02311" "02312" "0232" "0233" "031" "0321" "0322" "0323" "03311" "03312"
#> [41] "03313" "03321" "03322" "03323" "0333"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:kmeans 1 3 434 42283 1.12e-01 FALSE
#> 2 01 ATC:kmeans 2 3 140 16943 4.50e-02 FALSE
#> 3 011 ATC:kmeans 3 3 49 18153 4.83e-02 FALSE
#> 4 0111 ATC:skmeans 4 2 17 1443 3.84e-03 FALSE
#> 5 01111 not applied 5 NA 5 NA NA TRUE
#> 6 01112 SD:kmeans 5 3 12 644 1.71e-03 TRUE
#> 7 0112 ATC:kmeans 4 4 21 2615 6.95e-03 FALSE
#> 8 01121 not applied 5 NA 8 NA NA TRUE
#> 9 01122 not applied 5 NA 6 NA NA TRUE
#> 10 01123 not applied 5 NA 4 NA NA TRUE
#> 11 01124 not applied 5 NA 3 NA NA TRUE
#> 12 0113 not applied 4 NA 11 NA NA TRUE
#> 13 012 ATC:kmeans 3 3 49 11356 3.02e-02 FALSE
#> 14 0121 ATC:kmeans 4 3 23 12451 3.31e-02 FALSE
#> 15 01211 SD:kmeans 5 2 12 90 2.39e-04 TRUE
#> 16 01212 not applied 5 NA 7 NA NA TRUE
#> 17 01213 not applied 5 NA 4 NA NA TRUE
#> 18 0122 ATC:skmeans 4 3 15 311 8.27e-04 TRUE
#> 19 0123 not applied 4 NA 11 NA NA TRUE
#> 20 013 ATC:skmeans 3 4 42 21477 5.71e-02 FALSE
#> 21 0131 ATC:kmeans 4 2 12 35 9.31e-05 TRUE
#> 22 0132 ATC:kmeans 4 4 12 2447 6.51e-03 FALSE
#> 23 01321 not applied 5 NA 2 NA NA TRUE
#> 24 01322 not applied 5 NA 4 NA NA TRUE
#> 25 01323 not applied 5 NA 3 NA NA TRUE
#> 26 01324 not applied 5 NA 3 NA NA TRUE
#> 27 0133 not applied 4 NA 11 NA NA TRUE
#> 28 0134 not applied 4 NA 7 NA NA TRUE
#> 29 02 ATC:kmeans 2 3 118 10747 2.86e-02 FALSE
#> 30 021 ATC:skmeans 3 4 34 54159 1.44e-01 FALSE
#> 31 0211 not applied 4 NA 2 NA NA TRUE
#> 32 0212 not applied 4 NA 9 NA NA TRUE
#> 33 0213 SD:kmeans 4 2 15 3167 8.42e-03 FALSE
#> 34 02131 not applied 5 NA 6 NA NA TRUE
#> 35 02132 not applied 5 NA 9 NA NA TRUE
#> 36 0214 not applied 4 NA 8 NA NA TRUE
#> 37 022 SD:kmeans 3 2 59 2929 7.79e-03 FALSE
#> 38 0221 ATC:kmeans 4 2 16 1210 3.22e-03 FALSE
#> 39 02211 not applied 5 NA 10 NA NA TRUE
#> 40 02212 not applied 5 NA 6 NA NA TRUE
#> 41 0222 ATC:skmeans 4 3 43 2275 6.05e-03 FALSE
#> 42 02221 ATC:skmeans 5 3 14 834 2.22e-03 TRUE
#> 43 02222 ATC:kmeans 5 2 14 1601 4.26e-03 FALSE
#> 44 022221 not applied 6 NA 11 NA NA TRUE
#> 45 022222 not applied 6 NA 3 NA NA TRUE
#> 46 02223 SD:kmeans 5 2 15 15 3.99e-05 TRUE
#> 47 023 ATC:skmeans 3 3 25 7299 1.94e-02 FALSE
#> 48 0231 ATC:kmeans 4 2 15 3632 9.66e-03 FALSE
#> 49 02311 not applied 5 NA 2 NA NA TRUE
#> 50 02312 ATC:skmeans 5 3 13 618 1.64e-03 TRUE
#> 51 0232 not applied 4 NA 7 NA NA TRUE
#> 52 0233 not applied 4 NA 3 NA NA TRUE
#> 53 03 ATC:kmeans 2 3 176 12363 3.29e-02 FALSE
#> 54 031 SD:kmeans 3 2 60 582 1.55e-03 TRUE
#> 55 032 ATC:kmeans 3 3 50 7050 1.87e-02 FALSE
#> 56 0321 ATC:kmeans 4 2 22 521 1.39e-03 TRUE
#> 57 0322 ATC:kmeans 4 3 17 954 2.54e-03 TRUE
#> 58 0323 not applied 4 NA 11 NA NA TRUE
#> 59 033 ATC:skmeans 3 3 66 9518 2.53e-02 FALSE
#> 60 0331 ATC:kmeans 4 3 24 4378 1.16e-02 FALSE
#> 61 03311 not applied 5 NA 9 NA NA TRUE
#> 62 03312 not applied 5 NA 9 NA NA TRUE
#> 63 03313 not applied 5 NA 6 NA NA TRUE
#> 64 0332 ATC:skmeans 4 3 31 3264 8.68e-03 FALSE
#> 65 03321 ATC:kmeans 5 2 14 110 2.92e-04 TRUE
#> 66 03322 not applied 5 NA 6 NA NA TRUE
#> 67 03323 not applied 5 NA 11 NA NA TRUE
#> 68 0333 not applied 4 NA 11 NA NA TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 434 | ** | |
| Node01 | ATC:kmeans | 4 | 0.93 | 0.89 | 0.95 | 140 | * | |
| Node011 | ATC:kmeans | 3 | 0.94 | 0.97 | 0.98 | 49 | * | |
| Node0111 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 17 | ** | |
| Node01111-leaf | not applied | ✓ (b) | 5 | |||||
| Node01112-leaf | SD:kmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 12 | ** |
| Node0112 | ATC:kmeans | 4 | 0.91 | 0.97 | 0.94 | 21 | * | |
| Node01121-leaf | not applied | ✓ (b) | 8 | |||||
| Node01122-leaf | not applied | ✓ (b) | 6 | |||||
| Node01123-leaf | not applied | ✓ (b) | 4 | |||||
| Node01124-leaf | not applied | ✓ (b) | 3 | |||||
| Node0113-leaf | not applied | ✓ (b) | 11 | |||||
| Node012 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.96 | 49 | ** | |
| Node0121 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 23 | ** | |
| Node01211-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.98 | 12 | ** |
| Node01212-leaf | not applied | ✓ (b) | 7 | |||||
| Node01213-leaf | not applied | ✓ (b) | 4 | |||||
| Node0122-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 15 | ** |
| Node0123-leaf | not applied | ✓ (b) | 11 | |||||
| Node013 | ATC:skmeans | 5 | 0.92 | 0.89 | 0.93 | 42 | * | |
| Node0131-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 12 | ** |
| Node0132 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 12 | ** | |
| Node01321-leaf | not applied | ✓ (b) | 2 | |||||
| Node01322-leaf | not applied | ✓ (b) | 4 | |||||
| Node01323-leaf | not applied | ✓ (b) | 3 | |||||
| Node01324-leaf | not applied | ✓ (b) | 3 | |||||
| Node0133-leaf | not applied | ✓ (b) | 11 | |||||
| Node0134-leaf | not applied | ✓ (b) | 7 | |||||
| Node02 | ATC:kmeans | 3 | 1.00 | 0.99 | 1.00 | 118 | ** | |
| Node021 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 34 | ** | |
| Node0211-leaf | not applied | ✓ (b) | 2 | |||||
| Node0212-leaf | not applied | ✓ (b) | 9 | |||||
| Node0213 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 15 | ** | |
| Node02131-leaf | not applied | ✓ (b) | 6 | |||||
| Node02132-leaf | not applied | ✓ (b) | 9 | |||||
| Node0214-leaf | not applied | ✓ (b) | 8 | |||||
| Node022 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 59 | ** | |
| Node0221 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node02211-leaf | not applied | ✓ (b) | 10 | |||||
| Node02212-leaf | not applied | ✓ (b) | 6 | |||||
| Node0222 | ATC:skmeans | 3 | 1.00 | 0.96 | 0.98 | 43 | ** | |
| Node02221-leaf | ATC:skmeans | ✓ (c) | 4 | 0.95 | 0.76 | 0.96 | 14 | * |
| Node02222 | ATC:kmeans | 8 | 0.90 | 0.61 | 0.92 | 14 | * | |
| Node022221-leaf | not applied | ✓ (b) | 11 | |||||
| Node022222-leaf | not applied | ✓ (b) | 3 | |||||
| Node02223-leaf | SD:kmeans | ✓ (c) | 2 | 0.91 | 0.98 | 0.97 | 15 | * |
| Node023 | ATC:skmeans | 4 | 0.91 | 0.93 | 0.94 | 25 | * | |
| Node0231 | ATC:kmeans | 3 | 1.00 | 0.99 | 0.97 | 15 | ** | |
| Node02311-leaf | not applied | ✓ (b) | 2 | |||||
| Node02312-leaf | ATC:skmeans | ✓ (c) | 8 | 1.00 | 0.62 | 1.00 | 13 | ** |
| Node0232-leaf | not applied | ✓ (b) | 7 | |||||
| Node0233-leaf | not applied | ✓ (b) | 3 | |||||
| Node03 | ATC:kmeans | 3 | 0.99 | 0.97 | 0.99 | 176 | ** | |
| Node031-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 0.99 | 60 | ** |
| Node032 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 50 | ** | |
| Node0321-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 22 | ** |
| Node0322-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 17 | ** |
| Node0323-leaf | not applied | ✓ (b) | 11 | |||||
| Node033 | ATC:skmeans | 4 | 0.93 | 0.89 | 0.95 | 66 | * | |
| Node0331 | ATC:kmeans | 4 | 0.90 | 0.94 | 0.90 | 24 | * | |
| Node03311-leaf | not applied | ✓ (b) | 9 | |||||
| Node03312-leaf | not applied | ✓ (b) | 9 | |||||
| Node03313-leaf | not applied | ✓ (b) | 6 | |||||
| Node0332 | ATC:skmeans | 3 | 0.98 | 0.98 | 0.98 | 31 | ** | |
| Node03321-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 14 | ** |
| Node03322-leaf | not applied | ✓ (b) | 6 | |||||
| Node03323-leaf | not applied | ✓ (b) | 11 | |||||
| Node0333-leaf | not applied | ✓ (b) | 11 |
Stop reason: b) Subgroup had too few columns. c) There were too few signatures.
**: 1-PAC > 0.95, *: 1-PAC > 0.9
The nodes of the hierarchy can be merged by setting the merge_node parameters. Here we
control the hierarchy with the min_n_signatures parameter. The value of min_n_signatures is
from node_info().
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1210))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1443))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1601))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2275))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2447))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2615))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2929))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3167))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3264))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3632))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4378))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7050))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7299))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9518))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10747))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11356))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12363))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12451))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 16943))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 18153))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21477))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 42283))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 54159))
#> Error in max(children_height): invalid 'type' (list) of argument
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 = 1210))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02211" "02223" "0212" "031" "02221" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "02212" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "01112" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "022221" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022221" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01322" "0122" "02212" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02221" "0321" "03311" "0321" "01212" "02211"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "01121" "031" "02221" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "01121" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "02223" "0322" "0131" "02221" "01324"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "01121" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "01112" "031" "0214" "0333" "01121"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "02212" "02211" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "01121" "01122" "031" "02223" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022221" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "01112" "022221" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02223" "01124" "0133" "02223" "02211" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "02221" "0321" "02312" "03312" "01124"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "01111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01322" "0123" "01123" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022221" "0131" "03312" "02131" "01323" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "01123" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02221" "031" "031" "0333" "0333" "02211"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01121" "022221" "01212" "02223" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "02221" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01123" "0131" "02223" "02223" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "02221"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "01323" "022222" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "01122" "01111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "02211" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "01112" "02312" "03321" "02221" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "01112"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02221" "02212" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "02211" "0134" "01112"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "02212" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "01123" "031" "01121" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02221" "0113" "01322" "03312" "01122" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "01324" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "02223" "02211"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "02211" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "01122" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "022221" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "01112" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "02223" "01321" "0321" "01323" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "02211" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01122" "01112" "01111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "01322" "03322" "022221" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "01112" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01324" "01211" "0122" "0323" "0131" "02221"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01122" "02223" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "02223" "01124" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02223" "0323" "0323" "01112" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "01321" "01212" "01111" "02212" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02223" "02221" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "01121" "01112" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "022221"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "01112" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "02221" "022222" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "022221" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "01111" "0113" "022222" "0211" "022221"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "02223"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1443))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "0221" "02223" "0212" "031" "02221" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "0221" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "01112" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "022221" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022221" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01322" "0122" "0221" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02221" "0321" "03311" "0321" "01212" "0221"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "01121" "031" "02221" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "01121" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "02223" "0322" "0131" "02221" "01324"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "01121" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "01112" "031" "0214" "0333" "01121"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "0221" "0221" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "01121" "01122" "031" "02223" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022221" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "01112" "022221" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02223" "01124" "0133" "02223" "0221" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "02221" "0321" "02312" "03312" "01124"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "01111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01322" "0123" "01123" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022221" "0131" "03312" "02131" "01323" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "01123" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02221" "031" "031" "0333" "0333" "0221"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01121" "022221" "01212" "02223" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "02221" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01123" "0131" "02223" "02223" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "02221"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "01323" "022222" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "01122" "01111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "0221" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "01112" "02312" "03321" "02221" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "01112"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02221" "0221" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "0221" "0134" "01112"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "0221" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "01123" "031" "01121" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02221" "0113" "01322" "03312" "01122" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "01324" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "02223" "0221"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "0221" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "01122" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "022221" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "01112" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "02223" "01321" "0321" "01323" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "0221" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01122" "01112" "01111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "01322" "03322" "022221" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "01112" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01324" "01211" "0122" "0323" "0131" "02221"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01122" "02223" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "02223" "01124" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02223" "0323" "0323" "01112" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "01321" "01212" "01111" "0221" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02223" "02221" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "01121" "01112" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "022221"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "01112" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "02221" "022222" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "022221" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "01111" "0113" "022222" "0211" "022221"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "02223"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1601))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "0221" "02223" "0212" "031" "02221" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "0221" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "022221" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022221" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01322" "0122" "0221" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02221" "0321" "03311" "0321" "01212" "0221"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "01121" "031" "02221" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "01121" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "02223" "0322" "0131" "02221" "01324"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "01121" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "0111" "031" "0214" "0333" "01121"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "0221" "0221" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "01121" "01122" "031" "02223" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022221" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022221" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02223" "01124" "0133" "02223" "0221" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "02221" "0321" "02312" "03312" "01124"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01322" "0123" "01123" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022221" "0131" "03312" "02131" "01323" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "01123" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02221" "031" "031" "0333" "0333" "0221"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01121" "022221" "01212" "02223" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "02221" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01123" "0131" "02223" "02223" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "02221"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "01323" "022222" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "01122" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "0221" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "03321" "02221" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02221" "0221" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "0221" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "0221" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "01123" "031" "01121" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02221" "0113" "01322" "03312" "01122" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "01324" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "02223" "0221"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "0221" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "01122" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "022221" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "02223" "01321" "0321" "01323" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "0221" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01122" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "01322" "03322" "022221" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01324" "01211" "0122" "0323" "0131" "02221"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01122" "02223" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "02223" "01124" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02223" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "01321" "01212" "0111" "0221" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02223" "02221" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "01121" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "022221"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "02221" "022222" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "022221" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022222" "0211" "022221"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "02223"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2275))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "0221" "02223" "0212" "031" "02221" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "0221" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "02222" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02222" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01322" "0122" "0221" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02221" "0321" "03311" "0321" "01212" "0221"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "01121" "031" "02221" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "01121" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "02223" "0322" "0131" "02221" "01324"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "01121" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "0111" "031" "0214" "0333" "01121"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "0221" "0221" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "01121" "01122" "031" "02223" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "02222" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "02222" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02223" "01124" "0133" "02223" "0221" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "02221" "0321" "02312" "03312" "01124"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01322" "0123" "01123" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02222" "0131" "03312" "02131" "01323" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "01123" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02221" "031" "031" "0333" "0333" "0221"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01121" "02222" "01212" "02223" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "02221" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01123" "0131" "02223" "02223" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "02221"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "01323" "02222" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "01122" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "0221" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "03321" "02221" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02221" "0221" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "0221" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "0221" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "01123" "031" "01121" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02221" "0113" "01322" "03312" "01122" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "01324" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "02223" "0221"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "0221" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "01122" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "02222" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "02223" "01321" "0321" "01323" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "0221" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01122" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "01322" "03322" "02222" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01324" "01211" "0122" "0323" "0131" "02221"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01122" "02223" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "02223" "01124" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02223" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "01321" "01212" "0111" "0221" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02223" "02221" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "01121" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "02222"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "02221" "02222" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "02222" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "02222" "0211" "02222"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "02223"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2447))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "0221" "0222" "0212" "031" "0222" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "0221" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "0222" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "0222" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01322" "0122" "0221" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "0222" "0321" "03311" "0321" "01212" "0221"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "01121" "031" "0222" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "01121" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "0222" "0322" "0131" "0222" "01324"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "01121" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "0111" "031" "0214" "0333" "01121"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "0221" "0221" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "01121" "01122" "031" "0222" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "0222" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "0222" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "0222" "01124" "0133" "0222" "0221" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "0222" "0321" "02312" "03312" "01124"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01322" "0123" "01123" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "0222" "0131" "03312" "02131" "01323" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "01123" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "0222" "031" "031" "0333" "0333" "0221"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01121" "0222" "01212" "0222" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "0222" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01123" "0131" "0222" "0222" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "0222"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "01323" "0222" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "01122" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "0221" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "03321" "0222" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "0222" "0221" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "0221" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "0221" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "01123" "031" "01121" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "0222" "0113" "01322" "03312" "01122" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "01324" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "0222" "0221"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "0221" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "01122" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "0222" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "0222" "01321" "0321" "01323" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "0221" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01122" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "01322" "03322" "0222" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01324" "01211" "0122" "0323" "0131" "0222"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01122" "0222" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "0222" "01124" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "0222" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "01321" "01212" "0111" "0221" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "0222" "0222" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "01121" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "0222"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "0222" "0222" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "0222" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "0222" "0211" "0222"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "0222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2615))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "0221" "0222" "0212" "031" "0222" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "0221" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "0222" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "0222" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "0221" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "0222" "0321" "03311" "0321" "01212" "0221"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "01121" "031" "0222" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "01121" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "0222" "0322" "0131" "0222" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "01121" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "0111" "031" "0214" "0333" "01121"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "0221" "0221" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "01121" "01122" "031" "0222" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "0222" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "0222" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "0222" "01124" "0133" "0222" "0221" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "0222" "0321" "02312" "03312" "01124"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "01123" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "0222" "0131" "03312" "02131" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "01123" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "0222" "031" "031" "0333" "0333" "0221"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01121" "0222" "01212" "0222" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "0222" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01123" "0131" "0222" "0222" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "0222"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "0132" "0222" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "01122" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "0221" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "03321" "0222" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "0222" "0221" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "0221" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "0221" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "01123" "031" "01121" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "0222" "0113" "0132" "03312" "01122" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "0132" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "0222" "0221"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "0221" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "01122" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "0222" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "0222" "0132" "0321" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "0221" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01122" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "03322" "0222" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "0323" "0131" "0222"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01122" "0222" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "0222" "01124" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "0222" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "0221" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "0222" "0222" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "01121" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "0222"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "0222" "0222" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "0222" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "0222" "0211" "0222"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "0222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2929))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "0221" "0222" "0212" "031" "0222" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "0221" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "0222" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "0222" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "0221" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "0222" "0321" "03311" "0321" "01212" "0221"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "0112" "031" "0222" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "0222" "0322" "0131" "0222" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "0112" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "0221" "0221" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "0112" "0112" "031" "0222" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "0222" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "0222" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "0222" "0112" "0133" "0222" "0221" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "0222" "0321" "02312" "03312" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "0222" "0131" "03312" "02131" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "0222" "031" "031" "0333" "0333" "0221"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "0222" "01212" "0222" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "0222" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "0222" "0222" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "0222"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "0132" "0222" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "0221" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "03321" "0222" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "0222" "0221" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "0221" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "0221" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "0112" "031" "0112" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "0222" "0113" "0132" "03312" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "0132" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "0222" "0221"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "0221" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "0222" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "0222" "0132" "0321" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "0221" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "03322" "0222" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "0323" "0131" "0222"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "0222" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "0222" "0112" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "0222" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "0221" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "0222" "0222" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "0112" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "0222"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "0222" "0222" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "0222" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "0222" "0211" "0222"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "0222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3167))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "022" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02132" "022" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "0321" "03311" "0321" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "0112" "031" "022" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "022" "0322" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02132" "0112" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "0112" "0112" "031" "022" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "02131"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02132" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "0321" "02312" "03312" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "02131" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "03312" "02131" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "0333" "0333" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "022" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "02132" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "0132" "022" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "03321" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "02132" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "0112" "031" "0112" "03323" "02131"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "02132" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "03312" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02132" "0321" "0132" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "02132" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "022" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "022" "0132" "0321" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "03322" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "0323" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02132" "0233" "01212" "022" "0112" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "0112" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "022" "022" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02131" "0233" "0321" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "02131"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3264))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "022" "03323" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "03321"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "0213" "022" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "0333" "03323" "03323" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "0321" "03311" "0321" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "0112" "031" "022" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "03323"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "022" "0322" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "0213" "0112" "03311" "031" "03323" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03321" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "03323" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03321" "0112" "0112" "031" "022" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "03323"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "03321" "0322" "0321" "0213"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "0213" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "0321" "02312" "03312" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "0213" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "02312" "03312" "03322"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "03312" "0213" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "03322"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "0333" "0333" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "03321" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03323" "022" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03321" "02312" "0232" "031" "0213" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03322" "0113" "0132" "022" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "03321" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "0213" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "0333" "03321" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "03322" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "0112" "031" "0112" "03323" "0213"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "03323" "03321" "0323" "0213" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "03312" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "0213" "0321" "0132" "0322" "0212" "03321"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "03321" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "0213" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "03321" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "03323" "022" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03321" "022" "0132" "0321" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "03322" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "0323" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "0213" "0233" "01212" "022" "0112" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "0112" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03322" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "022" "022" "03321" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "0213" "0233" "0321" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "0213"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3632))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "022" "0332" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "0332"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "0213" "022" "03313" "02312" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "0333" "0332" "0332" "0321" "02312"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "02312" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "0321" "03311" "0321" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02312" "0112" "031" "022" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "0332"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "022" "0322" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "0213" "0112" "03311" "031" "0332" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "0332" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "0332" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "0332" "0112" "0112" "031" "022" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02312" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "0332"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "0332" "0322" "0321" "0213"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "0213" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "0321" "02312" "03312" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "0213" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "02312" "03312" "0332"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "03312" "0213" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "0332"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "0333" "0333" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "0332" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "0332" "022" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "0332" "02312" "0232" "031" "0213" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "0332" "0113" "0132" "022" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "0321" "0123" "02312"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "02312" "0332" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02312" "0213" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "0333" "0332" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "0332" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "0112" "031" "0112" "0332" "0213"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "0332" "0332" "0323" "0213" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "03312" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "0213" "0321" "0132" "0322" "0212" "0332"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "0332" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "0213" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "0332" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "0332" "022" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "0332" "022" "0132" "0321" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02312"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "0332" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "0323" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "0213" "0233" "01212" "022" "0112" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "02311"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "0112" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "0332" "031" "0123" "0111" "02312" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "022" "022" "0332" "02311" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "0213" "0233" "0321" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "0213"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4378))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "022" "0332" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "0332"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "03313"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "0213" "022" "03313" "0231" "03311" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "0333" "0332" "0332" "0321" "0231"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "0231" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "0321" "03311" "0321" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "0231" "0112" "031" "022" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "0332"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "022" "0322" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "0213" "0112" "03311" "031" "0332" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "0332" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "0332" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "0332" "0112" "0112" "031" "022" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "0231" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "0332"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "0332" "0322" "0321" "0213"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "0213" "031" "0322" "03313" "03311"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "0321" "0231" "03312" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "0213" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "0231" "03312" "0332"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "03312" "0213" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "0332"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "0333" "0333" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "0332" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "0332" "022" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "0321" "03313"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "0332" "0231" "0232" "031" "0213" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "0332" "0113" "0132" "022" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "0321" "0123" "0231"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "0231" "0332" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "0231" "0213" "03312" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "0333" "0332" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "0332" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03311" "0112" "031" "0112" "0332" "0213"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "0332" "0332" "0323" "0213" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "03312" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "0213" "0321" "0132" "0322" "0212" "0332"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "0332" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "0213" "03311" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "0332" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "0332" "022" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "03311"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "0332" "022" "0132" "0321" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "0231"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "0332" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "03312" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "0323" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "0213" "0233" "01212" "022" "0112" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "0231"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "03313" "0122" "0112" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03312" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "0332" "031" "0123" "0111" "0231" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "022" "022" "0332" "0231" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "0213" "0233" "0321" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "03312" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "03311" "03312" "031" "03313" "0213"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03311" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7050))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "0322" "022" "0332" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "0322" "0111" "0113" "0211" "0232" "0332"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "0321" "0123" "0321" "0214" "031" "0323"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "0331"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "0213" "022" "0331" "0231" "0331" "0321"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "0333" "0332" "0332" "0321" "0231"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "0231" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "0321" "0331" "0321" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "0231" "0112" "031" "022" "0323"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "0332"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "0322" "022" "0322" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "0213" "0112" "0331" "031" "0332" "0321"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "0332" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "0332" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "0332" "0112" "0112" "031" "022" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "0333" "0322"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "0231" "01211" "0123" "0322"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "0332"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "0332" "0322" "0321" "0213"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "0213" "031" "0322" "0331" "0331"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "0321" "0231" "0331" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "0213" "0111" "0322" "0323" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "0231" "0331" "0332"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "0331" "0213" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "0332"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "0333" "0333" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "0332" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "0332" "022" "0322" "0123" "0233" "0322"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "0321" "0331"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "0332" "0231" "0232" "031" "0213" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "0332" "0113" "0132" "022" "031" "0321"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "0321" "0123" "0231"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "0322" "0111" "0231" "0332" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "0231" "0213" "0331" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "0333" "0332" "0322" "0321"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "0332" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "0232" "0321" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "0331" "0112" "031" "0112" "0332" "0213"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "0323" "0214" "01211" "0322"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "0332" "0332" "0323" "0213" "0321"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "0331" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "0213" "0321" "0132" "0322" "0212" "0332"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "0322" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "0323" "0122" "0332" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "0213" "0331" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "0332" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "0332" "022" "031" "0321"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "0331"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "0332" "022" "0132" "0321" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "0231"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "0332" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "0331" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "0323" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "0321" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "0213" "0233" "01212" "022" "0112" "0321"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "0323" "0323" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "0231"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "0321" "0331" "0122" "0112" "0111" "0322"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "0331" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "0332" "031" "0123" "0111" "0231" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "0323" "022" "022" "0332" "0231" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "0213" "0233" "0321" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "0331" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "0323" "0331" "0331" "031" "0331" "0213"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "0331" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7299))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "032" "022" "0332" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "032" "0111" "0113" "0211" "0232" "0332"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "032" "0123" "032" "0214" "031" "032"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "0331"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "0213" "022" "0331" "0231" "0331" "032"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "0333" "0332" "0332" "032" "0231"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "0231" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "032" "0331" "032" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "0231" "0112" "031" "022" "032"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "0332"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "032" "022" "032" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "0213" "0112" "0331" "031" "0332" "032"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "0332" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "0332" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "0332" "0112" "0112" "031" "022" "0232"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "0333" "032"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "0231" "01211" "0123" "032"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "0332"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "0332" "032" "032" "0213"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "0213" "031" "032" "0331" "0331"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "032" "0231" "0331" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "0213" "0111" "032" "032" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "0231" "0331" "0332"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "0331" "0213" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "0332"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "0333" "0333" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "0332" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "0332" "022" "032" "0123" "0233" "032"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "032" "0331"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "0332" "0231" "0232" "031" "0213" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "0332" "0113" "0132" "022" "031" "032"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "032" "0123" "0231"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "0333" "0232" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "032" "0111" "0231" "0332" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "0231" "0213" "0331" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "0333" "0332" "032" "032"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "0332" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "0232" "032" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "0331" "0112" "031" "0112" "0332" "0213"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "032" "0214" "01211" "032"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "0332" "0332" "032" "0213" "032"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "0331" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "0213" "032" "0132" "032" "0212" "0332"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "032" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "032" "0122" "0332" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "0213" "0331" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "0332" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "0332" "022" "031" "032"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "0232" "0214" "0111" "0333" "031" "0331"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "0332" "022" "0132" "032" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "0231"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "0332" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "0331" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "032" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "032" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "0213" "0233" "01212" "022" "0112" "032"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "032" "032" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "0231"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "032" "0331" "0122" "0112" "0111" "032"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "0331" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "0332" "031" "0123" "0111" "0231" "0232"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "032" "022" "022" "0332" "0231" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "0213" "0233" "032" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "0331" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "032" "0331" "0331" "031" "0331" "0213"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "0331" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9518))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "032" "022" "0332" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "032" "0111" "0113" "0211" "023" "0332"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "032" "0123" "032" "0214" "031" "032"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "0331"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "0213" "022" "0331" "023" "0331" "032"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "0333" "0332" "0332" "032" "023"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "023" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "032" "0331" "032" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "023" "0112" "031" "022" "032"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "0332"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "032" "022" "032" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "0213" "0112" "0331" "031" "0332" "032"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "0332" "0111" "031" "0214" "0333" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "0332" "0333"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "0332" "0112" "0112" "031" "022" "023"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "0333" "032"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "023" "01211" "0123" "032"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "0332"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "0332" "032" "032" "0213"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "0213" "031" "032" "0331" "0331"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "032" "023" "0331" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "0213" "0111" "032" "032" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "023" "0331" "0332"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "0331" "0213" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "0332"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "0333" "0333" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "0332" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "0332" "022" "032" "0123" "023" "032"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "032" "0331"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "0332" "023" "023" "031" "0213" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "0332" "0113" "0132" "022" "031" "032"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "032" "0123" "023"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "0333" "023" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "032" "0111" "023" "0332" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "023" "0213" "0331" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "0333" "0332" "032" "032"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "0332" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "023" "032" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "0331" "0112" "031" "0112" "0332" "0213"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "032" "0214" "01211" "032"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "0332" "0332" "032" "0213" "032"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "0331" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "0213" "032" "0132" "032" "0212" "0332"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "032" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "032" "0122" "0332" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "0213" "0331" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "0332" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "0332" "022" "031" "032"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "023" "0214" "0111" "0333" "031" "0331"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "0332" "022" "0132" "032" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "023"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "0332" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "0331" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "032" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "032" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "0213" "023" "01212" "022" "0112" "032"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "032" "032" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "023"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "0333"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "032" "0331" "0122" "0112" "0111" "032"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "0331" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "0332" "031" "0123" "0111" "023" "023"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "032" "022" "022" "0332" "023" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "0213" "023" "032" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "0331" "0333" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "032" "0331" "0331" "031" "0331" "0213"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "0331" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10747))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "022" "022" "0212" "031" "022" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "032" "022" "033" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "032" "0111" "0113" "0211" "023" "033"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "032" "0123" "032" "0214" "031" "032"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "033"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "0213" "022" "033" "023" "033" "032"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "022" "033" "033" "033" "032" "023"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "022" "023" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "022" "032" "033" "032" "01212" "022"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "023" "0112" "031" "022" "032"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "0214" "031" "033"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "032" "022" "032" "0131" "022" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "0213" "0112" "033" "031" "033" "032"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "033" "0111" "031" "0214" "033" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "022" "022" "033" "033"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "0214" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "033" "0112" "0112" "031" "022" "023"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "0212" "022" "033" "032"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "022" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "023" "01211" "0123" "032"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "022" "0112" "0133" "022" "022" "033"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "033" "032" "032" "0213"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "0213" "031" "032" "033" "033"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "022" "032" "023" "033" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "0212" "0213" "0111" "032" "032" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "023" "033" "033"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "022" "0131" "033" "0213" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "033"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "022" "031" "031" "033" "033" "022"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "022" "01212" "022" "033" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "033" "022" "032" "0123" "023" "032"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "022" "022" "032" "033"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "033" "023" "023" "031" "0213" "022"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "033" "0113" "0132" "022" "031" "032"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "032" "0123" "023"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "022" "0131" "033" "023" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "032" "0111" "023" "033" "022" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "023" "0213" "033" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "022" "022" "033" "033" "032" "032"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "033" "022" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "022" "023" "032" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "033" "0112" "031" "0112" "033" "0213"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "032" "0214" "01211" "032"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "033" "033" "032" "0213" "032"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "022" "0113" "0132" "033" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "0213" "032" "0132" "032" "0212" "033"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "0214" "01211" "032" "031" "022" "022"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "032" "0122" "033" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "0212" "022" "0213" "033" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "0214" "0112" "033" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "033" "022" "031" "032"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "023" "0214" "0111" "033" "031" "033"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "033" "022" "0132" "032" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "022" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "023"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "033" "022" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "033" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "032" "0131" "022"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "022" "031" "032" "031" "0212"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "0213" "023" "01212" "022" "0112" "032"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "022" "032" "032" "0111" "0131" "0212"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "022" "023"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "022" "022" "01211" "0134" "031" "033"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "032" "033" "0122" "0112" "0111" "032"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "033" "0133" "0131" "0134" "031" "022"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "033" "031" "0123" "0111" "023" "023"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "032" "022" "022" "033" "023" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "0213" "023" "032" "0212" "022" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "022" "0211" "022"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "0212" "033" "033" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "032" "033" "033" "031" "033" "0213"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "033" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11356))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02" "02" "02" "031" "02" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "0122" "032" "02" "033" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "032" "0111" "0113" "02" "02" "033"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "032" "0123" "032" "02" "031" "032"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "033"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02" "02" "033" "02" "033" "032"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02" "033" "033" "033" "032" "02"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "0122" "02" "02" "0123" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02" "032" "033" "032" "01212" "02"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02" "0112" "031" "02" "032"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "02" "031" "033"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "032" "02" "032" "0131" "02" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02" "0112" "033" "031" "033" "032"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "033" "0111" "031" "02" "033" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01213" "031" "02" "02" "033" "033"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "01213" "02" "031" "01211" "01211"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "033" "0112" "0112" "031" "02" "02"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01211" "031" "02" "02" "033" "032"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "02" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "0122" "02" "01211" "0123" "032"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02" "0112" "0133" "02" "02" "033"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "0122" "031" "033" "032" "032" "02"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "0122" "02" "031" "032" "033" "033"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01212" "02" "032" "02" "033" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "02" "02" "0111" "032" "032" "01211"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "0123" "0112" "02" "033" "033"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02" "0131" "033" "02" "0132" "01213"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "033"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02" "031" "031" "033" "033" "02"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "02" "01212" "02" "033" "0123"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "033" "02" "032" "0123" "02" "032"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "0122" "01212" "0123"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "02" "02" "032" "033"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "033" "02" "02" "031" "02" "02"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "033" "0113" "0132" "02" "031" "032"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "0122" "0112" "0111" "032" "0123" "02"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "02" "0131" "033" "02" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "032" "0111" "02" "033" "02" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01211" "01213" "02" "02" "033" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02" "02" "033" "033" "032" "032"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "033" "02" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "0122" "0133" "02" "02" "032" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "033" "0112" "031" "0112" "033" "02"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "0122" "032" "02" "01211" "032"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "033" "033" "032" "02" "032"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02" "0113" "0132" "033" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02" "032" "0132" "032" "02" "033"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "02" "01211" "032" "031" "02" "02"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "032" "0122" "033" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "02" "02" "02" "033" "0133" "0122"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "02" "0112" "033" "0122" "01211" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01211" "0113" "033" "02" "031" "032"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "02" "02" "0111" "033" "031" "033"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "033" "02" "0132" "032" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "0122" "0131" "031" "0134" "02" "0123"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "033" "02" "01212"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "033" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "01211" "0122" "032" "0131" "02"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "02" "031" "032" "031" "02"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02" "02" "01212" "02" "0112" "032"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02" "032" "032" "0111" "0131" "02"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "0123" "0132" "01212" "0111" "02" "02"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02" "02" "01211" "0134" "031" "033"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "032" "033" "0122" "0112" "0111" "032"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "033" "0133" "0131" "0134" "031" "02"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "033" "031" "0123" "0111" "02" "02"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "032" "02" "02" "033" "02" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02" "02" "032" "02" "02" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "02" "02" "02"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "02" "033" "033" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "032" "033" "033" "031" "033" "02"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "033" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12363))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02" "02" "02" "031" "02" "031"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "031" "012" "032" "02" "033" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "032" "0111" "0113" "02" "02" "033"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "032" "012" "032" "02" "031" "032"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "031" "031" "031" "031" "031" "033"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02" "02" "033" "02" "033" "032"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02" "033" "033" "033" "032" "02"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "012" "02" "02" "012" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02" "032" "033" "032" "012" "02"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02" "0112" "031" "02" "032"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "02" "031" "033"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "032" "02" "032" "0131" "02" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02" "0112" "033" "031" "033" "032"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "033" "0111" "031" "02" "033" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "012" "031" "02" "02" "033" "033"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "031" "012" "02" "031" "012" "012"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "033" "0112" "0112" "031" "02" "02"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "012" "031" "02" "02" "033" "032"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "031" "0111" "02" "031" "031"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "012" "02" "012" "012" "032"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02" "0112" "0133" "02" "02" "033"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "012" "031" "033" "032" "032" "02"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "012" "02" "031" "032" "033" "033"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "012" "02" "032" "02" "033" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "02" "02" "0111" "032" "032" "012"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "012" "0112" "02" "033" "033"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02" "0131" "033" "02" "0132" "012"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "031" "031" "031" "0134" "0112" "033"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02" "031" "031" "033" "033" "02"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "02" "012" "02" "033" "012"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "033" "02" "032" "012" "02" "032"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "031" "0131" "031" "012" "012" "012"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "02" "02" "032" "033"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "033" "02" "02" "031" "02" "02"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "033" "0113" "0132" "02" "031" "032"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "012" "0112" "0111" "032" "012" "02"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "02" "0131" "033" "02" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "032" "0111" "02" "033" "02" "031"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "012" "012" "02" "02" "033" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02" "02" "033" "033" "032" "032"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "031" "031" "033" "02" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "012" "0133" "02" "02" "032" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "033" "0112" "031" "0112" "033" "02"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "031" "012" "032" "02" "012" "032"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "031" "033" "033" "032" "02" "032"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02" "0113" "0132" "033" "0112" "031"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02" "032" "0132" "032" "02" "033"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "02" "012" "032" "031" "02" "02"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "032" "012" "033" "031" "031" "031"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "02" "02" "02" "033" "0133" "012"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "02" "0112" "033" "012" "012" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "012" "0113" "033" "02" "031" "032"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "02" "02" "0111" "033" "031" "033"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "033" "02" "0132" "032" "0132" "031"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "012" "0131" "031" "0134" "02" "012"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "031" "0134" "0132" "033" "02" "012"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "031" "031" "0113" "0111" "033" "031"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "012" "012" "032" "0131" "02"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "02" "031" "032" "031" "02"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02" "02" "012" "02" "0112" "032"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02" "032" "032" "0111" "0131" "02"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "012" "0132" "012" "0111" "02" "02"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02" "02" "012" "0134" "031" "033"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "032" "033" "012" "0112" "0111" "032"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "033" "0133" "0131" "0134" "031" "02"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "033" "031" "012" "0111" "02" "02"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "032" "02" "02" "033" "02" "031"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02" "02" "032" "02" "02" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "02" "02" "02"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "031" "031" "02" "033" "033" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "032" "033" "033" "031" "033" "02"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "033" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12451))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02" "02" "02" "03" "02" "03"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "03" "012" "03" "02" "03" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "03" "0111" "0113" "02" "02" "03"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "03" "012" "03" "02" "03" "03"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02" "02" "03" "02" "03" "03"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "012" "02" "02" "012" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02" "03" "03" "03" "012" "02"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02" "0112" "03" "02" "03"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "02" "03" "03"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "03" "02" "03" "0131" "02" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02" "0112" "03" "03" "03" "03"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03" "0111" "03" "02" "03" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "012" "03" "02" "02" "03" "03"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "03" "012" "02" "03" "012" "012"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03" "0112" "0112" "03" "02" "02"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "012" "03" "02" "02" "03" "03"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "03" "0111" "02" "03" "03"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "012" "02" "012" "012" "03"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02" "0112" "0133" "02" "02" "03"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "012" "03" "03" "03" "03" "02"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "012" "02" "03" "03" "03" "03"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "012" "02" "03" "02" "03" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "02" "02" "0111" "03" "03" "012"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "012" "0112" "02" "03" "03"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02" "0131" "03" "02" "0132" "012"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "03" "03" "03" "0134" "0112" "03"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "02" "012" "02" "03" "012"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03" "02" "03" "012" "02" "03"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "03" "0131" "03" "012" "012" "012"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "02" "02" "03" "03"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03" "02" "02" "03" "02" "02"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03" "0113" "0132" "02" "03" "03"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "012" "0112" "0111" "03" "012" "02"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "02" "0131" "03" "02" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "03" "0111" "02" "03" "02" "03"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "012" "012" "02" "02" "03" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02" "02" "03" "03" "03" "03"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "03" "03" "03" "02" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "012" "0133" "02" "02" "03" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03" "0112" "03" "0112" "03" "02"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "03" "012" "03" "02" "012" "03"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "03" "03" "03" "03" "02" "03"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02" "0113" "0132" "03" "0112" "03"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02" "03" "0132" "03" "02" "03"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "02" "012" "03" "03" "02" "02"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "03" "012" "03" "03" "03" "03"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "02" "02" "02" "03" "0133" "012"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "02" "0112" "03" "012" "012" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "012" "0113" "03" "02" "03" "03"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "02" "02" "0111" "03" "03" "03"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03" "02" "0132" "03" "0132" "03"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "012" "0131" "03" "0134" "02" "012"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "03" "0134" "0132" "03" "02" "012"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "03" "03" "0113" "0111" "03" "03"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "012" "012" "03" "0131" "02"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "02" "03" "03" "03" "02"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02" "02" "012" "02" "0112" "03"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02" "03" "03" "0111" "0131" "02"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "012" "0132" "012" "0111" "02" "02"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02" "02" "012" "0134" "03" "03"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "03" "03" "012" "0112" "0111" "03"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03" "0133" "0131" "0134" "03" "02"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03" "03" "012" "0111" "02" "02"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "03" "02" "02" "03" "02" "03"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02" "02" "03" "02" "02" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "02" "02" "02"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "03" "03" "02" "03" "03" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "03" "03" "03" "03" "03" "02"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 16943))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02" "02" "02" "03" "02" "03"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "03" "012" "03" "02" "03" "0133"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "03" "0111" "0113" "02" "02" "03"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "03" "012" "03" "02" "03" "03"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02" "02" "03" "02" "03" "03"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "0132" "012" "02" "02" "012" "0131"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02" "03" "03" "03" "012" "02"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "0131" "02" "0112" "03" "02" "03"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "0134" "0112" "0133" "02" "03" "03"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "03" "02" "03" "0131" "02" "0132"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02" "0112" "03" "03" "03" "03"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03" "0111" "03" "02" "03" "0112"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "012" "03" "02" "02" "03" "03"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "03" "012" "02" "03" "012" "012"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03" "0112" "0112" "03" "02" "02"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "012" "03" "02" "02" "03" "03"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "0131" "03" "0111" "02" "03" "03"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "0113" "012" "02" "012" "012" "03"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02" "0112" "0133" "02" "02" "03"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "012" "03" "03" "03" "03" "02"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "012" "02" "03" "03" "03" "03"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "012" "02" "03" "02" "03" "0112"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "02" "02" "0111" "03" "03" "012"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "0132" "012" "0112" "02" "03" "03"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02" "0131" "03" "02" "0132" "012"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "03" "03" "03" "0134" "0112" "03"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "0112" "02" "012" "02" "03" "012"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03" "02" "03" "012" "02" "03"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "03" "0131" "03" "012" "012" "012"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "0112" "0131" "02" "02" "03" "03"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03" "02" "02" "03" "02" "02"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03" "0113" "0132" "02" "03" "03"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "012" "0112" "0111" "03" "012" "02"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "0113" "02" "0131" "03" "02" "0113"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "03" "0111" "02" "03" "02" "03"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "012" "012" "02" "02" "03" "0111"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02" "02" "03" "03" "03" "03"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "03" "03" "03" "02" "0134" "0111"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "012" "0133" "02" "02" "03" "0133"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03" "0112" "03" "0112" "03" "02"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "03" "012" "03" "02" "012" "03"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "03" "03" "03" "03" "02" "03"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02" "0113" "0132" "03" "0112" "03"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02" "03" "0132" "03" "02" "03"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "02" "012" "03" "03" "02" "02"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "03" "012" "03" "03" "03" "03"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "02" "02" "02" "03" "0133" "012"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "02" "0112" "03" "012" "012" "0133"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "012" "0113" "03" "02" "03" "03"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "02" "02" "0111" "03" "03" "03"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03" "02" "0132" "03" "0132" "03"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "012" "0131" "03" "0134" "02" "012"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "0112" "0111" "0111" "0113" "0133" "02"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "03" "0134" "0132" "03" "02" "012"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "03" "03" "0113" "0111" "03" "03"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "0132" "012" "012" "03" "0131" "02"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "0112" "02" "03" "03" "03" "02"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02" "02" "012" "02" "0112" "03"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02" "03" "03" "0111" "0131" "02"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "012" "0132" "012" "0111" "02" "02"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02" "02" "012" "0134" "03" "03"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "03" "03" "012" "0112" "0111" "03"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03" "0133" "0131" "0134" "03" "02"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03" "03" "012" "0111" "02" "02"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "03" "02" "02" "03" "02" "03"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02" "02" "03" "02" "02" "0133"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "0133" "0111" "0113" "02" "02" "02"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "03" "03" "02" "03" "03" "0113"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "03" "03" "03" "03" "03" "02"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 18153))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02" "02" "02" "03" "02" "03"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "03" "01" "03" "02" "03" "01"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "03" "01" "01" "02" "02" "03"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "03" "01" "03" "02" "03" "03"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02" "02" "03" "02" "03" "03"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01" "01" "02" "02" "01" "01"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02" "03" "03" "03" "01" "02"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "01" "02" "01" "03" "02" "03"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "01" "01" "01" "02" "03" "03"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "03" "02" "03" "01" "02" "01"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02" "01" "03" "03" "03" "03"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03" "01" "03" "02" "03" "01"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "03" "01" "02" "03" "01" "01"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03" "01" "01" "03" "02" "02"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "01" "03" "01" "02" "03" "03"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "01" "01" "02" "01" "01" "03"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02" "01" "01" "02" "02" "03"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "01" "03" "03" "03" "03" "02"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "01" "02" "03" "03" "03" "03"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01" "02" "03" "02" "03" "01"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "02" "02" "01" "03" "03" "01"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01" "01" "01" "02" "03" "03"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02" "01" "03" "02" "01" "01"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "03" "03" "03" "01" "01" "03"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01" "02" "01" "02" "03" "01"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03" "02" "03" "01" "02" "03"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "03" "01" "03" "01" "01" "01"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01" "01" "02" "02" "03" "03"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03" "02" "02" "03" "02" "02"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03" "01" "01" "02" "03" "03"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "01" "01" "01" "03" "01" "02"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "01" "02" "01" "03" "02" "01"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "03" "01" "02" "03" "02" "03"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02" "02" "03" "03" "03" "03"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "03" "03" "03" "02" "01" "01"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03" "01" "03" "01" "03" "02"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "03" "01" "03" "02" "01" "03"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "03" "03" "03" "03" "02" "03"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02" "01" "01" "03" "01" "03"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02" "03" "01" "03" "02" "03"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "02" "01" "03" "03" "02" "02"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "03" "01" "03" "03" "03" "03"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "02" "02" "02" "03" "01" "01"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "02" "01" "03" "01" "01" "01"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01" "01" "03" "02" "03" "03"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "02" "02" "01" "03" "03" "03"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03" "02" "01" "03" "01" "03"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "01" "01" "03" "01" "02" "01"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01" "01" "01" "01" "01" "02"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "03" "01" "01" "03" "02" "01"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "03" "03" "01" "01" "03" "03"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01" "01" "01" "03" "01" "02"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01" "02" "03" "03" "03" "02"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02" "02" "01" "02" "01" "03"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02" "03" "03" "01" "01" "02"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "01" "01" "01" "01" "02" "02"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02" "02" "01" "01" "03" "03"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "03" "03" "01" "01" "01" "03"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03" "01" "01" "01" "03" "02"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03" "03" "01" "01" "02" "02"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "03" "02" "02" "03" "02" "03"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02" "02" "03" "02" "02" "01"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "01" "01" "01" "02" "02" "02"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "03" "03" "02" "03" "03" "01"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "03" "03" "03" "03" "03" "02"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21477))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02" "02" "02" "03" "02" "03"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "03" "01" "03" "02" "03" "01"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "03" "01" "01" "02" "02" "03"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "03" "01" "03" "02" "03" "03"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02" "02" "03" "02" "03" "03"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01" "01" "02" "02" "01" "01"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02" "03" "03" "03" "01" "02"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "01" "02" "01" "03" "02" "03"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "01" "01" "01" "02" "03" "03"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "03" "02" "03" "01" "02" "01"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02" "01" "03" "03" "03" "03"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03" "01" "03" "02" "03" "01"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "03" "01" "02" "03" "01" "01"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03" "01" "01" "03" "02" "02"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "01" "03" "01" "02" "03" "03"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "01" "01" "02" "01" "01" "03"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02" "01" "01" "02" "02" "03"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "01" "03" "03" "03" "03" "02"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "01" "02" "03" "03" "03" "03"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01" "02" "03" "02" "03" "01"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "02" "02" "01" "03" "03" "01"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01" "01" "01" "02" "03" "03"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02" "01" "03" "02" "01" "01"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "03" "03" "03" "01" "01" "03"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01" "02" "01" "02" "03" "01"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03" "02" "03" "01" "02" "03"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "03" "01" "03" "01" "01" "01"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01" "01" "02" "02" "03" "03"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03" "02" "02" "03" "02" "02"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03" "01" "01" "02" "03" "03"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "01" "01" "01" "03" "01" "02"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "01" "02" "01" "03" "02" "01"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "03" "01" "02" "03" "02" "03"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02" "02" "03" "03" "03" "03"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "03" "03" "03" "02" "01" "01"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03" "01" "03" "01" "03" "02"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "03" "01" "03" "02" "01" "03"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "03" "03" "03" "03" "02" "03"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02" "01" "01" "03" "01" "03"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02" "03" "01" "03" "02" "03"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "02" "01" "03" "03" "02" "02"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "03" "01" "03" "03" "03" "03"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "02" "02" "02" "03" "01" "01"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "02" "01" "03" "01" "01" "01"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01" "01" "03" "02" "03" "03"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "02" "02" "01" "03" "03" "03"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03" "02" "01" "03" "01" "03"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "01" "01" "03" "01" "02" "01"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01" "01" "01" "01" "01" "02"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "03" "01" "01" "03" "02" "01"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "03" "03" "01" "01" "03" "03"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01" "01" "01" "03" "01" "02"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01" "02" "03" "03" "03" "02"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02" "02" "01" "02" "01" "03"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02" "03" "03" "01" "01" "02"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "01" "01" "01" "01" "02" "02"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02" "02" "01" "01" "03" "03"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "03" "03" "01" "01" "01" "03"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03" "01" "01" "01" "03" "02"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03" "03" "01" "01" "02" "02"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "03" "02" "02" "03" "02" "03"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02" "02" "03" "02" "02" "01"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "01" "01" "01" "02" "02" "02"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "03" "03" "02" "03" "03" "01"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "03" "03" "03" "03" "03" "02"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 42283))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> "02" "02" "02" "03" "02" "03"
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> "03" "01" "03" "02" "03" "01"
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> "03" "01" "01" "02" "02" "03"
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> "03" "01" "03" "02" "03" "03"
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> "02" "02" "03" "02" "03" "03"
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> "01" "01" "02" "02" "01" "01"
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> "02" "03" "03" "03" "01" "02"
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> "01" "02" "01" "03" "02" "03"
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> "01" "01" "01" "02" "03" "03"
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> "03" "02" "03" "01" "02" "01"
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> "02" "01" "03" "03" "03" "03"
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> "03" "01" "03" "02" "03" "01"
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> "03" "01" "02" "03" "01" "01"
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> "03" "01" "01" "03" "02" "02"
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> "01" "03" "01" "02" "03" "03"
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> "01" "01" "02" "01" "01" "03"
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> "02" "01" "01" "02" "02" "03"
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> "01" "03" "03" "03" "03" "02"
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> "01" "02" "03" "03" "03" "03"
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> "01" "02" "03" "02" "03" "01"
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> "02" "02" "01" "03" "03" "01"
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> "01" "01" "01" "02" "03" "03"
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> "02" "01" "03" "02" "01" "01"
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> "03" "03" "03" "01" "01" "03"
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> "02" "03" "03" "03" "03" "02"
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> "01" "02" "01" "02" "03" "01"
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> "03" "02" "03" "01" "02" "03"
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> "03" "01" "03" "01" "01" "01"
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> "01" "01" "02" "02" "03" "03"
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> "03" "02" "02" "03" "02" "02"
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> "03" "01" "01" "02" "03" "03"
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> "01" "01" "01" "03" "01" "02"
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> "01" "02" "01" "03" "02" "01"
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> "03" "01" "02" "03" "02" "03"
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> "02" "02" "03" "03" "03" "03"
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> "03" "03" "03" "02" "01" "01"
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> "03" "01" "03" "01" "03" "02"
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> "03" "01" "03" "02" "01" "03"
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> "03" "03" "03" "03" "02" "03"
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> "02" "01" "01" "03" "01" "03"
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> "02" "03" "01" "03" "02" "03"
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> "02" "01" "03" "03" "02" "02"
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> "03" "01" "03" "03" "03" "03"
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> "02" "02" "02" "03" "01" "01"
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> "02" "01" "03" "01" "01" "01"
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> "01" "01" "03" "02" "03" "03"
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> "02" "02" "01" "03" "03" "03"
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> "03" "02" "01" "03" "01" "03"
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> "01" "01" "03" "01" "02" "01"
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> "01" "01" "01" "01" "01" "02"
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> "03" "01" "01" "03" "02" "01"
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> "03" "03" "01" "01" "03" "03"
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> "01" "01" "01" "03" "01" "02"
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> "01" "02" "03" "03" "03" "02"
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> "02" "02" "01" "02" "01" "03"
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> "02" "03" "03" "01" "01" "02"
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> "01" "01" "01" "01" "02" "02"
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> "02" "02" "01" "01" "03" "03"
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> "03" "03" "01" "01" "01" "03"
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> "03" "01" "01" "01" "03" "02"
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> "03" "03" "01" "01" "02" "02"
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> "03" "02" "02" "03" "02" "03"
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> "02" "02" "03" "02" "02" "01"
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> "01" "01" "01" "02" "02" "02"
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> "03" "03" "02" "03" "03" "01"
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> "03" "03" "03" "03" "03" "02"
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> "03" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 54159))
#> TCGA.GD.A3OP.01 TCGA.4Z.AA86.01 TCGA.BL.A13J.11 TCGA.2F.A9KO.01 TCGA.GU.A42Q.01 TCGA.HQ.A5NE.01
#> NA NA NA NA NA NA
#> TCGA.PQ.A6FI.01 TCGA.E5.A2PC.01 TCGA.FD.A3SL.01 TCGA.FD.A5BU.01 TCGA.UY.A9PE.01 TCGA.FD.A3N6.01
#> NA NA NA NA NA NA
#> TCGA.CU.A3YL.01 TCGA.GV.A3JW.01 TCGA.ZF.A9R3.01 TCGA.E7.A6MF.01 TCGA.FD.A43P.01 TCGA.ZF.AA52.01
#> NA NA NA NA NA NA
#> TCGA.E7.A541.01 TCGA.DK.AA6L.01 TCGA.FD.A6TI.01 TCGA.BT.A20W.11 TCGA.XF.A9SZ.01 TCGA.C4.A0EZ.01
#> NA NA NA NA NA NA
#> TCGA.FD.A3SJ.01 TCGA.ZF.AA56.01 TCGA.XF.AAMH.01 TCGA.FD.A3NA.01 TCGA.DK.A3IK.01 TCGA.ZF.A9RF.01
#> NA NA NA NA NA NA
#> TCGA.UY.A78P.01 TCGA.DK.AA6X.01 TCGA.BT.A3PJ.01 TCGA.K4.A6FZ.01 TCGA.YC.A9TC.01 TCGA.ZF.A9R7.01
#> NA NA NA NA NA NA
#> TCGA.GC.A3OO.01 TCGA.DK.A1A7.01 TCGA.BT.A2LB.01 TCGA.GV.A3QF.01 TCGA.ZF.A9R9.01 TCGA.XF.AAN5.01
#> NA NA NA NA NA NA
#> TCGA.XF.A8HG.01 TCGA.DK.AA76.01 TCGA.DK.A2I2.01 TCGA.CF.A1HS.01 TCGA.KQ.A41O.01 TCGA.CF.A47T.01
#> NA NA NA NA NA NA
#> TCGA.4Z.AA7W.01 TCGA.XF.A8HB.01 TCGA.E7.A97P.01 TCGA.ZF.AA4V.01 TCGA.HQ.A2OE.01 TCGA.XF.A9SI.01
#> NA NA NA NA NA NA
#> TCGA.DK.A1AA.01 TCGA.K4.A5RH.01 TCGA.XF.AAN1.01 TCGA.CU.A5W6.01 TCGA.XF.A9SM.01 TCGA.C4.A0F7.01
#> NA NA NA NA NA NA
#> TCGA.GC.A3RD.01 TCGA.4Z.AA7S.01 TCGA.DK.A1AE.01 TCGA.GC.A3BM.11 TCGA.4Z.AA7Q.01 TCGA.DK.AA6S.01
#> NA NA NA NA NA NA
#> TCGA.XF.A8HD.01 TCGA.DK.A3IU.01 TCGA.KQ.A41S.01 TCGA.4Z.AA7O.01 TCGA.E7.A7XN.01 TCGA.G2.AA3B.01
#> NA NA NA NA NA NA
#> TCGA.K4.A5RI.11 TCGA.UY.A78O.01 TCGA.XF.AAMW.01 TCGA.BT.A0YX.01 TCGA.FD.A6TC.01 TCGA.GC.A3I6.01
#> NA NA NA NA NA NA
#> TCGA.XF.A9SK.01 TCGA.CF.A5U8.01 TCGA.GU.AATP.01 TCGA.K4.A3WV.11 TCGA.BT.A20T.01 TCGA.FD.A62O.01
#> NA NA NA NA NA NA
#> TCGA.MV.A51V.01 TCGA.UY.A9PH.01 TCGA.FD.A3B3.01 TCGA.FD.A6TF.01 TCGA.UY.A78K.01 TCGA.BT.A20W.01
#> NA NA NA NA NA NA
#> TCGA.E7.A7DV.01 TCGA.DK.A2I6.01 TCGA.GD.A3OQ.11 TCGA.BT.A20R.01 TCGA.FJ.A3ZF.01 TCGA.4Z.AA87.01
#> NA NA NA NA NA NA
#> TCGA.E7.A6MD.01 TCGA.XF.A9SV.01 TCGA.GV.A3JX.01 TCGA.ZF.A9RC.01 TCGA.FD.A43Y.01 TCGA.GU.A767.01
#> NA NA NA NA NA NA
#> TCGA.UY.A9PD.01 TCGA.DK.A6B2.01 TCGA.CU.A0YN.11 TCGA.YC.A8S6.01 TCGA.DK.A6B6.01 TCGA.DK.AA6M.01
#> NA NA NA NA NA NA
#> TCGA.GU.A763.01 TCGA.DK.A3IN.01 TCGA.E7.A5KF.01 TCGA.CU.A0YO.01 TCGA.XF.A9T3.01 TCGA.CF.A47Y.01
#> NA NA NA NA NA NA
#> TCGA.4Z.AA83.01 TCGA.CU.A72E.01 TCGA.XF.A9T5.01 TCGA.G2.A2EL.01 TCGA.BT.A3PH.01 TCGA.BL.A13J.01
#> NA NA NA NA NA NA
#> TCGA.FD.A62P.01 TCGA.FD.A6TH.01 TCGA.2F.A9KR.01 TCGA.DK.AA74.01 TCGA.BT.A20U.11 TCGA.GD.A2C5.01
#> NA NA NA NA NA NA
#> TCGA.ZF.AA4U.01 TCGA.XF.A9SP.01 TCGA.FD.A3SR.01 TCGA.G2.A2EO.01 TCGA.ZF.AA5N.01 TCGA.K4.A83P.01
#> NA NA NA NA NA NA
#> TCGA.ZF.A9RE.01 TCGA.XF.AAN8.01 TCGA.DK.A6B0.01 TCGA.BT.A20N.01 TCGA.ZF.AA5H.01 TCGA.G2.A2EJ.01
#> NA NA NA NA NA NA
#> TCGA.GC.A3RB.01 TCGA.BT.A42F.01 TCGA.FD.A3SN.01 TCGA.FT.A61P.01 TCGA.G2.A2EF.01 TCGA.XF.AAMF.01
#> NA NA NA NA NA NA
#> TCGA.BT.A20J.11 TCGA.FD.A5BS.01 TCGA.CF.A3MH.01 TCGA.GV.A3QK.01 TCGA.LT.A5Z6.01 TCGA.DK.A1AD.01
#> NA NA NA NA NA NA
#> TCGA.CF.A8HX.01 TCGA.C4.A0F6.01 TCGA.XF.AAMQ.01 TCGA.XF.A9SX.01 TCGA.FD.A5C1.01 TCGA.XF.A8HH.01
#> NA NA NA NA NA NA
#> TCGA.DK.A3IQ.01 TCGA.CF.A27C.01 TCGA.LC.A66R.01 TCGA.FD.A3B8.01 TCGA.BL.A0C8.01 TCGA.G2.A3VY.01
#> NA NA NA NA NA NA
#> TCGA.BT.A2LA.01 TCGA.ZF.AA54.01 TCGA.DK.AA6R.01 TCGA.YF.AA3M.01 TCGA.UY.A78N.01 TCGA.FT.A3EE.01
#> NA NA NA NA NA NA
#> TCGA.FD.A3B7.01 TCGA.ZF.AA4T.01 TCGA.2F.A9KW.01 TCGA.ZF.A9R1.01 TCGA.CF.A47S.01 TCGA.DK.A1AB.01
#> NA NA NA NA NA NA
#> TCGA.G2.AA3F.01 TCGA.K4.A3WU.01 TCGA.K4.A6MB.01 TCGA.FD.A62N.01 TCGA.E7.A3X6.01 TCGA.XF.AAN7.01
#> NA NA NA NA NA NA
#> TCGA.FD.A6TG.01 TCGA.UY.A9PB.01 TCGA.CF.A47V.01 TCGA.KQ.A41R.01 TCGA.XF.A9ST.01 TCGA.ZF.AA4X.01
#> NA NA NA NA NA NA
#> TCGA.FD.A5BZ.01 TCGA.GC.A3BM.01 TCGA.UY.A9PF.01 TCGA.CF.A7I0.01 TCGA.E7.A4IJ.01 TCGA.FD.A5BV.01
#> NA NA NA NA NA NA
#> TCGA.DK.A3IL.01 TCGA.FD.A43X.01 TCGA.GU.A766.01 TCGA.FD.A6TB.01 TCGA.DK.A1A5.01 TCGA.UY.A78L.01
#> NA NA NA NA NA NA
#> TCGA.FD.A6TA.01 TCGA.GU.A762.01 TCGA.K4.A3WS.01 TCGA.DK.A3X1.01 TCGA.XF.AAME.01 TCGA.XF.A9T8.01
#> NA NA NA NA NA NA
#> TCGA.YC.A89H.01 TCGA.4Z.AA7Y.01 TCGA.KQ.A41Q.01 TCGA.G2.AA3D.01 TCGA.XF.AAMY.01 TCGA.4Z.AA81.01
#> NA NA NA NA NA NA
#> TCGA.GU.AATQ.01 TCGA.FD.A6TE.01 TCGA.CF.A3MG.01 TCGA.UY.A8OC.01 TCGA.UY.A8OB.01 TCGA.K4.A5RJ.01
#> NA NA NA NA NA NA
#> TCGA.GD.A3OQ.01 TCGA.ZF.A9RG.01 TCGA.CF.A47X.01 TCGA.BT.A20Q.01 TCGA.FD.A5C0.01 TCGA.ZF.A9R4.01
#> NA NA NA NA NA NA
#> TCGA.FD.A3SS.01 TCGA.FJ.A3ZE.01 TCGA.ZF.A9RD.01 TCGA.E7.A6ME.01 TCGA.BT.A20O.01 TCGA.G2.A2EK.01
#> NA NA NA NA NA NA
#> TCGA.DK.AA75.01 TCGA.GV.A3JZ.01 TCGA.FD.A3SO.01 TCGA.FD.A43S.01 TCGA.SY.A9G5.01 TCGA.4Z.AA89.01
#> NA NA NA NA NA NA
#> TCGA.XF.A8HE.01 TCGA.GC.A3WC.01 TCGA.ZF.A9RM.01 TCGA.FD.A5BR.01 TCGA.G2.A2EC.01 TCGA.XF.A9T4.01
#> NA NA NA NA NA NA
#> TCGA.FD.A62S.01 TCGA.DK.A6B5.01 TCGA.ZF.AA51.01 TCGA.XF.A9SY.01 TCGA.GD.A6C6.01 TCGA.XF.A8HI.01
#> NA NA NA NA NA NA
#> TCGA.2F.A9KQ.01 TCGA.G2.A3IB.01 TCGA.GD.A2C5.11 TCGA.CU.A0YR.01 TCGA.BT.A42B.01 TCGA.CU.A3KJ.01
#> NA NA NA NA NA NA
#> TCGA.DK.A3WW.01 TCGA.YF.AA3L.01 TCGA.GV.A40E.01 TCGA.DK.A1A6.01 TCGA.DK.A1A6.06 TCGA.4Z.AA7N.01
#> NA NA NA NA NA NA
#> TCGA.DK.A2I1.01 TCGA.K4.A4AB.01 TCGA.DK.A2HX.01 TCGA.K4.A54R.11 TCGA.4Z.AA7M.01 TCGA.BL.A3JM.01
#> NA NA NA NA NA NA
#> TCGA.XF.A9SU.01 TCGA.GD.A76B.01 TCGA.BT.A20J.01 TCGA.DK.AA71.01 TCGA.DK.A3WY.01 TCGA.GC.A3RC.01
#> NA NA NA NA NA NA
#> TCGA.ZF.AA53.01 TCGA.CF.A9FF.01 TCGA.LT.A8JT.01 TCGA.GC.A3YS.01 TCGA.XF.AAML.01 TCGA.CF.A47W.01
#> NA NA NA NA NA NA
#> TCGA.DK.A1AF.01 TCGA.XF.AAN3.01 TCGA.5N.A9KM.01 TCGA.XF.AAN2.01 TCGA.BT.A20P.11 TCGA.DK.A3IV.01
#> NA NA NA NA NA NA
#> TCGA.BT.A2LA.11 TCGA.4Z.AA7R.01 TCGA.XF.A9SJ.01 TCGA.C4.A0F0.01 TCGA.DK.AA6T.01 TCGA.ZF.AA58.01
#> NA NA NA NA NA NA
#> TCGA.ZF.AA4R.01 TCGA.DK.A3IS.01 TCGA.FD.A3SQ.01 TCGA.K4.AAQO.01 TCGA.GC.A6I3.01 TCGA.XF.AAMT.01
#> NA NA NA NA NA NA
#> TCGA.BT.A20X.11 TCGA.GC.A6I3.11 TCGA.XF.AAN4.01 TCGA.DK.A3IM.01 TCGA.DK.AA6P.01 TCGA.E5.A4TZ.01
#> NA NA NA NA NA NA
#> TCGA.GD.A3OP.11 TCGA.E7.A7PW.01 TCGA.S5.A6DX.01 TCGA.GV.A6ZA.01 TCGA.FD.A43N.01 TCGA.FD.A3B5.01
#> NA NA NA NA NA NA
#> TCGA.4Z.AA80.01 TCGA.CF.A3MF.01 TCGA.ZF.A9R0.01 TCGA.XF.AAMJ.01 TCGA.BT.A0S7.01 TCGA.BT.A42E.01
#> NA NA NA NA NA NA
#> TCGA.XF.AAMZ.01 TCGA.BT.A20V.11 TCGA.E7.A7DU.01 TCGA.GU.A42R.01 TCGA.FD.A3SM.01 TCGA.ZF.AA4N.01
#> NA NA NA NA NA NA
#> TCGA.CF.A1HR.01 TCGA.FD.A5BT.01 TCGA.DK.A6B1.01 TCGA.FD.A5BY.01 TCGA.5N.A9KI.01 TCGA.GV.A3QH.01
#> NA NA NA NA NA NA
#> TCGA.CF.A9FL.01 TCGA.S5.AA26.01 TCGA.BL.A5ZZ.01 TCGA.E5.A4U1.01 TCGA.PQ.A6FN.01 TCGA.E7.A5KE.01
#> NA NA NA NA NA NA
#> TCGA.GV.A40G.01 TCGA.CF.A8HY.01 TCGA.CF.A3MI.01 TCGA.ZF.A9RL.01 TCGA.HQ.A5ND.01 TCGA.BT.A20U.01
#> NA NA NA NA NA NA
#> TCGA.G2.A3IE.01 TCGA.BT.A42C.01 TCGA.E7.A8O8.01 TCGA.UY.A8OD.01 TCGA.SY.A9G0.01 TCGA.XF.A9T0.01
#> NA NA NA NA NA NA
#> TCGA.DK.A1A3.01 TCGA.H4.A2HO.01 TCGA.DK.A6AW.01 TCGA.ZF.A9R5.01 TCGA.4Z.AA84.01 TCGA.XF.A9SG.01
#> NA NA NA NA NA NA
#> TCGA.2F.A9KP.01 TCGA.GU.A42P.01 TCGA.KQ.A41N.01 TCGA.GC.A4ZW.01 TCGA.ZF.A9R2.01 TCGA.K4.A4AC.01
#> NA NA NA NA NA NA
#> TCGA.XF.A8HC.01 TCGA.FD.A43U.01 TCGA.BT.A2LD.01 TCGA.GV.A3JV.01 TCGA.DK.A1AC.01 TCGA.GC.A3WC.11
#> NA NA NA NA NA NA
#> TCGA.DK.A3WX.01 TCGA.E7.A85H.01 TCGA.XF.AAMG.01 TCGA.GU.A764.01 TCGA.XF.A9T6.01 TCGA.G2.A2ES.01
#> NA NA NA NA NA NA
#> TCGA.DK.A2I4.01 TCGA.HQ.A2OF.01 TCGA.GU.AATO.01 TCGA.DK.A1AG.01 TCGA.E7.A3Y1.01 TCGA.CU.A0YR.11
#> NA NA NA NA NA NA
#> TCGA.XF.A8HF.01 TCGA.CU.A3QU.01 TCGA.KQ.A41P.01 TCGA.XF.A9T2.01 TCGA.BL.A13I.01 TCGA.GD.A3OS.01
#> NA NA NA NA NA NA
#> TCGA.FD.A6TK.01 TCGA.BT.A3PK.01 TCGA.DK.AA6U.01 TCGA.UY.A78M.01 TCGA.C4.A0F1.01 TCGA.E7.A8O7.01
#> NA NA NA NA NA NA
#> TCGA.DK.AA6Q.01 TCGA.GV.A3QG.01 TCGA.H4.A2HQ.01 TCGA.E7.A4XJ.01 TCGA.E7.A678.01 TCGA.K4.A54R.01
#> NA NA NA NA NA NA
#> TCGA.FD.A6TD.01 TCGA.K4.A5RI.01 TCGA.DK.AA77.01 TCGA.E7.A97Q.01 TCGA.2F.A9KT.01 TCGA.XF.A9SW.01
#> NA NA NA NA NA NA
#> TCGA.DK.A6AV.01 TCGA.K4.A3WV.01 TCGA.XF.AAMX.01 TCGA.XF.A9SH.01 TCGA.FD.A3B4.01 TCGA.XF.AAN0.01
#> NA NA NA NA NA NA
#> TCGA.BT.A20P.01 TCGA.ZF.AA4W.01 TCGA.UY.A9PA.01 TCGA.DK.A3IT.01 TCGA.FJ.A871.01 TCGA.DK.AA6W.01
#> NA NA NA NA NA NA
#> TCGA.XF.A9SL.01 TCGA.CF.A5UA.01 TCGA.FD.A3N5.01 TCGA.BT.A20R.11 TCGA.R3.A69X.01 TCGA.DK.A3X2.01
#> NA NA NA NA NA NA
#> TCGA.ZF.A9RN.01 TCGA.FJ.A3Z9.01 TCGA.E7.A677.01 TCGA.E7.A519.01 TCGA.CF.A9FM.01 TCGA.XF.AAMR.01
#> NA NA NA NA NA NA
#> TCGA.BT.A20X.01 TCGA.G2.AA3C.01 TCGA.BT.A20N.11 TCGA.CU.A0YN.01 TCGA.FJ.A3Z7.01 TCGA.CF.A9FH.01
#> NA NA NA NA NA NA
#> TCGA.GV.A3QI.01 TCGA.4Z.AA82.01 TCGA.GC.A6I1.01 TCGA.FD.A5BX.01 TCGA.FD.A3B6.01 TCGA.ZF.AA5P.01
#> NA NA NA NA NA NA
#> TCGA.BT.A20V.01 TCGA.FD.A3SP.01
#> NA NA
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 = 1210),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1210),
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 = 1443),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1443),
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 = 1601),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1601),
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 = 2275),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2275),
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 = 2447),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2447),
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 = 2615),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2615),
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 = 2929),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2929),
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 = 3167),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3167),
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 = 3264),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3264),
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 = 3632),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3632),
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 = 4378),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4378),
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 = 7050),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7050),
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 = 7299),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7299),
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 = 9518),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9518),
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 = 10747),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10747),
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 = 11356),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 11356),
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 = 12363),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12363),
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 = 12451),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12451),
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 = 16943),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 16943),
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 = 18153),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 18153),
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 = 21477),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 21477),
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 = 42283),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 42283),
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 = 54159),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 54159),
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 = 1210))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1443))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1601))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2275))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2447))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2615))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2929))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3167))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3264))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3632))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4378))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7050))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7299))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9518))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10747))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 11356))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 12363))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 12451))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 16943))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 18153))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 21477))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 42283))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 54159))
#> Error in names(x) <- value: 'names' attribute [1] must be the same length as the vector [0]
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 434 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 0.971 0.965 0.985 0.4996 0.499 0.499
#> 3 3 1.000 0.981 0.993 0.3188 0.677 0.445
#> 4 4 0.677 0.736 0.852 0.1089 0.798 0.493
#> 5 5 0.759 0.642 0.840 0.0560 0.895 0.654
#> 6 6 0.858 0.871 0.926 0.0477 0.879 0.573
#> 7 7 0.811 0.638 0.794 0.0257 0.886 0.515
#> 8 8 0.812 0.537 0.780 0.0249 0.905 0.543
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.GD.A3OP.01 2 0.000 0.976 0.00 1.00
#> TCGA.4Z.AA86.01 2 0.000 0.976 0.00 1.00
#> TCGA.BL.A13J.11 2 0.000 0.976 0.00 1.00
#> TCGA.2F.A9KO.01 2 0.000 0.976 0.00 1.00
#> TCGA.GU.A42Q.01 2 0.000 0.976 0.00 1.00
#> TCGA.HQ.A5NE.01 2 0.469 0.886 0.10 0.90
#> TCGA.PQ.A6FI.01 1 0.000 0.992 1.00 0.00
#> TCGA.E5.A2PC.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A3SL.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A5BU.01 2 0.000 0.976 0.00 1.00
#> TCGA.UY.A9PE.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A3N6.01 1 0.000 0.992 1.00 0.00
#> TCGA.CU.A3YL.01 1 0.000 0.992 1.00 0.00
#> TCGA.GV.A3JW.01 1 0.000 0.992 1.00 0.00
#> TCGA.ZF.A9R3.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A6MF.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A43P.01 2 0.000 0.976 0.00 1.00
#> TCGA.ZF.AA52.01 2 0.000 0.976 0.00 1.00
#> TCGA.E7.A541.01 1 0.995 0.101 0.54 0.46
#> TCGA.DK.AA6L.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A6TI.01 1 0.000 0.992 1.00 0.00
#> TCGA.BT.A20W.11 2 0.000 0.976 0.00 1.00
#> TCGA.XF.A9SZ.01 2 0.000 0.976 0.00 1.00
#> TCGA.C4.A0EZ.01 2 0.242 0.943 0.04 0.96
#> TCGA.FD.A3SJ.01 2 0.469 0.886 0.10 0.90
#> TCGA.ZF.AA56.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.AAMH.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A3NA.01 1 0.000 0.992 1.00 0.00
#> TCGA.DK.A3IK.01 1 0.000 0.992 1.00 0.00
#> TCGA.ZF.A9RF.01 2 0.760 0.738 0.22 0.78
#> TCGA.UY.A78P.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.AA6X.01 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A3PJ.01 1 0.000 0.992 1.00 0.00
#> TCGA.K4.A6FZ.01 2 0.000 0.976 0.00 1.00
#> TCGA.YC.A9TC.01 1 0.000 0.992 1.00 0.00
#> TCGA.ZF.A9R7.01 1 0.000 0.992 1.00 0.00
#> TCGA.GC.A3OO.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.A1A7.01 1 0.000 0.992 1.00 0.00
#> TCGA.BT.A2LB.01 1 0.000 0.992 1.00 0.00
#> TCGA.GV.A3QF.01 1 0.000 0.992 1.00 0.00
#> TCGA.ZF.A9R9.01 1 0.000 0.992 1.00 0.00
#> TCGA.XF.AAN5.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.A8HG.01 1 0.000 0.992 1.00 0.00
#> TCGA.DK.AA76.01 1 0.000 0.992 1.00 0.00
#> TCGA.DK.A2I2.01 2 0.000 0.976 0.00 1.00
#> TCGA.CF.A1HS.01 2 0.000 0.976 0.00 1.00
#> TCGA.KQ.A41O.01 1 0.000 0.992 1.00 0.00
#> TCGA.CF.A47T.01 1 0.000 0.992 1.00 0.00
#> TCGA.4Z.AA7W.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.A8HB.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A97P.01 2 0.000 0.976 0.00 1.00
#> TCGA.ZF.AA4V.01 1 0.000 0.992 1.00 0.00
#> TCGA.HQ.A2OE.01 1 0.000 0.992 1.00 0.00
#> TCGA.XF.A9SI.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.A1AA.01 1 0.000 0.992 1.00 0.00
#> TCGA.K4.A5RH.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.AAN1.01 1 0.000 0.992 1.00 0.00
#> TCGA.CU.A5W6.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.A9SM.01 2 0.000 0.976 0.00 1.00
#> TCGA.C4.A0F7.01 2 0.584 0.842 0.14 0.86
#> TCGA.GC.A3RD.01 1 0.000 0.992 1.00 0.00
#> TCGA.4Z.AA7S.01 1 0.000 0.992 1.00 0.00
#> TCGA.DK.A1AE.01 1 0.000 0.992 1.00 0.00
#> TCGA.GC.A3BM.11 2 0.000 0.976 0.00 1.00
#> TCGA.4Z.AA7Q.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.AA6S.01 1 0.000 0.992 1.00 0.00
#> TCGA.XF.A8HD.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.A3IU.01 2 0.000 0.976 0.00 1.00
#> TCGA.KQ.A41S.01 2 0.000 0.976 0.00 1.00
#> TCGA.4Z.AA7O.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A7XN.01 2 0.000 0.976 0.00 1.00
#> TCGA.G2.AA3B.01 1 0.000 0.992 1.00 0.00
#> TCGA.K4.A5RI.11 2 0.000 0.976 0.00 1.00
#> TCGA.UY.A78O.01 1 0.000 0.992 1.00 0.00
#> TCGA.XF.AAMW.01 1 0.000 0.992 1.00 0.00
#> TCGA.BT.A0YX.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A6TC.01 1 0.000 0.992 1.00 0.00
#> TCGA.GC.A3I6.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.A9SK.01 1 0.000 0.992 1.00 0.00
#> TCGA.CF.A5U8.01 1 0.000 0.992 1.00 0.00
#> TCGA.GU.AATP.01 1 0.000 0.992 1.00 0.00
#> TCGA.K4.A3WV.11 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A20T.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A62O.01 1 0.000 0.992 1.00 0.00
#> TCGA.MV.A51V.01 1 0.000 0.992 1.00 0.00
#> TCGA.UY.A9PH.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A3B3.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A6TF.01 2 0.000 0.976 0.00 1.00
#> TCGA.UY.A78K.01 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A20W.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A7DV.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.A2I6.01 1 0.000 0.992 1.00 0.00
#> TCGA.GD.A3OQ.11 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A20R.01 2 0.795 0.707 0.24 0.76
#> TCGA.FJ.A3ZF.01 1 0.000 0.992 1.00 0.00
#> TCGA.4Z.AA87.01 1 0.000 0.992 1.00 0.00
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#> TCGA.E7.A8O7.01 2 0.529 0.865 0.12 0.88
#> TCGA.DK.AA6Q.01 2 0.680 0.793 0.18 0.82
#> TCGA.GV.A3QG.01 2 0.000 0.976 0.00 1.00
#> TCGA.H4.A2HQ.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A4XJ.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A678.01 1 0.000 0.992 1.00 0.00
#> TCGA.K4.A54R.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A6TD.01 2 0.000 0.976 0.00 1.00
#> TCGA.K4.A5RI.01 1 0.000 0.992 1.00 0.00
#> TCGA.DK.AA77.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A97Q.01 1 0.000 0.992 1.00 0.00
#> TCGA.2F.A9KT.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.A9SW.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.A6AV.01 1 0.000 0.992 1.00 0.00
#> TCGA.K4.A3WV.01 1 0.958 0.358 0.62 0.38
#> TCGA.XF.AAMX.01 1 0.000 0.992 1.00 0.00
#> TCGA.XF.A9SH.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A3B4.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.AAN0.01 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A20P.01 2 0.000 0.976 0.00 1.00
#> TCGA.ZF.AA4W.01 2 0.000 0.976 0.00 1.00
#> TCGA.UY.A9PA.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.A3IT.01 2 0.000 0.976 0.00 1.00
#> TCGA.FJ.A871.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.AA6W.01 1 0.000 0.992 1.00 0.00
#> TCGA.XF.A9SL.01 2 0.000 0.976 0.00 1.00
#> TCGA.CF.A5UA.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A3N5.01 1 0.000 0.992 1.00 0.00
#> TCGA.BT.A20R.11 2 0.000 0.976 0.00 1.00
#> TCGA.R3.A69X.01 2 0.000 0.976 0.00 1.00
#> TCGA.DK.A3X2.01 1 0.000 0.992 1.00 0.00
#> TCGA.ZF.A9RN.01 1 0.000 0.992 1.00 0.00
#> TCGA.FJ.A3Z9.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A677.01 1 0.000 0.992 1.00 0.00
#> TCGA.E7.A519.01 2 0.000 0.976 0.00 1.00
#> TCGA.CF.A9FM.01 2 0.000 0.976 0.00 1.00
#> TCGA.XF.AAMR.01 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A20X.01 2 0.000 0.976 0.00 1.00
#> TCGA.G2.AA3C.01 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A20N.11 2 0.000 0.976 0.00 1.00
#> TCGA.CU.A0YN.01 2 0.000 0.976 0.00 1.00
#> TCGA.FJ.A3Z7.01 2 0.795 0.707 0.24 0.76
#> TCGA.CF.A9FH.01 1 0.000 0.992 1.00 0.00
#> TCGA.GV.A3QI.01 2 0.722 0.766 0.20 0.80
#> TCGA.4Z.AA82.01 2 0.000 0.976 0.00 1.00
#> TCGA.GC.A6I1.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A5BX.01 2 0.000 0.976 0.00 1.00
#> TCGA.FD.A3B6.01 2 0.000 0.976 0.00 1.00
#> TCGA.ZF.AA5P.01 2 0.000 0.976 0.00 1.00
#> TCGA.BT.A20V.01 1 0.000 0.992 1.00 0.00
#> TCGA.FD.A3SP.01 2 0.000 0.976 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GD.A3OP.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.4Z.AA86.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BL.A13J.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.2F.A9KO.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GU.A42Q.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.HQ.A5NE.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.PQ.A6FI.01 3 0.1529 0.9506 0.04 0.00 0.96
#> TCGA.E5.A2PC.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A3SL.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A5BU.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.UY.A9PE.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3N6.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CU.A3YL.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GV.A3JW.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9R3.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A6MF.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A43P.01 2 0.5835 0.4971 0.00 0.66 0.34
#> TCGA.ZF.AA52.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.E7.A541.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.AA6L.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A6TI.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20W.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A9SZ.01 3 0.0892 0.9725 0.00 0.02 0.98
#> TCGA.C4.A0EZ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3SJ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA56.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAMH.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3NA.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A3IK.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.A9RF.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.UY.A78P.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.AA6X.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A3PJ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.A6FZ.01 2 0.3340 0.8617 0.00 0.88 0.12
#> TCGA.YC.A9TC.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.A9R7.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A3OO.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A1A7.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A2LB.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GV.A3QF.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.A9R9.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAN5.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A8HG.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.AA76.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A2I2.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A1HS.01 2 0.3340 0.8617 0.00 0.88 0.12
#> TCGA.KQ.A41O.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.4Z.AA7W.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A8HB.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.E7.A97P.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA4V.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.HQ.A2OE.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9SI.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A1AA.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.K4.A5RH.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.AAN1.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CU.A5W6.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9SM.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.C4.A0F7.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A3RD.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.4Z.AA7S.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A1AE.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GC.A3BM.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.4Z.AA7Q.01 3 0.1529 0.9523 0.00 0.04 0.96
#> TCGA.DK.AA6S.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A8HD.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A3IU.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.KQ.A41S.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.4Z.AA7O.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A7XN.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.G2.AA3B.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.K4.A5RI.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.AAMW.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A0YX.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A6TC.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A3I6.01 3 0.5706 0.5157 0.00 0.32 0.68
#> TCGA.XF.A9SK.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CF.A5U8.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GU.AATP.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.A3WV.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A20T.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A62O.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.MV.A51V.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.UY.A9PH.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3B3.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A6TF.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.UY.A78K.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20W.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.E7.A7DV.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A2I6.01 1 0.0892 0.9779 0.98 0.00 0.02
#> TCGA.GD.A3OQ.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A20R.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FJ.A3ZF.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.4Z.AA87.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9SV.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GV.A3JX.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9RC.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A43Y.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GU.A767.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.UY.A9PD.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A6B2.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CU.A0YN.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.YC.A8S6.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A6B6.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.AA6M.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GU.A763.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A3IN.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.E7.A5KF.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CU.A0YO.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A9T3.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CF.A47Y.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.4Z.AA83.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CU.A72E.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9T5.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.G2.A2EL.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BT.A3PH.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BL.A13J.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A62P.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A6TH.01 1 0.0892 0.9779 0.98 0.00 0.02
#> TCGA.2F.A9KR.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.AA74.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A20U.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GD.A2C5.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA4U.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9SP.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3SR.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.G2.A2EO.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA5N.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.A83P.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.ZF.A9RE.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.AAN8.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A6B0.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20N.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA5H.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.G2.A2EJ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A3RB.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BT.A42F.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A3SN.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FT.A61P.01 2 0.0892 0.9671 0.00 0.98 0.02
#> TCGA.G2.A2EF.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAMF.01 1 0.2959 0.8857 0.90 0.00 0.10
#> TCGA.BT.A20J.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A5BS.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A3MH.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GV.A3QK.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.LT.A5Z6.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A1AD.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CF.A8HX.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.C4.A0F6.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.AAMQ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9SX.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A5C1.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A8HH.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A3IQ.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A27C.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.LC.A66R.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3B8.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BL.A0C8.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.G2.A3VY.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BT.A2LA.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA54.01 3 0.0892 0.9725 0.00 0.02 0.98
#> TCGA.DK.AA6R.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.YF.AA3M.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.UY.A78N.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FT.A3EE.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3B7.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.ZF.AA4T.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.2F.A9KW.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.A9R1.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CF.A47S.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A1AB.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.G2.AA3F.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.K4.A3WU.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.K4.A6MB.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A62N.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.E7.A3X6.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAN7.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A6TG.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.UY.A9PB.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A47V.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.KQ.A41R.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9ST.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.ZF.AA4X.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A5BZ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A3BM.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.UY.A9PF.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CF.A7I0.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A4IJ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A5BV.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A3IL.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A43X.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GU.A766.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A6TB.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A1A5.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.UY.A78L.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A6TA.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GU.A762.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.K4.A3WS.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A3X1.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAME.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A9T8.01 2 0.1529 0.9476 0.00 0.96 0.04
#> TCGA.YC.A89H.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.4Z.AA7Y.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.KQ.A41Q.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.G2.AA3D.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.AAMY.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.4Z.AA81.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GU.AATQ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A6TE.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CF.A3MG.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.UY.A8OC.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.UY.A8OB.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.K4.A5RJ.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GD.A3OQ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9RG.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A47X.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BT.A20Q.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A5C0.01 2 0.5560 0.5810 0.00 0.70 0.30
#> TCGA.ZF.A9R4.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A3SS.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FJ.A3ZE.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9RD.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.E7.A6ME.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20O.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.G2.A2EK.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.AA75.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GV.A3JZ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A3SO.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A43S.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.SY.A9G5.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.4Z.AA89.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A8HE.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GC.A3WC.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.ZF.A9RM.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A5BR.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.G2.A2EC.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9T4.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A62S.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A6B5.01 3 0.5835 0.4828 0.34 0.00 0.66
#> TCGA.ZF.AA51.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9SY.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GD.A6C6.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A8HI.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.2F.A9KQ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.G2.A3IB.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GD.A2C5.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CU.A0YR.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A42B.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CU.A3KJ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A3WW.01 3 0.0892 0.9725 0.00 0.02 0.98
#> TCGA.YF.AA3L.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GV.A40E.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A1A6.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.4Z.AA7N.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A2I1.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.A4AB.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A2HX.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.A54R.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.4Z.AA7M.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BL.A3JM.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9SU.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GD.A76B.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20J.01 3 0.0892 0.9725 0.00 0.02 0.98
#> TCGA.DK.AA71.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A3WY.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GC.A3RC.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA53.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A9FF.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.LT.A8JT.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAML.01 1 0.0892 0.9779 0.98 0.00 0.02
#> TCGA.CF.A47W.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A1AF.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.AAN3.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.5N.A9KM.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.AAN2.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20P.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A3IV.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A2LA.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.4Z.AA7R.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9SJ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.C4.A0F0.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.AA6T.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.ZF.AA58.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.ZF.AA4R.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A3IS.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A3SQ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.AAQO.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A6I3.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAMT.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20X.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GC.A6I3.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.AAN4.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A3IM.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.AA6P.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E5.A4TZ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GD.A3OP.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.E7.A7PW.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.S5.A6DX.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GV.A6ZA.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A43N.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A3B5.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.4Z.AA80.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CF.A3MF.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9R0.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAMJ.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A0S7.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A42E.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAMZ.01 2 0.3686 0.8369 0.00 0.86 0.14
#> TCGA.BT.A20V.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GU.A42R.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3SM.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA4N.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CF.A1HR.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A5BT.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A6B1.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A5BY.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.5N.A9KI.01 1 0.0892 0.9779 0.98 0.00 0.02
#> TCGA.GV.A3QH.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CF.A9FL.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.S5.AA26.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BL.A5ZZ.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.E5.A4U1.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.PQ.A6FN.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.E7.A5KE.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GV.A40G.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CF.A8HY.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.HQ.A5ND.01 1 0.0892 0.9779 0.98 0.00 0.02
#> TCGA.BT.A20U.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.G2.A3IE.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A42C.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A8O8.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.UY.A8OD.01 3 0.0892 0.9717 0.02 0.00 0.98
#> TCGA.SY.A9G0.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A9T0.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.DK.A1A3.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.H4.A2HO.01 3 0.6309 -0.0023 0.50 0.00 0.50
#> TCGA.DK.A6AW.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9R5.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9SG.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.2F.A9KP.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GU.A42P.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.KQ.A41N.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GC.A4ZW.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.A9R2.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.K4.A4AC.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A8HC.01 1 0.2066 0.9334 0.94 0.00 0.06
#> TCGA.FD.A43U.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A2LD.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GV.A3JV.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A1AC.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A3WC.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A3WX.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.E7.A85H.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.AAMG.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GU.A764.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A9T6.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.G2.A2ES.01 3 0.1529 0.9522 0.00 0.04 0.96
#> TCGA.DK.A2I4.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.HQ.A2OF.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GU.AATO.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.A1AG.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A3Y1.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CU.A0YR.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.A8HF.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.CU.A3QU.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.KQ.A41P.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9T2.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.BL.A13I.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.GD.A3OS.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A6TK.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A3PK.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.AA6U.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.UY.A78M.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.C4.A0F1.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.E7.A8O7.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.DK.AA6Q.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GV.A3QG.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.H4.A2HQ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A4XJ.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A678.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.K4.A54R.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A6TD.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.A5RI.01 1 0.0892 0.9779 0.98 0.00 0.02
#> TCGA.DK.AA77.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A97Q.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.2F.A9KT.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9SW.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A6AV.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.K4.A3WV.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.AAMX.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.XF.A9SH.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FD.A3B4.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.XF.AAN0.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A20P.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA4W.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A3IT.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FJ.A871.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.AA6W.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.XF.A9SL.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A5UA.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.FD.A3N5.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20R.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.R3.A69X.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.DK.A3X2.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.ZF.A9RN.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.FJ.A3Z9.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.E7.A677.01 1 0.0892 0.9779 0.98 0.00 0.02
#> TCGA.E7.A519.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CF.A9FM.01 2 0.6280 0.1674 0.00 0.54 0.46
#> TCGA.XF.AAMR.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A20X.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.G2.AA3C.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.BT.A20N.11 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.CU.A0YN.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FJ.A3Z7.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.CF.A9FH.01 1 0.0000 0.9976 1.00 0.00 0.00
#> TCGA.GV.A3QI.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.4Z.AA82.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.GC.A6I1.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A5BX.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3B6.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.ZF.AA5P.01 2 0.0000 0.9860 0.00 1.00 0.00
#> TCGA.BT.A20V.01 3 0.0000 0.9917 0.00 0.00 1.00
#> TCGA.FD.A3SP.01 2 0.0000 0.9860 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.GD.A3OP.01 2 0.4994 0.3311 0.00 0.52 0.48 0.00
#> TCGA.4Z.AA86.01 2 0.1637 0.8702 0.00 0.94 0.06 0.00
#> TCGA.BL.A13J.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.2F.A9KO.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.GU.A42Q.01 2 0.4994 0.3311 0.00 0.52 0.48 0.00
#> TCGA.HQ.A5NE.01 3 0.3975 0.6565 0.00 0.00 0.76 0.24
#> TCGA.PQ.A6FI.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.E5.A2PC.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.FD.A5BU.01 2 0.4977 0.3845 0.00 0.54 0.46 0.00
#> TCGA.UY.A9PE.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.FD.A3N6.01 1 0.2647 0.8098 0.88 0.00 0.00 0.12
#> TCGA.CU.A3YL.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.GV.A3JW.01 1 0.4277 0.5261 0.72 0.00 0.00 0.28
#> TCGA.ZF.A9R3.01 4 0.4406 0.6092 0.30 0.00 0.00 0.70
#> TCGA.E7.A6MF.01 2 0.7274 0.5663 0.00 0.54 0.24 0.22
#> TCGA.FD.A43P.01 3 0.2921 0.6695 0.00 0.14 0.86 0.00
#> TCGA.ZF.AA52.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.E7.A541.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.DK.AA6L.01 4 0.4713 0.5180 0.36 0.00 0.00 0.64
#> TCGA.FD.A6TI.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.BT.A20W.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SZ.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.C4.A0EZ.01 3 0.3400 0.7071 0.00 0.00 0.82 0.18
#> TCGA.FD.A3SJ.01 3 0.3975 0.6565 0.00 0.00 0.76 0.24
#> TCGA.ZF.AA56.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.XF.AAMH.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.FD.A3NA.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
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#> TCGA.K4.A83P.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
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#> TCGA.DK.A6B0.01 3 0.3801 0.6560 0.00 0.00 0.78 0.22
#> TCGA.BT.A20N.01 4 0.4134 0.6903 0.00 0.00 0.26 0.74
#> TCGA.ZF.AA5H.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
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#> TCGA.FT.A61P.01 3 0.3801 0.5442 0.00 0.22 0.78 0.00
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#> TCGA.DK.A1A6.06 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.4Z.AA7N.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.A2I1.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.K4.A4AB.01 4 0.4994 0.2347 0.48 0.00 0.00 0.52
#> TCGA.DK.A2HX.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.K4.A54R.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7M.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.BL.A3JM.01 3 0.4406 0.5732 0.00 0.00 0.70 0.30
#> TCGA.XF.A9SU.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.GD.A76B.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.BT.A20J.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.DK.AA71.01 3 0.4994 0.5410 0.00 0.00 0.52 0.48
#> TCGA.DK.A3WY.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.GC.A3RC.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.ZF.AA53.01 2 0.4134 0.7333 0.00 0.74 0.26 0.00
#> TCGA.CF.A9FF.01 4 0.4134 0.6584 0.26 0.00 0.00 0.74
#> TCGA.LT.A8JT.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.2921 0.7352 0.00 0.00 0.86 0.14
#> TCGA.XF.AAML.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.CF.A47W.01 3 0.4855 0.6212 0.00 0.00 0.60 0.40
#> TCGA.DK.A1AF.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN3.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.5N.A9KM.01 4 0.4134 0.6584 0.26 0.00 0.00 0.74
#> TCGA.XF.AAN2.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.BT.A20P.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IV.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.BT.A2LA.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7R.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SJ.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.C4.A0F0.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.DK.AA6T.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA58.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA4R.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.DK.A3IS.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.FD.A3SQ.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.K4.AAQO.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.GC.A6I3.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.XF.AAMT.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.BT.A20X.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN4.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IM.01 4 0.4994 0.1023 0.00 0.00 0.48 0.52
#> TCGA.DK.AA6P.01 4 0.3975 0.6793 0.24 0.00 0.00 0.76
#> TCGA.E5.A4TZ.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.GD.A3OP.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.E7.A7PW.01 4 0.4713 0.5186 0.36 0.00 0.00 0.64
#> TCGA.S5.A6DX.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.GV.A6ZA.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.FD.A43N.01 4 0.4994 0.2347 0.48 0.00 0.00 0.52
#> TCGA.FD.A3B5.01 4 0.4790 0.4803 0.38 0.00 0.00 0.62
#> TCGA.4Z.AA80.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.CF.A3MF.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R0.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.XF.AAMJ.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.BT.A0S7.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.BT.A42E.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.XF.AAMZ.01 3 0.3801 0.5442 0.00 0.22 0.78 0.00
#> TCGA.BT.A20V.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.GU.A42R.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.FD.A3SM.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.ZF.AA4N.01 3 0.4713 0.4480 0.00 0.00 0.64 0.36
#> TCGA.CF.A1HR.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.FD.A5BT.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.A6B1.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BY.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.5N.A9KI.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.GV.A3QH.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.CF.A9FL.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.S5.AA26.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.BL.A5ZZ.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.E5.A4U1.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.PQ.A6FN.01 2 0.4134 0.7333 0.00 0.74 0.26 0.00
#> TCGA.E7.A5KE.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 1 0.4406 0.4804 0.70 0.00 0.00 0.30
#> TCGA.CF.A8HY.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 4 0.4894 0.7456 0.10 0.00 0.12 0.78
#> TCGA.BT.A20U.01 3 0.3801 0.5442 0.00 0.22 0.78 0.00
#> TCGA.G2.A3IE.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.BT.A42C.01 4 0.4948 0.3451 0.44 0.00 0.00 0.56
#> TCGA.E7.A8O8.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.SY.A9G0.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.XF.A9T0.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.DK.A1A3.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.H4.A2HO.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.DK.A6AW.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R5.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.4977 0.1409 0.00 0.00 0.54 0.46
#> TCGA.XF.A9SG.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.2F.A9KP.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.GU.A42P.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.KQ.A41N.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.GC.A4ZW.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.ZF.A9R2.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.K4.A4AC.01 3 0.4624 0.2734 0.00 0.34 0.66 0.00
#> TCGA.XF.A8HC.01 4 0.0000 0.6690 0.00 0.00 0.00 1.00
#> TCGA.FD.A43U.01 2 0.4790 0.5563 0.00 0.62 0.38 0.00
#> TCGA.BT.A2LD.01 3 0.4948 0.2143 0.00 0.00 0.56 0.44
#> TCGA.GV.A3JV.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.DK.A1AC.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.GC.A3WC.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.A3WX.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.E7.A85H.01 2 0.4134 0.7333 0.00 0.74 0.26 0.00
#> TCGA.XF.AAMG.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.GU.A764.01 2 0.4977 0.3845 0.00 0.54 0.46 0.00
#> TCGA.XF.A9T6.01 4 0.4790 0.4805 0.38 0.00 0.00 0.62
#> TCGA.G2.A2ES.01 3 0.0707 0.7907 0.00 0.02 0.98 0.00
#> TCGA.DK.A2I4.01 2 0.4134 0.7333 0.00 0.74 0.26 0.00
#> TCGA.HQ.A2OF.01 3 0.4994 0.5410 0.00 0.00 0.52 0.48
#> TCGA.GU.AATO.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.DK.A1AG.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.E7.A3Y1.01 4 0.4994 0.2347 0.48 0.00 0.00 0.52
#> TCGA.CU.A0YR.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.XF.A8HF.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.KQ.A41P.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 1 0.2647 0.8104 0.88 0.00 0.00 0.12
#> TCGA.BL.A13I.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.GD.A3OS.01 2 0.4948 0.4326 0.00 0.56 0.44 0.00
#> TCGA.FD.A6TK.01 3 0.4522 0.3296 0.00 0.32 0.68 0.00
#> TCGA.BT.A3PK.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.AA6U.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 4 0.4713 0.5180 0.36 0.00 0.00 0.64
#> TCGA.C4.A0F1.01 4 0.4277 0.6579 0.00 0.00 0.28 0.72
#> TCGA.E7.A8O7.01 3 0.4977 0.5658 0.00 0.00 0.54 0.46
#> TCGA.DK.AA6Q.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.GV.A3QG.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.H4.A2HQ.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.E7.A678.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.K4.A54R.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TD.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.K4.A5RI.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.DK.AA77.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.E7.A97Q.01 1 0.4855 0.1949 0.60 0.00 0.00 0.40
#> TCGA.2F.A9KT.01 3 0.2647 0.7470 0.00 0.00 0.88 0.12
#> TCGA.XF.A9SW.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.A6AV.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.K4.A3WV.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.XF.AAMX.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.FD.A3B4.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN0.01 3 0.4977 -0.1538 0.00 0.46 0.54 0.00
#> TCGA.BT.A20P.01 3 0.3801 0.6560 0.00 0.00 0.78 0.22
#> TCGA.ZF.AA4W.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IT.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.FJ.A871.01 2 0.4713 0.5914 0.00 0.64 0.36 0.00
#> TCGA.DK.AA6W.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.XF.A9SL.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.CF.A5UA.01 3 0.3801 0.6560 0.00 0.00 0.78 0.22
#> TCGA.FD.A3N5.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.BT.A20R.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.R3.A69X.01 2 0.4134 0.7333 0.00 0.74 0.26 0.00
#> TCGA.DK.A3X2.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9RN.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.FJ.A3Z9.01 1 0.0000 0.9519 1.00 0.00 0.00 0.00
#> TCGA.E7.A677.01 4 0.3801 0.6973 0.22 0.00 0.00 0.78
#> TCGA.E7.A519.01 3 0.3801 0.6560 0.00 0.00 0.78 0.22
#> TCGA.CF.A9FM.01 3 0.3801 0.6560 0.00 0.00 0.78 0.22
#> TCGA.XF.AAMR.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.BT.A20X.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.G2.AA3C.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.BT.A20N.11 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.FJ.A3Z7.01 3 0.4134 0.6364 0.00 0.00 0.74 0.26
#> TCGA.CF.A9FH.01 4 0.2921 0.6917 0.14 0.00 0.00 0.86
#> TCGA.GV.A3QI.01 3 0.4977 0.5658 0.00 0.00 0.54 0.46
#> TCGA.4Z.AA82.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.GC.A6I1.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.FD.A5BX.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.FD.A3B6.01 3 0.0000 0.8022 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA5P.01 2 0.0000 0.9011 0.00 1.00 0.00 0.00
#> TCGA.BT.A20V.01 4 0.3801 0.7438 0.00 0.00 0.22 0.78
#> TCGA.FD.A3SP.01 2 0.3172 0.8090 0.00 0.84 0.16 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GD.A3OP.01 3 0.3684 0.1396 0.00 0.28 0.72 0.00 0.00
#> TCGA.4Z.AA86.01 2 0.4060 0.6469 0.00 0.64 0.36 0.00 0.00
#> TCGA.BL.A13J.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.2F.A9KO.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.GU.A42Q.01 3 0.3274 0.2744 0.00 0.22 0.78 0.00 0.00
#> TCGA.HQ.A5NE.01 3 0.6593 0.3345 0.00 0.00 0.44 0.22 0.34
#> TCGA.PQ.A6FI.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.E5.A2PC.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.FD.A5BU.01 3 0.2929 0.3234 0.00 0.18 0.82 0.00 0.00
#> TCGA.UY.A9PE.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A3N6.01 4 0.4302 0.1310 0.48 0.00 0.00 0.52 0.00
#> TCGA.CU.A3YL.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.GV.A3JW.01 4 0.4060 0.4469 0.36 0.00 0.00 0.64 0.00
#> TCGA.ZF.A9R3.01 4 0.0609 0.8236 0.02 0.00 0.00 0.98 0.00
#> TCGA.E7.A6MF.01 5 0.3983 0.5041 0.00 0.00 0.34 0.00 0.66
#> TCGA.FD.A43P.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA52.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.E7.A541.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.DK.AA6L.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TI.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20W.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SZ.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.C4.A0EZ.01 3 0.5927 0.4058 0.00 0.00 0.54 0.12 0.34
#> TCGA.FD.A3SJ.01 3 0.6593 0.3345 0.00 0.00 0.44 0.22 0.34
#> TCGA.ZF.AA56.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.XF.AAMH.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A3NA.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.DK.A3IK.01 4 0.2280 0.7186 0.00 0.00 0.00 0.88 0.12
#> TCGA.ZF.A9RF.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.UY.A78P.01 3 0.4182 -0.1861 0.00 0.40 0.60 0.00 0.00
#> TCGA.DK.AA6X.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A3PJ.01 4 0.0609 0.8187 0.00 0.00 0.00 0.98 0.02
#> TCGA.K4.A6FZ.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.YC.A9TC.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.A9R7.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.GC.A3OO.01 2 0.1043 0.8580 0.00 0.96 0.04 0.00 0.00
#> TCGA.DK.A1A7.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A2LB.01 4 0.3274 0.5826 0.00 0.00 0.00 0.78 0.22
#> TCGA.GV.A3QF.01 4 0.6808 -0.3048 0.00 0.00 0.30 0.36 0.34
#> TCGA.ZF.A9R9.01 4 0.0609 0.8233 0.00 0.00 0.00 0.98 0.02
#> TCGA.XF.AAN5.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A8HG.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA76.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I2.01 3 0.4182 -0.1861 0.00 0.40 0.60 0.00 0.00
#> TCGA.CF.A1HS.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.KQ.A41O.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7W.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
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#> TCGA.K4.A4AB.01 4 0.3424 0.6362 0.24 0.00 0.00 0.76 0.00
#> TCGA.DK.A2HX.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.K4.A54R.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7M.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.BL.A3JM.01 3 0.6778 0.2785 0.00 0.00 0.38 0.28 0.34
#> TCGA.XF.A9SU.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.GD.A76B.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.BT.A20J.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.AA71.01 5 0.0000 0.8398 0.00 0.00 0.00 0.00 1.00
#> TCGA.DK.A3WY.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.GC.A3RC.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.ZF.AA53.01 3 0.4182 -0.1861 0.00 0.40 0.60 0.00 0.00
#> TCGA.CF.A9FF.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.LT.A8JT.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.4921 0.4655 0.00 0.00 0.62 0.04 0.34
#> TCGA.XF.AAML.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.CF.A47W.01 5 0.0000 0.8398 0.00 0.00 0.00 0.00 1.00
#> TCGA.DK.A1AF.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN3.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.5N.A9KM.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAN2.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.BT.A20P.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IV.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.BT.A2LA.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7R.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SJ.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.C4.A0F0.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.DK.AA6T.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA58.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.DK.A3IS.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SQ.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.K4.AAQO.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.GC.A6I3.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.XF.AAMT.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.BT.A20X.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN4.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 4 0.6593 -0.1000 0.00 0.00 0.22 0.44 0.34
#> TCGA.DK.AA6P.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.E5.A4TZ.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A3OP.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 4 0.1410 0.7967 0.06 0.00 0.00 0.94 0.00
#> TCGA.S5.A6DX.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.GV.A6ZA.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43N.01 4 0.3561 0.6166 0.26 0.00 0.00 0.74 0.00
#> TCGA.FD.A3B5.01 4 0.0609 0.8236 0.02 0.00 0.00 0.98 0.00
#> TCGA.4Z.AA80.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.CF.A3MF.01 1 0.1043 0.9372 0.96 0.00 0.00 0.04 0.00
#> TCGA.ZF.A9R0.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAMJ.01 2 0.2732 0.7898 0.00 0.84 0.16 0.00 0.00
#> TCGA.BT.A0S7.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.BT.A42E.01 3 0.2020 0.4858 0.00 0.00 0.90 0.00 0.10
#> TCGA.XF.AAMZ.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20V.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A42R.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.FD.A3SM.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA4N.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.CF.A1HR.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.FD.A5BT.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BY.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.5N.A9KI.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.GV.A3QH.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.CF.A9FL.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.S5.AA26.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A5ZZ.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.E5.A4U1.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.PQ.A6FN.01 3 0.4126 -0.1358 0.00 0.38 0.62 0.00 0.00
#> TCGA.E7.A5KE.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 4 0.3684 0.5919 0.28 0.00 0.00 0.72 0.00
#> TCGA.CF.A8HY.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20U.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.A3IE.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A42C.01 4 0.0609 0.8236 0.02 0.00 0.00 0.98 0.00
#> TCGA.E7.A8O8.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.SY.A9G0.01 2 0.1043 0.8580 0.00 0.96 0.04 0.00 0.00
#> TCGA.XF.A9T0.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A3.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.H4.A2HO.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A6AW.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R5.01 1 0.1410 0.9103 0.94 0.00 0.00 0.06 0.00
#> TCGA.4Z.AA84.01 3 0.6824 0.2185 0.00 0.00 0.34 0.32 0.34
#> TCGA.XF.A9SG.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.2F.A9KP.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A42P.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41N.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A4ZW.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.A9R2.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A4AC.01 3 0.0609 0.4576 0.00 0.02 0.98 0.00 0.00
#> TCGA.XF.A8HC.01 4 0.2020 0.7659 0.00 0.00 0.00 0.90 0.10
#> TCGA.FD.A43U.01 3 0.3796 0.0884 0.00 0.30 0.70 0.00 0.00
#> TCGA.BT.A2LD.01 3 0.6824 0.2183 0.00 0.00 0.34 0.32 0.34
#> TCGA.GV.A3JV.01 4 0.3796 0.4520 0.00 0.00 0.00 0.70 0.30
#> TCGA.DK.A1AC.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.GC.A3WC.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 2 0.3983 0.6722 0.00 0.66 0.34 0.00 0.00
#> TCGA.E7.A85H.01 3 0.4307 -0.4198 0.00 0.50 0.50 0.00 0.00
#> TCGA.XF.AAMG.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A764.01 3 0.2732 0.3403 0.00 0.16 0.84 0.00 0.00
#> TCGA.XF.A9T6.01 4 0.0609 0.8236 0.02 0.00 0.00 0.98 0.00
#> TCGA.G2.A2ES.01 3 0.0000 0.4717 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A2I4.01 3 0.4182 -0.1861 0.00 0.40 0.60 0.00 0.00
#> TCGA.HQ.A2OF.01 5 0.0000 0.8398 0.00 0.00 0.00 0.00 1.00
#> TCGA.GU.AATO.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.DK.A1AG.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A3Y1.01 4 0.3561 0.6166 0.26 0.00 0.00 0.74 0.00
#> TCGA.CU.A0YR.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A8HF.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41P.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 4 0.4302 0.1279 0.48 0.00 0.00 0.52 0.00
#> TCGA.BL.A13I.01 2 0.3983 0.6722 0.00 0.66 0.34 0.00 0.00
#> TCGA.GD.A3OS.01 3 0.3109 0.3063 0.00 0.20 0.80 0.00 0.00
#> TCGA.FD.A6TK.01 3 0.0609 0.4576 0.00 0.02 0.98 0.00 0.00
#> TCGA.BT.A3PK.01 2 0.3983 0.6722 0.00 0.66 0.34 0.00 0.00
#> TCGA.DK.AA6U.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.C4.A0F1.01 4 0.6386 0.0224 0.00 0.00 0.18 0.48 0.34
#> TCGA.E7.A8O7.01 5 0.0000 0.8398 0.00 0.00 0.00 0.00 1.00
#> TCGA.DK.AA6Q.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.GV.A3QG.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.H4.A2HQ.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.E7.A678.01 4 0.0609 0.8236 0.02 0.00 0.00 0.98 0.00
#> TCGA.K4.A54R.01 3 0.2280 0.4856 0.00 0.00 0.88 0.00 0.12
#> TCGA.FD.A6TD.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.K4.A5RI.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.AA77.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A97Q.01 4 0.3561 0.6166 0.26 0.00 0.00 0.74 0.00
#> TCGA.2F.A9KT.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.XF.A9SW.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.K4.A3WV.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.XF.AAMX.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A3B4.01 2 0.3274 0.7512 0.00 0.78 0.22 0.00 0.00
#> TCGA.XF.AAN0.01 3 0.3684 0.1398 0.00 0.28 0.72 0.00 0.00
#> TCGA.BT.A20P.01 5 0.0000 0.8398 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZF.AA4W.01 2 0.1043 0.8580 0.00 0.96 0.04 0.00 0.00
#> TCGA.UY.A9PA.01 2 0.3983 0.6722 0.00 0.66 0.34 0.00 0.00
#> TCGA.DK.A3IT.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.FJ.A871.01 3 0.3796 0.0904 0.00 0.30 0.70 0.00 0.00
#> TCGA.DK.AA6W.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.A9SL.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A5UA.01 5 0.3983 0.5041 0.00 0.00 0.34 0.00 0.66
#> TCGA.FD.A3N5.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20R.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 3 0.4182 -0.1861 0.00 0.40 0.60 0.00 0.00
#> TCGA.DK.A3X2.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RN.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.FJ.A3Z9.01 1 0.0000 0.9875 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A677.01 4 0.0000 0.8334 0.00 0.00 0.00 1.00 0.00
#> TCGA.E7.A519.01 5 0.3983 0.5041 0.00 0.00 0.34 0.00 0.66
#> TCGA.CF.A9FM.01 5 0.3983 0.5041 0.00 0.00 0.34 0.00 0.66
#> TCGA.XF.AAMR.01 2 0.1043 0.8580 0.00 0.96 0.04 0.00 0.00
#> TCGA.BT.A20X.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.G2.AA3C.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.BT.A20N.11 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.FJ.A3Z7.01 3 0.6732 0.3071 0.00 0.00 0.40 0.26 0.34
#> TCGA.CF.A9FH.01 4 0.2929 0.6878 0.00 0.00 0.00 0.82 0.18
#> TCGA.GV.A3QI.01 5 0.0000 0.8398 0.00 0.00 0.00 0.00 1.00
#> TCGA.4Z.AA82.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.GC.A6I1.01 3 0.1043 0.4845 0.00 0.00 0.96 0.00 0.04
#> TCGA.FD.A5BX.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.FD.A3B6.01 3 0.3983 0.4921 0.00 0.00 0.66 0.00 0.34
#> TCGA.ZF.AA5P.01 2 0.0000 0.8669 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20V.01 4 0.3983 0.3784 0.00 0.00 0.00 0.66 0.34
#> TCGA.FD.A3SP.01 3 0.4302 -0.3760 0.00 0.48 0.52 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.GD.A3OP.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.4Z.AA86.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.BL.A13J.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KO.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GU.A42Q.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.HQ.A5NE.01 3 0.0547 0.8858 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.PQ.A6FI.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.E5.A2PC.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 3 0.2260 0.6874 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.FD.A5BU.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.UY.A9PE.01 4 0.4377 0.7309 0.00 0.00 0.12 0.72 0.16 0.00
#> TCGA.FD.A3N6.01 4 0.1092 0.8831 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.CU.A3YL.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.GV.A3JW.01 4 0.0547 0.8899 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.ZF.A9R3.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A6MF.01 5 0.3156 0.7668 0.00 0.00 0.02 0.00 0.80 0.18
#> TCGA.FD.A43P.01 6 0.1814 0.8699 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.ZF.AA52.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A541.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.DK.AA6L.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TI.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.BT.A20W.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SZ.01 6 0.2048 0.8564 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.C4.A0EZ.01 3 0.1807 0.8847 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.FD.A3SJ.01 3 0.1267 0.8881 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.ZF.AA56.01 6 0.2941 0.7488 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.XF.AAMH.01 4 0.2793 0.8507 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.FD.A3NA.01 3 0.2048 0.8726 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.DK.A3IK.01 3 0.5150 0.5291 0.00 0.00 0.62 0.22 0.16 0.00
#> TCGA.ZF.A9RF.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.UY.A78P.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.DK.AA6X.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BT.A3PJ.01 3 0.4737 0.6335 0.00 0.00 0.68 0.16 0.16 0.00
#> TCGA.K4.A6FZ.01 6 0.1556 0.8834 0.00 0.00 0.08 0.00 0.00 0.92
#> TCGA.YC.A9TC.01 4 0.2793 0.8507 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.ZF.A9R7.01 4 0.4377 0.7303 0.00 0.00 0.12 0.72 0.16 0.00
#> TCGA.GC.A3OO.01 2 0.2631 0.7837 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.DK.A1A7.01 4 0.2793 0.8507 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.BT.A2LB.01 3 0.4890 0.5999 0.00 0.00 0.66 0.18 0.16 0.00
#> TCGA.GV.A3QF.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.ZF.A9R9.01 4 0.0547 0.9015 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.XF.AAN5.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HG.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA76.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I2.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.CF.A1HS.01 6 0.1556 0.8834 0.00 0.00 0.08 0.00 0.00 0.92
#> TCGA.KQ.A41O.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7W.01 6 0.0937 0.9054 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.XF.A8HB.01 5 0.1267 0.8082 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.E7.A97P.01 6 0.2793 0.7749 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.ZF.AA4V.01 3 0.2454 0.8494 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.HQ.A2OE.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SI.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AA.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RH.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.XF.AAN1.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A5W6.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SM.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.C4.A0F7.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.GC.A3RD.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7S.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A1AE.01 4 0.0547 0.8959 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.GC.A3BM.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7Q.01 6 0.1814 0.8719 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.DK.AA6S.01 3 0.2048 0.8726 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.XF.A8HD.01 6 0.2793 0.7749 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.DK.A3IU.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.KQ.A41S.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7O.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7XN.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.G2.AA3B.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RI.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 4 0.5698 0.0673 0.00 0.00 0.40 0.44 0.16 0.00
#> TCGA.BT.A0YX.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A6TC.01 4 0.2454 0.8642 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.GC.A3I6.01 5 0.3985 0.8176 0.00 0.00 0.10 0.00 0.76 0.14
#> TCGA.XF.A9SK.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.CF.A5U8.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GU.AATP.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.K4.A3WV.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20T.01 3 0.2581 0.8602 0.00 0.00 0.86 0.02 0.12 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MV.A51V.01 4 0.3523 0.6703 0.18 0.00 0.00 0.78 0.04 0.00
#> TCGA.UY.A9PH.01 3 0.2260 0.8625 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.FD.A3B3.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.FD.A6TF.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.UY.A78K.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20W.01 3 0.1814 0.8802 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.E7.A7DV.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A2I6.01 4 0.2048 0.8838 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.GD.A3OQ.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 3 0.1556 0.8862 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.FJ.A3ZF.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA87.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.XF.A9SV.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GV.A3JX.01 4 0.0547 0.8959 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.ZF.A9RC.01 6 0.3198 0.6870 0.00 0.00 0.26 0.00 0.00 0.74
#> TCGA.FD.A43Y.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.GU.A767.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.UY.A9PD.01 4 0.0547 0.8899 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DK.A6B2.01 3 0.5438 0.4196 0.00 0.00 0.56 0.28 0.16 0.00
#> TCGA.CU.A0YN.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A8S6.01 2 0.3198 0.6823 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.DK.A6B6.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.DK.AA6M.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IN.01 3 0.1556 0.8862 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.E7.A5KF.01 4 0.1556 0.8518 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.CU.A0YO.01 6 0.3409 0.5072 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.XF.A9T3.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A47Y.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.4Z.AA83.01 1 0.3198 0.6719 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.CU.A72E.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.A9T5.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.G2.A2EL.01 1 0.3523 0.7473 0.78 0.00 0.00 0.18 0.04 0.00
#> TCGA.BT.A3PH.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A13J.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.FD.A62P.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FD.A6TH.01 4 0.1267 0.8976 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.2F.A9KR.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.AA74.01 2 0.2631 0.7837 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.BT.A20U.11 2 0.2793 0.7612 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.GD.A2C5.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.ZF.AA4U.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SP.01 3 0.0547 0.8858 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FD.A3SR.01 3 0.0937 0.8883 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.G2.A2EO.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA5N.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.K4.A83P.01 2 0.2631 0.7837 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.ZF.A9RE.01 4 0.1092 0.8831 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.XF.AAN8.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B0.01 5 0.3351 0.9006 0.00 0.00 0.16 0.00 0.80 0.04
#> TCGA.BT.A20N.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.ZF.AA5H.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.G2.A2EJ.01 6 0.2793 0.7749 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.GC.A3RB.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.FD.A3SN.01 3 0.0547 0.8858 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FT.A61P.01 6 0.0937 0.9054 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.G2.A2EF.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.XF.AAMF.01 4 0.1556 0.8940 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.BT.A20J.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BS.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MH.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QK.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.LT.A5Z6.01 4 0.4737 0.6693 0.00 0.00 0.16 0.68 0.16 0.00
#> TCGA.DK.A1AD.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C4.A0F6.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMQ.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SX.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.FD.A5C1.01 6 0.2793 0.7749 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.XF.A8HH.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.DK.A3IQ.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.CF.A27C.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LC.A66R.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A3B8.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A0C8.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.A3VY.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A2LA.01 3 0.1480 0.8851 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.ZF.AA54.01 6 0.2048 0.8574 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.DK.AA6R.01 3 0.2260 0.8616 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.YF.AA3M.01 1 0.2793 0.7553 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.UY.A78N.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FT.A3EE.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.FD.A3B7.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.ZF.AA4T.01 4 0.3351 0.8302 0.00 0.00 0.04 0.80 0.16 0.00
#> TCGA.2F.A9KW.01 4 0.3660 0.8083 0.00 0.00 0.06 0.78 0.16 0.00
#> TCGA.ZF.A9R1.01 3 0.3928 0.7548 0.00 0.00 0.76 0.08 0.16 0.00
#> TCGA.CF.A47S.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.DK.A1AB.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.AA3F.01 4 0.0937 0.8747 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.K4.A3WU.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.K4.A6MB.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62N.01 2 0.2631 0.7837 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.E7.A3X6.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.XF.AAN7.01 1 0.3351 0.7724 0.80 0.00 0.00 0.16 0.04 0.00
#> TCGA.FD.A6TG.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.UY.A9PB.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.CF.A47V.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.KQ.A41R.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9ST.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4X.01 4 0.2454 0.8642 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.FD.A5BZ.01 3 0.2048 0.8726 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.GC.A3BM.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A9PF.01 3 0.1556 0.8862 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.CF.A7I0.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A4IJ.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A5BV.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IL.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A43X.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A766.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.FD.A6TB.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.DK.A1A5.01 4 0.3660 0.8089 0.00 0.00 0.06 0.78 0.16 0.00
#> TCGA.UY.A78L.01 4 0.4737 0.6689 0.00 0.00 0.16 0.68 0.16 0.00
#> TCGA.FD.A6TA.01 4 0.3928 0.7843 0.00 0.00 0.08 0.76 0.16 0.00
#> TCGA.GU.A762.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.K4.A3WS.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DK.A3X1.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.XF.AAME.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T8.01 6 0.0937 0.9054 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.YC.A89H.01 4 0.3660 0.8083 0.00 0.00 0.06 0.78 0.16 0.00
#> TCGA.4Z.AA7Y.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.AA3D.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.XF.AAMY.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.4Z.AA81.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.GU.AATQ.01 1 0.2454 0.8027 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.FD.A6TE.01 4 0.0547 0.8959 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.CF.A3MG.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OC.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.UY.A8OB.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A5RJ.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.GD.A3OQ.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9RG.01 2 0.2793 0.7612 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.CF.A47X.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20Q.01 3 0.0547 0.8858 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FD.A5C0.01 6 0.2048 0.8553 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.ZF.A9R4.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SS.01 3 0.0547 0.8858 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FJ.A3ZE.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9RD.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.E7.A6ME.01 4 0.2631 0.8653 0.00 0.00 0.00 0.82 0.18 0.00
#> TCGA.BT.A20O.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EK.01 3 0.2454 0.8494 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.DK.AA75.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 4 0.0937 0.8890 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.FD.A3SO.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.FD.A43S.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.SY.A9G5.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA89.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.A8HE.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.GC.A3WC.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.ZF.A9RM.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.FD.A5BR.01 3 0.1556 0.8862 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.G2.A2EC.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T4.01 3 0.3163 0.8296 0.00 0.00 0.82 0.04 0.14 0.00
#> TCGA.FD.A62S.01 6 0.2793 0.7749 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.DK.A6B5.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.ZF.AA51.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.XF.A9SY.01 2 0.3828 0.3413 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.GD.A6C6.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HI.01 4 0.0547 0.8899 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.2F.A9KQ.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A3IB.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.11 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.CU.A0YR.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.BT.A42B.01 4 0.2454 0.8642 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.CU.A3KJ.01 4 0.0937 0.8890 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.DK.A3WW.01 6 0.2048 0.8564 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.YF.AA3L.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40E.01 3 0.0547 0.8858 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DK.A1A6.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A1A6.06 4 0.2454 0.8642 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.4Z.AA7N.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I1.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.K4.A4AB.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A2HX.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A54R.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7M.01 4 0.1267 0.8976 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.BL.A3JM.01 3 0.2260 0.8625 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.XF.A9SU.01 6 0.2793 0.7764 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.GD.A76B.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20J.01 6 0.2048 0.8564 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.DK.AA71.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.DK.A3WY.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RC.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.ZF.AA53.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.CF.A9FF.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.LT.A8JT.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.0937 0.8883 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.XF.AAML.01 4 0.0937 0.8890 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.CF.A47W.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.DK.A1AF.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN3.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.5N.A9KM.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN2.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20P.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IV.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A2LA.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7R.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SJ.01 6 0.2454 0.8198 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.C4.A0F0.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.DK.AA6T.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA58.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IS.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SQ.01 6 0.2941 0.7488 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.K4.AAQO.01 6 0.2941 0.7488 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.GC.A6I3.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMT.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20X.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN4.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.DK.AA6P.01 4 0.0937 0.8890 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E5.A4TZ.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A3OP.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S5.A6DX.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GV.A6ZA.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43N.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A3B5.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA80.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CF.A3MF.01 1 0.3409 0.6080 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.ZF.A9R0.01 4 0.2454 0.8642 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.XF.AAMJ.01 2 0.3578 0.5631 0.00 0.66 0.00 0.00 0.00 0.34
#> TCGA.BT.A0S7.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A42E.01 6 0.3869 0.2101 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.XF.AAMZ.01 6 0.1814 0.8699 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.BT.A20V.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A42R.01 3 0.1267 0.8865 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.FD.A3SM.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.ZF.AA4N.01 3 0.2260 0.8616 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.CF.A1HR.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BT.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BY.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.5N.A9KI.01 4 0.1267 0.8976 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.GV.A3QH.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.CF.A9FL.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S5.AA26.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A5ZZ.01 6 0.2454 0.8199 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.E5.A4U1.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PQ.A6FN.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.E7.A5KE.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 4 0.0547 0.8899 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CF.A8HY.01 1 0.2260 0.8237 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 4 0.1814 0.8896 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.BT.A20U.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.G2.A3IE.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.BT.A42C.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A8O8.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 4 0.2260 0.8773 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.SY.A9G0.01 2 0.2631 0.7837 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.XF.A9T0.01 1 0.3309 0.6409 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.DK.A1A3.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.H4.A2HO.01 4 0.2048 0.8838 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.DK.A6AW.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R5.01 1 0.3756 0.4346 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.XF.A9SG.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.2F.A9KP.01 1 0.2260 0.8237 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.GU.A42P.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41N.01 1 0.3076 0.7014 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.GC.A4ZW.01 4 0.2793 0.8507 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.ZF.A9R2.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A4AC.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.XF.A8HC.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A43U.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.BT.A2LD.01 3 0.2454 0.8494 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.GV.A3JV.01 3 0.5698 0.0761 0.00 0.00 0.44 0.40 0.16 0.00
#> TCGA.DK.A1AC.01 4 0.2631 0.8653 0.00 0.00 0.00 0.82 0.18 0.00
#> TCGA.GC.A3WC.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.E7.A85H.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.XF.AAMG.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A764.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.XF.A9T6.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.A2ES.01 6 0.2048 0.8564 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.DK.A2I4.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.HQ.A2OF.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.GU.AATO.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A1AG.01 1 0.2631 0.7807 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.E7.A3Y1.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YR.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HF.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41P.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 4 0.1267 0.8566 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.BL.A13I.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.GD.A3OS.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.FD.A6TK.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BT.A3PK.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.DK.AA6U.01 1 0.2454 0.8027 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.UY.A78M.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C4.A0F1.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.E7.A8O7.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.DK.AA6Q.01 3 0.1556 0.8862 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.GV.A3QG.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.H4.A2HQ.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A678.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A54R.01 6 0.3647 0.5051 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.FD.A6TD.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A5RI.01 4 0.1814 0.8930 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.DK.AA77.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A97Q.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.2F.A9KT.01 3 0.0547 0.8858 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.XF.A9SW.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 4 0.2454 0.8642 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.K4.A3WV.01 3 0.1814 0.8816 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.XF.AAMX.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A3B4.01 2 0.3706 0.4980 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.XF.AAN0.01 6 0.0547 0.9121 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BT.A20P.01 5 0.2793 0.9000 0.00 0.00 0.20 0.00 0.80 0.00
#> TCGA.ZF.AA4W.01 2 0.2631 0.7837 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.UY.A9PA.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.DK.A3IT.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FJ.A871.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.DK.AA6W.01 4 0.2793 0.8507 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.XF.A9SL.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A5UA.01 5 0.3567 0.8535 0.00 0.00 0.10 0.00 0.80 0.10
#> TCGA.FD.A3N5.01 4 0.3928 0.7844 0.00 0.00 0.08 0.76 0.16 0.00
#> TCGA.BT.A20R.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.DK.A3X2.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RN.01 4 0.0937 0.8890 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.FJ.A3Z9.01 1 0.0000 0.9531 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A677.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A519.01 5 0.3567 0.8535 0.00 0.00 0.10 0.00 0.80 0.10
#> TCGA.CF.A9FM.01 5 0.3475 0.8870 0.00 0.00 0.14 0.00 0.80 0.06
#> TCGA.XF.AAMR.01 2 0.2631 0.7837 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.BT.A20X.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G2.AA3C.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20N.11 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 6 0.2793 0.7749 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.FJ.A3Z7.01 3 0.1556 0.8862 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.CF.A9FH.01 4 0.0000 0.9024 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GV.A3QI.01 5 0.2454 0.9294 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.4Z.AA82.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GC.A6I1.01 6 0.2793 0.7749 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.FD.A5BX.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A3B6.01 3 0.0000 0.8838 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA5P.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20V.01 3 0.2981 0.8339 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.FD.A3SP.01 6 0.0547 0.9141 0.00 0.02 0.00 0.00 0.00 0.98
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GD.A3OP.01 6 0.1433 0.80581 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.4Z.AA86.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.BL.A13J.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KO.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.GU.A42Q.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HQ.A5NE.01 3 0.3358 -0.25130 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.PQ.A6FI.01 4 0.4175 0.32848 0.00 0.00 0.38 0.58 0.00 0.00 0.04
#> TCGA.E5.A2PC.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 7 0.4848 0.67860 0.00 0.00 0.40 0.00 0.00 0.10 0.50
#> TCGA.FD.A5BU.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.UY.A9PE.01 3 0.3413 0.28737 0.00 0.00 0.62 0.38 0.00 0.00 0.00
#> TCGA.FD.A3N6.01 4 0.2313 0.71468 0.06 0.00 0.00 0.88 0.00 0.00 0.06
#> TCGA.CU.A3YL.01 4 0.3525 0.20485 0.00 0.00 0.44 0.56 0.00 0.00 0.00
#> TCGA.GV.A3JW.01 4 0.3086 0.68022 0.04 0.00 0.00 0.80 0.00 0.00 0.16
#> TCGA.ZF.A9R3.01 4 0.3228 0.68929 0.02 0.00 0.02 0.80 0.00 0.00 0.16
#> TCGA.E7.A6MF.01 5 0.2745 0.90031 0.00 0.00 0.00 0.00 0.82 0.02 0.16
#> TCGA.FD.A43P.01 6 0.3459 0.04162 0.00 0.00 0.00 0.00 0.00 0.60 0.40
#> TCGA.ZF.AA52.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.E7.A541.01 3 0.2708 0.22755 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.DK.AA6L.01 4 0.0863 0.73005 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.FD.A6TI.01 4 0.3221 0.45624 0.00 0.00 0.32 0.68 0.00 0.00 0.00
#> TCGA.BT.A20W.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SZ.01 7 0.3994 0.37599 0.00 0.00 0.02 0.00 0.00 0.48 0.50
#> TCGA.C4.A0EZ.01 3 0.4577 -0.13766 0.00 0.00 0.58 0.04 0.02 0.00 0.36
#> TCGA.FD.A3SJ.01 3 0.3047 0.04653 0.00 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.ZF.AA56.01 7 0.4505 0.46433 0.00 0.00 0.06 0.00 0.00 0.44 0.50
#> TCGA.XF.AAMH.01 3 0.4945 0.20509 0.00 0.00 0.52 0.36 0.00 0.00 0.12
#> TCGA.FD.A3NA.01 3 0.0504 0.54368 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DK.A3IK.01 3 0.2945 0.46230 0.00 0.00 0.74 0.26 0.00 0.00 0.00
#> TCGA.ZF.A9RF.01 3 0.2945 0.11837 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.UY.A78P.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.AA6X.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A3PJ.01 3 0.2945 0.46230 0.00 0.00 0.74 0.26 0.00 0.00 0.00
#> TCGA.K4.A6FZ.01 6 0.3139 0.38696 0.00 0.00 0.00 0.00 0.00 0.70 0.30
#> TCGA.YC.A9TC.01 3 0.4978 0.11594 0.00 0.00 0.50 0.38 0.00 0.00 0.12
#> TCGA.ZF.A9R7.01 3 0.3413 0.28737 0.00 0.00 0.62 0.38 0.00 0.00 0.00
#> TCGA.GC.A3OO.01 6 0.3525 0.29371 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.DK.A1A7.01 3 0.4978 0.11597 0.00 0.00 0.50 0.38 0.00 0.00 0.12
#> TCGA.BT.A2LB.01 3 0.2708 0.50704 0.00 0.00 0.78 0.22 0.00 0.00 0.00
#> TCGA.GV.A3QF.01 3 0.0000 0.56009 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R9.01 4 0.4204 0.56576 0.00 0.00 0.00 0.70 0.14 0.00 0.16
#> TCGA.XF.AAN5.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HG.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA76.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I2.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CF.A1HS.01 6 0.3047 0.43829 0.00 0.00 0.00 0.00 0.00 0.72 0.28
#> TCGA.KQ.A41O.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7W.01 6 0.2945 0.48400 0.00 0.00 0.00 0.00 0.00 0.74 0.26
#> TCGA.XF.A8HB.01 5 0.1363 0.92995 0.00 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.E7.A97P.01 7 0.4505 0.46433 0.00 0.00 0.06 0.00 0.00 0.44 0.50
#> TCGA.ZF.AA4V.01 3 0.0863 0.56094 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.HQ.A2OE.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SI.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AA.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RH.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAN1.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A5W6.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.XF.A9SM.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.C4.A0F7.01 5 0.1928 0.91127 0.00 0.00 0.02 0.00 0.90 0.00 0.08
#> TCGA.GC.A3RD.01 4 0.1006 0.73512 0.02 0.00 0.02 0.96 0.00 0.00 0.00
#> TCGA.4Z.AA7S.01 4 0.3086 0.68022 0.04 0.00 0.00 0.80 0.00 0.00 0.16
#> TCGA.DK.A1AE.01 4 0.2016 0.72282 0.04 0.00 0.00 0.90 0.00 0.00 0.06
#> TCGA.GC.A3BM.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7Q.01 7 0.3994 0.37599 0.00 0.00 0.02 0.00 0.00 0.48 0.50
#> TCGA.DK.AA6S.01 3 0.1166 0.52932 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.XF.A8HD.01 7 0.4505 0.46433 0.00 0.00 0.06 0.00 0.00 0.44 0.50
#> TCGA.DK.A3IU.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.KQ.A41S.01 7 0.4266 0.68423 0.00 0.00 0.44 0.00 0.00 0.04 0.52
#> TCGA.4Z.AA7O.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7XN.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G2.AA3B.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RI.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 3 0.3294 0.35633 0.00 0.00 0.66 0.34 0.00 0.00 0.00
#> TCGA.BT.A0YX.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.FD.A6TC.01 3 0.3546 0.08835 0.00 0.00 0.54 0.46 0.00 0.00 0.00
#> TCGA.GC.A3I6.01 5 0.2832 0.86180 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.XF.A9SK.01 3 0.0504 0.57054 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.CF.A5U8.01 4 0.3086 0.68022 0.04 0.00 0.00 0.80 0.00 0.00 0.16
#> TCGA.GU.AATP.01 4 0.3459 0.30196 0.00 0.00 0.40 0.60 0.00 0.00 0.00
#> TCGA.K4.A3WV.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20T.01 3 0.1433 0.56139 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.FD.A62O.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MV.A51V.01 4 0.3011 0.67402 0.12 0.00 0.00 0.82 0.00 0.00 0.06
#> TCGA.UY.A9PH.01 3 0.0000 0.56009 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B3.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.FD.A6TF.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.UY.A78K.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.BT.A20W.01 3 0.0863 0.56094 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.E7.A7DV.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.DK.A2I6.01 4 0.3755 0.41763 0.00 0.00 0.34 0.64 0.00 0.00 0.02
#> TCGA.GD.A3OQ.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 3 0.2945 0.11837 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.FJ.A3ZF.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA87.01 4 0.0863 0.73650 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.0000 0.56009 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SV.01 4 0.3086 0.68022 0.04 0.00 0.00 0.80 0.00 0.00 0.16
#> TCGA.GV.A3JX.01 4 0.2016 0.72321 0.00 0.00 0.04 0.90 0.00 0.00 0.06
#> TCGA.ZF.A9RC.01 7 0.4848 0.51305 0.00 0.00 0.10 0.00 0.00 0.40 0.50
#> TCGA.FD.A43Y.01 6 0.0863 0.80617 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.GU.A767.01 6 0.1433 0.80581 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.UY.A9PD.01 4 0.0863 0.73650 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DK.A6B2.01 3 0.3221 0.38530 0.00 0.00 0.68 0.32 0.00 0.00 0.00
#> TCGA.CU.A0YN.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A8S6.01 6 0.3525 0.29371 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.DK.A6B6.01 3 0.1006 0.57201 0.00 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.DK.AA6M.01 7 0.4266 0.68423 0.00 0.00 0.44 0.00 0.00 0.04 0.52
#> TCGA.GU.A763.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IN.01 3 0.2945 0.11837 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.E7.A5KF.01 4 0.4502 0.51091 0.00 0.00 0.00 0.66 0.18 0.00 0.16
#> TCGA.CU.A0YO.01 6 0.3086 0.71646 0.00 0.16 0.00 0.00 0.00 0.80 0.04
#> TCGA.XF.A9T3.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.CF.A47Y.01 5 0.0504 0.94523 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.4Z.AA83.01 4 0.4930 0.43032 0.26 0.00 0.00 0.58 0.00 0.00 0.16
#> TCGA.CU.A72E.01 4 0.0863 0.73650 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.XF.A9T5.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.G2.A2EL.01 4 0.4514 0.01136 0.46 0.00 0.00 0.48 0.00 0.00 0.06
#> TCGA.BT.A3PH.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A13J.01 3 0.1363 0.57051 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.FD.A62P.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TH.01 4 0.3047 0.51599 0.00 0.00 0.28 0.72 0.00 0.00 0.00
#> TCGA.2F.A9KR.01 4 0.3386 0.68443 0.02 0.00 0.02 0.78 0.00 0.00 0.18
#> TCGA.DK.AA74.01 6 0.3525 0.29371 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.BT.A20U.11 6 0.3525 0.29371 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.GD.A2C5.01 4 0.3546 0.15062 0.00 0.00 0.46 0.54 0.00 0.00 0.00
#> TCGA.ZF.AA4U.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SP.01 3 0.4244 -0.54346 0.00 0.00 0.54 0.00 0.00 0.04 0.42
#> TCGA.FD.A3SR.01 3 0.3139 0.13115 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.G2.A2EO.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.ZF.AA5N.01 4 0.3546 0.15062 0.00 0.00 0.46 0.54 0.00 0.00 0.00
#> TCGA.K4.A83P.01 6 0.3525 0.29371 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.ZF.A9RE.01 4 0.2016 0.72282 0.04 0.00 0.00 0.90 0.00 0.00 0.06
#> TCGA.XF.AAN8.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B0.01 5 0.2081 0.92052 0.00 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.BT.A20N.01 3 0.0504 0.57054 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 3 0.3558 0.02576 0.00 0.00 0.52 0.48 0.00 0.00 0.00
#> TCGA.G2.A2EJ.01 7 0.4278 0.42316 0.00 0.00 0.04 0.00 0.00 0.46 0.50
#> TCGA.GC.A3RB.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A3SN.01 3 0.3496 -0.31319 0.00 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.FT.A61P.01 6 0.3139 0.38696 0.00 0.00 0.00 0.00 0.00 0.70 0.30
#> TCGA.G2.A2EF.01 3 0.2832 0.17797 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.XF.AAMF.01 4 0.3047 0.51599 0.00 0.00 0.28 0.72 0.00 0.00 0.00
#> TCGA.BT.A20J.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BS.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MH.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QK.01 4 0.3496 0.25616 0.00 0.00 0.42 0.58 0.00 0.00 0.00
#> TCGA.LT.A5Z6.01 3 0.4681 0.31147 0.00 0.00 0.58 0.32 0.00 0.00 0.10
#> TCGA.DK.A1AD.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C4.A0F6.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMQ.01 4 0.0863 0.73005 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.XF.A9SX.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A5C1.01 7 0.4505 0.46433 0.00 0.00 0.06 0.00 0.00 0.44 0.50
#> TCGA.XF.A8HH.01 3 0.0504 0.57054 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DK.A3IQ.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CF.A27C.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LC.A66R.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.FD.A3B8.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A0C8.01 4 0.0863 0.73650 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.G2.A3VY.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A2LA.01 3 0.4577 -0.05391 0.00 0.00 0.58 0.04 0.02 0.00 0.36
#> TCGA.ZF.AA54.01 7 0.3994 0.37599 0.00 0.00 0.02 0.00 0.00 0.48 0.50
#> TCGA.DK.AA6R.01 3 0.0000 0.56009 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 4 0.3943 0.20407 0.42 0.00 0.00 0.56 0.00 0.00 0.02
#> TCGA.UY.A78N.01 4 0.1718 0.73021 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.FT.A3EE.01 4 0.3546 0.15062 0.00 0.00 0.46 0.54 0.00 0.00 0.00
#> TCGA.FD.A3B7.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.ZF.AA4T.01 3 0.3496 0.19629 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.2F.A9KW.01 3 0.3496 0.19629 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.ZF.A9R1.01 3 0.2259 0.56186 0.00 0.00 0.84 0.16 0.00 0.00 0.00
#> TCGA.CF.A47S.01 5 0.0504 0.94523 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DK.A1AB.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.AA3F.01 4 0.2722 0.68662 0.12 0.00 0.00 0.84 0.00 0.00 0.04
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#> TCGA.XF.A8HC.01 4 0.4204 0.56576 0.00 0.00 0.00 0.70 0.14 0.00 0.16
#> TCGA.FD.A43U.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A2LD.01 3 0.0000 0.56009 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JV.01 3 0.5335 0.43189 0.00 0.00 0.64 0.14 0.14 0.00 0.08
#> TCGA.DK.A1AC.01 3 0.5002 0.05746 0.00 0.00 0.48 0.40 0.00 0.00 0.12
#> TCGA.GC.A3WC.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.E7.A85H.01 6 0.2259 0.74732 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.XF.AAMG.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A764.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.A9T6.01 4 0.0863 0.73005 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.G2.A2ES.01 7 0.3994 0.37599 0.00 0.00 0.02 0.00 0.00 0.48 0.50
#> TCGA.DK.A2I4.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HQ.A2OF.01 5 0.0504 0.94523 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.GU.AATO.01 7 0.4244 0.67483 0.00 0.00 0.42 0.00 0.00 0.04 0.54
#> TCGA.DK.A1AG.01 4 0.4939 0.38779 0.30 0.00 0.00 0.56 0.00 0.00 0.14
#> TCGA.E7.A3Y1.01 4 0.3086 0.68022 0.04 0.00 0.00 0.80 0.00 0.00 0.16
#> TCGA.CU.A0YR.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HF.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41P.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 4 0.3086 0.68022 0.04 0.00 0.00 0.80 0.00 0.00 0.16
#> TCGA.BL.A13I.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.GD.A3OS.01 6 0.0504 0.82889 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.FD.A6TK.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A3PK.01 6 0.0863 0.82868 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.DK.AA6U.01 1 0.3525 0.22251 0.56 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.UY.A78M.01 4 0.0863 0.73005 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.C4.A0F1.01 3 0.0504 0.57054 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.E7.A8O7.01 5 0.0504 0.94523 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DK.AA6Q.01 3 0.3047 0.18140 0.00 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.GV.A3QG.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.H4.A2HQ.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 4 0.2912 0.70526 0.00 0.00 0.04 0.82 0.00 0.00 0.14
#> TCGA.E7.A678.01 4 0.3370 0.65440 0.00 0.00 0.00 0.78 0.06 0.00 0.16
#> TCGA.K4.A54R.01 7 0.5173 0.58535 0.00 0.00 0.16 0.00 0.00 0.34 0.50
#> TCGA.FD.A6TD.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.K4.A5RI.01 4 0.4108 0.50116 0.00 0.00 0.28 0.66 0.00 0.00 0.06
#> TCGA.DK.AA77.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A97Q.01 4 0.0863 0.73650 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.2F.A9KT.01 3 0.4278 -0.62818 0.00 0.00 0.50 0.00 0.00 0.04 0.46
#> TCGA.XF.A9SW.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 3 0.3546 0.08835 0.00 0.00 0.54 0.46 0.00 0.00 0.00
#> TCGA.K4.A3WV.01 3 0.2163 0.52158 0.00 0.00 0.88 0.02 0.00 0.00 0.10
#> TCGA.XF.AAMX.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.2016 0.73288 0.00 0.00 0.04 0.90 0.00 0.00 0.06
#> TCGA.FD.A3B4.01 6 0.4070 0.46245 0.00 0.34 0.00 0.00 0.00 0.62 0.04
#> TCGA.XF.AAN0.01 6 0.1433 0.80581 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.BT.A20P.01 5 0.2081 0.92052 0.00 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.ZF.AA4W.01 6 0.3525 0.29371 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.UY.A9PA.01 6 0.2259 0.74732 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.DK.A3IT.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.FJ.A871.01 6 0.0504 0.82889 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.DK.AA6W.01 3 0.4978 0.15968 0.00 0.00 0.50 0.38 0.00 0.00 0.12
#> TCGA.XF.A9SL.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A5UA.01 5 0.2422 0.90735 0.00 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.FD.A3N5.01 3 0.3459 0.24706 0.00 0.00 0.60 0.40 0.00 0.00 0.00
#> TCGA.BT.A20R.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 6 0.0000 0.83462 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A3X2.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RN.01 4 0.2016 0.72321 0.00 0.00 0.04 0.90 0.00 0.00 0.06
#> TCGA.FJ.A3Z9.01 1 0.0000 0.96561 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A677.01 4 0.2912 0.70526 0.00 0.00 0.04 0.82 0.00 0.00 0.14
#> TCGA.E7.A519.01 5 0.2422 0.90735 0.00 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.CF.A9FM.01 5 0.2259 0.91428 0.00 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.XF.AAMR.01 6 0.4214 0.33208 0.00 0.40 0.00 0.00 0.00 0.56 0.04
#> TCGA.BT.A20X.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.G2.AA3C.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.BT.A20N.11 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 7 0.4278 0.42345 0.00 0.00 0.04 0.00 0.00 0.46 0.50
#> TCGA.FJ.A3Z7.01 3 0.2832 0.17797 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.CF.A9FH.01 4 0.4204 0.56576 0.00 0.00 0.00 0.70 0.14 0.00 0.16
#> TCGA.GV.A3QI.01 5 0.0504 0.94523 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.4Z.AA82.01 7 0.4684 0.66168 0.00 0.00 0.42 0.00 0.02 0.04 0.52
#> TCGA.GC.A6I1.01 7 0.4505 0.46433 0.00 0.00 0.06 0.00 0.00 0.44 0.50
#> TCGA.FD.A5BX.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.FD.A3B6.01 7 0.4278 0.68992 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.ZF.AA5P.01 2 0.0000 0.99829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20V.01 3 0.2313 0.57675 0.00 0.00 0.88 0.06 0.00 0.00 0.06
#> TCGA.FD.A3SP.01 6 0.0504 0.83306 0.00 0.02 0.00 0.00 0.00 0.98 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GD.A3OP.01 6 0.1765 0.8129 0.00 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.4Z.AA86.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BL.A13J.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KO.01 7 0.1341 0.5590 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.GU.A42Q.01 6 0.1091 0.8283 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.HQ.A5NE.01 7 0.3036 0.3196 0.00 0.00 0.04 0.00 0.00 0.00 0.78 0.18
#> TCGA.PQ.A6FI.01 3 0.3771 0.4259 0.00 0.00 0.72 0.12 0.00 0.00 0.00 0.16
#> TCGA.E5.A2PC.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 7 0.2224 0.5484 0.00 0.00 0.00 0.00 0.00 0.02 0.86 0.12
#> TCGA.FD.A5BU.01 6 0.1091 0.8283 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.UY.A9PE.01 3 0.3675 0.1619 0.00 0.00 0.66 0.00 0.00 0.00 0.04 0.30
#> TCGA.FD.A3N6.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.CU.A3YL.01 3 0.2981 0.3899 0.00 0.00 0.76 0.02 0.00 0.00 0.00 0.22
#> TCGA.GV.A3JW.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R3.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MF.01 5 0.1765 0.9132 0.00 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.FD.A43P.01 7 0.4407 -0.0162 0.00 0.00 0.00 0.00 0.00 0.46 0.46 0.08
#> TCGA.ZF.AA52.01 7 0.1091 0.5635 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.E7.A541.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.DK.AA6L.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TI.01 3 0.3385 0.4530 0.00 0.00 0.76 0.08 0.00 0.00 0.00 0.16
#> TCGA.BT.A20W.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SZ.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.C4.A0EZ.01 7 0.4399 -0.1093 0.00 0.00 0.04 0.02 0.00 0.00 0.50 0.44
#> TCGA.FD.A3SJ.01 7 0.3299 0.2785 0.00 0.00 0.06 0.00 0.00 0.00 0.76 0.18
#> TCGA.ZF.AA56.01 7 0.4059 0.4172 0.00 0.00 0.00 0.00 0.00 0.28 0.64 0.08
#> TCGA.XF.AAMH.01 8 0.4224 -0.1842 0.00 0.00 0.46 0.06 0.00 0.00 0.00 0.48
#> TCGA.FD.A3NA.01 7 0.5211 -0.6387 0.00 0.00 0.26 0.00 0.00 0.00 0.40 0.34
#> TCGA.DK.A3IK.01 3 0.4318 -0.0432 0.00 0.00 0.60 0.00 0.00 0.00 0.10 0.30
#> TCGA.ZF.A9RF.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.UY.A78P.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.AA6X.01 6 0.2132 0.7879 0.00 0.00 0.00 0.00 0.00 0.88 0.04 0.08
#> TCGA.BT.A3PJ.01 3 0.4318 -0.0432 0.00 0.00 0.60 0.00 0.00 0.00 0.10 0.30
#> TCGA.K4.A6FZ.01 6 0.4370 0.1914 0.00 0.00 0.00 0.00 0.00 0.52 0.40 0.08
#> TCGA.YC.A9TC.01 3 0.4199 0.1878 0.00 0.00 0.52 0.06 0.00 0.00 0.00 0.42
#> TCGA.ZF.A9R7.01 3 0.3374 0.2168 0.00 0.00 0.68 0.00 0.00 0.00 0.02 0.30
#> TCGA.GC.A3OO.01 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.DK.A1A7.01 3 0.4174 0.2129 0.00 0.00 0.54 0.06 0.00 0.00 0.00 0.40
#> TCGA.BT.A2LB.01 3 0.4318 -0.0432 0.00 0.00 0.60 0.00 0.00 0.00 0.10 0.30
#> TCGA.GV.A3QF.01 7 0.5270 -0.6616 0.00 0.00 0.30 0.00 0.00 0.00 0.36 0.34
#> TCGA.ZF.A9R9.01 4 0.3270 0.5656 0.00 0.00 0.12 0.80 0.06 0.00 0.00 0.02
#> TCGA.XF.AAN5.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HG.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA76.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I2.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CF.A1HS.01 6 0.4199 0.4009 0.00 0.00 0.00 0.00 0.00 0.60 0.32 0.08
#> TCGA.KQ.A41O.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7W.01 6 0.4134 0.4437 0.00 0.00 0.00 0.00 0.00 0.62 0.30 0.08
#> TCGA.XF.A8HB.01 5 0.2350 0.8998 0.00 0.00 0.00 0.10 0.86 0.00 0.00 0.04
#> TCGA.E7.A97P.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.ZF.AA4V.01 8 0.5211 0.6521 0.00 0.00 0.26 0.00 0.00 0.00 0.34 0.40
#> TCGA.HQ.A2OE.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SI.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AA.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RH.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN1.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A5W6.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.A9SM.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C4.A0F7.01 5 0.2534 0.8430 0.00 0.00 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.GC.A3RD.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7S.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AE.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.GC.A3BM.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7Q.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.DK.AA6S.01 7 0.5221 -0.6568 0.00 0.00 0.26 0.00 0.00 0.00 0.38 0.36
#> TCGA.XF.A8HD.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.DK.A3IU.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.KQ.A41S.01 7 0.1091 0.5580 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.4Z.AA7O.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7XN.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.AA3B.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RI.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 3 0.4134 0.0261 0.00 0.00 0.62 0.00 0.00 0.00 0.08 0.30
#> TCGA.BT.A0YX.01 7 0.1341 0.5590 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.FD.A6TC.01 3 0.2534 0.3670 0.00 0.00 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.GC.A3I6.01 5 0.3303 0.8481 0.00 0.00 0.00 0.00 0.76 0.02 0.02 0.20
#> TCGA.XF.A9SK.01 3 0.5270 -0.6335 0.00 0.00 0.36 0.00 0.00 0.00 0.30 0.34
#> TCGA.CF.A5U8.01 4 0.1804 0.6591 0.00 0.00 0.08 0.90 0.00 0.00 0.00 0.02
#> TCGA.GU.AATP.01 3 0.3154 0.4493 0.00 0.00 0.78 0.06 0.00 0.00 0.00 0.16
#> TCGA.K4.A3WV.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20T.01 8 0.4747 0.6893 0.00 0.00 0.16 0.00 0.00 0.00 0.30 0.54
#> TCGA.FD.A62O.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MV.A51V.01 4 0.4877 0.4976 0.04 0.00 0.42 0.48 0.00 0.00 0.00 0.06
#> TCGA.UY.A9PH.01 7 0.5211 -0.6387 0.00 0.00 0.26 0.00 0.00 0.00 0.40 0.34
#> TCGA.FD.A3B3.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TF.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.UY.A78K.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20W.01 8 0.5211 0.6521 0.00 0.00 0.26 0.00 0.00 0.00 0.34 0.40
#> TCGA.E7.A7DV.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A2I6.01 3 0.1947 0.3262 0.00 0.00 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.GD.A3OQ.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.FJ.A3ZF.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA87.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 7 0.5246 -0.6532 0.00 0.00 0.28 0.00 0.00 0.00 0.38 0.34
#> TCGA.XF.A9SV.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.ZF.A9RC.01 7 0.3880 0.4703 0.00 0.00 0.00 0.00 0.00 0.24 0.68 0.08
#> TCGA.FD.A43Y.01 6 0.3385 0.6682 0.00 0.00 0.00 0.00 0.00 0.76 0.16 0.08
#> TCGA.GU.A767.01 6 0.1341 0.8166 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.UY.A9PD.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B2.01 3 0.4318 -0.0432 0.00 0.00 0.60 0.00 0.00 0.00 0.10 0.30
#> TCGA.CU.A0YN.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A8S6.01 6 0.2938 0.5634 0.00 0.30 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.DK.A6B6.01 3 0.5138 -0.5287 0.00 0.00 0.44 0.00 0.00 0.00 0.24 0.32
#> TCGA.DK.AA6M.01 7 0.1341 0.5530 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.GU.A763.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IN.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.E7.A5KF.01 4 0.3078 0.5455 0.00 0.00 0.06 0.82 0.10 0.00 0.00 0.02
#> TCGA.CU.A0YO.01 6 0.2623 0.7557 0.00 0.10 0.00 0.00 0.00 0.84 0.00 0.06
#> TCGA.XF.A9T3.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CF.A47Y.01 5 0.0808 0.9418 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 4 0.3771 0.6559 0.12 0.00 0.16 0.72 0.00 0.00 0.00 0.00
#> TCGA.CU.A72E.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T5.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.A2EL.01 4 0.5738 0.5465 0.20 0.00 0.26 0.48 0.00 0.00 0.00 0.06
#> TCGA.BT.A3PH.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A13J.01 8 0.5133 0.5897 0.00 0.00 0.38 0.00 0.00 0.00 0.22 0.40
#> TCGA.FD.A62P.01 6 0.1341 0.8174 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.FD.A6TH.01 3 0.1765 0.2679 0.00 0.00 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KR.01 4 0.1341 0.6741 0.00 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.DK.AA74.01 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.BT.A20U.11 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.GD.A2C5.01 3 0.2569 0.4371 0.00 0.00 0.82 0.02 0.00 0.00 0.00 0.16
#> TCGA.ZF.AA4U.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SP.01 7 0.2114 0.4151 0.00 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.FD.A3SR.01 7 0.3808 0.0201 0.00 0.00 0.04 0.00 0.00 0.00 0.62 0.34
#> TCGA.G2.A2EO.01 7 0.0471 0.5655 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.ZF.AA5N.01 3 0.2114 0.4239 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.K4.A83P.01 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.ZF.A9RE.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.XF.AAN8.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B0.01 5 0.0808 0.9386 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.BT.A20N.01 3 0.5246 -0.6154 0.00 0.00 0.38 0.00 0.00 0.00 0.28 0.34
#> TCGA.ZF.AA5H.01 3 0.2114 0.4239 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.G2.A2EJ.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.GC.A3RB.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A3SN.01 7 0.3404 0.3270 0.00 0.00 0.04 0.00 0.00 0.00 0.72 0.24
#> TCGA.FT.A61P.01 6 0.4199 0.4011 0.00 0.00 0.00 0.00 0.00 0.60 0.32 0.08
#> TCGA.G2.A2EF.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.XF.AAMF.01 3 0.3263 0.4536 0.00 0.00 0.78 0.10 0.00 0.00 0.00 0.12
#> TCGA.BT.A20J.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BS.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MH.01 1 0.1341 0.9039 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QK.01 3 0.2569 0.4371 0.00 0.00 0.82 0.02 0.00 0.00 0.00 0.16
#> TCGA.LT.A5Z6.01 3 0.3618 0.0423 0.00 0.00 0.60 0.00 0.00 0.00 0.02 0.38
#> TCGA.DK.A1AD.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C4.A0F6.01 1 0.3154 0.6779 0.78 0.00 0.16 0.06 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMQ.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SX.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A5C1.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.XF.A8HH.01 3 0.5246 -0.6154 0.00 0.00 0.38 0.00 0.00 0.00 0.28 0.34
#> TCGA.DK.A3IQ.01 6 0.0808 0.8361 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CF.A27C.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LC.A66R.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A3B8.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A0C8.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.G2.A3VY.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A2LA.01 8 0.4004 0.0908 0.00 0.00 0.04 0.00 0.00 0.00 0.46 0.50
#> TCGA.ZF.AA54.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.DK.AA6R.01 7 0.5211 -0.6387 0.00 0.00 0.26 0.00 0.00 0.00 0.40 0.34
#> TCGA.YF.AA3M.01 4 0.5535 0.5429 0.18 0.00 0.30 0.48 0.00 0.00 0.00 0.04
#> TCGA.UY.A78N.01 3 0.3299 -0.3912 0.00 0.00 0.56 0.44 0.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 3 0.2406 0.3875 0.00 0.00 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.FD.A3B7.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA4T.01 3 0.3374 0.2168 0.00 0.00 0.68 0.00 0.00 0.00 0.02 0.30
#> TCGA.2F.A9KW.01 3 0.3374 0.2168 0.00 0.00 0.68 0.00 0.00 0.00 0.02 0.30
#> TCGA.ZF.A9R1.01 3 0.4480 -0.1130 0.00 0.00 0.58 0.00 0.00 0.00 0.12 0.30
#> TCGA.CF.A47S.01 5 0.1275 0.9373 0.00 0.00 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.DK.A1AB.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.AA3F.01 4 0.4698 0.5270 0.12 0.00 0.44 0.44 0.00 0.00 0.00 0.00
#> TCGA.K4.A3WU.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A6MB.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62N.01 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.E7.A3X6.01 3 0.2114 0.4239 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.XF.AAN7.01 4 0.5865 0.5238 0.22 0.00 0.28 0.44 0.00 0.00 0.00 0.06
#> TCGA.FD.A6TG.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.UY.A9PB.01 6 0.3227 0.6906 0.00 0.00 0.00 0.00 0.00 0.78 0.14 0.08
#> TCGA.CF.A47V.01 5 0.0808 0.9418 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.KQ.A41R.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9ST.01 2 0.0471 0.9741 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZF.AA4X.01 3 0.3746 0.2057 0.00 0.00 0.64 0.04 0.00 0.00 0.00 0.32
#> TCGA.FD.A5BZ.01 7 0.5211 -0.6387 0.00 0.00 0.26 0.00 0.00 0.00 0.40 0.34
#> TCGA.GC.A3BM.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A9PF.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.CF.A7I0.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.E7.A4IJ.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BV.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IL.01 4 0.3142 0.5447 0.00 0.00 0.36 0.64 0.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A766.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TB.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A1A5.01 3 0.3374 0.2168 0.00 0.00 0.68 0.00 0.00 0.00 0.02 0.30
#> TCGA.UY.A78L.01 3 0.3675 0.1668 0.00 0.00 0.66 0.00 0.00 0.00 0.04 0.30
#> TCGA.FD.A6TA.01 3 0.3374 0.2168 0.00 0.00 0.68 0.00 0.00 0.00 0.02 0.30
#> TCGA.GU.A762.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A3WS.01 6 0.1091 0.8283 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.DK.A3X1.01 3 0.5246 -0.6154 0.00 0.00 0.38 0.00 0.00 0.00 0.28 0.34
#> TCGA.XF.AAME.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T8.01 6 0.4199 0.4012 0.00 0.00 0.00 0.00 0.00 0.60 0.32 0.08
#> TCGA.YC.A89H.01 3 0.3374 0.2168 0.00 0.00 0.68 0.00 0.00 0.00 0.02 0.30
#> TCGA.4Z.AA7Y.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.G2.AA3D.01 6 0.2547 0.7609 0.00 0.00 0.00 0.00 0.04 0.84 0.00 0.12
#> TCGA.XF.AAMY.01 3 0.2114 0.4239 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.4Z.AA81.01 3 0.2114 0.4239 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.GU.AATQ.01 4 0.5163 0.5020 0.34 0.00 0.24 0.42 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TE.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.CF.A3MG.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OC.01 7 0.5270 -0.6616 0.00 0.00 0.30 0.00 0.00 0.00 0.36 0.34
#> TCGA.UY.A8OB.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RJ.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GD.A3OQ.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RG.01 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.CF.A47X.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20Q.01 7 0.3880 0.2224 0.00 0.00 0.08 0.00 0.00 0.00 0.68 0.24
#> TCGA.FD.A5C0.01 7 0.5550 0.0158 0.00 0.00 0.00 0.00 0.02 0.34 0.40 0.24
#> TCGA.ZF.A9R4.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SS.01 7 0.3504 0.3131 0.00 0.00 0.04 0.00 0.00 0.00 0.70 0.26
#> TCGA.FJ.A3ZE.01 4 0.2864 0.6035 0.00 0.00 0.08 0.84 0.06 0.00 0.00 0.02
#> TCGA.ZF.A9RD.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A6ME.01 3 0.4199 0.3248 0.00 0.00 0.60 0.08 0.00 0.00 0.00 0.32
#> TCGA.BT.A20O.01 2 0.1091 0.9227 0.00 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.G2.A2EK.01 7 0.5211 -0.6387 0.00 0.00 0.26 0.00 0.00 0.00 0.40 0.34
#> TCGA.DK.AA75.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.FD.A3SO.01 6 0.0808 0.8316 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.FD.A43S.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SY.A9G5.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.4Z.AA89.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HE.01 6 0.1091 0.8283 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.GC.A3WC.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9RM.01 5 0.1275 0.9373 0.00 0.00 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.FD.A5BR.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.G2.A2EC.01 7 0.1563 0.5580 0.00 0.00 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.XF.A9T4.01 8 0.5068 0.5806 0.00 0.00 0.38 0.00 0.00 0.00 0.20 0.42
#> TCGA.FD.A62S.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.DK.A6B5.01 3 0.2888 0.4444 0.00 0.00 0.80 0.04 0.00 0.00 0.00 0.16
#> TCGA.ZF.AA51.01 7 0.4144 0.1125 0.00 0.00 0.12 0.00 0.00 0.00 0.66 0.22
#> TCGA.XF.A9SY.01 6 0.2406 0.6928 0.00 0.20 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.GD.A6C6.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HI.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KQ.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A3IB.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.11 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YR.01 6 0.1341 0.8166 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.BT.A42B.01 3 0.2756 0.3153 0.00 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.CU.A3KJ.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.DK.A3WW.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.YF.AA3L.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40E.01 7 0.2114 0.4160 0.00 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.DK.A1A6.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.2756 0.3153 0.00 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.4Z.AA7N.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I1.01 3 0.2569 0.4371 0.00 0.00 0.82 0.02 0.00 0.00 0.00 0.16
#> TCGA.K4.A4AB.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 7 0.1563 0.5574 0.00 0.00 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.K4.A54R.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7M.01 3 0.1947 0.2286 0.00 0.00 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.BL.A3JM.01 8 0.4433 0.6482 0.00 0.00 0.10 0.00 0.00 0.00 0.34 0.56
#> TCGA.XF.A9SU.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.GD.A76B.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20J.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.DK.AA71.01 5 0.0471 0.9423 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DK.A3WY.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RC.01 7 0.4896 -0.5333 0.00 0.00 0.16 0.00 0.00 0.00 0.46 0.38
#> TCGA.ZF.AA53.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CF.A9FF.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.LT.A8JT.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 7 0.2267 0.3861 0.00 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.XF.AAML.01 4 0.4174 0.4908 0.00 0.00 0.40 0.54 0.00 0.00 0.00 0.06
#> TCGA.CF.A47W.01 5 0.0000 0.9431 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A1AF.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN3.01 7 0.1341 0.5435 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.5N.A9KM.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN2.01 7 0.1341 0.5520 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.BT.A20P.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IV.01 7 0.0808 0.5622 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.BT.A2LA.11 2 0.1341 0.9156 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.4Z.AA7R.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SJ.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.C4.A0F0.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.DK.AA6T.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA58.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 7 0.1563 0.5384 0.00 0.00 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.DK.A3IS.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SQ.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.K4.AAQO.01 7 0.4059 0.4172 0.00 0.00 0.00 0.00 0.00 0.28 0.64 0.08
#> TCGA.GC.A6I3.01 7 0.0808 0.5657 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.XF.AAMT.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20X.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN4.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 8 0.4730 0.6841 0.00 0.00 0.18 0.00 0.00 0.00 0.26 0.56
#> TCGA.DK.AA6P.01 4 0.4747 0.5426 0.00 0.00 0.30 0.54 0.00 0.00 0.00 0.16
#> TCGA.E5.A4TZ.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A3OP.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.S5.A6DX.01 7 0.0808 0.5657 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.GV.A6ZA.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43N.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B5.01 3 0.3329 -0.4046 0.00 0.00 0.52 0.48 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA80.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MF.01 4 0.2132 0.6505 0.08 0.00 0.04 0.88 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R0.01 3 0.2756 0.3153 0.00 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.XF.AAMJ.01 6 0.3198 0.6070 0.00 0.26 0.00 0.00 0.00 0.72 0.00 0.02
#> TCGA.BT.A0S7.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A42E.01 7 0.3227 0.5159 0.00 0.00 0.00 0.00 0.00 0.14 0.78 0.08
#> TCGA.XF.AAMZ.01 6 0.4433 0.3367 0.00 0.00 0.00 0.00 0.00 0.56 0.34 0.10
#> TCGA.BT.A20V.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A42R.01 8 0.4370 0.5330 0.00 0.00 0.08 0.00 0.00 0.00 0.40 0.52
#> TCGA.FD.A3SM.01 3 0.2114 0.4239 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.ZF.AA4N.01 7 0.5211 -0.6387 0.00 0.00 0.26 0.00 0.00 0.00 0.40 0.34
#> TCGA.CF.A1HR.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A5BT.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BY.01 7 0.1341 0.5591 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.5N.A9KI.01 3 0.1947 0.2286 0.00 0.00 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QH.01 3 0.3154 0.4395 0.00 0.00 0.78 0.06 0.00 0.00 0.00 0.16
#> TCGA.CF.A9FL.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S5.AA26.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A5ZZ.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.E5.A4U1.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PQ.A6FN.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A5KE.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 4 0.1765 0.6773 0.00 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HY.01 4 0.1947 0.5895 0.14 0.00 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 3 0.1563 0.3038 0.00 0.00 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.BT.A20U.01 6 0.2648 0.7525 0.00 0.00 0.00 0.00 0.00 0.84 0.08 0.08
#> TCGA.G2.A3IE.01 3 0.2534 0.3670 0.00 0.00 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.BT.A42C.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.E7.A8O8.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 3 0.2569 0.4371 0.00 0.00 0.82 0.02 0.00 0.00 0.00 0.16
#> TCGA.SY.A9G0.01 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.XF.A9T0.01 4 0.5190 0.5156 0.32 0.00 0.26 0.42 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A3.01 7 0.0808 0.5403 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.H4.A2HO.01 3 0.3154 0.4502 0.00 0.00 0.78 0.06 0.00 0.00 0.00 0.16
#> TCGA.DK.A6AW.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R5.01 4 0.2025 0.6331 0.10 0.00 0.02 0.88 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 7 0.5270 -0.6616 0.00 0.00 0.30 0.00 0.00 0.00 0.36 0.34
#> TCGA.XF.A9SG.01 7 0.3909 0.1402 0.00 0.00 0.12 0.00 0.00 0.00 0.70 0.18
#> TCGA.2F.A9KP.01 4 0.4999 0.4326 0.40 0.00 0.18 0.42 0.00 0.00 0.00 0.00
#> TCGA.GU.A42P.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41N.01 4 0.5203 0.5256 0.28 0.00 0.30 0.42 0.00 0.00 0.00 0.00
#> TCGA.GC.A4ZW.01 3 0.4004 0.1442 0.00 0.00 0.50 0.04 0.00 0.00 0.00 0.46
#> TCGA.ZF.A9R2.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A4AC.01 6 0.1341 0.8174 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.XF.A8HC.01 4 0.2864 0.6035 0.00 0.00 0.08 0.84 0.06 0.00 0.00 0.02
#> TCGA.FD.A43U.01 6 0.0808 0.8361 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BT.A2LD.01 7 0.5270 -0.6616 0.00 0.00 0.30 0.00 0.00 0.00 0.36 0.34
#> TCGA.GV.A3JV.01 3 0.6068 -0.2782 0.00 0.00 0.44 0.08 0.04 0.00 0.08 0.36
#> TCGA.DK.A1AC.01 3 0.3991 0.2995 0.00 0.00 0.62 0.06 0.00 0.00 0.00 0.32
#> TCGA.GC.A3WC.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A85H.01 6 0.2547 0.7609 0.00 0.00 0.00 0.00 0.04 0.84 0.00 0.12
#> TCGA.XF.AAMG.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A764.01 6 0.1091 0.8283 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.XF.A9T6.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.G2.A2ES.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.DK.A2I4.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HQ.A2OF.01 5 0.1607 0.9332 0.00 0.00 0.00 0.04 0.92 0.00 0.00 0.04
#> TCGA.GU.AATO.01 7 0.1563 0.5384 0.00 0.00 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.DK.A1AG.01 4 0.3771 0.6559 0.12 0.00 0.16 0.72 0.00 0.00 0.00 0.00
#> TCGA.E7.A3Y1.01 4 0.2406 0.6752 0.00 0.00 0.20 0.80 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YR.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HF.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41P.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 4 0.2650 0.6675 0.00 0.00 0.24 0.76 0.00 0.00 0.00 0.00
#> TCGA.BL.A13I.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GD.A3OS.01 6 0.1341 0.8174 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.FD.A6TK.01 6 0.1341 0.8174 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.BT.A3PK.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.AA6U.01 4 0.5123 0.4929 0.36 0.00 0.22 0.42 0.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.C4.A0F1.01 3 0.5270 -0.6335 0.00 0.00 0.36 0.00 0.00 0.00 0.30 0.34
#> TCGA.E7.A8O7.01 5 0.0808 0.9418 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.DK.AA6Q.01 7 0.4073 0.1709 0.00 0.00 0.10 0.00 0.00 0.00 0.66 0.24
#> TCGA.GV.A3QG.01 7 0.0808 0.5657 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.H4.A2HQ.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 4 0.2534 0.6269 0.00 0.00 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 4 0.1804 0.6591 0.00 0.00 0.08 0.90 0.00 0.00 0.00 0.02
#> TCGA.K4.A54R.01 7 0.3785 0.4997 0.00 0.00 0.00 0.00 0.00 0.14 0.72 0.14
#> TCGA.FD.A6TD.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.K4.A5RI.01 3 0.3170 0.1771 0.00 0.00 0.76 0.20 0.00 0.00 0.00 0.04
#> TCGA.DK.AA77.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A97Q.01 3 0.3272 -0.3507 0.00 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KT.01 7 0.1765 0.4651 0.00 0.00 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.XF.A9SW.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 3 0.2938 0.2505 0.00 0.00 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.K4.A3WV.01 8 0.4255 0.6004 0.00 0.00 0.08 0.00 0.00 0.00 0.34 0.58
#> TCGA.XF.AAMX.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.3299 0.4634 0.00 0.00 0.44 0.56 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B4.01 6 0.3660 0.6078 0.00 0.24 0.00 0.00 0.00 0.70 0.00 0.06
#> TCGA.XF.AAN0.01 6 0.1563 0.8168 0.00 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.BT.A20P.01 5 0.0808 0.9386 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.ZF.AA4W.01 6 0.3015 0.5292 0.00 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.UY.A9PA.01 6 0.2224 0.7777 0.00 0.00 0.00 0.00 0.02 0.86 0.00 0.12
#> TCGA.DK.A3IT.01 7 0.0808 0.5622 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.FJ.A871.01 6 0.1091 0.8283 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.DK.AA6W.01 3 0.4216 0.1581 0.00 0.00 0.50 0.06 0.00 0.00 0.00 0.44
#> TCGA.XF.A9SL.01 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A5UA.01 5 0.1765 0.9132 0.00 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.FD.A3N5.01 3 0.2938 0.2505 0.00 0.00 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.BT.A20R.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A3X2.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RN.01 4 0.4224 0.4613 0.00 0.00 0.46 0.48 0.00 0.00 0.00 0.06
#> TCGA.FJ.A3Z9.01 1 0.0000 0.9943 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A677.01 4 0.2650 0.6107 0.00 0.00 0.24 0.76 0.00 0.00 0.00 0.00
#> TCGA.E7.A519.01 5 0.1765 0.9132 0.00 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.CF.A9FM.01 5 0.0808 0.9386 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.XF.AAMR.01 6 0.3675 0.5281 0.00 0.30 0.00 0.00 0.00 0.66 0.00 0.04
#> TCGA.BT.A20X.01 7 0.1341 0.5590 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.G2.AA3C.01 7 0.0471 0.5655 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BT.A20N.11 2 0.0000 0.9933 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 7 0.4199 0.3629 0.00 0.00 0.00 0.00 0.00 0.32 0.60 0.08
#> TCGA.FJ.A3Z7.01 7 0.3808 0.0201 0.00 0.00 0.04 0.00 0.00 0.00 0.62 0.34
#> TCGA.CF.A9FH.01 4 0.2864 0.6035 0.00 0.00 0.08 0.84 0.06 0.00 0.00 0.02
#> TCGA.GV.A3QI.01 5 0.0471 0.9423 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.4Z.AA82.01 7 0.1765 0.5370 0.00 0.00 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.GC.A6I1.01 7 0.4134 0.3911 0.00 0.00 0.00 0.00 0.00 0.30 0.62 0.08
#> TCGA.FD.A5BX.01 7 0.1341 0.5590 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.FD.A3B6.01 7 0.0000 0.5630 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA5P.01 2 0.1091 0.9227 0.00 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.BT.A20V.01 8 0.5183 0.5791 0.00 0.00 0.38 0.00 0.00 0.00 0.24 0.38
#> TCGA.FD.A3SP.01 6 0.0000 0.8477 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031-leaf , Node032 , Node033 .
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 140 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.990 0.997 0.5019 0.499 0.499
#> 3 3 1.000 0.981 0.992 0.3346 0.746 0.531
#> 4 4 0.931 0.886 0.955 0.1104 0.869 0.636
#> 5 5 0.798 0.610 0.773 0.0632 0.946 0.797
#> 6 6 0.760 0.482 0.692 0.0367 0.869 0.503
#> 7 7 0.795 0.657 0.781 0.0261 0.901 0.545
#> 8 8 0.807 0.797 0.826 0.0192 0.931 0.616
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.E5.A2PC.01 2 0.000 0.994 0.00 1.00
#> TCGA.FD.A3N6.01 2 0.000 0.994 0.00 1.00
#> TCGA.GV.A3JW.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZF.A9R3.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.AA6L.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A8HG.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.AA76.01 2 0.000 0.994 0.00 1.00
#> TCGA.KQ.A41O.01 2 0.000 0.994 0.00 1.00
#> TCGA.CF.A47T.01 2 0.000 0.994 0.00 1.00
#> TCGA.HQ.A2OE.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A1AA.01 1 0.000 1.000 1.00 0.00
#> TCGA.XF.AAN1.01 1 0.000 1.000 1.00 0.00
#> TCGA.GC.A3RD.01 2 0.000 0.994 0.00 1.00
#> TCGA.4Z.AA7S.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A1AE.01 1 0.000 1.000 1.00 0.00
#> TCGA.4Z.AA7O.01 1 0.000 1.000 1.00 0.00
#> TCGA.G2.AA3B.01 2 0.000 0.994 0.00 1.00
#> TCGA.UY.A78O.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A5U8.01 1 0.000 1.000 1.00 0.00
#> TCGA.FD.A62O.01 1 0.000 1.000 1.00 0.00
#> TCGA.MV.A51V.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A2I6.01 2 0.000 0.994 0.00 1.00
#> TCGA.FJ.A3ZF.01 2 0.000 0.994 0.00 1.00
#> TCGA.4Z.AA87.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A9SV.01 1 0.000 1.000 1.00 0.00
#> TCGA.GV.A3JX.01 1 0.000 1.000 1.00 0.00
#> TCGA.UY.A9PD.01 2 0.000 0.994 0.00 1.00
#> TCGA.GU.A763.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A5KF.01 1 0.000 1.000 1.00 0.00
#> TCGA.4Z.AA83.01 1 0.000 1.000 1.00 0.00
#> TCGA.CU.A72E.01 2 0.000 0.994 0.00 1.00
#> TCGA.G2.A2EL.01 2 0.000 0.994 0.00 1.00
#> TCGA.BT.A3PH.01 2 0.000 0.994 0.00 1.00
#> TCGA.FD.A6TH.01 1 0.000 1.000 1.00 0.00
#> TCGA.2F.A9KR.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZF.AA4U.01 2 0.000 0.994 0.00 1.00
#> TCGA.ZF.A9RE.01 2 0.000 0.994 0.00 1.00
#> TCGA.GC.A3RB.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.AAMF.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A3MH.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A1AD.01 2 0.000 0.994 0.00 1.00
#> TCGA.CF.A8HX.01 2 0.000 0.994 0.00 1.00
#> TCGA.C4.A0F6.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.AAMQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A27C.01 1 0.000 1.000 1.00 0.00
#> TCGA.BL.A0C8.01 2 0.000 0.994 0.00 1.00
#> TCGA.G2.A3VY.01 2 0.000 0.994 0.00 1.00
#> TCGA.YF.AA3M.01 1 0.000 1.000 1.00 0.00
#> TCGA.UY.A78N.01 1 0.000 1.000 1.00 0.00
#> TCGA.G2.AA3F.01 1 0.000 1.000 1.00 0.00
#> TCGA.K4.A6MB.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.AAN7.01 2 0.000 0.994 0.00 1.00
#> TCGA.KQ.A41R.01 2 0.000 0.994 0.00 1.00
#> TCGA.GC.A3BM.01 2 0.000 0.994 0.00 1.00
#> TCGA.CF.A7I0.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A4IJ.01 2 0.000 0.994 0.00 1.00
#> TCGA.FD.A5BV.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A3IL.01 1 0.000 1.000 1.00 0.00
#> TCGA.FD.A43X.01 1 0.000 1.000 1.00 0.00
#> TCGA.4Z.AA7Y.01 1 0.000 1.000 1.00 0.00
#> TCGA.KQ.A41Q.01 2 0.000 0.994 0.00 1.00
#> TCGA.GU.AATQ.01 2 0.000 0.994 0.00 1.00
#> TCGA.FD.A6TE.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A3MG.01 1 0.000 1.000 1.00 0.00
#> TCGA.UY.A8OB.01 2 0.000 0.994 0.00 1.00
#> TCGA.GD.A3OQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A47X.01 2 0.000 0.994 0.00 1.00
#> TCGA.ZF.A9R4.01 1 0.000 1.000 1.00 0.00
#> TCGA.FJ.A3ZE.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.AA75.01 2 0.000 0.994 0.00 1.00
#> TCGA.GV.A3JZ.01 2 0.000 0.994 0.00 1.00
#> TCGA.4Z.AA89.01 1 0.000 1.000 1.00 0.00
#> TCGA.GD.A6C6.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A8HI.01 1 0.000 1.000 1.00 0.00
#> TCGA.2F.A9KQ.01 2 0.000 0.994 0.00 1.00
#> TCGA.G2.A3IB.01 1 0.000 1.000 1.00 0.00
#> TCGA.CU.A3KJ.01 2 0.000 0.994 0.00 1.00
#> TCGA.YF.AA3L.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A1A6.01 1 0.000 1.000 1.00 0.00
#> TCGA.K4.A4AB.01 2 0.000 0.994 0.00 1.00
#> TCGA.4Z.AA7M.01 2 0.000 0.994 0.00 1.00
#> TCGA.CF.A9FF.01 1 0.000 1.000 1.00 0.00
#> TCGA.LT.A8JT.01 1 0.000 1.000 1.00 0.00
#> TCGA.XF.AAML.01 1 0.000 1.000 1.00 0.00
#> TCGA.5N.A9KM.01 1 0.000 1.000 1.00 0.00
#> TCGA.4Z.AA7R.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A3IS.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.AA6P.01 1 0.141 0.979 0.98 0.02
#> TCGA.E5.A4TZ.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A7PW.01 1 0.000 1.000 1.00 0.00
#> TCGA.GV.A6ZA.01 2 0.000 0.994 0.00 1.00
#> TCGA.FD.A43N.01 2 0.000 0.994 0.00 1.00
#> TCGA.FD.A3B5.01 2 0.000 0.994 0.00 1.00
#> TCGA.4Z.AA80.01 2 0.000 0.994 0.00 1.00
#> TCGA.CF.A3MF.01 1 0.000 1.000 1.00 0.00
#> TCGA.E7.A7DU.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A6B1.01 2 0.000 0.994 0.00 1.00
#> TCGA.5N.A9KI.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A9FL.01 2 0.000 0.994 0.00 1.00
#> TCGA.S5.AA26.01 2 0.995 0.147 0.46 0.54
#> TCGA.E5.A4U1.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A5KE.01 2 0.000 0.994 0.00 1.00
#> TCGA.GV.A40G.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A8HY.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A3MI.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZF.A9RL.01 1 0.000 1.000 1.00 0.00
#> TCGA.HQ.A5ND.01 2 0.000 0.994 0.00 1.00
#> TCGA.BT.A42C.01 1 0.000 1.000 1.00 0.00
#> TCGA.E7.A8O8.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A9T0.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A6AW.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZF.A9R5.01 1 0.000 1.000 1.00 0.00
#> TCGA.2F.A9KP.01 2 0.000 0.994 0.00 1.00
#> TCGA.GU.A42P.01 2 0.000 0.994 0.00 1.00
#> TCGA.KQ.A41N.01 2 0.000 0.994 0.00 1.00
#> TCGA.ZF.A9R2.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A8HC.01 1 0.000 1.000 1.00 0.00
#> TCGA.XF.AAMG.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A9T6.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A1AG.01 1 0.000 1.000 1.00 0.00
#> TCGA.E7.A3Y1.01 1 0.000 1.000 1.00 0.00
#> TCGA.XF.A8HF.01 2 0.000 0.994 0.00 1.00
#> TCGA.CU.A3QU.01 1 0.000 1.000 1.00 0.00
#> TCGA.KQ.A41P.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A9T2.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.AA6U.01 2 0.000 0.994 0.00 1.00
#> TCGA.UY.A78M.01 2 0.000 0.994 0.00 1.00
#> TCGA.H4.A2HQ.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A4XJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.E7.A678.01 1 0.000 1.000 1.00 0.00
#> TCGA.K4.A5RI.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.AA77.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A97Q.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.AAMX.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A9SH.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A3X2.01 2 0.000 0.994 0.00 1.00
#> TCGA.ZF.A9RN.01 1 0.000 1.000 1.00 0.00
#> TCGA.FJ.A3Z9.01 1 0.000 1.000 1.00 0.00
#> TCGA.E7.A677.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A9FH.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.E5.A2PC.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.FD.A3N6.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.GV.A3JW.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.ZF.A9R3.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.AA6L.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.A8HG.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.DK.AA76.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.KQ.A41O.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.CF.A47T.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.HQ.A2OE.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.DK.A1AA.01 3 0.0892 0.9700 0.02 0.00 0.98
#> TCGA.XF.AAN1.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.GC.A3RD.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.4Z.AA7S.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.A1AE.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.4Z.AA7O.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.G2.AA3B.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.UY.A78O.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A5U8.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.MV.A51V.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.DK.A2I6.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.FJ.A3ZF.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.4Z.AA87.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.A9SV.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.GV.A3JX.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.UY.A9PD.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.GU.A763.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.E7.A5KF.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.4Z.AA83.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CU.A72E.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.G2.A2EL.01 2 0.0892 0.9803 0.00 0.98 0.02
#> TCGA.BT.A3PH.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.FD.A6TH.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.2F.A9KR.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.ZF.AA4U.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.ZF.A9RE.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.GC.A3RB.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.AAMF.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A3MH.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.A1AD.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.CF.A8HX.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.C4.A0F6.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.AAMQ.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A27C.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.BL.A0C8.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.G2.A3VY.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.YF.AA3M.01 3 0.5216 0.6583 0.26 0.00 0.74
#> TCGA.UY.A78N.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.G2.AA3F.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.K4.A6MB.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.AAN7.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.KQ.A41R.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.GC.A3BM.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.CF.A7I0.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.E7.A4IJ.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.FD.A5BV.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.DK.A3IL.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.FD.A43X.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.4Z.AA7Y.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.KQ.A41Q.01 3 0.0892 0.9687 0.00 0.02 0.98
#> TCGA.GU.AATQ.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.FD.A6TE.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A3MG.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.UY.A8OB.01 2 0.0892 0.9803 0.00 0.98 0.02
#> TCGA.GD.A3OQ.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A47X.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.ZF.A9R4.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.FJ.A3ZE.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.AA75.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.GV.A3JZ.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.4Z.AA89.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.GD.A6C6.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.XF.A8HI.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.2F.A9KQ.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.G2.A3IB.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.CU.A3KJ.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.YF.AA3L.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.A1A6.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.K4.A4AB.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.4Z.AA7M.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.CF.A9FF.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.LT.A8JT.01 3 0.2959 0.8912 0.10 0.00 0.90
#> TCGA.XF.AAML.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.5N.A9KM.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.4Z.AA7R.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.DK.A3IS.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.DK.AA6P.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.E5.A4TZ.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.E7.A7PW.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.GV.A6ZA.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.FD.A43N.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.FD.A3B5.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.4Z.AA80.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.CF.A3MF.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.A6B1.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.5N.A9KI.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.CF.A9FL.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.S5.AA26.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.E5.A4U1.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.E7.A5KE.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.GV.A40G.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A8HY.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.HQ.A5ND.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.BT.A42C.01 3 0.2959 0.8912 0.10 0.00 0.90
#> TCGA.E7.A8O8.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.XF.A9T0.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.DK.A6AW.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.ZF.A9R5.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.2F.A9KP.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.GU.A42P.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.KQ.A41N.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.ZF.A9R2.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.XF.A8HC.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.XF.AAMG.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.A9T6.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.A1AG.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.E7.A3Y1.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.XF.A8HF.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.CU.A3QU.01 3 0.2066 0.9330 0.06 0.00 0.94
#> TCGA.KQ.A41P.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.A9T2.01 1 0.6302 0.0422 0.52 0.00 0.48
#> TCGA.DK.AA6U.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.UY.A78M.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.H4.A2HQ.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.E7.A4XJ.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.E7.A678.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.K4.A5RI.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.DK.AA77.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.E7.A97Q.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.XF.AAMX.01 2 0.0000 0.9992 0.00 1.00 0.00
#> TCGA.XF.A9SH.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.DK.A3X2.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.ZF.A9RN.01 3 0.0000 0.9862 0.00 0.00 1.00
#> TCGA.FJ.A3Z9.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.E7.A677.01 1 0.0000 0.9897 1.00 0.00 0.00
#> TCGA.CF.A9FH.01 1 0.0000 0.9897 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.E5.A2PC.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FD.A3N6.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.GV.A3JW.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R3.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.DK.AA6L.01 3 0.4624 0.4870 0.00 0.34 0.66 0.00
#> TCGA.XF.A8HG.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.DK.AA76.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.KQ.A41O.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CF.A47T.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.HQ.A2OE.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DK.A1AA.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.XF.AAN1.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.GC.A3RD.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.4Z.AA7S.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.DK.A1AE.01 4 0.4522 0.4499 0.00 0.00 0.32 0.68
#> TCGA.4Z.AA7O.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.G2.AA3B.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.CF.A5U8.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.MV.A51V.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DK.A2I6.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FJ.A3ZF.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA87.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SV.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.UY.A9PD.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.GU.A763.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.E7.A5KF.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.CU.A72E.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.G2.A2EL.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.BT.A3PH.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TH.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.2F.A9KR.01 4 0.3400 0.7236 0.00 0.00 0.18 0.82
#> TCGA.ZF.AA4U.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9RE.01 3 0.5000 0.0315 0.00 0.50 0.50 0.00
#> TCGA.GC.A3RB.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.XF.AAMF.01 1 0.5000 0.0538 0.50 0.00 0.00 0.50
#> TCGA.CF.A3MH.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.DK.A1AD.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CF.A8HX.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.C4.A0F6.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.XF.AAMQ.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.CF.A27C.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.BL.A0C8.01 3 0.3801 0.7131 0.00 0.00 0.78 0.22
#> TCGA.G2.A3VY.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.YF.AA3M.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.UY.A78N.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.G2.AA3F.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.K4.A6MB.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN7.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.KQ.A41R.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.GC.A3BM.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.CF.A7I0.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E7.A4IJ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FD.A5BV.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IL.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.4Z.AA7Y.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.GU.AATQ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TE.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.CF.A3MG.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.UY.A8OB.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.GD.A3OQ.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.ZF.A9R4.01 1 0.0707 0.9231 0.98 0.00 0.00 0.02
#> TCGA.FJ.A3ZE.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.DK.AA75.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.GV.A3JZ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA89.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.GD.A6C6.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.XF.A8HI.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.2F.A9KQ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.G2.A3IB.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.CU.A3KJ.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.YF.AA3L.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.K4.A4AB.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7M.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CF.A9FF.01 1 0.1211 0.9051 0.96 0.00 0.00 0.04
#> TCGA.LT.A8JT.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.XF.AAML.01 1 0.4855 0.3580 0.60 0.00 0.00 0.40
#> TCGA.5N.A9KM.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.4Z.AA7R.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IS.01 3 0.4713 0.4446 0.00 0.36 0.64 0.00
#> TCGA.DK.AA6P.01 3 0.4977 0.2171 0.00 0.00 0.54 0.46
#> TCGA.E5.A4TZ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E7.A7PW.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.GV.A6ZA.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FD.A43N.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FD.A3B5.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.4Z.AA80.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CF.A3MF.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.DK.A6B1.01 3 0.3801 0.7131 0.00 0.00 0.78 0.22
#> TCGA.5N.A9KI.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.CF.A9FL.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S5.AA26.01 3 0.3975 0.6870 0.00 0.00 0.76 0.24
#> TCGA.E5.A4U1.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.E7.A5KE.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.GV.A40G.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.CF.A8HY.01 1 0.4713 0.4479 0.64 0.00 0.00 0.36
#> TCGA.CF.A3MI.01 4 0.3975 0.6493 0.24 0.00 0.00 0.76
#> TCGA.ZF.A9RL.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.BT.A42C.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.E7.A8O8.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.XF.A9T0.01 3 0.1211 0.8652 0.00 0.04 0.96 0.00
#> TCGA.DK.A6AW.01 1 0.4948 0.2497 0.56 0.00 0.00 0.44
#> TCGA.ZF.A9R5.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.2F.A9KP.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.GU.A42P.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.KQ.A41N.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9R2.01 3 0.3801 0.7131 0.00 0.00 0.78 0.22
#> TCGA.XF.A8HC.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMG.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.XF.A9T6.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.DK.A1AG.01 4 0.3801 0.6830 0.22 0.00 0.00 0.78
#> TCGA.E7.A3Y1.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.XF.A8HF.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CU.A3QU.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.KQ.A41P.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.XF.A9T2.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.DK.AA6U.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.UY.A78M.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.H4.A2HQ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E7.A4XJ.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.K4.A5RI.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.DK.AA77.01 3 0.0707 0.8852 0.00 0.00 0.98 0.02
#> TCGA.E7.A97Q.01 3 0.0000 0.8971 0.00 0.00 1.00 0.00
#> TCGA.XF.AAMX.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.3975 0.6493 0.24 0.00 0.00 0.76
#> TCGA.DK.A3X2.01 3 0.3801 0.7131 0.00 0.00 0.78 0.22
#> TCGA.ZF.A9RN.01 4 0.0000 0.9337 0.00 0.00 0.00 1.00
#> TCGA.FJ.A3Z9.01 1 0.5000 0.0538 0.50 0.00 0.00 0.50
#> TCGA.E7.A677.01 1 0.0000 0.9394 1.00 0.00 0.00 0.00
#> TCGA.CF.A9FH.01 1 0.0000 0.9394 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.E5.A2PC.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A3N6.01 5 0.4307 -0.2957 0.00 0.00 0.50 0.00 0.50
#> TCGA.GV.A3JW.01 1 0.1043 0.6048 0.96 0.00 0.00 0.00 0.04
#> TCGA.ZF.A9R3.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.DK.AA6L.01 3 0.1410 0.4443 0.00 0.06 0.94 0.00 0.00
#> TCGA.XF.A8HG.01 3 0.4287 0.2996 0.00 0.00 0.54 0.00 0.46
#> TCGA.DK.AA76.01 2 0.4060 0.7222 0.00 0.64 0.36 0.00 0.00
#> TCGA.KQ.A41O.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 3 0.4307 0.1997 0.00 0.00 0.50 0.00 0.50
#> TCGA.HQ.A2OE.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A1AA.01 4 0.0000 0.8056 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAN1.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.GC.A3RD.01 3 0.4060 0.4808 0.00 0.00 0.64 0.00 0.36
#> TCGA.4Z.AA7S.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.DK.A1AE.01 5 0.5157 0.2986 0.00 0.00 0.04 0.44 0.52
#> TCGA.4Z.AA7O.01 4 0.0609 0.8022 0.00 0.00 0.00 0.98 0.02
#> TCGA.G2.AA3B.01 3 0.4262 0.3434 0.00 0.00 0.56 0.00 0.44
#> TCGA.UY.A78O.01 1 0.4302 0.7637 0.52 0.00 0.00 0.00 0.48
#> TCGA.CF.A5U8.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.MV.A51V.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A2I6.01 2 0.4262 0.6286 0.00 0.56 0.44 0.00 0.00
#> TCGA.FJ.A3ZF.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA87.01 2 0.4182 0.6795 0.00 0.60 0.40 0.00 0.00
#> TCGA.XF.A9SV.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.GV.A3JX.01 4 0.2020 0.8019 0.00 0.00 0.00 0.90 0.10
#> TCGA.UY.A9PD.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 5 0.5447 -0.1624 0.00 0.00 0.44 0.06 0.50
#> TCGA.E7.A5KF.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.CU.A72E.01 2 0.3983 0.7400 0.00 0.66 0.34 0.00 0.00
#> TCGA.G2.A2EL.01 3 0.0000 0.4893 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A3PH.01 2 0.2929 0.8151 0.00 0.82 0.18 0.00 0.00
#> TCGA.FD.A6TH.01 1 0.4227 0.7986 0.58 0.00 0.00 0.00 0.42
#> TCGA.2F.A9KR.01 4 0.5131 -0.1719 0.00 0.00 0.04 0.54 0.42
#> TCGA.ZF.AA4U.01 2 0.3895 0.7545 0.00 0.68 0.32 0.00 0.00
#> TCGA.ZF.A9RE.01 3 0.1410 0.4443 0.00 0.06 0.94 0.00 0.00
#> TCGA.GC.A3RB.01 2 0.3983 0.7400 0.00 0.66 0.34 0.00 0.00
#> TCGA.XF.AAMF.01 4 0.6054 0.5914 0.28 0.00 0.00 0.56 0.16
#> TCGA.CF.A3MH.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AD.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 3 0.4060 0.4808 0.00 0.00 0.64 0.00 0.36
#> TCGA.C4.A0F6.01 2 0.3895 0.7545 0.00 0.68 0.32 0.00 0.00
#> TCGA.XF.AAMQ.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.CF.A27C.01 4 0.0000 0.8056 0.00 0.00 0.00 1.00 0.00
#> TCGA.BL.A0C8.01 5 0.6102 0.1707 0.00 0.00 0.34 0.14 0.52
#> TCGA.G2.A3VY.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 4 0.2020 0.8019 0.00 0.00 0.00 0.90 0.10
#> TCGA.UY.A78N.01 1 0.4287 0.7775 0.54 0.00 0.00 0.00 0.46
#> TCGA.G2.AA3F.01 4 0.2020 0.8019 0.00 0.00 0.00 0.90 0.10
#> TCGA.K4.A6MB.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN7.01 2 0.0609 0.8591 0.00 0.98 0.02 0.00 0.00
#> TCGA.KQ.A41R.01 2 0.1732 0.8472 0.00 0.92 0.08 0.00 0.00
#> TCGA.GC.A3BM.01 3 0.4307 0.1997 0.00 0.00 0.50 0.00 0.50
#> TCGA.CF.A7I0.01 2 0.3983 0.7400 0.00 0.66 0.34 0.00 0.00
#> TCGA.E7.A4IJ.01 2 0.0609 0.8591 0.00 0.98 0.02 0.00 0.00
#> TCGA.FD.A5BV.01 2 0.4307 0.5348 0.00 0.50 0.50 0.00 0.00
#> TCGA.DK.A3IL.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.FD.A43X.01 4 0.0000 0.8056 0.00 0.00 0.00 1.00 0.00
#> TCGA.4Z.AA7Y.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.KQ.A41Q.01 3 0.1732 0.5142 0.00 0.00 0.92 0.00 0.08
#> TCGA.GU.AATQ.01 2 0.3895 0.7545 0.00 0.68 0.32 0.00 0.00
#> TCGA.FD.A6TE.01 1 0.4227 0.7986 0.58 0.00 0.00 0.00 0.42
#> TCGA.CF.A3MG.01 1 0.1043 0.6596 0.96 0.00 0.00 0.00 0.04
#> TCGA.UY.A8OB.01 3 0.0000 0.4893 0.00 0.00 1.00 0.00 0.00
#> TCGA.GD.A3OQ.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.CF.A47X.01 3 0.3983 0.5005 0.00 0.00 0.66 0.00 0.34
#> TCGA.ZF.A9R4.01 5 0.6047 -0.6811 0.40 0.00 0.00 0.12 0.48
#> TCGA.FJ.A3ZE.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA75.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA89.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A6C6.01 3 0.2280 0.5162 0.00 0.00 0.88 0.00 0.12
#> TCGA.XF.A8HI.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KQ.01 2 0.3895 0.7545 0.00 0.68 0.32 0.00 0.00
#> TCGA.G2.A3IB.01 4 0.2020 0.7315 0.00 0.00 0.00 0.90 0.10
#> TCGA.CU.A3KJ.01 5 0.4307 -0.2957 0.00 0.00 0.50 0.00 0.50
#> TCGA.YF.AA3L.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.DK.A1A6.01 4 0.2020 0.8019 0.00 0.00 0.00 0.90 0.10
#> TCGA.K4.A4AB.01 2 0.3895 0.7545 0.00 0.68 0.32 0.00 0.00
#> TCGA.4Z.AA7M.01 2 0.3796 0.7651 0.00 0.70 0.30 0.00 0.00
#> TCGA.CF.A9FF.01 1 0.3922 0.2884 0.78 0.00 0.00 0.18 0.04
#> TCGA.LT.A8JT.01 4 0.0000 0.8056 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAML.01 5 0.5895 -0.3522 0.10 0.00 0.00 0.44 0.46
#> TCGA.5N.A9KM.01 4 0.0609 0.8022 0.00 0.00 0.00 0.98 0.02
#> TCGA.4Z.AA7R.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IS.01 3 0.1043 0.4612 0.00 0.04 0.96 0.00 0.00
#> TCGA.DK.AA6P.01 5 0.5425 0.3111 0.00 0.00 0.06 0.42 0.52
#> TCGA.E5.A4TZ.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.GV.A6ZA.01 2 0.1732 0.8472 0.00 0.92 0.08 0.00 0.00
#> TCGA.FD.A43N.01 3 0.4307 -0.5640 0.00 0.50 0.50 0.00 0.00
#> TCGA.FD.A3B5.01 3 0.3983 0.5005 0.00 0.00 0.66 0.00 0.34
#> TCGA.4Z.AA80.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A3MF.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.E7.A7DU.01 4 0.5095 0.5732 0.40 0.00 0.00 0.56 0.04
#> TCGA.DK.A6B1.01 5 0.6327 0.2445 0.00 0.00 0.28 0.20 0.52
#> TCGA.5N.A9KI.01 4 0.1043 0.8046 0.00 0.00 0.00 0.96 0.04
#> TCGA.CF.A9FL.01 2 0.3796 0.7651 0.00 0.70 0.30 0.00 0.00
#> TCGA.S5.AA26.01 5 0.6275 0.3004 0.00 0.00 0.18 0.30 0.52
#> TCGA.E5.A4U1.01 3 0.4307 0.1997 0.00 0.00 0.50 0.00 0.50
#> TCGA.E7.A5KE.01 2 0.1732 0.8472 0.00 0.92 0.08 0.00 0.00
#> TCGA.GV.A40G.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.CF.A8HY.01 1 0.4921 -0.1803 0.62 0.00 0.00 0.34 0.04
#> TCGA.CF.A3MI.01 4 0.5394 0.5714 0.40 0.00 0.00 0.54 0.06
#> TCGA.ZF.A9RL.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.HQ.A5ND.01 3 0.3983 0.5005 0.00 0.00 0.66 0.00 0.34
#> TCGA.BT.A42C.01 4 0.2020 0.8019 0.00 0.00 0.00 0.90 0.10
#> TCGA.E7.A8O8.01 3 0.4060 0.4808 0.00 0.00 0.64 0.00 0.36
#> TCGA.XF.A9T0.01 3 0.0000 0.4893 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A6AW.01 1 0.5673 -0.4357 0.50 0.00 0.00 0.42 0.08
#> TCGA.ZF.A9R5.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KP.01 3 0.3895 0.5063 0.00 0.00 0.68 0.00 0.32
#> TCGA.GU.A42P.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.KQ.A41N.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R2.01 5 0.5828 0.0897 0.00 0.00 0.38 0.10 0.52
#> TCGA.XF.A8HC.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.XF.AAMG.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T6.01 1 0.4829 0.7485 0.50 0.00 0.00 0.02 0.48
#> TCGA.DK.A1AG.01 4 0.5498 0.6062 0.34 0.00 0.00 0.58 0.08
#> TCGA.E7.A3Y1.01 4 0.0000 0.8056 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.A8HF.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 4 0.2020 0.8019 0.00 0.00 0.00 0.90 0.10
#> TCGA.KQ.A41P.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 4 0.0609 0.8033 0.02 0.00 0.00 0.98 0.00
#> TCGA.DK.AA6U.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 3 0.3895 0.5063 0.00 0.00 0.68 0.00 0.32
#> TCGA.H4.A2HQ.01 2 0.0000 0.8616 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.E7.A678.01 1 0.0000 0.6379 1.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RI.01 3 0.3983 0.5005 0.00 0.00 0.66 0.00 0.34
#> TCGA.DK.AA77.01 3 0.4307 0.1997 0.00 0.00 0.50 0.00 0.50
#> TCGA.E7.A97Q.01 3 0.1732 0.5142 0.00 0.00 0.92 0.00 0.08
#> TCGA.XF.AAMX.01 2 0.4302 0.5682 0.00 0.52 0.48 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.5394 0.5714 0.40 0.00 0.00 0.54 0.06
#> TCGA.DK.A3X2.01 5 0.5828 0.0897 0.00 0.00 0.38 0.10 0.52
#> TCGA.ZF.A9RN.01 4 0.0609 0.8022 0.00 0.00 0.00 0.98 0.02
#> TCGA.FJ.A3Z9.01 4 0.5689 0.5131 0.44 0.00 0.00 0.48 0.08
#> TCGA.E7.A677.01 1 0.4182 0.8088 0.60 0.00 0.00 0.00 0.40
#> TCGA.CF.A9FH.01 1 0.4182 0.8088 0.60 0.00 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.E5.A2PC.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3N6.01 3 0.2793 0.66183 0.00 0.00 0.80 0.20 0.00 0.00
#> TCGA.GV.A3JW.01 5 0.3828 0.17307 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.ZF.A9R3.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6L.01 6 0.3873 0.46504 0.00 0.04 0.16 0.00 0.02 0.78
#> TCGA.XF.A8HG.01 3 0.3045 0.67638 0.00 0.00 0.84 0.06 0.00 0.10
#> TCGA.DK.AA76.01 6 0.3797 0.26009 0.00 0.42 0.00 0.00 0.00 0.58
#> TCGA.KQ.A41O.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 3 0.1267 0.68184 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.HQ.A2OE.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AA.01 5 0.6319 -0.60045 0.00 0.00 0.02 0.36 0.42 0.20
#> TCGA.XF.AAN1.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RD.01 3 0.3460 0.63296 0.00 0.00 0.76 0.02 0.00 0.22
#> TCGA.4Z.AA7S.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AE.01 4 0.6319 -0.14615 0.00 0.00 0.36 0.42 0.02 0.20
#> TCGA.4Z.AA7O.01 4 0.6228 0.57753 0.00 0.00 0.02 0.44 0.36 0.18
#> TCGA.G2.AA3B.01 3 0.3795 0.67176 0.00 0.00 0.80 0.06 0.02 0.12
#> TCGA.UY.A78O.01 1 0.3270 0.70484 0.82 0.00 0.00 0.12 0.06 0.00
#> TCGA.CF.A5U8.01 5 0.3851 0.14888 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MV.A51V.01 2 0.0547 0.77273 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DK.A2I6.01 6 0.3409 0.49407 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.FJ.A3ZF.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA87.01 6 0.3409 0.49407 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.XF.A9SV.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 4 0.3797 0.59915 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.UY.A9PD.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 3 0.5684 0.35301 0.00 0.00 0.52 0.28 0.00 0.20
#> TCGA.E7.A5KF.01 5 0.3864 0.09516 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.4Z.AA83.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A72E.01 6 0.3828 0.20594 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.G2.A2EL.01 6 0.4246 -0.00282 0.00 0.00 0.40 0.02 0.00 0.58
#> TCGA.BT.A3PH.01 2 0.4806 0.22373 0.00 0.56 0.00 0.06 0.00 0.38
#> TCGA.FD.A6TH.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KR.01 4 0.6471 0.04645 0.00 0.00 0.28 0.48 0.04 0.20
#> TCGA.ZF.AA4U.01 2 0.4902 -0.03346 0.00 0.48 0.00 0.06 0.00 0.46
#> TCGA.ZF.A9RE.01 6 0.3351 0.47784 0.00 0.04 0.16 0.00 0.00 0.80
#> TCGA.GC.A3RB.01 6 0.4328 0.11111 0.00 0.46 0.00 0.02 0.00 0.52
#> TCGA.XF.AAMF.01 5 0.4534 -0.27451 0.04 0.00 0.00 0.38 0.58 0.00
#> TCGA.CF.A3MH.01 5 0.3864 0.09516 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.DK.A1AD.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 3 0.2631 0.64707 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.C4.A0F6.01 2 0.4902 -0.03346 0.00 0.48 0.00 0.06 0.00 0.46
#> TCGA.XF.AAMQ.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A27C.01 5 0.6331 -0.59264 0.00 0.00 0.02 0.38 0.40 0.20
#> TCGA.BL.A0C8.01 3 0.3309 0.60733 0.00 0.00 0.72 0.28 0.00 0.00
#> TCGA.G2.A3VY.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 4 0.3797 0.59915 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.UY.A78N.01 1 0.2190 0.80456 0.90 0.00 0.00 0.06 0.04 0.00
#> TCGA.G2.AA3F.01 4 0.3797 0.59915 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.K4.A6MB.01 2 0.0937 0.76146 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.XF.AAN7.01 2 0.3982 0.57216 0.00 0.74 0.00 0.06 0.00 0.20
#> TCGA.KQ.A41R.01 2 0.4360 0.49454 0.00 0.68 0.00 0.06 0.00 0.26
#> TCGA.GC.A3BM.01 3 0.2631 0.66334 0.00 0.00 0.82 0.18 0.00 0.00
#> TCGA.CF.A7I0.01 6 0.3828 0.20594 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.E7.A4IJ.01 2 0.2941 0.60624 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.FD.A5BV.01 6 0.4495 0.56961 0.00 0.20 0.00 0.06 0.02 0.72
#> TCGA.DK.A3IL.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 4 0.6319 0.56785 0.00 0.00 0.02 0.42 0.36 0.20
#> TCGA.4Z.AA7Y.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 3 0.4310 0.34864 0.00 0.00 0.54 0.00 0.02 0.44
#> TCGA.GU.AATQ.01 2 0.4902 -0.03346 0.00 0.48 0.00 0.06 0.00 0.46
#> TCGA.FD.A6TE.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MG.01 1 0.3797 0.10887 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.UY.A8OB.01 6 0.4864 0.30305 0.00 0.00 0.26 0.06 0.02 0.66
#> TCGA.GD.A3OQ.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 3 0.3309 0.59910 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.ZF.A9R4.01 1 0.5292 0.29581 0.60 0.00 0.00 0.22 0.18 0.00
#> TCGA.FJ.A3ZE.01 5 0.3869 0.03519 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.DK.AA75.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA89.01 5 0.3851 0.14888 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.GD.A6C6.01 3 0.4609 0.34810 0.00 0.00 0.54 0.04 0.00 0.42
#> TCGA.XF.A8HI.01 1 0.3869 -0.11315 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.2F.A9KQ.01 2 0.4902 -0.03346 0.00 0.48 0.00 0.06 0.00 0.46
#> TCGA.G2.A3IB.01 4 0.6373 0.42547 0.00 0.00 0.08 0.56 0.16 0.20
#> TCGA.CU.A3KJ.01 3 0.2631 0.66334 0.00 0.00 0.82 0.18 0.00 0.00
#> TCGA.YF.AA3L.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.01 4 0.3828 0.59562 0.00 0.00 0.00 0.56 0.44 0.00
#> TCGA.K4.A4AB.01 2 0.4902 -0.03346 0.00 0.48 0.00 0.06 0.00 0.46
#> TCGA.4Z.AA7M.01 6 0.3864 0.05536 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.CF.A9FF.01 5 0.2793 0.41213 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.LT.A8JT.01 4 0.5586 0.59687 0.00 0.00 0.00 0.44 0.42 0.14
#> TCGA.XF.AAML.01 5 0.6039 -0.19204 0.28 0.00 0.00 0.30 0.42 0.00
#> TCGA.5N.A9KM.01 4 0.5791 0.58806 0.00 0.00 0.00 0.44 0.38 0.18
#> TCGA.4Z.AA7R.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IS.01 6 0.4971 0.13747 0.00 0.04 0.36 0.02 0.00 0.58
#> TCGA.DK.AA6P.01 3 0.5618 0.36151 0.00 0.00 0.50 0.34 0.00 0.16
#> TCGA.E5.A4TZ.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A6ZA.01 2 0.4360 0.49454 0.00 0.68 0.00 0.06 0.00 0.26
#> TCGA.FD.A43N.01 6 0.2793 0.57720 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.FD.A3B5.01 3 0.3309 0.59910 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.4Z.AA80.01 2 0.0547 0.77273 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CF.A3MF.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 5 0.0937 0.21339 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.DK.A6B1.01 3 0.3309 0.60733 0.00 0.00 0.72 0.28 0.00 0.00
#> TCGA.5N.A9KI.01 4 0.4689 0.61236 0.00 0.00 0.02 0.58 0.38 0.02
#> TCGA.CF.A9FL.01 2 0.4902 -0.03346 0.00 0.48 0.00 0.06 0.00 0.46
#> TCGA.S5.AA26.01 3 0.5202 0.45240 0.00 0.00 0.60 0.26 0.00 0.14
#> TCGA.E5.A4U1.01 3 0.2631 0.66899 0.00 0.00 0.82 0.18 0.00 0.00
#> TCGA.E7.A5KE.01 2 0.4360 0.49454 0.00 0.68 0.00 0.06 0.00 0.26
#> TCGA.GV.A40G.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HY.01 5 0.1814 0.34698 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.CF.A3MI.01 5 0.0547 0.26124 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 3 0.3309 0.59910 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.BT.A42C.01 4 0.3797 0.59915 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.E7.A8O8.01 3 0.2631 0.64707 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.XF.A9T0.01 6 0.4576 -0.01217 0.00 0.00 0.40 0.04 0.00 0.56
#> TCGA.DK.A6AW.01 5 0.4121 0.11668 0.06 0.00 0.00 0.22 0.72 0.00
#> TCGA.ZF.A9R5.01 5 0.3851 0.14888 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.2F.A9KP.01 3 0.3198 0.60938 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.GU.A42P.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41N.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R2.01 3 0.4002 0.58792 0.00 0.00 0.66 0.32 0.00 0.02
#> TCGA.XF.A8HC.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMG.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T6.01 1 0.4475 0.51595 0.70 0.00 0.00 0.20 0.10 0.00
#> TCGA.DK.A1AG.01 5 0.4002 -0.21019 0.02 0.00 0.00 0.32 0.66 0.00
#> TCGA.E7.A3Y1.01 5 0.6331 -0.59264 0.00 0.00 0.02 0.38 0.40 0.20
#> TCGA.XF.A8HF.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 4 0.3797 0.59915 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.KQ.A41P.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 5 0.5802 -0.60402 0.00 0.00 0.00 0.40 0.42 0.18
#> TCGA.DK.AA6U.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 3 0.3578 0.53369 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.H4.A2HQ.01 2 0.0000 0.78128 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 5 0.3851 0.14888 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.K4.A5RI.01 3 0.3309 0.59910 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.DK.AA77.01 3 0.4608 0.57522 0.00 0.00 0.68 0.22 0.00 0.10
#> TCGA.E7.A97Q.01 3 0.4337 0.23576 0.00 0.00 0.50 0.02 0.00 0.48
#> TCGA.XF.AAMX.01 6 0.4495 0.56961 0.00 0.20 0.00 0.06 0.02 0.72
#> TCGA.XF.A9SH.01 5 0.0547 0.26124 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DK.A3X2.01 3 0.3916 0.60221 0.00 0.00 0.68 0.30 0.00 0.02
#> TCGA.ZF.A9RN.01 4 0.6245 0.58525 0.00 0.00 0.02 0.42 0.38 0.18
#> TCGA.FJ.A3Z9.01 5 0.3821 0.06434 0.04 0.00 0.00 0.22 0.74 0.00
#> TCGA.E7.A677.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A9FH.01 1 0.0000 0.90381 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E5.A2PC.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3N6.01 3 0.1363 0.8255 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.GV.A3JW.01 5 0.3606 0.7996 0.30 0.00 0.00 0.00 0.68 0.00 0.02
#> TCGA.ZF.A9R3.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6L.01 6 0.3770 0.5163 0.00 0.00 0.00 0.00 0.18 0.74 0.08
#> TCGA.XF.A8HG.01 3 0.2864 0.7459 0.00 0.00 0.84 0.00 0.02 0.12 0.02
#> TCGA.DK.AA76.01 2 0.6367 0.4513 0.00 0.40 0.00 0.00 0.24 0.30 0.06
#> TCGA.KQ.A41O.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 3 0.5362 0.1520 0.00 0.00 0.52 0.02 0.04 0.38 0.04
#> TCGA.HQ.A2OE.01 2 0.0504 0.7493 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.A1AA.01 4 0.1363 0.7670 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.XF.AAN1.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RD.01 6 0.4328 0.3643 0.00 0.00 0.34 0.00 0.00 0.60 0.06
#> TCGA.4Z.AA7S.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AE.01 4 0.4623 0.4462 0.00 0.00 0.28 0.64 0.04 0.00 0.04
#> TCGA.4Z.AA7O.01 4 0.1166 0.7589 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.G2.AA3B.01 3 0.1886 0.7700 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.UY.A78O.01 1 0.3413 0.3007 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.CF.A5U8.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MV.A51V.01 2 0.1166 0.7423 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DK.A2I6.01 6 0.5755 0.2562 0.00 0.16 0.00 0.00 0.18 0.58 0.08
#> TCGA.FJ.A3ZF.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA87.01 6 0.6166 0.0102 0.00 0.24 0.00 0.00 0.18 0.50 0.08
#> TCGA.XF.A9SV.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 7 0.3047 0.7073 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.UY.A9PD.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 4 0.6393 -0.1162 0.00 0.00 0.38 0.42 0.04 0.12 0.04
#> TCGA.E7.A5KF.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.4Z.AA83.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A72E.01 2 0.6308 0.4736 0.00 0.42 0.00 0.00 0.22 0.30 0.06
#> TCGA.G2.A2EL.01 6 0.2509 0.5362 0.00 0.00 0.02 0.00 0.04 0.88 0.06
#> TCGA.BT.A3PH.01 2 0.6329 0.5650 0.00 0.50 0.00 0.00 0.20 0.18 0.12
#> TCGA.FD.A6TH.01 1 0.0863 0.9078 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.2F.A9KR.01 4 0.3680 0.6414 0.00 0.00 0.14 0.78 0.02 0.00 0.06
#> TCGA.ZF.AA4U.01 2 0.6406 0.5141 0.00 0.44 0.00 0.00 0.22 0.26 0.08
#> TCGA.ZF.A9RE.01 6 0.3770 0.5163 0.00 0.00 0.00 0.00 0.18 0.74 0.08
#> TCGA.GC.A3RB.01 2 0.6284 0.5141 0.00 0.44 0.00 0.00 0.26 0.24 0.06
#> TCGA.XF.AAMF.01 7 0.4908 0.7027 0.04 0.00 0.00 0.20 0.10 0.00 0.66
#> TCGA.CF.A3MH.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.DK.A1AD.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 6 0.4408 0.2005 0.00 0.00 0.44 0.00 0.02 0.52 0.02
#> TCGA.C4.A0F6.01 2 0.6512 0.5147 0.00 0.44 0.00 0.00 0.22 0.24 0.10
#> TCGA.XF.AAMQ.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A27C.01 4 0.1363 0.7670 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.BL.A0C8.01 3 0.2654 0.8192 0.00 0.00 0.86 0.00 0.02 0.02 0.10
#> TCGA.G2.A3VY.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 7 0.3047 0.7073 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.UY.A78N.01 1 0.3047 0.5584 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.G2.AA3F.01 7 0.3139 0.6975 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.K4.A6MB.01 2 0.1166 0.7423 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.XF.AAN7.01 2 0.5001 0.6649 0.00 0.68 0.00 0.00 0.12 0.08 0.12
#> TCGA.KQ.A41R.01 2 0.5575 0.6304 0.00 0.60 0.00 0.00 0.20 0.08 0.12
#> TCGA.GC.A3BM.01 3 0.1363 0.8255 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.CF.A7I0.01 2 0.6337 0.4394 0.00 0.40 0.00 0.00 0.22 0.32 0.06
#> TCGA.E7.A4IJ.01 2 0.4635 0.6725 0.00 0.70 0.00 0.00 0.16 0.10 0.04
#> TCGA.FD.A5BV.01 6 0.5106 0.4621 0.00 0.06 0.00 0.00 0.14 0.66 0.14
#> TCGA.DK.A3IL.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 4 0.0504 0.7686 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.4Z.AA7Y.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 6 0.3606 0.4462 0.00 0.00 0.30 0.00 0.00 0.68 0.02
#> TCGA.GU.AATQ.01 2 0.6284 0.5121 0.00 0.44 0.00 0.00 0.24 0.26 0.06
#> TCGA.FD.A6TE.01 1 0.0863 0.9078 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CF.A3MG.01 5 0.3562 0.4693 0.50 0.00 0.00 0.00 0.50 0.00 0.00
#> TCGA.UY.A8OB.01 6 0.4045 0.5130 0.00 0.00 0.00 0.00 0.14 0.72 0.14
#> TCGA.GD.A3OQ.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 6 0.3867 0.3674 0.00 0.00 0.38 0.00 0.00 0.60 0.02
#> TCGA.ZF.A9R4.01 7 0.4070 0.4935 0.34 0.00 0.00 0.04 0.00 0.00 0.62
#> TCGA.FJ.A3ZE.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.DK.AA75.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA89.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.GD.A6C6.01 6 0.4092 0.4699 0.00 0.00 0.16 0.00 0.02 0.74 0.08
#> TCGA.XF.A8HI.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.2F.A9KQ.01 2 0.6406 0.5141 0.00 0.44 0.00 0.00 0.22 0.26 0.08
#> TCGA.G2.A3IB.01 4 0.1433 0.7247 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.CU.A3KJ.01 3 0.2213 0.8302 0.00 0.00 0.90 0.00 0.02 0.04 0.04
#> TCGA.YF.AA3L.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.01 7 0.3139 0.6975 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.K4.A4AB.01 2 0.6284 0.5121 0.00 0.44 0.00 0.00 0.24 0.26 0.06
#> TCGA.4Z.AA7M.01 2 0.6284 0.5121 0.00 0.44 0.00 0.00 0.24 0.26 0.06
#> TCGA.CF.A9FF.01 5 0.5448 0.5973 0.10 0.00 0.02 0.08 0.66 0.00 0.14
#> TCGA.LT.A8JT.01 4 0.1886 0.7055 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.XF.AAML.01 7 0.4502 0.6542 0.16 0.00 0.00 0.18 0.00 0.00 0.66
#> TCGA.5N.A9KM.01 4 0.1433 0.7468 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.4Z.AA7R.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IS.01 6 0.1363 0.5445 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.DK.AA6P.01 3 0.4824 0.5989 0.00 0.00 0.68 0.16 0.04 0.00 0.12
#> TCGA.E5.A4TZ.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A6ZA.01 2 0.5575 0.6304 0.00 0.60 0.00 0.00 0.20 0.08 0.12
#> TCGA.FD.A43N.01 6 0.4569 0.4872 0.00 0.04 0.00 0.00 0.18 0.70 0.08
#> TCGA.FD.A3B5.01 6 0.3867 0.3674 0.00 0.00 0.38 0.00 0.00 0.60 0.02
#> TCGA.4Z.AA80.01 2 0.0504 0.7493 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CF.A3MF.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 5 0.4146 0.4330 0.00 0.00 0.02 0.32 0.64 0.00 0.02
#> TCGA.DK.A6B1.01 3 0.2654 0.8192 0.00 0.00 0.86 0.00 0.02 0.02 0.10
#> TCGA.5N.A9KI.01 4 0.4425 -0.2395 0.00 0.00 0.02 0.48 0.02 0.00 0.48
#> TCGA.CF.A9FL.01 2 0.6284 0.5121 0.00 0.44 0.00 0.00 0.24 0.26 0.06
#> TCGA.S5.AA26.01 3 0.1363 0.8235 0.00 0.00 0.94 0.04 0.02 0.00 0.00
#> TCGA.E5.A4U1.01 3 0.1166 0.8199 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.E7.A5KE.01 2 0.5575 0.6304 0.00 0.60 0.00 0.00 0.20 0.08 0.12
#> TCGA.GV.A40G.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HY.01 5 0.5401 0.5517 0.06 0.00 0.02 0.14 0.66 0.00 0.12
#> TCGA.CF.A3MI.01 5 0.4812 0.4594 0.00 0.00 0.02 0.18 0.66 0.00 0.14
#> TCGA.ZF.A9RL.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 6 0.3755 0.4139 0.00 0.00 0.34 0.00 0.00 0.64 0.02
#> TCGA.BT.A42C.01 7 0.3047 0.7073 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.E7.A8O8.01 6 0.4408 0.2005 0.00 0.00 0.44 0.00 0.02 0.52 0.02
#> TCGA.XF.A9T0.01 6 0.2313 0.5374 0.00 0.00 0.00 0.00 0.06 0.88 0.06
#> TCGA.DK.A6AW.01 7 0.5512 0.5081 0.02 0.00 0.02 0.10 0.30 0.00 0.56
#> TCGA.ZF.A9R5.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.2F.A9KP.01 6 0.3755 0.4139 0.00 0.00 0.34 0.00 0.00 0.64 0.02
#> TCGA.GU.A42P.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41N.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R2.01 3 0.3485 0.7966 0.00 0.00 0.82 0.04 0.02 0.02 0.10
#> TCGA.XF.A8HC.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMG.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T6.01 7 0.3459 0.3476 0.40 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.DK.A1AG.01 7 0.5526 0.6095 0.00 0.00 0.02 0.24 0.20 0.00 0.54
#> TCGA.E7.A3Y1.01 4 0.1363 0.7670 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.XF.A8HF.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 7 0.3047 0.7073 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.KQ.A41P.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 4 0.1363 0.7540 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.DK.AA6U.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 6 0.3755 0.4139 0.00 0.00 0.34 0.00 0.00 0.64 0.02
#> TCGA.H4.A2HQ.01 2 0.0000 0.7513 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 5 0.3221 0.8053 0.32 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.K4.A5RI.01 6 0.3755 0.4139 0.00 0.00 0.34 0.00 0.00 0.64 0.02
#> TCGA.DK.AA77.01 3 0.3630 0.7738 0.00 0.00 0.80 0.10 0.04 0.00 0.06
#> TCGA.E7.A97Q.01 6 0.2803 0.5216 0.00 0.00 0.10 0.00 0.00 0.84 0.06
#> TCGA.XF.AAMX.01 6 0.6005 0.2904 0.00 0.14 0.00 0.00 0.16 0.56 0.14
#> TCGA.XF.A9SH.01 5 0.4825 0.4500 0.00 0.00 0.02 0.16 0.66 0.00 0.16
#> TCGA.DK.A3X2.01 3 0.2654 0.8192 0.00 0.00 0.86 0.00 0.02 0.02 0.10
#> TCGA.ZF.A9RN.01 4 0.0863 0.7627 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.FJ.A3Z9.01 7 0.5625 0.5027 0.00 0.00 0.02 0.18 0.30 0.00 0.50
#> TCGA.E7.A677.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A9FH.01 1 0.0000 0.9526 1.00 0.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E5.A2PC.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.FD.A3N6.01 3 0.3426 0.862 0.00 0.00 0.74 0.02 0.02 0.22 0.00 0.00
#> TCGA.GV.A3JW.01 5 0.3728 0.818 0.28 0.02 0.00 0.00 0.68 0.00 0.02 0.00
#> TCGA.ZF.A9R3.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6L.01 8 0.3036 0.672 0.00 0.00 0.00 0.00 0.04 0.18 0.00 0.78
#> TCGA.XF.A8HG.01 3 0.4233 0.755 0.00 0.00 0.60 0.04 0.02 0.34 0.00 0.00
#> TCGA.DK.AA76.01 8 0.0471 0.824 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.KQ.A41O.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CF.A47T.01 6 0.4046 0.475 0.00 0.06 0.16 0.02 0.02 0.74 0.00 0.00
#> TCGA.HQ.A2OE.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.DK.A1AA.01 4 0.3291 0.741 0.00 0.00 0.00 0.70 0.02 0.00 0.28 0.00
#> TCGA.XF.AAN1.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RD.01 6 0.0471 0.803 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.4Z.AA7S.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AE.01 4 0.4975 0.437 0.00 0.06 0.22 0.64 0.06 0.02 0.00 0.00
#> TCGA.4Z.AA7O.01 4 0.4415 0.713 0.00 0.06 0.02 0.60 0.00 0.00 0.32 0.00
#> TCGA.G2.AA3B.01 3 0.3015 0.800 0.00 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.UY.A78O.01 1 0.3291 0.540 0.70 0.00 0.02 0.00 0.00 0.00 0.28 0.00
#> TCGA.CF.A5U8.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MV.A51V.01 2 0.2719 0.977 0.00 0.80 0.00 0.02 0.00 0.00 0.00 0.18
#> TCGA.DK.A2I6.01 8 0.2404 0.727 0.00 0.00 0.00 0.00 0.02 0.14 0.00 0.84
#> TCGA.FJ.A3ZF.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.4Z.AA87.01 8 0.2025 0.764 0.00 0.00 0.00 0.00 0.02 0.10 0.00 0.88
#> TCGA.XF.A9SV.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 7 0.0471 0.759 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.UY.A9PD.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.GU.A763.01 4 0.6112 0.245 0.00 0.06 0.10 0.50 0.06 0.28 0.00 0.00
#> TCGA.E7.A5KF.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A72E.01 8 0.0471 0.824 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.G2.A2EL.01 6 0.5563 0.653 0.00 0.00 0.08 0.04 0.12 0.62 0.00 0.14
#> TCGA.BT.A3PH.01 8 0.2407 0.784 0.00 0.06 0.00 0.08 0.00 0.00 0.00 0.86
#> TCGA.FD.A6TH.01 1 0.0471 0.954 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KR.01 4 0.5398 0.568 0.00 0.06 0.16 0.66 0.04 0.04 0.04 0.00
#> TCGA.ZF.AA4U.01 8 0.0941 0.821 0.00 0.02 0.00 0.02 0.00 0.00 0.00 0.96
#> TCGA.ZF.A9RE.01 8 0.2719 0.678 0.00 0.00 0.00 0.00 0.02 0.18 0.00 0.80
#> TCGA.GC.A3RB.01 8 0.3021 0.751 0.00 0.02 0.00 0.02 0.16 0.00 0.00 0.80
#> TCGA.XF.AAMF.01 7 0.1408 0.754 0.02 0.00 0.02 0.00 0.02 0.00 0.94 0.00
#> TCGA.CF.A3MH.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.DK.A1AD.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CF.A8HX.01 6 0.1741 0.772 0.00 0.00 0.02 0.04 0.02 0.92 0.00 0.00
#> TCGA.C4.A0F6.01 8 0.1275 0.818 0.00 0.02 0.00 0.04 0.00 0.00 0.00 0.94
#> TCGA.XF.AAMQ.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A27C.01 4 0.3291 0.741 0.00 0.00 0.00 0.70 0.02 0.00 0.28 0.00
#> TCGA.BL.A0C8.01 3 0.2719 0.858 0.00 0.00 0.80 0.00 0.00 0.18 0.02 0.00
#> TCGA.G2.A3VY.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.YF.AA3M.01 7 0.0941 0.749 0.00 0.00 0.02 0.02 0.00 0.00 0.96 0.00
#> TCGA.UY.A78N.01 1 0.2224 0.805 0.86 0.00 0.02 0.00 0.00 0.00 0.12 0.00
#> TCGA.G2.AA3F.01 7 0.0471 0.759 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.K4.A6MB.01 2 0.2406 0.974 0.00 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.XF.AAN7.01 8 0.4199 0.306 0.00 0.32 0.00 0.08 0.00 0.00 0.00 0.60
#> TCGA.KQ.A41R.01 8 0.2994 0.705 0.00 0.14 0.00 0.06 0.00 0.00 0.00 0.80
#> TCGA.GC.A3BM.01 3 0.2981 0.865 0.00 0.00 0.76 0.00 0.02 0.22 0.00 0.00
#> TCGA.CF.A7I0.01 8 0.0471 0.824 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.E7.A4IJ.01 8 0.3083 0.314 0.00 0.34 0.00 0.00 0.00 0.00 0.00 0.66
#> TCGA.FD.A5BV.01 8 0.3744 0.657 0.00 0.00 0.00 0.06 0.02 0.18 0.00 0.74
#> TCGA.DK.A3IL.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 4 0.2756 0.749 0.00 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.4Z.AA7Y.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 6 0.1741 0.806 0.00 0.00 0.00 0.02 0.02 0.92 0.00 0.04
#> TCGA.GU.AATQ.01 8 0.0471 0.824 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.FD.A6TE.01 1 0.0471 0.954 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MG.01 5 0.3318 0.525 0.46 0.00 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.UY.A8OB.01 8 0.4097 0.618 0.00 0.00 0.00 0.08 0.02 0.20 0.00 0.70
#> TCGA.GD.A3OQ.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 6 0.0471 0.820 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZF.A9R4.01 7 0.2856 0.628 0.20 0.00 0.02 0.00 0.00 0.00 0.78 0.00
#> TCGA.FJ.A3ZE.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.DK.AA75.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.GV.A3JZ.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.4Z.AA89.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.GD.A6C6.01 6 0.5660 0.632 0.00 0.00 0.10 0.06 0.22 0.58 0.00 0.04
#> TCGA.XF.A8HI.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.2F.A9KQ.01 8 0.0941 0.821 0.00 0.02 0.00 0.02 0.00 0.00 0.00 0.96
#> TCGA.G2.A3IB.01 4 0.4680 0.703 0.00 0.08 0.12 0.68 0.00 0.00 0.12 0.00
#> TCGA.CU.A3KJ.01 3 0.2406 0.866 0.00 0.00 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.YF.AA3L.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.01 7 0.0808 0.742 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.K4.A4AB.01 8 0.0471 0.824 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.4Z.AA7M.01 8 0.0941 0.822 0.00 0.02 0.00 0.00 0.02 0.00 0.00 0.96
#> TCGA.CF.A9FF.01 5 0.4779 0.736 0.18 0.02 0.02 0.00 0.66 0.00 0.12 0.00
#> TCGA.LT.A8JT.01 4 0.3907 0.658 0.00 0.04 0.00 0.58 0.00 0.00 0.38 0.00
#> TCGA.XF.AAML.01 7 0.2404 0.687 0.14 0.00 0.02 0.00 0.00 0.00 0.84 0.00
#> TCGA.5N.A9KM.01 4 0.4673 0.690 0.00 0.08 0.02 0.56 0.00 0.00 0.34 0.00
#> TCGA.4Z.AA7R.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.DK.A3IS.01 6 0.5132 0.671 0.00 0.00 0.08 0.04 0.06 0.66 0.00 0.16
#> TCGA.DK.AA6P.01 3 0.4734 0.659 0.00 0.04 0.70 0.14 0.04 0.08 0.00 0.00
#> TCGA.E5.A4TZ.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.E7.A7PW.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A6ZA.01 8 0.2994 0.705 0.00 0.14 0.00 0.06 0.00 0.00 0.00 0.80
#> TCGA.FD.A43N.01 8 0.2719 0.678 0.00 0.00 0.00 0.00 0.02 0.18 0.00 0.80
#> TCGA.FD.A3B5.01 6 0.0471 0.820 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.4Z.AA80.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CF.A3MF.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 5 0.5049 0.466 0.00 0.02 0.02 0.20 0.62 0.00 0.14 0.00
#> TCGA.DK.A6B1.01 3 0.3169 0.856 0.00 0.02 0.78 0.00 0.00 0.18 0.02 0.00
#> TCGA.5N.A9KI.01 7 0.2224 0.614 0.00 0.00 0.02 0.12 0.00 0.00 0.86 0.00
#> TCGA.CF.A9FL.01 8 0.0471 0.824 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.S5.AA26.01 3 0.4363 0.841 0.00 0.04 0.70 0.04 0.02 0.20 0.00 0.00
#> TCGA.E5.A4U1.01 3 0.2756 0.843 0.00 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.E7.A5KE.01 8 0.2994 0.705 0.00 0.14 0.00 0.06 0.00 0.00 0.00 0.80
#> TCGA.GV.A40G.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A8HY.01 5 0.5156 0.624 0.06 0.02 0.02 0.10 0.68 0.00 0.12 0.00
#> TCGA.CF.A3MI.01 5 0.4934 0.505 0.00 0.02 0.02 0.14 0.64 0.00 0.18 0.00
#> TCGA.ZF.A9RL.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HQ.A5ND.01 6 0.0471 0.820 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BT.A42C.01 7 0.0941 0.749 0.00 0.00 0.02 0.02 0.00 0.00 0.96 0.00
#> TCGA.E7.A8O8.01 6 0.1741 0.772 0.00 0.00 0.02 0.04 0.02 0.92 0.00 0.00
#> TCGA.XF.A9T0.01 6 0.6408 0.564 0.00 0.00 0.08 0.06 0.20 0.50 0.00 0.16
#> TCGA.DK.A6AW.01 7 0.4280 0.579 0.00 0.02 0.04 0.02 0.24 0.00 0.68 0.00
#> TCGA.ZF.A9R5.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.2F.A9KP.01 6 0.0471 0.820 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.GU.A42P.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.KQ.A41N.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.ZF.A9R2.01 3 0.3616 0.843 0.00 0.00 0.76 0.02 0.02 0.18 0.02 0.00
#> TCGA.XF.A8HC.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMG.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.XF.A9T6.01 7 0.3618 0.368 0.38 0.00 0.02 0.00 0.00 0.00 0.60 0.00
#> TCGA.DK.A1AG.01 7 0.3627 0.657 0.00 0.02 0.04 0.02 0.14 0.00 0.78 0.00
#> TCGA.E7.A3Y1.01 4 0.3291 0.741 0.00 0.00 0.00 0.70 0.02 0.00 0.28 0.00
#> TCGA.XF.A8HF.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CU.A3QU.01 7 0.1408 0.748 0.00 0.02 0.02 0.02 0.00 0.00 0.94 0.00
#> TCGA.KQ.A41P.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.XF.A9T2.01 4 0.4700 0.717 0.00 0.08 0.04 0.62 0.00 0.00 0.26 0.00
#> TCGA.DK.AA6U.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.UY.A78M.01 6 0.0471 0.820 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.H4.A2HQ.01 2 0.2267 0.998 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.E7.A4XJ.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 5 0.2852 0.832 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.K4.A5RI.01 6 0.0471 0.820 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DK.AA77.01 3 0.6106 0.607 0.00 0.04 0.50 0.14 0.06 0.26 0.00 0.00
#> TCGA.E7.A97Q.01 6 0.3319 0.762 0.00 0.00 0.08 0.02 0.02 0.82 0.00 0.06
#> TCGA.XF.AAMX.01 8 0.3830 0.686 0.00 0.00 0.00 0.08 0.02 0.16 0.00 0.74
#> TCGA.XF.A9SH.01 5 0.4934 0.505 0.00 0.02 0.02 0.14 0.64 0.00 0.18 0.00
#> TCGA.DK.A3X2.01 3 0.2719 0.856 0.00 0.00 0.80 0.00 0.00 0.18 0.02 0.00
#> TCGA.ZF.A9RN.01 4 0.4593 0.728 0.00 0.10 0.02 0.62 0.00 0.00 0.26 0.00
#> TCGA.FJ.A3Z9.01 7 0.4581 0.560 0.00 0.04 0.04 0.02 0.24 0.00 0.66 0.00
#> TCGA.E7.A677.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A9FH.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-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 49 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 0.5090 0.491 0.491
#> 3 3 0.936 0.973 0.984 0.2842 0.798 0.610
#> 4 4 0.880 0.834 0.928 0.1223 0.865 0.634
#> 5 5 0.842 0.739 0.842 0.0570 0.947 0.809
#> 6 6 0.781 0.704 0.855 0.0292 0.918 0.684
#> 7 7 0.832 0.643 0.839 0.0198 0.988 0.941
#> 8 8 0.817 0.594 0.785 0.0191 0.949 0.765
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.GV.A3JW.01 1 0 1 1 0
#> TCGA.ZF.A9R3.01 1 0 1 1 0
#> TCGA.XF.AAN1.01 2 0 1 0 1
#> TCGA.4Z.AA7S.01 2 0 1 0 1
#> TCGA.UY.A78O.01 2 0 1 0 1
#> TCGA.CF.A5U8.01 1 0 1 1 0
#> TCGA.FD.A62O.01 2 0 1 0 1
#> TCGA.XF.A9SV.01 2 0 1 0 1
#> TCGA.GV.A3JX.01 2 0 1 0 1
#> TCGA.E7.A5KF.01 1 0 1 1 0
#> TCGA.4Z.AA83.01 2 0 1 0 1
#> TCGA.FD.A6TH.01 2 0 1 0 1
#> TCGA.XF.AAMF.01 2 0 1 0 1
#> TCGA.CF.A3MH.01 1 0 1 1 0
#> TCGA.XF.AAMQ.01 2 0 1 0 1
#> TCGA.UY.A78N.01 2 0 1 0 1
#> TCGA.G2.AA3F.01 2 0 1 0 1
#> TCGA.DK.A3IL.01 2 0 1 0 1
#> TCGA.4Z.AA7Y.01 1 0 1 1 0
#> TCGA.FD.A6TE.01 2 0 1 0 1
#> TCGA.CF.A3MG.01 1 0 1 1 0
#> TCGA.GD.A3OQ.01 2 0 1 0 1
#> TCGA.ZF.A9R4.01 2 0 1 0 1
#> TCGA.FJ.A3ZE.01 1 0 1 1 0
#> TCGA.4Z.AA89.01 1 0 1 1 0
#> TCGA.XF.A8HI.01 1 0 1 1 0
#> TCGA.YF.AA3L.01 2 0 1 0 1
#> TCGA.DK.A1A6.01 2 0 1 0 1
#> TCGA.CF.A9FF.01 1 0 1 1 0
#> TCGA.XF.AAML.01 2 0 1 0 1
#> TCGA.E7.A7PW.01 2 0 1 0 1
#> TCGA.CF.A3MF.01 1 0 1 1 0
#> TCGA.E7.A7DU.01 1 0 1 1 0
#> TCGA.GV.A40G.01 2 0 1 0 1
#> TCGA.CF.A8HY.01 1 0 1 1 0
#> TCGA.CF.A3MI.01 1 0 1 1 0
#> TCGA.ZF.A9RL.01 1 0 1 1 0
#> TCGA.DK.A6AW.01 2 0 1 0 1
#> TCGA.ZF.A9R5.01 1 0 1 1 0
#> TCGA.XF.A8HC.01 2 0 1 0 1
#> TCGA.XF.A9T6.01 2 0 1 0 1
#> TCGA.DK.A1AG.01 1 0 1 1 0
#> TCGA.XF.A9T2.01 1 0 1 1 0
#> TCGA.E7.A4XJ.01 2 0 1 0 1
#> TCGA.E7.A678.01 1 0 1 1 0
#> TCGA.XF.A9SH.01 1 0 1 1 0
#> TCGA.FJ.A3Z9.01 1 0 1 1 0
#> TCGA.E7.A677.01 2 0 1 0 1
#> TCGA.CF.A9FH.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GV.A3JW.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.ZF.A9R3.01 3 0.000 0.925 0.00 0.00 1.00
#> TCGA.XF.AAN1.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.4Z.AA7S.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.UY.A78O.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CF.A5U8.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.FD.A62O.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.XF.A9SV.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.GV.A3JX.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E7.A5KF.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.4Z.AA83.01 3 0.000 0.925 0.00 0.00 1.00
#> TCGA.FD.A6TH.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.XF.AAMF.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CF.A3MH.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.XF.AAMQ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.UY.A78N.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.G2.AA3F.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DK.A3IL.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.4Z.AA7Y.01 3 0.369 0.872 0.14 0.00 0.86
#> TCGA.FD.A6TE.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CF.A3MG.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.GD.A3OQ.01 3 0.153 0.907 0.00 0.04 0.96
#> TCGA.ZF.A9R4.01 3 0.000 0.925 0.00 0.00 1.00
#> TCGA.FJ.A3ZE.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.4Z.AA89.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.XF.A8HI.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.YF.AA3L.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DK.A1A6.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CF.A9FF.01 3 0.000 0.925 0.00 0.00 1.00
#> TCGA.XF.AAML.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E7.A7PW.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CF.A3MF.01 3 0.369 0.872 0.14 0.00 0.86
#> TCGA.E7.A7DU.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.GV.A40G.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CF.A8HY.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.ZF.A9RL.01 3 0.369 0.872 0.14 0.00 0.86
#> TCGA.DK.A6AW.01 3 0.000 0.925 0.00 0.00 1.00
#> TCGA.ZF.A9R5.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.XF.A8HC.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.XF.A9T6.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DK.A1AG.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.XF.A9T2.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.E7.A4XJ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E7.A678.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.XF.A9SH.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.FJ.A3Z9.01 1 0.207 0.932 0.94 0.00 0.06
#> TCGA.E7.A677.01 3 0.153 0.907 0.00 0.04 0.96
#> TCGA.CF.A9FH.01 3 0.480 0.778 0.22 0.00 0.78
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GV.A3JW.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R3.01 3 0.4277 0.6510 0.00 0.00 0.72 0.28
#> TCGA.XF.AAN1.01 4 0.5062 0.6188 0.00 0.30 0.02 0.68
#> TCGA.4Z.AA7S.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.UY.A78O.01 2 0.0707 0.9206 0.00 0.98 0.02 0.00
#> TCGA.CF.A5U8.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SV.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.E7.A5KF.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 4 0.1637 0.7556 0.00 0.00 0.06 0.94
#> TCGA.FD.A6TH.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.XF.AAMF.01 2 0.5535 0.0712 0.00 0.56 0.02 0.42
#> TCGA.CF.A3MH.01 3 0.3801 0.7248 0.22 0.00 0.78 0.00
#> TCGA.XF.AAMQ.01 4 0.4936 0.6438 0.00 0.28 0.02 0.70
#> TCGA.UY.A78N.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.G2.AA3F.01 2 0.0707 0.9206 0.00 0.98 0.02 0.00
#> TCGA.DK.A3IL.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7Y.01 3 0.0707 0.8579 0.02 0.00 0.98 0.00
#> TCGA.FD.A6TE.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.CF.A3MG.01 3 0.3801 0.7248 0.22 0.00 0.78 0.00
#> TCGA.GD.A3OQ.01 4 0.0707 0.7814 0.00 0.00 0.02 0.98
#> TCGA.ZF.A9R4.01 4 0.0707 0.7814 0.00 0.00 0.02 0.98
#> TCGA.FJ.A3ZE.01 1 0.4277 0.5665 0.72 0.00 0.28 0.00
#> TCGA.4Z.AA89.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.XF.A8HI.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.YF.AA3L.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.DK.A1A6.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.CF.A9FF.01 3 0.4277 0.6510 0.00 0.00 0.72 0.28
#> TCGA.XF.AAML.01 2 0.0707 0.9206 0.00 0.98 0.02 0.00
#> TCGA.E7.A7PW.01 4 0.5062 0.6188 0.00 0.30 0.02 0.68
#> TCGA.CF.A3MF.01 3 0.0707 0.8579 0.02 0.00 0.98 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.CF.A8HY.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9RL.01 3 0.0707 0.8579 0.02 0.00 0.98 0.00
#> TCGA.DK.A6AW.01 4 0.1637 0.7417 0.00 0.00 0.06 0.94
#> TCGA.ZF.A9R5.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.XF.A8HC.01 2 0.0707 0.9206 0.00 0.98 0.02 0.00
#> TCGA.XF.A9T6.01 2 0.5594 -0.0821 0.00 0.52 0.02 0.46
#> TCGA.DK.A1AG.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 2 0.0000 0.9303 0.00 1.00 0.00 0.00
#> TCGA.E7.A678.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 1 0.0000 0.9760 1.00 0.00 0.00 0.00
#> TCGA.FJ.A3Z9.01 3 0.1211 0.8511 0.04 0.00 0.96 0.00
#> TCGA.E7.A677.01 4 0.0707 0.7814 0.00 0.00 0.02 0.98
#> TCGA.CF.A9FH.01 3 0.0707 0.8579 0.02 0.00 0.98 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GV.A3JW.01 1 0.1043 0.9389 0.96 0.00 0.00 0.00 0.04
#> TCGA.ZF.A9R3.01 5 0.6459 1.0000 0.00 0.00 0.40 0.18 0.42
#> TCGA.XF.AAN1.01 4 0.5425 0.5658 0.00 0.08 0.00 0.60 0.32
#> TCGA.4Z.AA7S.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.UY.A78O.01 2 0.4456 0.5751 0.00 0.66 0.00 0.02 0.32
#> TCGA.CF.A5U8.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SV.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A5KF.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 4 0.4227 -0.2052 0.00 0.00 0.00 0.58 0.42
#> TCGA.FD.A6TH.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMF.01 4 0.6816 0.2613 0.00 0.32 0.00 0.36 0.32
#> TCGA.CF.A3MH.01 3 0.2797 0.7080 0.06 0.00 0.88 0.00 0.06
#> TCGA.XF.AAMQ.01 4 0.5156 0.5624 0.00 0.06 0.00 0.62 0.32
#> TCGA.UY.A78N.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.G2.AA3F.01 2 0.3895 0.6044 0.00 0.68 0.00 0.00 0.32
#> TCGA.DK.A3IL.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7Y.01 3 0.2732 0.7222 0.00 0.00 0.84 0.00 0.16
#> TCGA.FD.A6TE.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A3MG.01 3 0.3110 0.7031 0.06 0.00 0.86 0.00 0.08
#> TCGA.GD.A3OQ.01 4 0.0000 0.4191 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.A9R4.01 4 0.3684 0.1109 0.00 0.00 0.00 0.72 0.28
#> TCGA.FJ.A3ZE.01 1 0.5579 0.3969 0.60 0.00 0.30 0.00 0.10
#> TCGA.4Z.AA89.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HI.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.YF.AA3L.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A9FF.01 5 0.6459 1.0000 0.00 0.00 0.40 0.18 0.42
#> TCGA.XF.AAML.01 2 0.3796 0.6291 0.00 0.70 0.00 0.00 0.30
#> TCGA.E7.A7PW.01 4 0.5425 0.5658 0.00 0.08 0.00 0.60 0.32
#> TCGA.CF.A3MF.01 3 0.2732 0.7222 0.00 0.00 0.84 0.00 0.16
#> TCGA.E7.A7DU.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A8HY.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RL.01 3 0.0609 0.7730 0.00 0.00 0.98 0.00 0.02
#> TCGA.DK.A6AW.01 4 0.4227 -0.0416 0.00 0.00 0.00 0.58 0.42
#> TCGA.ZF.A9R5.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HC.01 2 0.5156 0.5042 0.00 0.62 0.00 0.06 0.32
#> TCGA.XF.A9T6.01 4 0.6555 0.4654 0.00 0.22 0.00 0.46 0.32
#> TCGA.DK.A1AG.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T2.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 2 0.0000 0.8955 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 1 0.0000 0.9635 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 1 0.1043 0.9389 0.96 0.00 0.00 0.00 0.04
#> TCGA.FJ.A3Z9.01 3 0.0609 0.7730 0.00 0.00 0.98 0.00 0.02
#> TCGA.E7.A677.01 4 0.1043 0.4479 0.00 0.00 0.00 0.96 0.04
#> TCGA.CF.A9FH.01 3 0.2732 0.7222 0.00 0.00 0.84 0.00 0.16
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GV.A3JW.01 1 0.1814 0.8954 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.ZF.A9R3.01 3 0.4165 0.6018 0.00 0.00 0.74 0.00 0.10 0.16
#> TCGA.XF.AAN1.01 4 0.4631 0.0169 0.00 0.06 0.00 0.62 0.00 0.32
#> TCGA.4Z.AA7S.01 2 0.1556 0.8592 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.UY.A78O.01 2 0.3797 0.1091 0.00 0.58 0.00 0.42 0.00 0.00
#> TCGA.CF.A5U8.01 1 0.0000 0.9465 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 2 0.1556 0.8592 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.XF.A9SV.01 2 0.1556 0.8592 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.0937 0.8520 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.E7.A5KF.01 1 0.0000 0.9465 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 6 0.3483 0.5309 0.00 0.00 0.12 0.04 0.02 0.82
#> TCGA.FD.A6TH.01 2 0.0937 0.8520 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.XF.AAMF.01 4 0.1814 0.5710 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CF.A3MH.01 3 0.5394 0.7182 0.06 0.00 0.72 0.04 0.08 0.10
#> TCGA.XF.AAMQ.01 4 0.4631 0.0169 0.00 0.06 0.00 0.62 0.00 0.32
#> TCGA.UY.A78N.01 2 0.1556 0.8592 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.G2.AA3F.01 4 0.3706 0.3315 0.00 0.38 0.00 0.62 0.00 0.00
#> TCGA.DK.A3IL.01 2 0.2048 0.8335 0.00 0.88 0.00 0.12 0.00 0.00
#> TCGA.4Z.AA7Y.01 3 0.0547 0.7921 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FD.A6TE.01 2 0.3523 0.6435 0.00 0.78 0.00 0.18 0.04 0.00
#> TCGA.CF.A3MG.01 3 0.5343 0.7219 0.06 0.00 0.72 0.04 0.06 0.12
#> TCGA.GD.A3OQ.01 6 0.3409 0.7265 0.00 0.00 0.00 0.30 0.00 0.70
#> TCGA.ZF.A9R4.01 6 0.3985 0.5545 0.00 0.00 0.00 0.14 0.10 0.76
#> TCGA.FJ.A3ZE.01 1 0.6145 0.4746 0.60 0.00 0.22 0.02 0.12 0.04
#> TCGA.4Z.AA89.01 1 0.0547 0.9432 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.XF.A8HI.01 1 0.0547 0.9432 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.YF.AA3L.01 2 0.0937 0.8520 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DK.A1A6.01 2 0.1556 0.8592 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.CF.A9FF.01 3 0.4200 0.5994 0.00 0.00 0.74 0.00 0.12 0.14
#> TCGA.XF.AAML.01 4 0.3756 0.2856 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.E7.A7PW.01 4 0.1807 0.4561 0.00 0.02 0.00 0.92 0.00 0.06
#> TCGA.CF.A3MF.01 3 0.0547 0.7921 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.E7.A7DU.01 1 0.0000 0.9465 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 2 0.0937 0.8520 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.CF.A8HY.01 1 0.0000 0.9465 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0547 0.9432 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.ZF.A9RL.01 3 0.3483 0.7790 0.00 0.00 0.82 0.02 0.04 0.12
#> TCGA.DK.A6AW.01 5 0.3660 0.0000 0.00 0.00 0.00 0.06 0.78 0.16
#> TCGA.ZF.A9R5.01 1 0.0000 0.9465 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HC.01 4 0.4576 0.3701 0.00 0.40 0.00 0.56 0.04 0.00
#> TCGA.XF.A9T6.01 4 0.3258 0.5527 0.00 0.10 0.00 0.84 0.02 0.04
#> TCGA.DK.A1AG.01 1 0.1092 0.9342 0.96 0.00 0.02 0.00 0.02 0.00
#> TCGA.XF.A9T2.01 1 0.0000 0.9465 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 2 0.0937 0.8520 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.E7.A678.01 1 0.0000 0.9465 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 1 0.2048 0.8795 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.FJ.A3Z9.01 3 0.3483 0.7790 0.00 0.00 0.82 0.02 0.04 0.12
#> TCGA.E7.A677.01 6 0.3409 0.7265 0.00 0.00 0.00 0.30 0.00 0.70
#> TCGA.CF.A9FH.01 3 0.0000 0.7954 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GV.A3JW.01 1 0.2864 0.8414 0.84 0.00 0.00 0.02 0.02 0.12 0.00
#> TCGA.ZF.A9R3.01 3 0.2906 0.3811 0.00 0.00 0.80 0.00 0.02 0.00 0.18
#> TCGA.XF.AAN1.01 4 0.5152 0.2943 0.00 0.02 0.00 0.60 0.00 0.24 0.14
#> TCGA.4Z.AA7S.01 2 0.0504 0.8775 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.UY.A78O.01 2 0.4278 -0.1826 0.00 0.50 0.00 0.46 0.00 0.00 0.04
#> TCGA.CF.A5U8.01 1 0.0000 0.9121 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 2 0.0504 0.8775 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.XF.A9SV.01 2 0.0863 0.8673 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.0863 0.8758 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.E7.A5KF.01 1 0.0000 0.9121 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 6 0.4461 0.3969 0.00 0.00 0.32 0.00 0.02 0.62 0.04
#> TCGA.FD.A6TH.01 2 0.0863 0.8758 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.XF.AAMF.01 4 0.1166 0.6345 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CF.A3MH.01 3 0.4684 -0.4693 0.00 0.00 0.52 0.00 0.02 0.04 0.42
#> TCGA.XF.AAMQ.01 4 0.5240 0.2534 0.00 0.02 0.00 0.58 0.00 0.26 0.14
#> TCGA.UY.A78N.01 2 0.0504 0.8775 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.G2.AA3F.01 4 0.3358 0.4469 0.00 0.36 0.00 0.64 0.00 0.00 0.00
#> TCGA.DK.A3IL.01 2 0.2081 0.7785 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.4Z.AA7Y.01 3 0.0000 0.5172 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TE.01 2 0.3637 0.5930 0.00 0.72 0.00 0.24 0.00 0.00 0.04
#> TCGA.CF.A3MG.01 3 0.4266 -0.4924 0.00 0.00 0.52 0.00 0.00 0.04 0.44
#> TCGA.GD.A3OQ.01 6 0.2422 0.7498 0.00 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.ZF.A9R4.01 6 0.4812 0.6994 0.00 0.00 0.00 0.18 0.02 0.66 0.14
#> TCGA.FJ.A3ZE.01 1 0.7588 0.0431 0.38 0.00 0.20 0.02 0.02 0.18 0.20
#> TCGA.4Z.AA89.01 1 0.1363 0.9046 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.XF.A8HI.01 1 0.1363 0.9046 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.YF.AA3L.01 2 0.0863 0.8758 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DK.A1A6.01 2 0.0504 0.8775 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CF.A9FF.01 3 0.2745 0.4030 0.00 0.00 0.82 0.00 0.02 0.00 0.16
#> TCGA.XF.AAML.01 4 0.3358 0.4316 0.00 0.36 0.00 0.64 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 4 0.2159 0.5904 0.00 0.02 0.00 0.90 0.00 0.02 0.06
#> TCGA.CF.A3MF.01 3 0.0000 0.5172 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.9121 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 2 0.0863 0.8758 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CF.A8HY.01 1 0.0000 0.9121 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.1363 0.9046 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.ZF.A9RL.01 7 0.3558 1.0000 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.DK.A6AW.01 5 0.0504 0.0000 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.ZF.A9R5.01 1 0.0000 0.9121 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HC.01 4 0.3307 0.5811 0.00 0.24 0.00 0.74 0.00 0.00 0.02
#> TCGA.XF.A9T6.01 4 0.1718 0.6224 0.00 0.04 0.00 0.92 0.00 0.00 0.04
#> TCGA.DK.A1AG.01 1 0.1363 0.9046 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.XF.A9T2.01 1 0.0000 0.9121 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 2 0.0863 0.8758 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.E7.A678.01 1 0.0000 0.9121 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 1 0.2864 0.8414 0.84 0.00 0.00 0.02 0.02 0.12 0.00
#> TCGA.FJ.A3Z9.01 7 0.3558 1.0000 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.E7.A677.01 6 0.2906 0.7463 0.00 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.CF.A9FH.01 3 0.0000 0.5172 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GV.A3JW.01 1 0.4031 0.6949 0.72 0.00 0.00 0.00 0.02 0.00 0.10 0.16
#> TCGA.ZF.A9R3.01 3 0.5364 0.5714 0.00 0.00 0.60 0.00 0.06 0.24 0.06 0.04
#> TCGA.XF.AAN1.01 4 0.1341 0.5498 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.4Z.AA7S.01 2 0.0000 0.7662 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78O.01 2 0.5032 0.0441 0.00 0.56 0.00 0.26 0.00 0.00 0.02 0.16
#> TCGA.CF.A5U8.01 1 0.0000 0.8932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 2 0.0000 0.7662 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SV.01 2 0.1741 0.7380 0.00 0.92 0.00 0.02 0.00 0.00 0.02 0.04
#> TCGA.GV.A3JX.01 2 0.2025 0.7591 0.00 0.88 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.E7.A5KF.01 1 0.0000 0.8932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA83.01 6 0.4293 0.4118 0.00 0.00 0.20 0.10 0.02 0.68 0.00 0.00
#> TCGA.FD.A6TH.01 2 0.2025 0.7591 0.00 0.88 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.XF.AAMF.01 8 0.4954 0.2945 0.00 0.10 0.00 0.42 0.00 0.00 0.02 0.46
#> TCGA.CF.A3MH.01 7 0.3291 0.6910 0.00 0.00 0.28 0.00 0.00 0.00 0.70 0.02
#> TCGA.XF.AAMQ.01 4 0.2407 0.5495 0.00 0.00 0.00 0.86 0.00 0.08 0.00 0.06
#> TCGA.UY.A78N.01 2 0.0941 0.7556 0.00 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.G2.AA3F.01 2 0.5535 -0.3054 0.00 0.44 0.00 0.36 0.00 0.00 0.04 0.16
#> TCGA.DK.A3IL.01 2 0.2265 0.7286 0.00 0.88 0.00 0.02 0.00 0.00 0.02 0.08
#> TCGA.4Z.AA7Y.01 3 0.0000 0.6911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TE.01 2 0.3374 0.6006 0.00 0.68 0.00 0.02 0.00 0.00 0.00 0.30
#> TCGA.CF.A3MG.01 7 0.2852 0.7018 0.00 0.00 0.28 0.00 0.00 0.00 0.72 0.00
#> TCGA.GD.A3OQ.01 6 0.3237 0.5289 0.00 0.00 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.ZF.A9R4.01 6 0.2348 0.3838 0.00 0.00 0.00 0.02 0.04 0.88 0.00 0.06
#> TCGA.FJ.A3ZE.01 1 0.6856 -0.0794 0.32 0.00 0.16 0.00 0.02 0.00 0.22 0.28
#> TCGA.4Z.AA89.01 1 0.0941 0.8870 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.XF.A8HI.01 1 0.0941 0.8870 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.YF.AA3L.01 2 0.2025 0.7591 0.00 0.88 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.DK.A1A6.01 2 0.0000 0.7662 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A9FF.01 3 0.5125 0.5720 0.00 0.00 0.60 0.00 0.08 0.26 0.04 0.02
#> TCGA.XF.AAML.01 2 0.5622 -0.2040 0.00 0.46 0.00 0.30 0.00 0.00 0.04 0.20
#> TCGA.E7.A7PW.01 4 0.2224 0.3839 0.00 0.00 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.CF.A3MF.01 3 0.0471 0.6764 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E7.A7DU.01 1 0.0000 0.8932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A40G.01 2 0.2025 0.7591 0.00 0.88 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.CF.A8HY.01 1 0.0000 0.8932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MI.01 1 0.0941 0.8870 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.ZF.A9RL.01 7 0.4770 0.6459 0.00 0.00 0.40 0.00 0.04 0.02 0.52 0.02
#> TCGA.DK.A6AW.01 5 0.1091 0.0000 0.00 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.ZF.A9R5.01 1 0.0000 0.8932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HC.01 8 0.4686 0.4818 0.00 0.16 0.00 0.28 0.00 0.00 0.00 0.56
#> TCGA.XF.A9T6.01 4 0.4914 -0.3938 0.00 0.00 0.00 0.42 0.00 0.00 0.16 0.42
#> TCGA.DK.A1AG.01 1 0.0941 0.8870 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.XF.A9T2.01 1 0.0000 0.8932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A4XJ.01 2 0.2025 0.7591 0.00 0.88 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.E7.A678.01 1 0.0000 0.8932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 1 0.4211 0.6729 0.70 0.00 0.00 0.00 0.02 0.00 0.12 0.16
#> TCGA.FJ.A3Z9.01 7 0.4770 0.6459 0.00 0.00 0.40 0.00 0.04 0.02 0.52 0.02
#> TCGA.E7.A677.01 6 0.3690 0.4947 0.00 0.00 0.00 0.42 0.00 0.56 0.00 0.02
#> TCGA.CF.A9FH.01 3 0.0000 0.6911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-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 17 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 0.4417 0.559 0.559
#> 3 3 0.537 0.657 0.815 0.2507 0.956 0.921
#> 4 4 0.706 0.876 0.926 0.2437 0.772 0.569
#> 5 5 0.625 0.733 0.845 0.0605 0.985 0.953
#> 6 6 0.691 0.640 0.826 0.0435 0.934 0.786
#> 7 7 0.765 0.484 0.858 0.0478 0.919 0.686
#> 8 8 0.787 0.516 0.879 0.0319 0.934 0.667
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.GV.A3JW.01 2 0 1 0 1
#> TCGA.CF.A5U8.01 2 0 1 0 1
#> TCGA.E7.A5KF.01 2 0 1 0 1
#> TCGA.CF.A3MH.01 1 0 1 1 0
#> TCGA.CF.A3MG.01 1 0 1 1 0
#> TCGA.FJ.A3ZE.01 2 0 1 0 1
#> TCGA.4Z.AA89.01 2 0 1 0 1
#> TCGA.XF.A8HI.01 2 0 1 0 1
#> TCGA.E7.A7DU.01 2 0 1 0 1
#> TCGA.CF.A8HY.01 2 0 1 0 1
#> TCGA.CF.A3MI.01 1 0 1 1 0
#> TCGA.ZF.A9R5.01 2 0 1 0 1
#> TCGA.DK.A1AG.01 2 0 1 0 1
#> TCGA.XF.A9T2.01 1 0 1 1 0
#> TCGA.E7.A678.01 2 0 1 0 1
#> TCGA.XF.A9SH.01 2 0 1 0 1
#> TCGA.FJ.A3Z9.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GV.A3JW.01 2 0.2959 0.857 0.00 0.90 0.10
#> TCGA.CF.A5U8.01 2 0.2959 0.857 0.00 0.90 0.10
#> TCGA.E7.A5KF.01 2 0.2959 0.857 0.00 0.90 0.10
#> TCGA.CF.A3MH.01 1 0.7633 0.252 0.68 0.20 0.12
#> TCGA.CF.A3MG.01 1 0.0000 0.125 1.00 0.00 0.00
#> TCGA.FJ.A3ZE.01 2 0.5835 0.728 0.00 0.66 0.34
#> TCGA.4Z.AA89.01 2 0.0892 0.839 0.00 0.98 0.02
#> TCGA.XF.A8HI.01 2 0.0000 0.845 0.00 1.00 0.00
#> TCGA.E7.A7DU.01 2 0.2537 0.812 0.00 0.92 0.08
#> TCGA.CF.A8HY.01 2 0.2537 0.812 0.00 0.92 0.08
#> TCGA.CF.A3MI.01 1 0.6309 -0.938 0.50 0.00 0.50
#> TCGA.ZF.A9R5.01 2 0.5835 0.728 0.00 0.66 0.34
#> TCGA.DK.A1AG.01 2 0.2537 0.812 0.00 0.92 0.08
#> TCGA.XF.A9T2.01 3 0.6280 1.000 0.46 0.00 0.54
#> TCGA.E7.A678.01 2 0.2959 0.857 0.00 0.90 0.10
#> TCGA.XF.A9SH.01 2 0.5835 0.728 0.00 0.66 0.34
#> TCGA.FJ.A3Z9.01 3 0.6280 1.000 0.46 0.00 0.54
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GV.A3JW.01 2 0.3400 0.842 0.00 0.82 0.00 0.18
#> TCGA.CF.A5U8.01 2 0.3400 0.842 0.00 0.82 0.00 0.18
#> TCGA.E7.A5KF.01 2 0.3400 0.842 0.00 0.82 0.00 0.18
#> TCGA.CF.A3MH.01 1 0.0000 0.882 1.00 0.00 0.00 0.00
#> TCGA.CF.A3MG.01 1 0.2345 0.873 0.90 0.00 0.10 0.00
#> TCGA.FJ.A3ZE.01 4 0.2011 0.937 0.00 0.08 0.00 0.92
#> TCGA.4Z.AA89.01 2 0.0000 0.877 0.00 1.00 0.00 0.00
#> TCGA.XF.A8HI.01 2 0.0000 0.877 0.00 1.00 0.00 0.00
#> TCGA.E7.A7DU.01 2 0.1637 0.848 0.06 0.94 0.00 0.00
#> TCGA.CF.A8HY.01 2 0.0707 0.873 0.02 0.98 0.00 0.00
#> TCGA.CF.A3MI.01 3 0.3821 0.815 0.12 0.00 0.84 0.04
#> TCGA.ZF.A9R5.01 4 0.2011 0.932 0.00 0.08 0.00 0.92
#> TCGA.DK.A1AG.01 2 0.0707 0.873 0.02 0.98 0.00 0.00
#> TCGA.XF.A9T2.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.E7.A678.01 2 0.3400 0.842 0.00 0.82 0.00 0.18
#> TCGA.XF.A9SH.01 4 0.0707 0.899 0.00 0.02 0.00 0.98
#> TCGA.FJ.A3Z9.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GV.A3JW.01 2 0.3690 0.759 0.00 0.78 0.02 0.20 0.00
#> TCGA.CF.A5U8.01 2 0.3513 0.772 0.00 0.80 0.02 0.18 0.00
#> TCGA.E7.A5KF.01 2 0.3513 0.772 0.00 0.80 0.02 0.18 0.00
#> TCGA.CF.A3MH.01 1 0.0000 0.660 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MG.01 1 0.5210 0.606 0.68 0.00 0.12 0.00 0.20
#> TCGA.FJ.A3ZE.01 4 0.2020 0.877 0.00 0.10 0.00 0.90 0.00
#> TCGA.4Z.AA89.01 2 0.1648 0.768 0.00 0.94 0.04 0.02 0.00
#> TCGA.XF.A8HI.01 2 0.2020 0.785 0.00 0.90 0.00 0.10 0.00
#> TCGA.E7.A7DU.01 2 0.6149 0.495 0.06 0.64 0.22 0.00 0.08
#> TCGA.CF.A8HY.01 2 0.3106 0.705 0.02 0.84 0.14 0.00 0.00
#> TCGA.CF.A3MI.01 5 0.1410 0.000 0.06 0.00 0.00 0.00 0.94
#> TCGA.ZF.A9R5.01 4 0.3034 0.893 0.00 0.06 0.04 0.88 0.02
#> TCGA.DK.A1AG.01 2 0.2020 0.739 0.00 0.90 0.10 0.00 0.00
#> TCGA.XF.A9T2.01 3 0.4182 1.000 0.00 0.00 0.60 0.00 0.40
#> TCGA.E7.A678.01 2 0.3690 0.759 0.00 0.78 0.02 0.20 0.00
#> TCGA.XF.A9SH.01 4 0.0609 0.864 0.00 0.00 0.02 0.98 0.00
#> TCGA.FJ.A3Z9.01 3 0.4182 1.000 0.00 0.00 0.60 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.GV.A3JW.01 2 0.000 0.823 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A5U8.01 2 0.000 0.823 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A5KF.01 2 0.000 0.823 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MH.01 1 0.000 0.726 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MG.01 1 0.446 0.722 0.66 0.00 0.06 0.00 0.28 0.00
#> TCGA.FJ.A3ZE.01 4 0.308 0.681 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.4Z.AA89.01 2 0.279 0.700 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.XF.A8HI.01 2 0.000 0.823 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7DU.01 6 0.592 -0.204 0.00 0.30 0.00 0.00 0.24 0.46
#> TCGA.CF.A8HY.01 2 0.371 0.498 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.CF.A3MI.01 6 0.536 -0.213 0.00 0.00 0.14 0.00 0.30 0.56
#> TCGA.ZF.A9R5.01 4 0.399 0.693 0.00 0.10 0.00 0.76 0.14 0.00
#> TCGA.DK.A1AG.01 2 0.371 0.498 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.XF.A9T2.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 2 0.000 0.823 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.273 0.671 0.00 0.04 0.00 0.86 0.10 0.00
#> TCGA.FJ.A3Z9.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GV.A3JW.01 2 0.0000 0.844 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A5U8.01 2 0.0000 0.844 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A5KF.01 2 0.0000 0.844 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MH.01 1 0.0504 0.493 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CF.A3MG.01 1 0.5256 0.454 0.50 0.00 0.02 0.00 0.38 0.00 0.10
#> TCGA.FJ.A3ZE.01 4 0.4248 0.245 0.00 0.26 0.00 0.66 0.08 0.00 0.00
#> TCGA.4Z.AA89.01 2 0.2832 0.550 0.00 0.76 0.00 0.00 0.00 0.24 0.00
#> TCGA.XF.A8HI.01 2 0.0504 0.833 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E7.A7DU.01 6 0.0000 0.128 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CF.A8HY.01 6 0.3546 -0.113 0.00 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.CF.A3MI.01 7 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZF.A9R5.01 5 0.4718 0.000 0.00 0.06 0.00 0.32 0.60 0.02 0.00
#> TCGA.DK.A1AG.01 2 0.3413 0.148 0.00 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.XF.A9T2.01 3 0.0000 0.944 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 2 0.0000 0.844 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.0000 0.236 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FJ.A3Z9.01 3 0.1363 0.943 0.00 0.00 0.94 0.00 0.02 0.00 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GV.A3JW.01 2 0.0000 0.9223 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A5U8.01 2 0.0000 0.9223 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A5KF.01 2 0.0000 0.9223 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A3MH.01 1 0.1341 0.0000 0.92 0.00 0 0.00 0.00 0.00 0.00 0.08
#> TCGA.CF.A3MG.01 8 0.0000 0.0000 0.00 0.00 0 0.00 0.00 0.00 0.00 1.00
#> TCGA.FJ.A3ZE.01 4 0.4893 0.4500 0.06 0.18 0 0.64 0.12 0.00 0.00 0.00
#> TCGA.4Z.AA89.01 2 0.2534 0.5925 0.00 0.78 0 0.00 0.00 0.22 0.00 0.00
#> TCGA.XF.A8HI.01 2 0.0808 0.8895 0.00 0.96 0 0.00 0.00 0.04 0.00 0.00
#> TCGA.E7.A7DU.01 6 0.3080 0.0596 0.02 0.02 0 0.06 0.06 0.84 0.00 0.00
#> TCGA.CF.A8HY.01 6 0.3570 0.4634 0.02 0.36 0 0.00 0.00 0.62 0.00 0.00
#> TCGA.CF.A3MI.01 7 0.0000 0.0000 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.A9R5.01 5 0.1091 0.0000 0.00 0.00 0 0.06 0.94 0.00 0.00 0.00
#> TCGA.DK.A1AG.01 6 0.3333 0.2013 0.00 0.50 0 0.00 0.00 0.50 0.00 0.00
#> TCGA.XF.A9T2.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A678.01 2 0.0000 0.9223 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SH.01 4 0.2025 0.4324 0.00 0.00 0 0.88 0.10 0.00 0.02 0.00
#> TCGA.FJ.A3Z9.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0112"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 21 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5243 0.476 0.476
#> 3 3 0.779 0.820 0.868 0.2408 0.829 0.650
#> 4 4 0.905 0.969 0.935 0.1212 0.914 0.743
#> 5 5 0.763 0.882 0.929 0.0427 0.986 0.942
#> 6 6 0.842 0.558 0.846 0.0653 0.948 0.784
#> 7 7 0.863 0.641 0.853 0.0374 0.910 0.620
#> 8 8 0.862 0.703 0.896 0.0294 0.929 0.634
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
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.XF.AAN1.01 1 0 1 1 0
#> TCGA.4Z.AA7S.01 1 0 1 1 0
#> TCGA.UY.A78O.01 1 0 1 1 0
#> TCGA.FD.A62O.01 1 0 1 1 0
#> TCGA.XF.A9SV.01 1 0 1 1 0
#> TCGA.GV.A3JX.01 2 0 1 0 1
#> TCGA.FD.A6TH.01 2 0 1 0 1
#> TCGA.XF.AAMF.01 2 0 1 0 1
#> TCGA.XF.AAMQ.01 1 0 1 1 0
#> TCGA.UY.A78N.01 1 0 1 1 0
#> TCGA.G2.AA3F.01 1 0 1 1 0
#> TCGA.DK.A3IL.01 1 0 1 1 0
#> TCGA.FD.A6TE.01 2 0 1 0 1
#> TCGA.YF.AA3L.01 2 0 1 0 1
#> TCGA.DK.A1A6.01 1 0 1 1 0
#> TCGA.XF.AAML.01 2 0 1 0 1
#> TCGA.E7.A7PW.01 2 0 1 0 1
#> TCGA.GV.A40G.01 2 0 1 0 1
#> TCGA.XF.A8HC.01 2 0 1 0 1
#> TCGA.XF.A9T6.01 2 0 1 0 1
#> TCGA.E7.A4XJ.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.XF.AAN1.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.4Z.AA7S.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.XF.A9SV.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.0000 0.841 0.00 1.00 0.00
#> TCGA.FD.A6TH.01 2 0.6244 0.638 0.00 0.56 0.44
#> TCGA.XF.AAMF.01 2 0.6244 0.638 0.00 0.56 0.44
#> TCGA.XF.AAMQ.01 3 0.6302 0.662 0.48 0.00 0.52
#> TCGA.UY.A78N.01 3 0.6302 0.662 0.48 0.00 0.52
#> TCGA.G2.AA3F.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DK.A3IL.01 3 0.6302 0.662 0.48 0.00 0.52
#> TCGA.FD.A6TE.01 2 0.0000 0.841 0.00 1.00 0.00
#> TCGA.YF.AA3L.01 3 0.0000 0.273 0.00 0.00 1.00
#> TCGA.DK.A1A6.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.XF.AAML.01 2 0.0000 0.841 0.00 1.00 0.00
#> TCGA.E7.A7PW.01 2 0.0892 0.836 0.00 0.98 0.02
#> TCGA.GV.A40G.01 2 0.0000 0.841 0.00 1.00 0.00
#> TCGA.XF.A8HC.01 2 0.0000 0.841 0.00 1.00 0.00
#> TCGA.XF.A9T6.01 2 0.6244 0.638 0.00 0.56 0.44
#> TCGA.E7.A4XJ.01 1 0.0000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.XF.AAN1.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7S.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SV.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.4522 0.994 0.00 0.68 0.00 0.32
#> TCGA.FD.A6TH.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.XF.AAMF.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.XF.AAMQ.01 3 0.0707 0.907 0.02 0.00 0.98 0.00
#> TCGA.UY.A78N.01 3 0.0707 0.907 0.02 0.00 0.98 0.00
#> TCGA.G2.AA3F.01 1 0.0707 0.980 0.98 0.00 0.02 0.00
#> TCGA.DK.A3IL.01 3 0.0000 0.901 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TE.01 2 0.4522 0.994 0.00 0.68 0.00 0.32
#> TCGA.YF.AA3L.01 3 0.4522 0.731 0.00 0.32 0.68 0.00
#> TCGA.DK.A1A6.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.XF.AAML.01 2 0.4522 0.994 0.00 0.68 0.00 0.32
#> TCGA.E7.A7PW.01 2 0.5173 0.972 0.00 0.66 0.02 0.32
#> TCGA.GV.A40G.01 2 0.4522 0.994 0.00 0.68 0.00 0.32
#> TCGA.XF.A8HC.01 2 0.4522 0.994 0.00 0.68 0.00 0.32
#> TCGA.XF.A9T6.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.E7.A4XJ.01 1 0.0000 0.997 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.XF.AAN1.01 1 0.104 0.922 0.96 0.00 0.00 0.04 0.00
#> TCGA.4Z.AA7S.01 1 0.000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78O.01 1 0.000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SV.01 1 0.000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A6TH.01 4 0.273 1.000 0.00 0.16 0.00 0.84 0.00
#> TCGA.XF.AAMF.01 4 0.273 1.000 0.00 0.16 0.00 0.84 0.00
#> TCGA.XF.AAMQ.01 3 0.303 0.875 0.06 0.00 0.88 0.04 0.02
#> TCGA.UY.A78N.01 3 0.364 0.812 0.06 0.00 0.82 0.12 0.00
#> TCGA.G2.AA3F.01 1 0.422 0.775 0.78 0.00 0.10 0.12 0.00
#> TCGA.DK.A3IL.01 3 0.201 0.889 0.06 0.00 0.92 0.00 0.02
#> TCGA.FD.A6TE.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.YF.AA3L.01 5 0.104 0.000 0.00 0.00 0.04 0.00 0.96
#> TCGA.DK.A1A6.01 1 0.000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAML.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 2 0.244 0.918 0.00 0.90 0.06 0.00 0.04
#> TCGA.GV.A40G.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A8HC.01 2 0.244 0.918 0.00 0.90 0.06 0.00 0.04
#> TCGA.XF.A9T6.01 4 0.273 1.000 0.00 0.16 0.00 0.84 0.00
#> TCGA.E7.A4XJ.01 1 0.287 0.854 0.86 0.00 0.02 0.12 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.XF.AAN1.01 1 0.2260 0.7542 0.86 0.00 0.00 0.00 0 0.14
#> TCGA.4Z.AA7S.01 1 0.0000 0.8819 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.8819 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.8819 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.XF.A9SV.01 1 0.0000 0.8819 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.GV.A3JX.01 2 0.0000 0.8419 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.FD.A6TH.01 4 0.0547 0.9729 0.00 0.02 0.00 0.98 0 0.00
#> TCGA.XF.AAMF.01 4 0.1635 0.9586 0.00 0.02 0.02 0.94 0 0.02
#> TCGA.XF.AAMQ.01 6 0.4282 0.0000 0.02 0.00 0.42 0.00 0 0.56
#> TCGA.UY.A78N.01 3 0.0547 -0.0925 0.02 0.00 0.98 0.00 0 0.00
#> TCGA.G2.AA3F.01 3 0.3851 -0.2199 0.46 0.00 0.54 0.00 0 0.00
#> TCGA.DK.A3IL.01 3 0.4787 -0.7970 0.02 0.00 0.52 0.02 0 0.44
#> TCGA.FD.A6TE.01 2 0.0000 0.8419 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.YF.AA3L.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.DK.A1A6.01 1 0.0000 0.8819 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.XF.AAML.01 2 0.0000 0.8419 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.E7.A7PW.01 2 0.3756 0.6273 0.00 0.60 0.00 0.00 0 0.40
#> TCGA.GV.A40G.01 2 0.0000 0.8419 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.XF.A8HC.01 2 0.3706 0.6440 0.00 0.62 0.00 0.00 0 0.38
#> TCGA.XF.A9T6.01 4 0.1092 0.9684 0.00 0.02 0.00 0.96 0 0.02
#> TCGA.E7.A4XJ.01 1 0.3797 0.1337 0.58 0.00 0.42 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.XF.AAN1.01 1 0.3047 0.533 0.72 0.00 0.28 0.00 0 0.00 0.00
#> TCGA.4Z.AA7S.01 1 0.0000 0.764 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.764 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.764 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.XF.A9SV.01 1 0.0000 0.764 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.3139 1.000 0.00 0.70 0.00 0.00 0 0.00 0.30
#> TCGA.FD.A6TH.01 4 0.0000 0.899 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.XF.AAMF.01 4 0.1664 0.877 0.00 0.00 0.06 0.92 0 0.00 0.02
#> TCGA.XF.AAMQ.01 6 0.3459 0.529 0.00 0.00 0.40 0.00 0 0.60 0.00
#> TCGA.UY.A78N.01 3 0.5485 0.000 0.00 0.22 0.40 0.00 0 0.38 0.00
#> TCGA.G2.AA3F.01 1 0.6611 -0.292 0.34 0.28 0.30 0.00 0 0.08 0.00
#> TCGA.DK.A3IL.01 6 0.0000 0.457 0.00 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.FD.A6TE.01 2 0.3139 1.000 0.00 0.70 0.00 0.00 0 0.00 0.30
#> TCGA.YF.AA3L.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DK.A1A6.01 1 0.0000 0.764 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.XF.AAML.01 2 0.3139 1.000 0.00 0.70 0.00 0.00 0 0.00 0.30
#> TCGA.E7.A7PW.01 7 0.0863 0.943 0.00 0.00 0.04 0.00 0 0.00 0.96
#> TCGA.GV.A40G.01 2 0.3139 1.000 0.00 0.70 0.00 0.00 0 0.00 0.30
#> TCGA.XF.A8HC.01 7 0.0504 0.942 0.00 0.02 0.00 0.00 0 0.00 0.98
#> TCGA.XF.A9T6.01 4 0.2376 0.847 0.00 0.02 0.12 0.86 0 0.00 0.00
#> TCGA.E7.A4XJ.01 1 0.5560 -0.100 0.42 0.28 0.30 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.XF.AAN1.01 1 0.3618 0.345 0.60 0.00 0.00 0.00 0 0.38 0.02 0.00
#> TCGA.4Z.AA7S.01 1 0.0000 0.913 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.UY.A78O.01 1 0.0000 0.913 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.FD.A62O.01 1 0.0000 0.913 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.XF.A9SV.01 1 0.0000 0.913 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.GV.A3JX.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.FD.A6TH.01 4 0.0000 0.849 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.XF.AAMF.01 4 0.3601 0.741 0.00 0.00 0.02 0.76 0 0.00 0.06 0.16
#> TCGA.XF.AAMQ.01 6 0.0471 0.000 0.00 0.00 0.02 0.00 0 0.98 0.00 0.00
#> TCGA.UY.A78N.01 3 0.4304 0.468 0.00 0.00 0.72 0.00 0 0.08 0.12 0.08
#> TCGA.G2.AA3F.01 3 0.1341 0.682 0.08 0.00 0.92 0.00 0 0.00 0.00 0.00
#> TCGA.DK.A3IL.01 8 0.4560 0.000 0.00 0.00 0.18 0.00 0 0.22 0.00 0.60
#> TCGA.FD.A6TE.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.YF.AA3L.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.DK.A1A6.01 1 0.0000 0.913 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.XF.AAML.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.E7.A7PW.01 7 0.1947 0.827 0.00 0.14 0.00 0.00 0 0.00 0.86 0.00
#> TCGA.GV.A40G.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.XF.A8HC.01 7 0.4533 0.829 0.00 0.20 0.02 0.00 0 0.02 0.68 0.08
#> TCGA.XF.A9T6.01 4 0.1341 0.829 0.00 0.00 0.00 0.92 0 0.00 0.00 0.08
#> TCGA.E7.A4XJ.01 3 0.2534 0.624 0.22 0.00 0.78 0.00 0 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-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 49 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 0.633 0.880 0.917 0.4736 0.490 0.490
#> 3 3 1.000 0.971 0.961 0.3714 0.838 0.676
#> 4 4 0.833 0.930 0.900 0.1398 0.888 0.680
#> 5 5 0.821 0.828 0.893 0.0660 0.979 0.911
#> 6 6 0.791 0.661 0.818 0.0438 0.970 0.865
#> 7 7 0.792 0.592 0.791 0.0286 0.979 0.891
#> 8 8 0.786 0.354 0.649 0.0198 0.919 0.599
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.E5.A2PC.01 2 0.925 0.716 0.34 0.66
#> TCGA.DK.AA6L.01 2 0.000 0.814 0.00 1.00
#> TCGA.DK.AA76.01 2 0.981 0.575 0.42 0.58
#> TCGA.KQ.A41O.01 2 0.000 0.814 0.00 1.00
#> TCGA.HQ.A2OE.01 1 0.000 1.000 1.00 0.00
#> TCGA.MV.A51V.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A2I6.01 1 0.000 1.000 1.00 0.00
#> TCGA.FJ.A3ZF.01 1 0.000 1.000 1.00 0.00
#> TCGA.4Z.AA87.01 1 0.000 1.000 1.00 0.00
#> TCGA.UY.A9PD.01 1 0.000 1.000 1.00 0.00
#> TCGA.CU.A72E.01 2 0.925 0.716 0.34 0.66
#> TCGA.G2.A2EL.01 1 0.000 1.000 1.00 0.00
#> TCGA.BT.A3PH.01 2 0.000 0.814 0.00 1.00
#> TCGA.ZF.AA4U.01 2 0.925 0.716 0.34 0.66
#> TCGA.ZF.A9RE.01 2 0.925 0.716 0.34 0.66
#> TCGA.GC.A3RB.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A1AD.01 1 0.000 1.000 1.00 0.00
#> TCGA.C4.A0F6.01 2 0.000 0.814 0.00 1.00
#> TCGA.G2.A3VY.01 1 0.000 1.000 1.00 0.00
#> TCGA.K4.A6MB.01 1 0.000 1.000 1.00 0.00
#> TCGA.XF.AAN7.01 2 0.327 0.814 0.06 0.94
#> TCGA.KQ.A41R.01 2 0.000 0.814 0.00 1.00
#> TCGA.CF.A7I0.01 2 0.925 0.716 0.34 0.66
#> TCGA.E7.A4IJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.FD.A5BV.01 2 0.000 0.814 0.00 1.00
#> TCGA.GU.AATQ.01 2 0.925 0.716 0.34 0.66
#> TCGA.UY.A8OB.01 2 0.000 0.814 0.00 1.00
#> TCGA.DK.AA75.01 1 0.000 1.000 1.00 0.00
#> TCGA.GV.A3JZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.2F.A9KQ.01 2 0.242 0.815 0.04 0.96
#> TCGA.K4.A4AB.01 2 0.904 0.727 0.32 0.68
#> TCGA.4Z.AA7M.01 1 0.000 1.000 1.00 0.00
#> TCGA.4Z.AA7R.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.A3IS.01 2 0.925 0.716 0.34 0.66
#> TCGA.E5.A4TZ.01 2 0.327 0.814 0.06 0.94
#> TCGA.GV.A6ZA.01 2 0.529 0.802 0.12 0.88
#> TCGA.FD.A43N.01 1 0.000 1.000 1.00 0.00
#> TCGA.4Z.AA80.01 1 0.000 1.000 1.00 0.00
#> TCGA.CF.A9FL.01 2 0.925 0.716 0.34 0.66
#> TCGA.E7.A5KE.01 2 0.000 0.814 0.00 1.00
#> TCGA.XF.A9T0.01 1 0.000 1.000 1.00 0.00
#> TCGA.GU.A42P.01 1 0.000 1.000 1.00 0.00
#> TCGA.KQ.A41N.01 2 0.925 0.716 0.34 0.66
#> TCGA.XF.AAMG.01 1 0.000 1.000 1.00 0.00
#> TCGA.XF.A8HF.01 2 0.000 0.814 0.00 1.00
#> TCGA.KQ.A41P.01 1 0.000 1.000 1.00 0.00
#> TCGA.DK.AA6U.01 1 0.000 1.000 1.00 0.00
#> TCGA.H4.A2HQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.XF.AAMX.01 2 0.000 0.814 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E5.A2PC.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.DK.AA6L.01 3 0.0892 0.992 0.00 0.02 0.98
#> TCGA.DK.AA76.01 2 0.0892 0.905 0.02 0.98 0.00
#> TCGA.KQ.A41O.01 3 0.0892 0.992 0.00 0.02 0.98
#> TCGA.HQ.A2OE.01 1 0.2414 0.963 0.94 0.04 0.02
#> TCGA.MV.A51V.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.DK.A2I6.01 1 0.3340 0.914 0.88 0.12 0.00
#> TCGA.FJ.A3ZF.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.4Z.AA87.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.UY.A9PD.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.CU.A72E.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.G2.A2EL.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.BT.A3PH.01 3 0.0892 0.992 0.00 0.02 0.98
#> TCGA.ZF.AA4U.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.ZF.A9RE.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.GC.A3RB.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.DK.A1AD.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.C4.A0F6.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.G2.A3VY.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.K4.A6MB.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.XF.AAN7.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.KQ.A41R.01 3 0.0892 0.992 0.00 0.02 0.98
#> TCGA.CF.A7I0.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.E7.A4IJ.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.FD.A5BV.01 3 0.0892 0.992 0.00 0.02 0.98
#> TCGA.GU.AATQ.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.UY.A8OB.01 3 0.0892 0.992 0.00 0.02 0.98
#> TCGA.DK.AA75.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.GV.A3JZ.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.2F.A9KQ.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.K4.A4AB.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.4Z.AA7M.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.4Z.AA7R.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.DK.A3IS.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.E5.A4TZ.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.GV.A6ZA.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.FD.A43N.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.4Z.AA80.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.CF.A9FL.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.E7.A5KE.01 3 0.0892 0.992 0.00 0.02 0.98
#> TCGA.XF.A9T0.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.GU.A42P.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.KQ.A41N.01 2 0.2066 0.985 0.00 0.94 0.06
#> TCGA.XF.AAMG.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.XF.A8HF.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.KQ.A41P.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.DK.AA6U.01 1 0.2066 0.962 0.94 0.06 0.00
#> TCGA.H4.A2HQ.01 2 0.0892 0.905 0.02 0.98 0.00
#> TCGA.XF.AAMX.01 3 0.0892 0.992 0.00 0.02 0.98
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E5.A2PC.01 2 0.0707 0.964 0.00 0.98 0.00 0.02
#> TCGA.DK.AA6L.01 3 0.2011 0.931 0.00 0.00 0.92 0.08
#> TCGA.DK.AA76.01 2 0.2335 0.930 0.06 0.92 0.00 0.02
#> TCGA.KQ.A41O.01 3 0.0000 0.960 0.00 0.00 1.00 0.00
#> TCGA.HQ.A2OE.01 4 0.4624 0.843 0.34 0.00 0.00 0.66
#> TCGA.MV.A51V.01 1 0.2011 0.914 0.92 0.00 0.00 0.08
#> TCGA.DK.A2I6.01 1 0.1211 0.870 0.96 0.00 0.00 0.04
#> TCGA.FJ.A3ZF.01 4 0.4277 0.951 0.28 0.00 0.00 0.72
#> TCGA.4Z.AA87.01 4 0.4277 0.951 0.28 0.00 0.00 0.72
#> TCGA.UY.A9PD.01 4 0.3975 0.938 0.24 0.00 0.00 0.76
#> TCGA.CU.A72E.01 2 0.0000 0.965 0.00 1.00 0.00 0.00
#> TCGA.G2.A2EL.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.BT.A3PH.01 3 0.0707 0.960 0.00 0.00 0.98 0.02
#> TCGA.ZF.AA4U.01 2 0.0707 0.964 0.00 0.98 0.00 0.02
#> TCGA.ZF.A9RE.01 2 0.0707 0.964 0.00 0.98 0.00 0.02
#> TCGA.GC.A3RB.01 1 0.0707 0.891 0.98 0.00 0.00 0.02
#> TCGA.DK.A1AD.01 4 0.4277 0.947 0.28 0.00 0.00 0.72
#> TCGA.C4.A0F6.01 3 0.1211 0.956 0.00 0.00 0.96 0.04
#> TCGA.G2.A3VY.01 4 0.4277 0.951 0.28 0.00 0.00 0.72
#> TCGA.K4.A6MB.01 1 0.2011 0.912 0.92 0.00 0.00 0.08
#> TCGA.XF.AAN7.01 3 0.4642 0.814 0.02 0.00 0.74 0.24
#> TCGA.KQ.A41R.01 3 0.0000 0.960 0.00 0.00 1.00 0.00
#> TCGA.CF.A7I0.01 2 0.0000 0.965 0.00 1.00 0.00 0.00
#> TCGA.E7.A4IJ.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BV.01 3 0.2011 0.931 0.00 0.00 0.92 0.08
#> TCGA.GU.AATQ.01 2 0.0707 0.964 0.00 0.98 0.00 0.02
#> TCGA.UY.A8OB.01 3 0.0000 0.960 0.00 0.00 1.00 0.00
#> TCGA.DK.AA75.01 4 0.4277 0.951 0.28 0.00 0.00 0.72
#> TCGA.GV.A3JZ.01 1 0.2011 0.914 0.92 0.00 0.00 0.08
#> TCGA.2F.A9KQ.01 2 0.0000 0.965 0.00 1.00 0.00 0.00
#> TCGA.K4.A4AB.01 2 0.0000 0.965 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7M.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7R.01 4 0.4277 0.951 0.28 0.00 0.00 0.72
#> TCGA.DK.A3IS.01 2 0.0707 0.964 0.00 0.98 0.00 0.02
#> TCGA.E5.A4TZ.01 2 0.4472 0.780 0.00 0.76 0.02 0.22
#> TCGA.GV.A6ZA.01 2 0.2011 0.918 0.00 0.92 0.00 0.08
#> TCGA.FD.A43N.01 4 0.4134 0.938 0.26 0.00 0.00 0.74
#> TCGA.4Z.AA80.01 4 0.4277 0.947 0.28 0.00 0.00 0.72
#> TCGA.CF.A9FL.01 2 0.0000 0.965 0.00 1.00 0.00 0.00
#> TCGA.E7.A5KE.01 3 0.0707 0.960 0.00 0.00 0.98 0.02
#> TCGA.XF.A9T0.01 1 0.2345 0.905 0.90 0.00 0.00 0.10
#> TCGA.GU.A42P.01 1 0.2345 0.896 0.90 0.00 0.00 0.10
#> TCGA.KQ.A41N.01 2 0.0000 0.965 0.00 1.00 0.00 0.00
#> TCGA.XF.AAMG.01 1 0.3172 0.827 0.84 0.00 0.00 0.16
#> TCGA.XF.A8HF.01 3 0.1211 0.956 0.00 0.00 0.96 0.04
#> TCGA.KQ.A41P.01 4 0.3975 0.922 0.24 0.00 0.00 0.76
#> TCGA.DK.AA6U.01 1 0.2011 0.912 0.92 0.00 0.00 0.08
#> TCGA.H4.A2HQ.01 2 0.2706 0.916 0.08 0.90 0.00 0.02
#> TCGA.XF.AAMX.01 3 0.0707 0.960 0.00 0.00 0.98 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E5.A2PC.01 2 0.1216 0.901 0.02 0.96 0.00 0.00 0.02
#> TCGA.DK.AA6L.01 3 0.3999 0.680 0.00 0.00 0.74 0.02 0.24
#> TCGA.DK.AA76.01 2 0.4588 0.637 0.06 0.72 0.00 0.00 0.22
#> TCGA.KQ.A41O.01 3 0.1216 0.913 0.00 0.00 0.96 0.02 0.02
#> TCGA.HQ.A2OE.01 4 0.3390 0.807 0.06 0.00 0.00 0.84 0.10
#> TCGA.MV.A51V.01 1 0.2438 0.836 0.90 0.00 0.00 0.06 0.04
#> TCGA.DK.A2I6.01 1 0.3424 0.755 0.76 0.00 0.00 0.00 0.24
#> TCGA.FJ.A3ZF.01 4 0.2754 0.891 0.08 0.00 0.00 0.88 0.04
#> TCGA.4Z.AA87.01 4 0.2754 0.891 0.08 0.00 0.00 0.88 0.04
#> TCGA.UY.A9PD.01 4 0.0609 0.897 0.02 0.00 0.00 0.98 0.00
#> TCGA.CU.A72E.01 2 0.0000 0.902 0.00 1.00 0.00 0.00 0.00
#> TCGA.G2.A2EL.01 1 0.3852 0.788 0.76 0.00 0.00 0.02 0.22
#> TCGA.BT.A3PH.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA4U.01 2 0.1216 0.901 0.02 0.96 0.00 0.00 0.02
#> TCGA.ZF.A9RE.01 2 0.1216 0.901 0.02 0.96 0.00 0.00 0.02
#> TCGA.GC.A3RB.01 1 0.3999 0.775 0.74 0.00 0.00 0.02 0.24
#> TCGA.DK.A1AD.01 4 0.1043 0.897 0.04 0.00 0.00 0.96 0.00
#> TCGA.C4.A0F6.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.A3VY.01 4 0.4588 0.739 0.22 0.00 0.00 0.72 0.06
#> TCGA.K4.A6MB.01 1 0.2438 0.847 0.90 0.00 0.00 0.04 0.06
#> TCGA.XF.AAN7.01 5 0.4982 0.429 0.00 0.00 0.20 0.10 0.70
#> TCGA.KQ.A41R.01 3 0.1216 0.913 0.00 0.00 0.96 0.02 0.02
#> TCGA.CF.A7I0.01 2 0.0000 0.902 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A4IJ.01 1 0.2012 0.839 0.92 0.00 0.00 0.02 0.06
#> TCGA.FD.A5BV.01 3 0.3999 0.680 0.00 0.00 0.74 0.02 0.24
#> TCGA.GU.AATQ.01 2 0.1216 0.901 0.02 0.96 0.00 0.00 0.02
#> TCGA.UY.A8OB.01 3 0.1216 0.913 0.00 0.00 0.96 0.02 0.02
#> TCGA.DK.AA75.01 4 0.2754 0.891 0.08 0.00 0.00 0.88 0.04
#> TCGA.GV.A3JZ.01 1 0.2331 0.834 0.90 0.00 0.00 0.08 0.02
#> TCGA.2F.A9KQ.01 2 0.0000 0.902 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A4AB.01 2 0.0000 0.902 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7M.01 1 0.3513 0.807 0.80 0.00 0.00 0.02 0.18
#> TCGA.4Z.AA7R.01 4 0.3037 0.880 0.10 0.00 0.00 0.86 0.04
#> TCGA.DK.A3IS.01 2 0.1216 0.901 0.02 0.96 0.00 0.00 0.02
#> TCGA.E5.A4TZ.01 5 0.4456 0.462 0.00 0.32 0.00 0.02 0.66
#> TCGA.GV.A6ZA.01 2 0.3274 0.582 0.00 0.78 0.00 0.00 0.22
#> TCGA.FD.A43N.01 4 0.1043 0.897 0.04 0.00 0.00 0.96 0.00
#> TCGA.4Z.AA80.01 4 0.1043 0.897 0.04 0.00 0.00 0.96 0.00
#> TCGA.CF.A9FL.01 2 0.0000 0.902 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A5KE.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.A9T0.01 1 0.1732 0.841 0.92 0.00 0.00 0.08 0.00
#> TCGA.GU.A42P.01 1 0.3684 0.707 0.72 0.00 0.00 0.28 0.00
#> TCGA.KQ.A41N.01 2 0.0000 0.902 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMG.01 1 0.3110 0.810 0.86 0.00 0.00 0.08 0.06
#> TCGA.XF.A8HF.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.KQ.A41P.01 4 0.1648 0.886 0.04 0.00 0.00 0.94 0.02
#> TCGA.DK.AA6U.01 1 0.1410 0.845 0.94 0.00 0.00 0.06 0.00
#> TCGA.H4.A2HQ.01 2 0.4854 0.576 0.06 0.68 0.00 0.00 0.26
#> TCGA.XF.AAMX.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E5.A2PC.01 2 0.0000 0.7992 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6L.01 3 0.5120 0.5410 0.00 0.00 0.60 0.00 0.28 0.12
#> TCGA.DK.AA76.01 2 0.3756 0.0354 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.KQ.A41O.01 3 0.1267 0.8725 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.HQ.A2OE.01 4 0.4337 0.1414 0.02 0.00 0.00 0.50 0.00 0.48
#> TCGA.MV.A51V.01 1 0.1635 0.6699 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.DK.A2I6.01 6 0.3706 0.3504 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.FJ.A3ZF.01 4 0.4213 0.7537 0.08 0.00 0.00 0.78 0.04 0.10
#> TCGA.4Z.AA87.01 4 0.4213 0.7537 0.08 0.00 0.00 0.78 0.04 0.10
#> TCGA.UY.A9PD.01 4 0.0000 0.7623 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A72E.01 2 0.3163 0.8057 0.00 0.82 0.00 0.00 0.14 0.04
#> TCGA.G2.A2EL.01 1 0.4348 0.4000 0.64 0.00 0.00 0.00 0.04 0.32
#> TCGA.BT.A3PH.01 3 0.0000 0.8771 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4U.01 2 0.0000 0.7992 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RE.01 2 0.0000 0.7992 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RB.01 6 0.3706 0.3504 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.DK.A1AD.01 4 0.0547 0.7615 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.C4.A0F6.01 3 0.1267 0.8652 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.G2.A3VY.01 4 0.6209 0.4761 0.34 0.00 0.00 0.50 0.06 0.10
#> TCGA.K4.A6MB.01 1 0.3460 0.6120 0.76 0.00 0.00 0.02 0.00 0.22
#> TCGA.XF.AAN7.01 5 0.4784 0.6334 0.00 0.00 0.08 0.10 0.74 0.08
#> TCGA.KQ.A41R.01 3 0.1267 0.8725 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.CF.A7I0.01 2 0.4165 0.7586 0.00 0.74 0.00 0.00 0.16 0.10
#> TCGA.E7.A4IJ.01 1 0.3523 0.6219 0.78 0.00 0.00 0.00 0.04 0.18
#> TCGA.FD.A5BV.01 3 0.5120 0.5410 0.00 0.00 0.60 0.00 0.28 0.12
#> TCGA.GU.AATQ.01 2 0.0000 0.7992 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OB.01 3 0.2048 0.8523 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.DK.AA75.01 4 0.4213 0.7537 0.08 0.00 0.00 0.78 0.04 0.10
#> TCGA.GV.A3JZ.01 1 0.1092 0.6666 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.2F.A9KQ.01 2 0.4165 0.7586 0.00 0.74 0.00 0.00 0.16 0.10
#> TCGA.K4.A4AB.01 2 0.3163 0.8057 0.00 0.82 0.00 0.00 0.14 0.04
#> TCGA.4Z.AA7M.01 1 0.4172 0.4870 0.68 0.00 0.00 0.00 0.04 0.28
#> TCGA.4Z.AA7R.01 4 0.4453 0.7434 0.10 0.00 0.00 0.76 0.04 0.10
#> TCGA.DK.A3IS.01 2 0.0000 0.7992 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E5.A4TZ.01 5 0.1814 0.6440 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.GV.A6ZA.01 2 0.4609 0.4161 0.00 0.54 0.00 0.00 0.42 0.04
#> TCGA.FD.A43N.01 4 0.0547 0.7615 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.4Z.AA80.01 4 0.0547 0.7615 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CF.A9FL.01 2 0.3163 0.8057 0.00 0.82 0.00 0.00 0.14 0.04
#> TCGA.E7.A5KE.01 3 0.0000 0.8771 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T0.01 1 0.0937 0.6716 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.GU.A42P.01 1 0.5331 0.5239 0.66 0.00 0.00 0.20 0.04 0.10
#> TCGA.KQ.A41N.01 2 0.3163 0.8057 0.00 0.82 0.00 0.00 0.14 0.04
#> TCGA.XF.AAMG.01 1 0.4756 0.4520 0.74 0.00 0.00 0.10 0.06 0.10
#> TCGA.XF.A8HF.01 3 0.0000 0.8771 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KQ.A41P.01 4 0.2350 0.6975 0.02 0.00 0.00 0.88 0.00 0.10
#> TCGA.DK.AA6U.01 1 0.3258 0.6794 0.84 0.00 0.00 0.02 0.04 0.10
#> TCGA.H4.A2HQ.01 6 0.4337 0.0220 0.02 0.48 0.00 0.00 0.00 0.50
#> TCGA.XF.AAMX.01 3 0.0000 0.8771 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E5.A2PC.01 2 0.2906 0.8032 0.00 0.80 0.00 0.00 0.00 0.18 0.02
#> TCGA.DK.AA6L.01 3 0.5622 0.5516 0.00 0.00 0.52 0.00 0.24 0.02 0.22
#> TCGA.DK.AA76.01 6 0.2906 0.5333 0.00 0.18 0.00 0.00 0.00 0.80 0.02
#> TCGA.KQ.A41O.01 3 0.2163 0.8244 0.00 0.00 0.88 0.00 0.02 0.00 0.10
#> TCGA.HQ.A2OE.01 4 0.6464 -0.0691 0.02 0.00 0.00 0.42 0.04 0.32 0.20
#> TCGA.MV.A51V.01 1 0.2745 0.4702 0.82 0.00 0.00 0.00 0.00 0.02 0.16
#> TCGA.DK.A2I6.01 6 0.3991 0.5122 0.22 0.00 0.00 0.00 0.02 0.72 0.04
#> TCGA.FJ.A3ZF.01 4 0.4264 0.4305 0.06 0.00 0.00 0.62 0.00 0.00 0.32
#> TCGA.4Z.AA87.01 4 0.4264 0.4305 0.06 0.00 0.00 0.62 0.00 0.00 0.32
#> TCGA.UY.A9PD.01 4 0.0504 0.6329 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CU.A72E.01 2 0.0000 0.8315 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EL.01 1 0.3413 0.2414 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.BT.A3PH.01 3 0.0000 0.8319 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4U.01 2 0.2906 0.8032 0.00 0.80 0.00 0.00 0.00 0.18 0.02
#> TCGA.ZF.A9RE.01 2 0.2906 0.8032 0.00 0.80 0.00 0.00 0.00 0.18 0.02
#> TCGA.GC.A3RB.01 6 0.5025 0.4896 0.22 0.00 0.00 0.00 0.04 0.64 0.10
#> TCGA.DK.A1AD.01 4 0.0000 0.6352 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C4.A0F6.01 3 0.2376 0.8019 0.00 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.G2.A3VY.01 7 0.5735 0.0000 0.36 0.00 0.00 0.18 0.00 0.02 0.44
#> TCGA.K4.A6MB.01 1 0.4298 0.4628 0.74 0.00 0.00 0.00 0.04 0.12 0.10
#> TCGA.XF.AAN7.01 5 0.1505 0.9222 0.02 0.00 0.00 0.02 0.94 0.00 0.02
#> TCGA.KQ.A41R.01 3 0.2163 0.8244 0.00 0.00 0.88 0.00 0.02 0.00 0.10
#> TCGA.CF.A7I0.01 2 0.2569 0.7627 0.00 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.E7.A4IJ.01 1 0.1886 0.5867 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.FD.A5BV.01 3 0.5622 0.5516 0.00 0.00 0.52 0.00 0.24 0.02 0.22
#> TCGA.GU.AATQ.01 2 0.2906 0.8032 0.00 0.80 0.00 0.00 0.00 0.18 0.02
#> TCGA.UY.A8OB.01 3 0.3661 0.7772 0.00 0.00 0.74 0.00 0.02 0.02 0.22
#> TCGA.DK.AA75.01 4 0.4264 0.4305 0.06 0.00 0.00 0.62 0.00 0.00 0.32
#> TCGA.GV.A3JZ.01 1 0.2745 0.4702 0.82 0.00 0.00 0.00 0.00 0.02 0.16
#> TCGA.2F.A9KQ.01 2 0.2569 0.7627 0.00 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.K4.A4AB.01 2 0.0000 0.8315 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7M.01 1 0.3294 0.3335 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.4Z.AA7R.01 4 0.4681 0.3440 0.10 0.00 0.00 0.58 0.00 0.00 0.32
#> TCGA.DK.A3IS.01 2 0.3186 0.7748 0.00 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.E5.A4TZ.01 5 0.1363 0.9223 0.00 0.04 0.00 0.00 0.94 0.00 0.02
#> TCGA.GV.A6ZA.01 2 0.3388 0.6519 0.00 0.76 0.00 0.00 0.20 0.00 0.04
#> TCGA.FD.A43N.01 4 0.0000 0.6352 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA80.01 4 0.0000 0.6352 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A9FL.01 2 0.0863 0.8241 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.E7.A5KE.01 3 0.0000 0.8319 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T0.01 1 0.1166 0.5502 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.GU.A42P.01 1 0.3755 0.2879 0.64 0.00 0.00 0.34 0.00 0.02 0.00
#> TCGA.KQ.A41N.01 2 0.0863 0.8241 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.XF.AAMG.01 1 0.4266 -0.6361 0.52 0.00 0.00 0.04 0.00 0.00 0.44
#> TCGA.XF.A8HF.01 3 0.0000 0.8319 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41P.01 4 0.3927 0.4735 0.00 0.00 0.00 0.76 0.02 0.08 0.14
#> TCGA.DK.AA6U.01 1 0.0000 0.5726 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H4.A2HQ.01 6 0.2376 0.5987 0.02 0.12 0.00 0.00 0.00 0.86 0.00
#> TCGA.XF.AAMX.01 3 0.0000 0.8319 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E5.A2PC.01 2 0.0000 0.39321 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6L.01 5 0.3142 -0.01792 0.00 0.00 0.36 0.00 0.64 0.00 0.00 0.00
#> TCGA.DK.AA76.01 2 0.5162 0.09566 0.00 0.50 0.00 0.00 0.00 0.36 0.10 0.04
#> TCGA.KQ.A41O.01 3 0.3615 0.68348 0.00 0.00 0.74 0.00 0.20 0.02 0.04 0.00
#> TCGA.HQ.A2OE.01 6 0.4358 0.26686 0.04 0.00 0.00 0.40 0.00 0.54 0.00 0.02
#> TCGA.MV.A51V.01 1 0.4059 0.61312 0.64 0.00 0.00 0.00 0.00 0.08 0.28 0.00
#> TCGA.DK.A2I6.01 6 0.4041 0.58286 0.22 0.00 0.00 0.00 0.00 0.70 0.04 0.04
#> TCGA.FJ.A3ZF.01 4 0.3992 -0.08605 0.00 0.00 0.00 0.52 0.00 0.00 0.44 0.04
#> TCGA.4Z.AA87.01 4 0.3992 -0.08605 0.00 0.00 0.00 0.52 0.00 0.00 0.44 0.04
#> TCGA.UY.A9PD.01 4 0.0471 0.62088 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CU.A72E.01 2 0.3299 -0.66179 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.G2.A2EL.01 1 0.2807 0.67145 0.86 0.00 0.00 0.00 0.02 0.06 0.04 0.02
#> TCGA.BT.A3PH.01 3 0.0000 0.78205 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4U.01 2 0.0000 0.39321 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RE.01 2 0.0000 0.39321 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RB.01 6 0.2406 0.61127 0.20 0.00 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.DK.A1AD.01 4 0.0471 0.62493 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.C4.A0F6.01 3 0.4186 0.62737 0.00 0.00 0.72 0.02 0.18 0.00 0.06 0.02
#> TCGA.G2.A3VY.01 7 0.4409 0.49865 0.08 0.00 0.00 0.18 0.00 0.02 0.70 0.02
#> TCGA.K4.A6MB.01 1 0.4004 -0.01620 0.50 0.00 0.00 0.00 0.00 0.46 0.04 0.00
#> TCGA.XF.AAN7.01 5 0.5256 0.33604 0.00 0.00 0.00 0.00 0.54 0.10 0.06 0.30
#> TCGA.KQ.A41R.01 3 0.3483 0.69406 0.00 0.00 0.76 0.00 0.18 0.02 0.04 0.00
#> TCGA.CF.A7I0.01 8 0.3299 1.00000 0.00 0.44 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.E7.A4IJ.01 1 0.0471 0.72640 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FD.A5BV.01 5 0.3570 -0.00847 0.00 0.00 0.36 0.00 0.62 0.00 0.02 0.00
#> TCGA.GU.AATQ.01 2 0.0000 0.39321 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OB.01 3 0.3237 0.50366 0.00 0.00 0.60 0.00 0.40 0.00 0.00 0.00
#> TCGA.DK.AA75.01 4 0.3729 -0.09872 0.00 0.00 0.00 0.52 0.00 0.00 0.46 0.02
#> TCGA.GV.A3JZ.01 1 0.3504 0.63452 0.70 0.00 0.00 0.00 0.00 0.04 0.26 0.00
#> TCGA.2F.A9KQ.01 8 0.3299 1.00000 0.00 0.44 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.K4.A4AB.01 2 0.3299 -0.66179 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.4Z.AA7M.01 1 0.2532 0.67867 0.88 0.00 0.00 0.00 0.02 0.04 0.04 0.02
#> TCGA.4Z.AA7R.01 7 0.3333 -0.23629 0.00 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.DK.A3IS.01 2 0.1275 0.37802 0.00 0.94 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.E5.A4TZ.01 5 0.4740 0.34852 0.00 0.00 0.00 0.00 0.58 0.10 0.02 0.30
#> TCGA.GV.A6ZA.01 2 0.5055 -0.36137 0.00 0.48 0.00 0.00 0.24 0.00 0.00 0.28
#> TCGA.FD.A43N.01 4 0.0000 0.62339 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA80.01 4 0.0471 0.62493 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.CF.A9FL.01 2 0.3237 -0.58811 0.00 0.60 0.00 0.00 0.00 0.00 0.00 0.40
#> TCGA.E7.A5KE.01 3 0.0000 0.78205 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T0.01 1 0.2267 0.71036 0.82 0.00 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.GU.A42P.01 1 0.2859 0.63846 0.82 0.00 0.00 0.14 0.02 0.00 0.00 0.02
#> TCGA.KQ.A41N.01 2 0.3318 -0.70905 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.XF.AAMG.01 7 0.3504 0.42270 0.26 0.00 0.00 0.04 0.00 0.00 0.70 0.00
#> TCGA.XF.A8HF.01 3 0.1741 0.74752 0.00 0.00 0.92 0.02 0.00 0.00 0.04 0.02
#> TCGA.KQ.A41P.01 4 0.2406 0.39727 0.00 0.00 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.DK.AA6U.01 1 0.1091 0.73382 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.H4.A2HQ.01 2 0.6365 -0.12003 0.10 0.40 0.00 0.00 0.00 0.36 0.10 0.04
#> TCGA.XF.AAMX.01 3 0.0000 0.78205 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node012. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0121"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 23 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5222 0.478 0.478
#> 3 3 0.779 0.956 0.951 0.2180 0.889 0.769
#> 4 4 0.896 0.933 0.937 0.1223 0.893 0.710
#> 5 5 0.795 0.778 0.872 0.0872 1.000 1.000
#> 6 6 0.829 0.790 0.877 0.0556 0.905 0.636
#> 7 7 0.818 0.706 0.866 0.0264 0.980 0.881
#> 8 8 0.857 0.427 0.768 0.0258 0.945 0.689
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.HQ.A2OE.01 2 0 1 0 1
#> TCGA.MV.A51V.01 2 0 1 0 1
#> TCGA.DK.A2I6.01 2 0 1 0 1
#> TCGA.FJ.A3ZF.01 1 0 1 1 0
#> TCGA.4Z.AA87.01 1 0 1 1 0
#> TCGA.UY.A9PD.01 1 0 1 1 0
#> TCGA.G2.A2EL.01 1 0 1 1 0
#> TCGA.GC.A3RB.01 2 0 1 0 1
#> TCGA.DK.A1AD.01 1 0 1 1 0
#> TCGA.G2.A3VY.01 2 0 1 0 1
#> TCGA.K4.A6MB.01 2 0 1 0 1
#> TCGA.E7.A4IJ.01 2 0 1 0 1
#> TCGA.DK.AA75.01 1 0 1 1 0
#> TCGA.GV.A3JZ.01 2 0 1 0 1
#> TCGA.4Z.AA7M.01 1 0 1 1 0
#> TCGA.4Z.AA7R.01 1 0 1 1 0
#> TCGA.FD.A43N.01 1 0 1 1 0
#> TCGA.4Z.AA80.01 1 0 1 1 0
#> TCGA.XF.A9T0.01 2 0 1 0 1
#> TCGA.GU.A42P.01 1 0 1 1 0
#> TCGA.XF.AAMG.01 2 0 1 0 1
#> TCGA.KQ.A41P.01 2 0 1 0 1
#> TCGA.DK.AA6U.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HQ.A2OE.01 2 0.000 0.969 0.00 1.00 0.00
#> TCGA.MV.A51V.01 3 0.369 1.000 0.00 0.14 0.86
#> TCGA.DK.A2I6.01 3 0.369 1.000 0.00 0.14 0.86
#> TCGA.FJ.A3ZF.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.4Z.AA87.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.UY.A9PD.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.G2.A2EL.01 1 0.369 0.889 0.86 0.00 0.14
#> TCGA.GC.A3RB.01 2 0.000 0.969 0.00 1.00 0.00
#> TCGA.DK.A1AD.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.G2.A3VY.01 3 0.369 1.000 0.00 0.14 0.86
#> TCGA.K4.A6MB.01 2 0.000 0.969 0.00 1.00 0.00
#> TCGA.E7.A4IJ.01 2 0.369 0.817 0.00 0.86 0.14
#> TCGA.DK.AA75.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.GV.A3JZ.01 3 0.369 1.000 0.00 0.14 0.86
#> TCGA.4Z.AA7M.01 1 0.369 0.889 0.86 0.00 0.14
#> TCGA.4Z.AA7R.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.FD.A43N.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.4Z.AA80.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.XF.A9T0.01 2 0.000 0.969 0.00 1.00 0.00
#> TCGA.GU.A42P.01 1 0.000 0.965 1.00 0.00 0.00
#> TCGA.XF.AAMG.01 2 0.000 0.969 0.00 1.00 0.00
#> TCGA.KQ.A41P.01 2 0.000 0.969 0.00 1.00 0.00
#> TCGA.DK.AA6U.01 1 0.369 0.889 0.86 0.00 0.14
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.HQ.A2OE.01 2 0.0707 0.972 0.00 0.98 0 0.02
#> TCGA.MV.A51V.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.DK.A2I6.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.FJ.A3ZF.01 1 0.1637 0.928 0.94 0.00 0 0.06
#> TCGA.4Z.AA87.01 1 0.1637 0.928 0.94 0.00 0 0.06
#> TCGA.UY.A9PD.01 1 0.0000 0.964 1.00 0.00 0 0.00
#> TCGA.G2.A2EL.01 4 0.3400 0.642 0.18 0.00 0 0.82
#> TCGA.GC.A3RB.01 2 0.0707 0.972 0.00 0.98 0 0.02
#> TCGA.DK.A1AD.01 1 0.0000 0.964 1.00 0.00 0 0.00
#> TCGA.G2.A3VY.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.K4.A6MB.01 2 0.0707 0.972 0.00 0.98 0 0.02
#> TCGA.E7.A4IJ.01 2 0.1211 0.950 0.00 0.96 0 0.04
#> TCGA.DK.AA75.01 1 0.0000 0.964 1.00 0.00 0 0.00
#> TCGA.GV.A3JZ.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.4Z.AA7M.01 4 0.4948 0.768 0.44 0.00 0 0.56
#> TCGA.4Z.AA7R.01 1 0.1637 0.928 0.94 0.00 0 0.06
#> TCGA.FD.A43N.01 1 0.0000 0.964 1.00 0.00 0 0.00
#> TCGA.4Z.AA80.01 1 0.0000 0.964 1.00 0.00 0 0.00
#> TCGA.XF.A9T0.01 2 0.0000 0.971 0.00 1.00 0 0.00
#> TCGA.GU.A42P.01 1 0.0000 0.964 1.00 0.00 0 0.00
#> TCGA.XF.AAMG.01 2 0.2345 0.911 0.00 0.90 0 0.10
#> TCGA.KQ.A41P.01 2 0.0000 0.971 0.00 1.00 0 0.00
#> TCGA.DK.AA6U.01 4 0.4948 0.768 0.44 0.00 0 0.56
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.HQ.A2OE.01 5 0.141 0.869 0.00 0.06 0 0.00 0.94
#> TCGA.MV.A51V.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DK.A2I6.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FJ.A3ZF.01 1 0.625 0.442 0.50 0.34 0 0.16 0.00
#> TCGA.4Z.AA87.01 1 0.625 0.442 0.50 0.34 0 0.16 0.00
#> TCGA.UY.A9PD.01 1 0.000 0.766 1.00 0.00 0 0.00 0.00
#> TCGA.G2.A2EL.01 4 0.425 0.563 0.02 0.28 0 0.70 0.00
#> TCGA.GC.A3RB.01 5 0.000 0.893 0.00 0.00 0 0.00 1.00
#> TCGA.DK.A1AD.01 1 0.000 0.766 1.00 0.00 0 0.00 0.00
#> TCGA.G2.A3VY.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.K4.A6MB.01 5 0.000 0.893 0.00 0.00 0 0.00 1.00
#> TCGA.E7.A4IJ.01 5 0.437 0.775 0.00 0.08 0 0.16 0.76
#> TCGA.DK.AA75.01 1 0.000 0.766 1.00 0.00 0 0.00 0.00
#> TCGA.GV.A3JZ.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.4Z.AA7M.01 4 0.293 0.758 0.18 0.00 0 0.82 0.00
#> TCGA.4Z.AA7R.01 1 0.610 0.463 0.52 0.34 0 0.14 0.00
#> TCGA.FD.A43N.01 1 0.000 0.766 1.00 0.00 0 0.00 0.00
#> TCGA.4Z.AA80.01 1 0.000 0.766 1.00 0.00 0 0.00 0.00
#> TCGA.XF.A9T0.01 5 0.141 0.894 0.00 0.06 0 0.00 0.94
#> TCGA.GU.A42P.01 1 0.202 0.701 0.90 0.00 0 0.10 0.00
#> TCGA.XF.AAMG.01 5 0.446 0.711 0.00 0.32 0 0.02 0.66
#> TCGA.KQ.A41P.01 5 0.141 0.894 0.00 0.06 0 0.00 0.94
#> TCGA.DK.AA6U.01 4 0.293 0.758 0.18 0.00 0 0.82 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.HQ.A2OE.01 5 0.3706 0.4706 0.00 0.38 0 0.00 0.62 0.00
#> TCGA.MV.A51V.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.DK.A2I6.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.FJ.A3ZF.01 6 0.3309 0.9669 0.28 0.00 0 0.00 0.00 0.72
#> TCGA.4Z.AA87.01 6 0.3309 0.9669 0.28 0.00 0 0.00 0.00 0.72
#> TCGA.UY.A9PD.01 1 0.0000 0.9785 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.G2.A2EL.01 4 0.2474 0.6792 0.00 0.08 0 0.88 0.00 0.04
#> TCGA.GC.A3RB.01 5 0.2048 0.6821 0.00 0.12 0 0.00 0.88 0.00
#> TCGA.DK.A1AD.01 1 0.0000 0.9785 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.G2.A3VY.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.K4.A6MB.01 5 0.2048 0.6821 0.00 0.12 0 0.00 0.88 0.00
#> TCGA.E7.A4IJ.01 5 0.5896 0.0106 0.00 0.10 0 0.32 0.54 0.04
#> TCGA.DK.AA75.01 1 0.0000 0.9785 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.4Z.AA7M.01 4 0.3045 0.8519 0.06 0.00 0 0.84 0.00 0.10
#> TCGA.4Z.AA7R.01 6 0.4711 0.9330 0.28 0.08 0 0.00 0.00 0.64
#> TCGA.FD.A43N.01 1 0.0000 0.9785 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.4Z.AA80.01 1 0.0000 0.9785 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.XF.A9T0.01 5 0.0937 0.6361 0.00 0.00 0 0.00 0.96 0.04
#> TCGA.GU.A42P.01 1 0.1807 0.8865 0.92 0.00 0 0.06 0.00 0.02
#> TCGA.XF.AAMG.01 2 0.5837 0.0000 0.00 0.46 0 0.00 0.34 0.20
#> TCGA.KQ.A41P.01 5 0.0000 0.6590 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.DK.AA6U.01 4 0.3045 0.8519 0.06 0.00 0 0.84 0.00 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.HQ.A2OE.01 7 0.3358 0.000 0.00 0.00 0.00 0.00 0.36 0.00 0.64
#> TCGA.MV.A51V.01 3 0.0000 0.988 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I6.01 3 0.0000 0.988 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FJ.A3ZF.01 6 0.2572 0.896 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.4Z.AA87.01 6 0.2572 0.896 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.UY.A9PD.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EL.01 4 0.3887 0.601 0.02 0.02 0.00 0.70 0.00 0.00 0.26
#> TCGA.GC.A3RB.01 5 0.2376 0.510 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.DK.A1AD.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A3VY.01 3 0.0000 0.988 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A6MB.01 5 0.2376 0.510 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.E7.A4IJ.01 5 0.6853 -0.134 0.00 0.02 0.00 0.30 0.42 0.12 0.14
#> TCGA.DK.AA75.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 3 0.0863 0.964 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.4Z.AA7M.01 4 0.2016 0.820 0.06 0.00 0.00 0.90 0.00 0.04 0.00
#> TCGA.4Z.AA7R.01 6 0.5776 0.780 0.20 0.18 0.00 0.00 0.00 0.56 0.06
#> TCGA.FD.A43N.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA80.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T0.01 5 0.1363 0.536 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.GU.A42P.01 1 0.2422 0.751 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.XF.AAMG.01 2 0.2572 0.000 0.00 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.KQ.A41P.01 5 0.1006 0.539 0.00 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.DK.AA6U.01 4 0.2016 0.820 0.06 0.00 0.00 0.90 0.00 0.04 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.HQ.A2OE.01 7 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MV.A51V.01 3 0.0000 0.9318 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I6.01 3 0.0000 0.9318 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FJ.A3ZF.01 5 0.6608 -0.4922 0.08 0.04 0.00 0.00 0.36 0.34 0.00 0.18
#> TCGA.4Z.AA87.01 5 0.6364 -0.4922 0.08 0.02 0.00 0.00 0.38 0.34 0.00 0.18
#> TCGA.UY.A9PD.01 1 0.0000 0.9339 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EL.01 4 0.0000 0.2563 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RB.01 5 0.3729 0.0952 0.00 0.00 0.00 0.00 0.52 0.02 0.46 0.00
#> TCGA.DK.A1AD.01 1 0.0000 0.9339 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A3VY.01 3 0.0000 0.9318 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A6MB.01 5 0.3729 0.0952 0.00 0.00 0.00 0.00 0.52 0.02 0.46 0.00
#> TCGA.E7.A4IJ.01 8 0.6426 0.0000 0.00 0.02 0.00 0.16 0.10 0.00 0.34 0.38
#> TCGA.DK.AA75.01 1 0.0000 0.9339 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JZ.01 3 0.3154 0.7755 0.00 0.00 0.78 0.00 0.00 0.06 0.00 0.16
#> TCGA.4Z.AA7M.01 4 0.4562 0.6412 0.00 0.00 0.00 0.46 0.00 0.10 0.00 0.44
#> TCGA.4Z.AA7R.01 6 0.1341 0.0000 0.08 0.00 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.FD.A43N.01 1 0.0000 0.9339 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA80.01 1 0.0000 0.9339 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T0.01 5 0.3942 0.1117 0.00 0.02 0.00 0.00 0.62 0.00 0.34 0.02
#> TCGA.GU.A42P.01 1 0.2852 0.6058 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.XF.AAMG.01 2 0.0941 0.0000 0.00 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.KQ.A41P.01 5 0.3618 0.1293 0.00 0.02 0.00 0.00 0.60 0.00 0.38 0.00
#> TCGA.DK.AA6U.01 4 0.4562 0.6412 0.00 0.00 0.00 0.46 0.00 0.10 0.00 0.44
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["013"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 42 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.903 0.925 0.971 0.49865 0.498 0.498
#> 3 3 1.000 0.997 0.999 0.34889 0.708 0.478
#> 4 4 0.980 0.967 0.983 0.12172 0.891 0.678
#> 5 5 0.920 0.890 0.933 0.04348 0.944 0.779
#> 6 6 0.895 0.786 0.895 0.02967 0.991 0.955
#> 7 7 0.858 0.746 0.861 0.02105 0.981 0.908
#> 8 8 0.877 0.705 0.821 0.00952 0.986 0.929
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.FD.A3N6.01 1 0.000 0.9748 1.00 0.00
#> TCGA.XF.A8HG.01 2 0.000 0.9579 0.00 1.00
#> TCGA.CF.A47T.01 1 0.000 0.9748 1.00 0.00
#> TCGA.DK.A1AA.01 1 0.000 0.9748 1.00 0.00
#> TCGA.GC.A3RD.01 1 0.000 0.9748 1.00 0.00
#> TCGA.DK.A1AE.01 1 0.000 0.9748 1.00 0.00
#> TCGA.4Z.AA7O.01 2 0.634 0.8082 0.16 0.84
#> TCGA.G2.AA3B.01 2 0.000 0.9579 0.00 1.00
#> TCGA.GU.A763.01 1 0.000 0.9748 1.00 0.00
#> TCGA.2F.A9KR.01 1 0.000 0.9748 1.00 0.00
#> TCGA.CF.A8HX.01 2 0.000 0.9579 0.00 1.00
#> TCGA.CF.A27C.01 1 0.000 0.9748 1.00 0.00
#> TCGA.BL.A0C8.01 2 0.000 0.9579 0.00 1.00
#> TCGA.YF.AA3M.01 2 0.000 0.9579 0.00 1.00
#> TCGA.GC.A3BM.01 1 0.000 0.9748 1.00 0.00
#> TCGA.FD.A43X.01 2 0.634 0.8082 0.16 0.84
#> TCGA.KQ.A41Q.01 2 0.000 0.9579 0.00 1.00
#> TCGA.CF.A47X.01 1 0.000 0.9748 1.00 0.00
#> TCGA.GD.A6C6.01 1 0.000 0.9748 1.00 0.00
#> TCGA.G2.A3IB.01 1 0.000 0.9748 1.00 0.00
#> TCGA.CU.A3KJ.01 1 0.000 0.9748 1.00 0.00
#> TCGA.LT.A8JT.01 2 0.000 0.9579 0.00 1.00
#> TCGA.5N.A9KM.01 2 0.000 0.9579 0.00 1.00
#> TCGA.DK.AA6P.01 1 0.000 0.9748 1.00 0.00
#> TCGA.FD.A3B5.01 1 0.000 0.9748 1.00 0.00
#> TCGA.DK.A6B1.01 2 0.000 0.9579 0.00 1.00
#> TCGA.5N.A9KI.01 2 0.000 0.9579 0.00 1.00
#> TCGA.S5.AA26.01 1 0.995 0.0637 0.54 0.46
#> TCGA.E5.A4U1.01 2 0.943 0.4517 0.36 0.64
#> TCGA.HQ.A5ND.01 1 0.000 0.9748 1.00 0.00
#> TCGA.BT.A42C.01 2 0.000 0.9579 0.00 1.00
#> TCGA.E7.A8O8.01 2 0.000 0.9579 0.00 1.00
#> TCGA.2F.A9KP.01 2 0.000 0.9579 0.00 1.00
#> TCGA.ZF.A9R2.01 1 0.000 0.9748 1.00 0.00
#> TCGA.E7.A3Y1.01 1 0.000 0.9748 1.00 0.00
#> TCGA.CU.A3QU.01 2 0.000 0.9579 0.00 1.00
#> TCGA.UY.A78M.01 1 0.402 0.8916 0.92 0.08
#> TCGA.K4.A5RI.01 1 0.000 0.9748 1.00 0.00
#> TCGA.DK.AA77.01 1 0.000 0.9748 1.00 0.00
#> TCGA.E7.A97Q.01 2 0.000 0.9579 0.00 1.00
#> TCGA.DK.A3X2.01 1 0.000 0.9748 1.00 0.00
#> TCGA.ZF.A9RN.01 1 0.000 0.9748 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FD.A3N6.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.XF.A8HG.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.CF.A47T.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.DK.A1AA.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.GC.A3RD.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.DK.A1AE.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.4Z.AA7O.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.G2.AA3B.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.GU.A763.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.2F.A9KR.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.CF.A8HX.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.CF.A27C.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.BL.A0C8.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.YF.AA3M.01 2 0.0892 0.979 0.02 0.98 0
#> TCGA.GC.A3BM.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.FD.A43X.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.KQ.A41Q.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.CF.A47X.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.GD.A6C6.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.G2.A3IB.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.CU.A3KJ.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.LT.A8JT.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.5N.A9KM.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.DK.AA6P.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.FD.A3B5.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.DK.A6B1.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.5N.A9KI.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.S5.AA26.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.E5.A4U1.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.HQ.A5ND.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.BT.A42C.01 2 0.0892 0.979 0.02 0.98 0
#> TCGA.E7.A8O8.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.2F.A9KP.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.ZF.A9R2.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.E7.A3Y1.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.CU.A3QU.01 2 0.0000 0.997 0.00 1.00 0
#> TCGA.UY.A78M.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.K4.A5RI.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.DK.AA77.01 1 0.0000 0.999 1.00 0.00 0
#> TCGA.E7.A97Q.01 1 0.0892 0.979 0.98 0.02 0
#> TCGA.DK.A3X2.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.ZF.A9RN.01 3 0.0000 1.000 0.00 0.00 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FD.A3N6.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.XF.A8HG.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.CF.A47T.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.DK.A1AA.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.GC.A3RD.01 4 0.000 0.901 0.00 0.00 0 1.00
#> TCGA.DK.A1AE.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.4Z.AA7O.01 1 0.292 0.826 0.86 0.00 0 0.14
#> TCGA.G2.AA3B.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.GU.A763.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.2F.A9KR.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.CF.A8HX.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.CF.A27C.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.BL.A0C8.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.YF.AA3M.01 4 0.361 0.786 0.00 0.20 0 0.80
#> TCGA.GC.A3BM.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.FD.A43X.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.KQ.A41Q.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.CF.A47X.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.GD.A6C6.01 4 0.000 0.901 0.00 0.00 0 1.00
#> TCGA.G2.A3IB.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.CU.A3KJ.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.LT.A8JT.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.5N.A9KM.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.DK.AA6P.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.FD.A3B5.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.DK.A6B1.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.5N.A9KI.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.S5.AA26.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.E5.A4U1.01 4 0.317 0.781 0.16 0.00 0 0.84
#> TCGA.HQ.A5ND.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.BT.A42C.01 4 0.380 0.763 0.00 0.22 0 0.78
#> TCGA.E7.A8O8.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.2F.A9KP.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.ZF.A9R2.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.E7.A3Y1.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.CU.A3QU.01 2 0.000 1.000 0.00 1.00 0 0.00
#> TCGA.UY.A78M.01 4 0.000 0.901 0.00 0.00 0 1.00
#> TCGA.K4.A5RI.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.DK.AA77.01 1 0.000 0.986 1.00 0.00 0 0.00
#> TCGA.E7.A97Q.01 4 0.000 0.901 0.00 0.00 0 1.00
#> TCGA.DK.A3X2.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.ZF.A9RN.01 3 0.000 1.000 0.00 0.00 1 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FD.A3N6.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.A8HG.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AA.01 1 0.1410 0.870 0.94 0.00 0.00 0.00 0.06
#> TCGA.GC.A3RD.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A1AE.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7O.01 5 0.4456 0.507 0.32 0.00 0.00 0.02 0.66
#> TCGA.G2.AA3B.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 1 0.0609 0.895 0.98 0.00 0.00 0.00 0.02
#> TCGA.2F.A9KR.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.CF.A8HX.01 2 0.1410 0.944 0.00 0.94 0.00 0.00 0.06
#> TCGA.CF.A27C.01 1 0.3109 0.778 0.80 0.00 0.00 0.00 0.20
#> TCGA.BL.A0C8.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 5 0.5597 0.491 0.00 0.20 0.00 0.16 0.64
#> TCGA.GC.A3BM.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 5 0.3983 0.447 0.34 0.00 0.00 0.00 0.66
#> TCGA.KQ.A41Q.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 1 0.2929 0.798 0.82 0.00 0.00 0.00 0.18
#> TCGA.GD.A6C6.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.G2.A3IB.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A3KJ.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.LT.A8JT.01 2 0.1410 0.944 0.00 0.94 0.00 0.00 0.06
#> TCGA.5N.A9KM.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.AA6P.01 3 0.0609 0.981 0.00 0.00 0.98 0.00 0.02
#> TCGA.FD.A3B5.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A6B1.01 2 0.1043 0.956 0.00 0.96 0.00 0.00 0.04
#> TCGA.5N.A9KI.01 2 0.0609 0.972 0.00 0.98 0.00 0.00 0.02
#> TCGA.S5.AA26.01 5 0.2516 0.612 0.14 0.00 0.00 0.00 0.86
#> TCGA.E5.A4U1.01 5 0.5888 0.453 0.14 0.00 0.00 0.28 0.58
#> TCGA.HQ.A5ND.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A42C.01 5 0.5555 0.492 0.00 0.22 0.00 0.14 0.64
#> TCGA.E7.A8O8.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.2F.A9KP.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R2.01 1 0.2929 0.798 0.82 0.00 0.00 0.00 0.18
#> TCGA.E7.A3Y1.01 1 0.0609 0.895 0.98 0.00 0.00 0.00 0.02
#> TCGA.CU.A3QU.01 2 0.0000 0.984 0.00 1.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.K4.A5RI.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.AA77.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A97Q.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A3X2.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9RN.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FD.A3N6.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A8HG.01 2 0.0000 0.9372 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.1556 0.7059 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DK.A1AA.01 1 0.3409 0.4288 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.GC.A3RD.01 4 0.0547 0.9671 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DK.A1AE.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7O.01 6 0.6721 0.4805 0.20 0.00 0.00 0.06 0.28 0.46
#> TCGA.G2.AA3B.01 2 0.0000 0.9372 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 1 0.0000 0.7399 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KR.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 2 0.2094 0.8921 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.CF.A27C.01 1 0.4806 0.2177 0.56 0.00 0.00 0.00 0.06 0.38
#> TCGA.BL.A0C8.01 2 0.0000 0.9372 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 5 0.1556 0.5162 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.GC.A3BM.01 1 0.0000 0.7399 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 6 0.4613 0.5566 0.26 0.00 0.00 0.00 0.08 0.66
#> TCGA.KQ.A41Q.01 2 0.0000 0.9372 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 1 0.4798 0.4268 0.62 0.00 0.00 0.00 0.08 0.30
#> TCGA.GD.A6C6.01 4 0.0000 0.9822 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.A3IB.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CU.A3KJ.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LT.A8JT.01 2 0.2094 0.8921 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.5N.A9KM.01 2 0.0000 0.9372 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6P.01 3 0.0547 0.9777 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.FD.A3B5.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 2 0.3409 0.6183 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.5N.A9KI.01 2 0.2350 0.8548 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.S5.AA26.01 5 0.5265 -0.0643 0.10 0.00 0.00 0.00 0.50 0.40
#> TCGA.E5.A4U1.01 5 0.7023 0.1623 0.08 0.00 0.00 0.20 0.38 0.34
#> TCGA.HQ.A5ND.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A42C.01 5 0.1480 0.5116 0.00 0.02 0.00 0.04 0.94 0.00
#> TCGA.E7.A8O8.01 2 0.1807 0.9034 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.2F.A9KP.01 2 0.0000 0.9372 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R2.01 1 0.4328 0.5585 0.72 0.00 0.00 0.00 0.10 0.18
#> TCGA.E7.A3Y1.01 1 0.0000 0.7399 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 2 0.0000 0.9372 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 4 0.0000 0.9822 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A5RI.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.AA77.01 1 0.0937 0.7278 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.E7.A97Q.01 4 0.0547 0.9718 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DK.A3X2.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9RN.01 3 0.0000 0.9978 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FD.A3N6.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HG.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.1718 0.725 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.DK.A1AA.01 1 0.3745 0.545 0.70 0.00 0.00 0.00 0.00 0.26 0.04
#> TCGA.GC.A3RD.01 4 0.0000 0.985 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A1AE.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7O.01 6 0.6202 0.491 0.24 0.00 0.00 0.06 0.08 0.56 0.06
#> TCGA.G2.AA3B.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 1 0.0504 0.721 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.2F.A9KR.01 3 0.1664 0.931 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.CF.A8HX.01 2 0.4702 0.647 0.00 0.68 0.00 0.00 0.20 0.08 0.04
#> TCGA.CF.A27C.01 1 0.5047 0.275 0.52 0.00 0.00 0.00 0.00 0.34 0.14
#> TCGA.BL.A0C8.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 5 0.4392 0.974 0.00 0.06 0.00 0.10 0.76 0.02 0.06
#> TCGA.GC.A3BM.01 1 0.1664 0.716 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.FD.A43X.01 6 0.3208 0.509 0.12 0.00 0.00 0.00 0.02 0.82 0.04
#> TCGA.KQ.A41Q.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 7 0.3909 0.232 0.40 0.00 0.00 0.00 0.00 0.02 0.58
#> TCGA.GD.A6C6.01 4 0.0000 0.985 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G2.A3IB.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3KJ.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LT.A8JT.01 2 0.4569 0.664 0.00 0.70 0.00 0.00 0.18 0.08 0.04
#> TCGA.5N.A9KM.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6P.01 3 0.2159 0.914 0.02 0.00 0.90 0.00 0.00 0.02 0.06
#> TCGA.FD.A3B5.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 2 0.3459 0.330 0.00 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.5N.A9KI.01 2 0.3139 0.536 0.00 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.S5.AA26.01 6 0.6234 0.203 0.06 0.00 0.00 0.00 0.20 0.44 0.30
#> TCGA.E5.A4U1.01 7 0.6080 0.304 0.06 0.00 0.00 0.18 0.10 0.06 0.60
#> TCGA.HQ.A5ND.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42C.01 5 0.4110 0.974 0.00 0.06 0.00 0.10 0.78 0.02 0.04
#> TCGA.E7.A8O8.01 2 0.4298 0.689 0.00 0.74 0.00 0.00 0.10 0.04 0.12
#> TCGA.2F.A9KP.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R2.01 1 0.4244 -0.156 0.54 0.00 0.00 0.00 0.00 0.04 0.42
#> TCGA.E7.A3Y1.01 1 0.1006 0.703 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.CU.A3QU.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 4 0.0000 0.985 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A5RI.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA77.01 1 0.1664 0.724 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.E7.A97Q.01 4 0.1006 0.954 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.DK.A3X2.01 3 0.0504 0.972 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.ZF.A9RN.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FD.A3N6.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HG.01 2 0.0471 0.8017 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CF.A47T.01 1 0.0471 0.6951 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.A1AA.01 1 0.3431 0.5499 0.74 0.00 0.00 0.00 0.00 0.20 0.06 0.00
#> TCGA.GC.A3RD.01 8 0.0000 0.9480 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DK.A1AE.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7O.01 6 0.6957 0.3409 0.18 0.00 0.00 0.04 0.10 0.50 0.10 0.08
#> TCGA.G2.AA3B.01 2 0.0000 0.8094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A763.01 1 0.0941 0.6857 0.96 0.00 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.2F.A9KR.01 3 0.1408 0.9448 0.00 0.00 0.94 0.02 0.00 0.02 0.02 0.00
#> TCGA.CF.A8HX.01 2 0.4125 0.4357 0.00 0.52 0.00 0.44 0.02 0.02 0.00 0.00
#> TCGA.CF.A27C.01 1 0.5683 0.0852 0.42 0.00 0.00 0.04 0.00 0.34 0.20 0.00
#> TCGA.BL.A0C8.01 2 0.0000 0.8094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YF.AA3M.01 5 0.1887 0.9196 0.00 0.04 0.00 0.00 0.90 0.00 0.00 0.06
#> TCGA.GC.A3BM.01 1 0.0000 0.6971 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43X.01 6 0.3263 0.3026 0.10 0.00 0.00 0.00 0.00 0.78 0.12 0.00
#> TCGA.KQ.A41Q.01 2 0.0000 0.8094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A47X.01 1 0.6955 0.0780 0.40 0.00 0.00 0.16 0.06 0.14 0.24 0.00
#> TCGA.GD.A6C6.01 8 0.0000 0.9480 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G2.A3IB.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3KJ.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LT.A8JT.01 2 0.3658 0.5033 0.00 0.58 0.00 0.40 0.02 0.00 0.00 0.00
#> TCGA.5N.A9KM.01 2 0.0000 0.8094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6P.01 3 0.1408 0.9448 0.00 0.00 0.94 0.02 0.00 0.02 0.02 0.00
#> TCGA.FD.A3B5.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 2 0.2852 0.5587 0.00 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.5N.A9KI.01 2 0.3198 0.5501 0.00 0.72 0.00 0.02 0.26 0.00 0.00 0.00
#> TCGA.S5.AA26.01 7 0.4460 -0.1379 0.06 0.00 0.00 0.00 0.12 0.12 0.70 0.00
#> TCGA.E5.A4U1.01 7 0.8029 0.0993 0.06 0.00 0.00 0.22 0.12 0.10 0.30 0.20
#> TCGA.HQ.A5ND.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42C.01 5 0.2482 0.9196 0.00 0.06 0.00 0.00 0.88 0.02 0.02 0.02
#> TCGA.E7.A8O8.01 2 0.5044 0.3422 0.00 0.50 0.00 0.40 0.04 0.02 0.04 0.00
#> TCGA.2F.A9KP.01 2 0.0000 0.8094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R2.01 1 0.5322 0.4959 0.64 0.00 0.00 0.06 0.04 0.16 0.10 0.00
#> TCGA.E7.A3Y1.01 1 0.2071 0.6624 0.90 0.00 0.00 0.04 0.00 0.02 0.04 0.00
#> TCGA.CU.A3QU.01 2 0.0000 0.8094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78M.01 8 0.0471 0.9370 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.K4.A5RI.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA77.01 1 0.1741 0.6872 0.92 0.00 0.00 0.00 0.00 0.04 0.02 0.02
#> TCGA.E7.A97Q.01 8 0.2348 0.8626 0.00 0.00 0.00 0.06 0.02 0.04 0.00 0.88
#> TCGA.DK.A3X2.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RN.01 3 0.0000 0.9881 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node013. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0132"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 12 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.591 0.838 0.920 0.3763 0.697 0.697
#> 3 3 1.000 1.000 1.000 0.7725 0.636 0.478
#> 4 4 0.788 0.962 0.967 0.1907 0.803 0.458
#> 5 5 0.879 0.829 0.885 0.0503 1.000 1.000
#> 6 6 0.864 0.560 0.873 0.0449 0.924 0.615
#> 7 7 0.864 0.618 0.870 0.0344 0.970 0.750
#> 8 8 0.833 0.403 0.828 0.0235 0.985 0.833
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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.XF.A8HG.01 2 0.000 0.879 0.00 1.00
#> TCGA.G2.AA3B.01 2 0.000 0.879 0.00 1.00
#> TCGA.CF.A8HX.01 2 0.000 0.879 0.00 1.00
#> TCGA.BL.A0C8.01 2 0.904 0.634 0.32 0.68
#> TCGA.KQ.A41Q.01 2 0.904 0.634 0.32 0.68
#> TCGA.LT.A8JT.01 2 0.000 0.879 0.00 1.00
#> TCGA.5N.A9KM.01 2 0.000 0.879 0.00 1.00
#> TCGA.DK.A6B1.01 1 0.000 1.000 1.00 0.00
#> TCGA.5N.A9KI.01 2 0.904 0.634 0.32 0.68
#> TCGA.E7.A8O8.01 2 0.000 0.879 0.00 1.00
#> TCGA.2F.A9KP.01 2 0.000 0.879 0.00 1.00
#> TCGA.CU.A3QU.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.XF.A8HG.01 2 0 1 0 1 0
#> TCGA.G2.AA3B.01 3 0 1 0 0 1
#> TCGA.CF.A8HX.01 2 0 1 0 1 0
#> TCGA.BL.A0C8.01 3 0 1 0 0 1
#> TCGA.KQ.A41Q.01 3 0 1 0 0 1
#> TCGA.LT.A8JT.01 2 0 1 0 1 0
#> TCGA.5N.A9KM.01 2 0 1 0 1 0
#> TCGA.DK.A6B1.01 1 0 1 1 0 0
#> TCGA.5N.A9KI.01 3 0 1 0 0 1
#> TCGA.E7.A8O8.01 2 0 1 0 1 0
#> TCGA.2F.A9KP.01 2 0 1 0 1 0
#> TCGA.CU.A3QU.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.XF.A8HG.01 2 0.000 1.000 0 1.0 0.0 0.0
#> TCGA.G2.AA3B.01 4 0.234 0.861 0 0.0 0.1 0.9
#> TCGA.CF.A8HX.01 2 0.000 1.000 0 1.0 0.0 0.0
#> TCGA.BL.A0C8.01 3 0.000 0.954 0 0.0 1.0 0.0
#> TCGA.KQ.A41Q.01 3 0.000 0.954 0 0.0 1.0 0.0
#> TCGA.LT.A8JT.01 2 0.000 1.000 0 1.0 0.0 0.0
#> TCGA.5N.A9KM.01 4 0.234 0.932 0 0.1 0.0 0.9
#> TCGA.DK.A6B1.01 1 0.000 1.000 1 0.0 0.0 0.0
#> TCGA.5N.A9KI.01 3 0.234 0.907 0 0.0 0.9 0.1
#> TCGA.E7.A8O8.01 2 0.000 1.000 0 1.0 0.0 0.0
#> TCGA.2F.A9KP.01 4 0.234 0.932 0 0.1 0.0 0.9
#> TCGA.CU.A3QU.01 1 0.000 1.000 1 0.0 0.0 0.0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.XF.A8HG.01 2 0.389 0.785 0.32 0.68 0.00 0.00 0.00
#> TCGA.G2.AA3B.01 4 0.104 0.943 0.00 0.00 0.04 0.96 0.00
#> TCGA.CF.A8HX.01 2 0.000 0.844 0.00 1.00 0.00 0.00 0.00
#> TCGA.BL.A0C8.01 3 0.000 0.796 0.00 0.00 1.00 0.00 0.00
#> TCGA.KQ.A41Q.01 3 0.000 0.796 0.00 0.00 1.00 0.00 0.00
#> TCGA.LT.A8JT.01 2 0.327 0.832 0.22 0.78 0.00 0.00 0.00
#> TCGA.5N.A9KM.01 4 0.104 0.972 0.00 0.04 0.00 0.96 0.00
#> TCGA.DK.A6B1.01 5 0.425 0.806 0.22 0.00 0.00 0.04 0.74
#> TCGA.5N.A9KI.01 3 0.429 0.549 0.46 0.00 0.54 0.00 0.00
#> TCGA.E7.A8O8.01 2 0.000 0.844 0.00 1.00 0.00 0.00 0.00
#> TCGA.2F.A9KP.01 4 0.104 0.972 0.00 0.04 0.00 0.96 0.00
#> TCGA.CU.A3QU.01 5 0.000 0.806 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.XF.A8HG.01 1 0.5575 0.000 0.46 0.40 0.00 0.00 0.00 0.14
#> TCGA.G2.AA3B.01 4 0.0547 0.980 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.CF.A8HX.01 2 0.0000 0.577 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A0C8.01 3 0.2793 0.784 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 3 0.0000 0.784 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LT.A8JT.01 2 0.3864 -0.549 0.48 0.52 0.00 0.00 0.00 0.00
#> TCGA.5N.A9KM.01 4 0.0000 0.990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A6B1.01 5 0.3679 0.791 0.20 0.00 0.00 0.00 0.76 0.04
#> TCGA.5N.A9KI.01 6 0.2631 0.000 0.00 0.00 0.18 0.00 0.00 0.82
#> TCGA.E7.A8O8.01 2 0.0000 0.577 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KP.01 4 0.0000 0.990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A3QU.01 5 0.0000 0.791 0.00 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.XF.A8HG.01 1 0.341 0.000 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.G2.AA3B.01 4 0.208 0.863 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.CF.A8HX.01 2 0.384 0.955 0.00 0.68 0.00 0.00 0.00 0.04 0.28
#> TCGA.BL.A0C8.01 3 0.000 0.614 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 3 0.463 0.615 0.26 0.12 0.62 0.00 0.00 0.00 0.00
#> TCGA.LT.A8JT.01 7 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.5N.A9KM.01 4 0.000 0.934 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 5 0.418 0.770 0.06 0.16 0.00 0.00 0.74 0.04 0.00
#> TCGA.5N.A9KI.01 6 0.143 0.000 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.E7.A8O8.01 2 0.305 0.955 0.00 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.2F.A9KP.01 4 0.000 0.934 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 5 0.000 0.770 0.00 0.00 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.XF.A8HG.01 1 0.3329 0.000 0.52 0.00 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.G2.AA3B.01 4 0.4759 0.407 0.36 0.00 0.00 0.50 0.00 0.00 0.00 0.14
#> TCGA.CF.A8HX.01 2 0.2650 0.888 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.BL.A0C8.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41Q.01 8 0.2534 0.000 0.00 0.00 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.LT.A8JT.01 7 0.0471 0.000 0.00 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.5N.A9KM.01 4 0.1091 0.734 0.00 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B1.01 5 0.5593 0.591 0.12 0.18 0.00 0.00 0.56 0.00 0.00 0.14
#> TCGA.5N.A9KI.01 6 0.0471 0.000 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.E7.A8O8.01 2 0.4314 0.888 0.00 0.66 0.00 0.00 0.00 0.02 0.24 0.08
#> TCGA.2F.A9KP.01 4 0.0000 0.734 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A3QU.01 5 0.0000 0.591 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031-leaf , Node032 , Node033 .
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 118 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 0.964 0.937 0.973 0.5021 0.499 0.499
#> 3 3 1.000 0.995 0.997 0.2515 0.621 0.394
#> 4 4 0.690 0.809 0.873 0.1392 0.775 0.474
#> 5 5 0.763 0.454 0.784 0.0726 0.906 0.677
#> 6 6 0.767 0.717 0.861 0.0337 0.918 0.684
#> 7 7 0.771 0.664 0.856 0.0158 0.980 0.903
#> 8 8 0.822 0.745 0.872 0.0178 0.949 0.759
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.GD.A3OP.01 2 0.000 1.000 0.00 1.00
#> TCGA.4Z.AA86.01 2 0.000 1.000 0.00 1.00
#> TCGA.BL.A13J.11 1 0.000 0.948 1.00 0.00
#> TCGA.GU.A42Q.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A5BU.01 1 0.327 0.902 0.94 0.06
#> TCGA.E7.A6MF.01 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A43P.01 2 0.000 1.000 0.00 1.00
#> TCGA.BT.A20W.11 1 0.000 0.948 1.00 0.00
#> TCGA.UY.A78P.01 1 0.000 0.948 1.00 0.00
#> TCGA.DK.AA6X.01 2 0.000 1.000 0.00 1.00
#> TCGA.K4.A6FZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.GC.A3OO.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.AAN5.01 2 0.000 1.000 0.00 1.00
#> TCGA.DK.A2I2.01 1 0.981 0.361 0.58 0.42
#> TCGA.CF.A1HS.01 2 0.000 1.000 0.00 1.00
#> TCGA.4Z.AA7W.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.A9SI.01 1 0.000 0.948 1.00 0.00
#> TCGA.K4.A5RH.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.A9SM.01 1 0.000 0.948 1.00 0.00
#> TCGA.GC.A3BM.11 1 0.000 0.948 1.00 0.00
#> TCGA.DK.A3IU.01 2 0.000 1.000 0.00 1.00
#> TCGA.E7.A7XN.01 1 0.981 0.361 0.58 0.42
#> TCGA.K4.A5RI.11 1 0.000 0.948 1.00 0.00
#> TCGA.K4.A3WV.11 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A3B3.01 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A6TF.01 2 0.000 1.000 0.00 1.00
#> TCGA.GD.A3OQ.11 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A43Y.01 2 0.000 1.000 0.00 1.00
#> TCGA.GU.A767.01 2 0.000 1.000 0.00 1.00
#> TCGA.CU.A0YN.11 1 0.000 0.948 1.00 0.00
#> TCGA.YC.A8S6.01 1 0.000 0.948 1.00 0.00
#> TCGA.CU.A0YO.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.A9T5.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A62P.01 2 0.000 1.000 0.00 1.00
#> TCGA.DK.AA74.01 1 0.000 0.948 1.00 0.00
#> TCGA.BT.A20U.11 2 0.000 1.000 0.00 1.00
#> TCGA.K4.A83P.01 1 0.000 0.948 1.00 0.00
#> TCGA.XF.AAN8.01 1 0.000 0.948 1.00 0.00
#> TCGA.BT.A42F.01 1 0.958 0.454 0.62 0.38
#> TCGA.FT.A61P.01 2 0.000 1.000 0.00 1.00
#> TCGA.BT.A20J.11 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A5BS.01 1 0.000 0.948 1.00 0.00
#> TCGA.XF.A9SX.01 2 0.000 1.000 0.00 1.00
#> TCGA.DK.A3IQ.01 1 0.981 0.361 0.58 0.42
#> TCGA.FD.A3B8.01 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A3B7.01 1 0.000 0.948 1.00 0.00
#> TCGA.DK.A1AB.01 1 0.000 0.948 1.00 0.00
#> TCGA.K4.A3WU.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A62N.01 2 0.000 1.000 0.00 1.00
#> TCGA.UY.A9PB.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.A9ST.01 2 0.000 1.000 0.00 1.00
#> TCGA.GU.A766.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A6TB.01 1 0.242 0.919 0.96 0.04
#> TCGA.GU.A762.01 2 0.000 1.000 0.00 1.00
#> TCGA.K4.A3WS.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.AAME.01 1 0.000 0.948 1.00 0.00
#> TCGA.XF.A9T8.01 2 0.000 1.000 0.00 1.00
#> TCGA.G2.AA3D.01 2 0.000 1.000 0.00 1.00
#> TCGA.K4.A5RJ.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZF.A9RG.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A5C0.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZF.A9RD.01 2 0.000 1.000 0.00 1.00
#> TCGA.BT.A20O.01 1 0.141 0.935 0.98 0.02
#> TCGA.FD.A3SO.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A43S.01 1 0.000 0.948 1.00 0.00
#> TCGA.XF.A8HE.01 1 0.000 0.948 1.00 0.00
#> TCGA.GC.A3WC.01 1 0.000 0.948 1.00 0.00
#> TCGA.XF.A9SY.01 1 0.000 0.948 1.00 0.00
#> TCGA.GD.A2C5.11 1 0.000 0.948 1.00 0.00
#> TCGA.CU.A0YR.01 2 0.000 1.000 0.00 1.00
#> TCGA.4Z.AA7N.01 1 0.000 0.948 1.00 0.00
#> TCGA.K4.A54R.11 1 0.000 0.948 1.00 0.00
#> TCGA.DK.A3WY.01 1 0.000 0.948 1.00 0.00
#> TCGA.ZF.AA53.01 1 0.000 0.948 1.00 0.00
#> TCGA.DK.A1AF.01 1 0.000 0.948 1.00 0.00
#> TCGA.BT.A20P.11 1 0.000 0.948 1.00 0.00
#> TCGA.BT.A2LA.11 1 0.000 0.948 1.00 0.00
#> TCGA.DK.AA6T.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZF.AA58.01 2 0.000 1.000 0.00 1.00
#> TCGA.BT.A20X.11 1 0.000 0.948 1.00 0.00
#> TCGA.GC.A6I3.11 1 0.000 0.948 1.00 0.00
#> TCGA.XF.AAN4.01 1 0.000 0.948 1.00 0.00
#> TCGA.GD.A3OP.11 1 0.000 0.948 1.00 0.00
#> TCGA.XF.AAMJ.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.AAMZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.BT.A20V.11 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A5BT.01 1 0.000 0.948 1.00 0.00
#> TCGA.PQ.A6FN.01 2 0.000 1.000 0.00 1.00
#> TCGA.BT.A20U.01 2 0.000 1.000 0.00 1.00
#> TCGA.SY.A9G0.01 1 0.925 0.534 0.66 0.34
#> TCGA.K4.A4AC.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A43U.01 2 0.000 1.000 0.00 1.00
#> TCGA.GC.A3WC.11 1 0.000 0.948 1.00 0.00
#> TCGA.DK.A3WX.01 1 0.000 0.948 1.00 0.00
#> TCGA.E7.A85H.01 2 0.000 1.000 0.00 1.00
#> TCGA.GU.A764.01 1 0.000 0.948 1.00 0.00
#> TCGA.DK.A2I4.01 2 0.000 1.000 0.00 1.00
#> TCGA.CU.A0YR.11 1 0.000 0.948 1.00 0.00
#> TCGA.BL.A13I.01 1 0.242 0.919 0.96 0.04
#> TCGA.GD.A3OS.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A6TK.01 1 0.971 0.409 0.60 0.40
#> TCGA.BT.A3PK.01 1 0.981 0.361 0.58 0.42
#> TCGA.XF.A9SW.01 2 0.000 1.000 0.00 1.00
#> TCGA.FD.A3B4.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.AAN0.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZF.AA4W.01 1 0.000 0.948 1.00 0.00
#> TCGA.UY.A9PA.01 1 0.000 0.948 1.00 0.00
#> TCGA.FJ.A871.01 2 0.000 1.000 0.00 1.00
#> TCGA.XF.A9SL.01 1 0.000 0.948 1.00 0.00
#> TCGA.CF.A5UA.01 2 0.000 1.000 0.00 1.00
#> TCGA.BT.A20R.11 1 0.000 0.948 1.00 0.00
#> TCGA.R3.A69X.01 1 0.141 0.935 0.98 0.02
#> TCGA.E7.A519.01 2 0.000 1.000 0.00 1.00
#> TCGA.CF.A9FM.01 1 0.000 0.948 1.00 0.00
#> TCGA.XF.AAMR.01 1 0.722 0.751 0.80 0.20
#> TCGA.BT.A20N.11 1 0.000 0.948 1.00 0.00
#> TCGA.ZF.AA5P.01 1 0.000 0.948 1.00 0.00
#> TCGA.FD.A3SP.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.GD.A3OP.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.4Z.AA86.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.BL.A13J.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.GU.A42Q.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FD.A5BU.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.E7.A6MF.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.FD.A43P.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BT.A20W.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.UY.A78P.01 1 0.0892 0.977 0.98 0.02 0.00
#> TCGA.DK.AA6X.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.K4.A6FZ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.GC.A3OO.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.XF.AAN5.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DK.A2I2.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.CF.A1HS.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.4Z.AA7W.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.XF.A9SI.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.K4.A5RH.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.XF.A9SM.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.GC.A3BM.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.DK.A3IU.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.E7.A7XN.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.K4.A5RI.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.K4.A3WV.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.FD.A3B3.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FD.A6TF.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.GD.A3OQ.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.FD.A43Y.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.GU.A767.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CU.A0YN.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.YC.A8S6.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.CU.A0YO.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.XF.A9T5.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FD.A62P.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.DK.AA74.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.BT.A20U.11 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.K4.A83P.01 1 0.1529 0.953 0.96 0.04 0.00
#> TCGA.XF.AAN8.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.BT.A42F.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FT.A61P.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BT.A20J.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.FD.A5BS.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.XF.A9SX.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DK.A3IQ.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FD.A3B8.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.FD.A3B7.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.DK.A1AB.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.K4.A3WU.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FD.A62N.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.UY.A9PB.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.XF.A9ST.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.GU.A766.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FD.A6TB.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.GU.A762.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.K4.A3WS.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.XF.AAME.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.XF.A9T8.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.G2.AA3D.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.K4.A5RJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZF.A9RG.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.FD.A5C0.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZF.A9RD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BT.A20O.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FD.A3SO.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FD.A43S.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.XF.A8HE.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.GC.A3WC.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.XF.A9SY.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.GD.A2C5.11 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.CU.A0YR.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.4Z.AA7N.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.K4.A54R.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.DK.A3WY.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.ZF.AA53.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.DK.A1AF.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.BT.A20P.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.BT.A2LA.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.DK.AA6T.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.ZF.AA58.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.BT.A20X.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.XF.AAN4.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.GD.A3OP.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.XF.AAMJ.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.XF.AAMZ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BT.A20V.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.FD.A5BT.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.PQ.A6FN.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.BT.A20U.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.SY.A9G0.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.K4.A4AC.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.FD.A43U.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.GC.A3WC.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.DK.A3WX.01 1 0.0892 0.977 0.98 0.02 0.00
#> TCGA.E7.A85H.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.GU.A764.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.DK.A2I4.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.CU.A0YR.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.BL.A13I.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.GD.A3OS.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FD.A6TK.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.BT.A3PK.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.XF.A9SW.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FD.A3B4.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.XF.AAN0.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZF.AA4W.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.FJ.A871.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.XF.A9SL.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.CF.A5UA.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BT.A20R.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.R3.A69X.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.E7.A519.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.CF.A9FM.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.XF.AAMR.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.BT.A20N.11 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.ZF.AA5P.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.FD.A3SP.01 2 0.0000 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.GD.A3OP.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.4Z.AA86.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.BL.A13J.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.GU.A42Q.01 2 0.4994 0.475 0.00 0.52 0.00 0.48
#> TCGA.FD.A5BU.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.E7.A6MF.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.FD.A43P.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.BT.A20W.11 2 0.4277 0.548 0.28 0.72 0.00 0.00
#> TCGA.UY.A78P.01 2 0.3801 0.643 0.22 0.78 0.00 0.00
#> TCGA.DK.AA6X.01 4 0.1211 0.832 0.00 0.04 0.00 0.96
#> TCGA.K4.A6FZ.01 4 0.4624 0.409 0.00 0.00 0.34 0.66
#> TCGA.GC.A3OO.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.XF.AAN5.01 3 0.1637 0.946 0.00 0.00 0.94 0.06
#> TCGA.DK.A2I2.01 2 0.4624 0.761 0.00 0.66 0.00 0.34
#> TCGA.CF.A1HS.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.4Z.AA7W.01 4 0.1211 0.832 0.00 0.04 0.00 0.96
#> TCGA.XF.A9SI.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.K4.A5RH.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.XF.A9SM.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.GC.A3BM.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IU.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.E7.A7XN.01 2 0.4624 0.761 0.00 0.66 0.00 0.34
#> TCGA.K4.A5RI.11 2 0.4948 0.174 0.44 0.56 0.00 0.00
#> TCGA.K4.A3WV.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.FD.A3B3.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.FD.A6TF.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.GD.A3OQ.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.FD.A43Y.01 4 0.4994 -0.389 0.00 0.48 0.00 0.52
#> TCGA.GU.A767.01 4 0.3801 0.616 0.00 0.00 0.22 0.78
#> TCGA.CU.A0YN.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.YC.A8S6.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.CU.A0YO.01 4 0.4855 -0.100 0.00 0.40 0.00 0.60
#> TCGA.XF.A9T5.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.FD.A62P.01 4 0.2011 0.808 0.00 0.00 0.08 0.92
#> TCGA.DK.AA74.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.BT.A20U.11 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.K4.A83P.01 2 0.3801 0.643 0.22 0.78 0.00 0.00
#> TCGA.XF.AAN8.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 2 0.4134 0.838 0.00 0.74 0.00 0.26
#> TCGA.FT.A61P.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.BT.A20J.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BS.01 2 0.4855 0.292 0.40 0.60 0.00 0.00
#> TCGA.XF.A9SX.01 3 0.2647 0.908 0.00 0.00 0.88 0.12
#> TCGA.DK.A3IQ.01 2 0.4624 0.761 0.00 0.66 0.00 0.34
#> TCGA.FD.A3B8.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.FD.A3B7.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.DK.A1AB.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.K4.A3WU.01 4 0.1637 0.811 0.00 0.06 0.00 0.94
#> TCGA.FD.A62N.01 4 0.1637 0.826 0.00 0.00 0.06 0.94
#> TCGA.UY.A9PB.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.XF.A9ST.01 3 0.2011 0.889 0.00 0.08 0.92 0.00
#> TCGA.GU.A766.01 4 0.1211 0.832 0.00 0.04 0.00 0.96
#> TCGA.FD.A6TB.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.GU.A762.01 4 0.4624 0.409 0.00 0.00 0.34 0.66
#> TCGA.K4.A3WS.01 4 0.3801 0.616 0.00 0.00 0.22 0.78
#> TCGA.XF.AAME.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T8.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.G2.AA3D.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.K4.A5RJ.01 4 0.4713 0.364 0.00 0.00 0.36 0.64
#> TCGA.ZF.A9RG.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.FD.A5C0.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.ZF.A9RD.01 3 0.2647 0.908 0.00 0.00 0.88 0.12
#> TCGA.BT.A20O.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.FD.A3SO.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.FD.A43S.01 1 0.4948 0.213 0.56 0.44 0.00 0.00
#> TCGA.XF.A8HE.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.GC.A3WC.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.XF.A9SY.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.GD.A2C5.11 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.CU.A0YR.01 3 0.2345 0.923 0.00 0.00 0.90 0.10
#> TCGA.4Z.AA7N.01 1 0.2647 0.865 0.88 0.12 0.00 0.00
#> TCGA.K4.A54R.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.DK.A3WY.01 1 0.2647 0.865 0.88 0.12 0.00 0.00
#> TCGA.ZF.AA53.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.DK.A1AF.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.BT.A20P.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.BT.A2LA.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.DK.AA6T.01 4 0.0000 0.855 0.00 0.00 0.00 1.00
#> TCGA.ZF.AA58.01 4 0.1211 0.832 0.00 0.04 0.00 0.96
#> TCGA.BT.A20X.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.XF.AAN4.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.GD.A3OP.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMJ.01 4 0.1211 0.832 0.00 0.04 0.00 0.96
#> TCGA.XF.AAMZ.01 3 0.2647 0.908 0.00 0.00 0.88 0.12
#> TCGA.BT.A20V.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BT.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.PQ.A6FN.01 4 0.0707 0.845 0.00 0.02 0.00 0.98
#> TCGA.BT.A20U.01 4 0.4624 0.409 0.00 0.00 0.34 0.66
#> TCGA.SY.A9G0.01 2 0.4624 0.761 0.00 0.66 0.00 0.34
#> TCGA.K4.A4AC.01 4 0.1637 0.826 0.00 0.00 0.06 0.94
#> TCGA.FD.A43U.01 4 0.1211 0.839 0.00 0.00 0.04 0.96
#> TCGA.GC.A3WC.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 2 0.3801 0.643 0.22 0.78 0.00 0.00
#> TCGA.E7.A85H.01 3 0.2011 0.889 0.00 0.08 0.92 0.00
#> TCGA.GU.A764.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.DK.A2I4.01 4 0.2011 0.808 0.00 0.00 0.08 0.92
#> TCGA.CU.A0YR.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.BL.A13I.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.GD.A3OS.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.FD.A6TK.01 2 0.4624 0.761 0.00 0.66 0.00 0.34
#> TCGA.BT.A3PK.01 2 0.4624 0.761 0.00 0.66 0.00 0.34
#> TCGA.XF.A9SW.01 4 0.1637 0.811 0.00 0.06 0.00 0.94
#> TCGA.FD.A3B4.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.XF.AAN0.01 3 0.1211 0.954 0.00 0.00 0.96 0.04
#> TCGA.ZF.AA4W.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.UY.A9PA.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.FJ.A871.01 3 0.4491 0.864 0.00 0.06 0.80 0.14
#> TCGA.XF.A9SL.01 1 0.2647 0.865 0.88 0.12 0.00 0.00
#> TCGA.CF.A5UA.01 3 0.2011 0.889 0.00 0.08 0.92 0.00
#> TCGA.BT.A20R.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 2 0.3801 0.869 0.00 0.78 0.00 0.22
#> TCGA.E7.A519.01 4 0.1637 0.834 0.00 0.06 0.00 0.94
#> TCGA.CF.A9FM.01 2 0.4855 0.148 0.40 0.60 0.00 0.00
#> TCGA.XF.AAMR.01 2 0.4624 0.761 0.00 0.66 0.00 0.34
#> TCGA.BT.A20N.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA5P.01 1 0.2647 0.865 0.88 0.12 0.00 0.00
#> TCGA.FD.A3SP.01 4 0.1211 0.832 0.00 0.04 0.00 0.96
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GD.A3OP.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.4Z.AA86.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.BL.A13J.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A42Q.01 5 0.5245 0.5674 0.00 0.28 0.00 0.08 0.64
#> TCGA.FD.A5BU.01 5 0.4829 0.7961 0.00 0.48 0.00 0.02 0.50
#> TCGA.E7.A6MF.01 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43P.01 3 0.1648 0.9224 0.00 0.00 0.94 0.04 0.02
#> TCGA.BT.A20W.11 2 0.1043 0.1929 0.04 0.96 0.00 0.00 0.00
#> TCGA.UY.A78P.01 2 0.0000 0.1645 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.AA6X.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.K4.A6FZ.01 4 0.2516 0.8175 0.00 0.00 0.14 0.86 0.00
#> TCGA.GC.A3OO.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAN5.01 3 0.2516 0.8762 0.00 0.00 0.86 0.14 0.00
#> TCGA.DK.A2I2.01 5 0.5173 0.8276 0.00 0.46 0.00 0.04 0.50
#> TCGA.CF.A1HS.01 3 0.1648 0.9224 0.00 0.00 0.94 0.04 0.02
#> TCGA.4Z.AA7W.01 4 0.2438 0.8558 0.00 0.04 0.00 0.90 0.06
#> TCGA.XF.A9SI.01 2 0.2516 -0.0171 0.00 0.86 0.00 0.00 0.14
#> TCGA.K4.A5RH.01 3 0.1043 0.9210 0.00 0.00 0.96 0.04 0.00
#> TCGA.XF.A9SM.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.GC.A3BM.11 1 0.2516 0.8883 0.86 0.14 0.00 0.00 0.00
#> TCGA.DK.A3IU.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.E7.A7XN.01 2 0.5178 -0.8374 0.00 0.48 0.00 0.04 0.48
#> TCGA.K4.A5RI.11 2 0.2732 0.2431 0.16 0.84 0.00 0.00 0.00
#> TCGA.K4.A3WV.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B3.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.FD.A6TF.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.GD.A3OQ.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43Y.01 5 0.5673 0.7859 0.00 0.42 0.00 0.08 0.50
#> TCGA.GU.A767.01 4 0.0609 0.9166 0.00 0.00 0.02 0.98 0.00
#> TCGA.CU.A0YN.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A8S6.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.CU.A0YO.01 5 0.6296 0.6474 0.00 0.36 0.00 0.16 0.48
#> TCGA.XF.A9T5.01 3 0.1043 0.9210 0.00 0.00 0.96 0.04 0.00
#> TCGA.FD.A62P.01 4 0.0609 0.9166 0.00 0.00 0.02 0.98 0.00
#> TCGA.DK.AA74.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.BT.A20U.11 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.K4.A83P.01 2 0.0000 0.1645 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN8.01 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 2 0.4829 -0.7865 0.00 0.50 0.00 0.02 0.48
#> TCGA.FT.A61P.01 3 0.1043 0.9210 0.00 0.00 0.96 0.04 0.00
#> TCGA.BT.A20J.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BS.01 2 0.2516 0.2376 0.14 0.86 0.00 0.00 0.00
#> TCGA.XF.A9SX.01 3 0.2516 0.8762 0.00 0.00 0.86 0.14 0.00
#> TCGA.DK.A3IQ.01 5 0.5178 0.8122 0.00 0.48 0.00 0.04 0.48
#> TCGA.FD.A3B8.01 1 0.2516 0.8883 0.86 0.14 0.00 0.00 0.00
#> TCGA.FD.A3B7.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.DK.A1AB.01 2 0.4287 -0.6781 0.00 0.54 0.00 0.00 0.46
#> TCGA.K4.A3WU.01 4 0.4588 0.6173 0.00 0.06 0.00 0.72 0.22
#> TCGA.FD.A62N.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.UY.A9PB.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.A9ST.01 3 0.2280 0.8589 0.00 0.00 0.88 0.00 0.12
#> TCGA.GU.A766.01 4 0.1043 0.8992 0.00 0.04 0.00 0.96 0.00
#> TCGA.FD.A6TB.01 2 0.4829 -0.7865 0.00 0.50 0.00 0.02 0.48
#> TCGA.GU.A762.01 4 0.2516 0.8175 0.00 0.00 0.14 0.86 0.00
#> TCGA.K4.A3WS.01 4 0.1043 0.9052 0.00 0.00 0.04 0.96 0.00
#> TCGA.XF.AAME.01 2 0.4307 -0.4468 0.50 0.50 0.00 0.00 0.00
#> TCGA.XF.A9T8.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.G2.AA3D.01 4 0.2929 0.8052 0.00 0.00 0.00 0.82 0.18
#> TCGA.K4.A5RJ.01 4 0.2516 0.8175 0.00 0.00 0.14 0.86 0.00
#> TCGA.ZF.A9RG.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A5C0.01 3 0.1648 0.9224 0.00 0.00 0.94 0.04 0.02
#> TCGA.ZF.A9RD.01 3 0.2929 0.8334 0.00 0.00 0.82 0.18 0.00
#> TCGA.BT.A20O.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.FD.A3SO.01 3 0.1648 0.9224 0.00 0.00 0.94 0.04 0.02
#> TCGA.FD.A43S.01 2 0.3561 0.0918 0.26 0.74 0.00 0.00 0.00
#> TCGA.XF.A8HE.01 2 0.4262 -0.6570 0.00 0.56 0.00 0.00 0.44
#> TCGA.GC.A3WC.01 2 0.4262 -0.6570 0.00 0.56 0.00 0.00 0.44
#> TCGA.XF.A9SY.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.GD.A2C5.11 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.CU.A0YR.01 3 0.2516 0.8762 0.00 0.00 0.86 0.14 0.00
#> TCGA.4Z.AA7N.01 2 0.4302 -0.4120 0.48 0.52 0.00 0.00 0.00
#> TCGA.K4.A54R.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WY.01 2 0.4302 -0.4120 0.48 0.52 0.00 0.00 0.00
#> TCGA.ZF.AA53.01 2 0.2929 -0.0940 0.00 0.82 0.00 0.00 0.18
#> TCGA.DK.A1AF.01 2 0.4307 -0.4468 0.50 0.50 0.00 0.00 0.00
#> TCGA.BT.A20P.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A2LA.11 1 0.2516 0.8883 0.86 0.14 0.00 0.00 0.00
#> TCGA.DK.AA6T.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA58.01 4 0.2438 0.8558 0.00 0.04 0.00 0.90 0.06
#> TCGA.BT.A20X.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.2516 -0.0171 0.00 0.86 0.00 0.00 0.14
#> TCGA.XF.AAN4.01 1 0.3274 0.8111 0.78 0.22 0.00 0.00 0.00
#> TCGA.GD.A3OP.11 1 0.2516 0.8883 0.86 0.14 0.00 0.00 0.00
#> TCGA.XF.AAMJ.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAMZ.01 3 0.2516 0.8762 0.00 0.00 0.86 0.14 0.00
#> TCGA.BT.A20V.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BT.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.PQ.A6FN.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20U.01 4 0.2516 0.8175 0.00 0.00 0.14 0.86 0.00
#> TCGA.SY.A9G0.01 2 0.5178 -0.8374 0.00 0.48 0.00 0.04 0.48
#> TCGA.K4.A4AC.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A43U.01 4 0.0000 0.9262 0.00 0.00 0.00 1.00 0.00
#> TCGA.GC.A3WC.11 1 0.2516 0.8883 0.86 0.14 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 2 0.0000 0.1645 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A85H.01 3 0.2280 0.8589 0.00 0.00 0.88 0.00 0.12
#> TCGA.GU.A764.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.DK.A2I4.01 4 0.0609 0.9166 0.00 0.00 0.02 0.98 0.00
#> TCGA.CU.A0YR.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A13I.01 5 0.4829 0.7961 0.00 0.48 0.00 0.02 0.50
#> TCGA.GD.A3OS.01 3 0.1043 0.9044 0.00 0.00 0.96 0.00 0.04
#> TCGA.FD.A6TK.01 5 0.5178 0.8122 0.00 0.48 0.00 0.04 0.48
#> TCGA.BT.A3PK.01 2 0.5178 -0.8374 0.00 0.48 0.00 0.04 0.48
#> TCGA.XF.A9SW.01 4 0.4558 0.6529 0.00 0.08 0.00 0.74 0.18
#> TCGA.FD.A3B4.01 3 0.1648 0.9224 0.00 0.00 0.94 0.04 0.02
#> TCGA.XF.AAN0.01 3 0.1648 0.9224 0.00 0.00 0.94 0.04 0.02
#> TCGA.ZF.AA4W.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.UY.A9PA.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.FJ.A871.01 3 0.5783 0.6466 0.00 0.00 0.54 0.10 0.36
#> TCGA.XF.A9SL.01 2 0.4302 -0.4120 0.48 0.52 0.00 0.00 0.00
#> TCGA.CF.A5UA.01 3 0.2280 0.8589 0.00 0.00 0.88 0.00 0.12
#> TCGA.BT.A20R.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 2 0.4302 -0.7173 0.00 0.52 0.00 0.00 0.48
#> TCGA.E7.A519.01 4 0.4254 0.7444 0.00 0.04 0.00 0.74 0.22
#> TCGA.CF.A9FM.01 2 0.4254 0.1513 0.22 0.74 0.00 0.00 0.04
#> TCGA.XF.AAMR.01 5 0.5173 0.8276 0.00 0.46 0.00 0.04 0.50
#> TCGA.BT.A20N.11 1 0.0000 0.9527 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA5P.01 2 0.4302 -0.4120 0.48 0.52 0.00 0.00 0.00
#> TCGA.FD.A3SP.01 4 0.2438 0.8558 0.00 0.04 0.00 0.90 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GD.A3OP.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA86.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BL.A13J.11 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.GU.A42Q.01 5 0.5849 0.5402 0.00 0.06 0.00 0.10 0.60 0.24
#> TCGA.FD.A5BU.01 5 0.3572 0.7909 0.00 0.06 0.00 0.02 0.82 0.10
#> TCGA.E7.A6MF.01 1 0.0000 0.9276 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43P.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20W.11 2 0.3409 0.7515 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.UY.A78P.01 2 0.4265 0.7393 0.00 0.66 0.00 0.00 0.30 0.04
#> TCGA.DK.AA6X.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A6FZ.01 4 0.4067 0.4437 0.00 0.00 0.26 0.70 0.00 0.04
#> TCGA.GC.A3OO.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN5.01 3 0.3821 0.3134 0.00 0.00 0.74 0.22 0.00 0.04
#> TCGA.DK.A2I2.01 5 0.3572 0.7909 0.00 0.06 0.00 0.02 0.82 0.10
#> TCGA.CF.A1HS.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA7W.01 4 0.2793 0.6461 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.XF.A9SI.01 2 0.4482 0.6699 0.00 0.60 0.00 0.00 0.36 0.04
#> TCGA.K4.A5RH.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SM.01 5 0.0547 0.8789 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.GC.A3BM.11 1 0.2728 0.8585 0.86 0.10 0.00 0.00 0.00 0.04
#> TCGA.DK.A3IU.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A7XN.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.K4.A5RI.11 2 0.3409 0.7515 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.K4.A3WV.11 1 0.0000 0.9276 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B3.01 5 0.0547 0.8789 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.FD.A6TF.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GD.A3OQ.11 1 0.0000 0.9276 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43Y.01 5 0.5529 0.6051 0.00 0.06 0.00 0.16 0.66 0.12
#> TCGA.GU.A767.01 4 0.1480 0.7973 0.00 0.00 0.02 0.94 0.00 0.04
#> TCGA.CU.A0YN.11 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.YC.A8S6.01 5 0.0547 0.8789 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.CU.A0YO.01 5 0.3076 0.6207 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.XF.A9T5.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A62P.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.AA74.01 5 0.0547 0.8789 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BT.A20U.11 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A83P.01 2 0.4265 0.7393 0.00 0.66 0.00 0.00 0.30 0.04
#> TCGA.XF.AAN8.01 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BT.A42F.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.FT.A61P.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20J.11 1 0.0000 0.9276 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BS.01 2 0.3409 0.7515 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.XF.A9SX.01 3 0.3821 0.3134 0.00 0.00 0.74 0.22 0.00 0.04
#> TCGA.DK.A3IQ.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.FD.A3B8.01 1 0.2728 0.8585 0.86 0.10 0.00 0.00 0.00 0.04
#> TCGA.FD.A3B7.01 5 0.0547 0.8789 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DK.A1AB.01 5 0.5150 0.5481 0.00 0.16 0.00 0.00 0.62 0.22
#> TCGA.K4.A3WU.01 4 0.3797 0.2964 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.FD.A62N.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.UY.A9PB.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.A9ST.01 3 0.4536 0.3076 0.00 0.18 0.70 0.00 0.00 0.12
#> TCGA.GU.A766.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TB.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.GU.A762.01 4 0.4067 0.4437 0.00 0.00 0.26 0.70 0.00 0.04
#> TCGA.K4.A3WS.01 4 0.1480 0.7973 0.00 0.00 0.02 0.94 0.00 0.04
#> TCGA.XF.AAME.01 2 0.4326 0.5622 0.28 0.68 0.00 0.00 0.02 0.02
#> TCGA.XF.A9T8.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G2.AA3D.01 4 0.3409 0.5309 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.K4.A5RJ.01 4 0.4067 0.4437 0.00 0.00 0.26 0.70 0.00 0.04
#> TCGA.ZF.A9RG.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A5C0.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9RD.01 3 0.4172 0.1415 0.00 0.00 0.68 0.28 0.00 0.04
#> TCGA.BT.A20O.01 5 0.0000 0.8816 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A3SO.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A43S.01 2 0.3819 0.7536 0.02 0.70 0.00 0.00 0.28 0.00
#> TCGA.XF.A8HE.01 5 0.4004 0.6352 0.00 0.12 0.00 0.00 0.76 0.12
#> TCGA.GC.A3WC.01 5 0.5039 0.5481 0.00 0.18 0.00 0.00 0.64 0.18
#> TCGA.XF.A9SY.01 5 0.0547 0.8789 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.GD.A2C5.11 5 0.0937 0.8674 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.CU.A0YR.01 3 0.3821 0.3134 0.00 0.00 0.74 0.22 0.00 0.04
#> TCGA.4Z.AA7N.01 2 0.4067 0.6033 0.26 0.70 0.00 0.00 0.04 0.00
#> TCGA.K4.A54R.11 1 0.0000 0.9276 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WY.01 2 0.3819 0.5733 0.28 0.70 0.00 0.00 0.02 0.00
#> TCGA.ZF.AA53.01 2 0.4646 0.4674 0.00 0.50 0.00 0.00 0.46 0.04
#> TCGA.DK.A1AF.01 2 0.4326 0.5622 0.28 0.68 0.00 0.00 0.02 0.02
#> TCGA.BT.A20P.11 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BT.A2LA.11 1 0.2728 0.8585 0.86 0.10 0.00 0.00 0.00 0.04
#> TCGA.DK.AA6T.01 4 0.0937 0.8171 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.ZF.AA58.01 4 0.2793 0.6461 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.BT.A20X.11 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.GC.A6I3.11 2 0.4482 0.6699 0.00 0.60 0.00 0.00 0.36 0.04
#> TCGA.XF.AAN4.01 1 0.4534 0.3228 0.58 0.38 0.00 0.00 0.00 0.04
#> TCGA.GD.A3OP.11 1 0.2728 0.8585 0.86 0.10 0.00 0.00 0.00 0.04
#> TCGA.XF.AAMJ.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.AAMZ.01 3 0.3821 0.3134 0.00 0.00 0.74 0.22 0.00 0.04
#> TCGA.BT.A20V.11 1 0.0000 0.9276 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BT.01 5 0.0000 0.8816 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.PQ.A6FN.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20U.01 4 0.4067 0.4437 0.00 0.00 0.26 0.70 0.00 0.04
#> TCGA.SY.A9G0.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.K4.A4AC.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A43U.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GC.A3WC.11 1 0.2728 0.8585 0.86 0.10 0.00 0.00 0.00 0.04
#> TCGA.DK.A3WX.01 2 0.4798 0.7240 0.00 0.62 0.00 0.00 0.30 0.08
#> TCGA.E7.A85H.01 3 0.4536 0.3076 0.00 0.18 0.70 0.00 0.00 0.12
#> TCGA.GU.A764.01 5 0.0000 0.8816 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A2I4.01 4 0.0000 0.8399 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YR.11 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BL.A13I.01 5 0.3572 0.7909 0.00 0.06 0.00 0.02 0.82 0.10
#> TCGA.GD.A3OS.01 3 0.1267 0.6164 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.FD.A6TK.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.BT.A3PK.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.XF.A9SW.01 4 0.3756 0.3575 0.00 0.00 0.00 0.60 0.40 0.00
#> TCGA.FD.A3B4.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN0.01 3 0.0000 0.6846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4W.01 5 0.1480 0.8490 0.00 0.02 0.00 0.00 0.94 0.04
#> TCGA.UY.A9PA.01 5 0.0547 0.8789 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.FJ.A871.01 6 0.5514 0.0000 0.00 0.02 0.38 0.08 0.00 0.52
#> TCGA.XF.A9SL.01 2 0.4247 0.6291 0.24 0.70 0.00 0.00 0.06 0.00
#> TCGA.CF.A5UA.01 3 0.4536 0.3076 0.00 0.18 0.70 0.00 0.00 0.12
#> TCGA.BT.A20R.11 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.R3.A69X.01 5 0.0000 0.8816 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E7.A519.01 4 0.5878 0.0496 0.00 0.04 0.00 0.44 0.08 0.44
#> TCGA.CF.A9FM.01 2 0.5679 0.6062 0.06 0.64 0.00 0.00 0.12 0.18
#> TCGA.XF.AAMR.01 5 0.0547 0.8810 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.BT.A20N.11 1 0.0547 0.9274 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZF.AA5P.01 2 0.4326 0.5622 0.28 0.68 0.00 0.00 0.02 0.02
#> TCGA.FD.A3SP.01 4 0.2793 0.6461 0.00 0.00 0.00 0.80 0.20 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GD.A3OP.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA86.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BL.A13J.11 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.GU.A42Q.01 7 0.3968 -0.2144 0.00 0.00 0.00 0.02 0.44 0.00 0.54
#> TCGA.FD.A5BU.01 5 0.2708 0.6962 0.00 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.E7.A6MF.01 1 0.0000 0.9193 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43P.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20W.11 2 0.2708 0.7165 0.00 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.UY.A78P.01 2 0.3417 0.6953 0.00 0.72 0.00 0.00 0.26 0.00 0.02
#> TCGA.DK.AA6X.01 4 0.0504 0.8031 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.K4.A6FZ.01 4 0.4266 0.0869 0.00 0.04 0.44 0.52 0.00 0.00 0.00
#> TCGA.GC.A3OO.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN5.01 3 0.3086 0.5546 0.00 0.04 0.80 0.16 0.00 0.00 0.00
#> TCGA.DK.A2I2.01 5 0.2708 0.6962 0.00 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.CF.A1HS.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7W.01 4 0.2376 0.6625 0.00 0.00 0.00 0.86 0.12 0.00 0.02
#> TCGA.XF.A9SI.01 2 0.3815 0.5729 0.00 0.62 0.00 0.00 0.36 0.00 0.02
#> TCGA.K4.A5RH.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SM.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GC.A3BM.11 1 0.3370 0.7724 0.78 0.16 0.00 0.00 0.00 0.00 0.06
#> TCGA.DK.A3IU.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A7XN.01 5 0.1166 0.8368 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.K4.A5RI.11 2 0.3244 0.7361 0.04 0.78 0.00 0.00 0.18 0.00 0.00
#> TCGA.K4.A3WV.11 1 0.0000 0.9193 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B3.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TF.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GD.A3OQ.11 1 0.0000 0.9193 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43Y.01 5 0.3417 0.5839 0.00 0.00 0.00 0.02 0.72 0.00 0.26
#> TCGA.GU.A767.01 4 0.0863 0.7940 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.CU.A0YN.11 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.YC.A8S6.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YO.01 5 0.3370 0.5436 0.00 0.00 0.00 0.16 0.78 0.00 0.06
#> TCGA.XF.A9T5.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62P.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.AA74.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20U.11 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A83P.01 2 0.3417 0.6953 0.00 0.72 0.00 0.00 0.26 0.00 0.02
#> TCGA.XF.AAN8.01 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BT.A42F.01 5 0.1166 0.8368 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.FT.A61P.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20J.11 1 0.0000 0.9193 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BS.01 2 0.3244 0.7361 0.04 0.78 0.00 0.00 0.18 0.00 0.00
#> TCGA.XF.A9SX.01 3 0.3086 0.5546 0.00 0.04 0.80 0.16 0.00 0.00 0.00
#> TCGA.DK.A3IQ.01 5 0.1166 0.8368 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.FD.A3B8.01 1 0.3370 0.7724 0.78 0.16 0.00 0.00 0.00 0.00 0.06
#> TCGA.FD.A3B7.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A1AB.01 5 0.3994 -0.1642 0.00 0.02 0.00 0.00 0.50 0.00 0.48
#> TCGA.K4.A3WU.01 4 0.4191 0.2104 0.00 0.00 0.00 0.64 0.30 0.00 0.06
#> TCGA.FD.A62N.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.UY.A9PB.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9ST.01 3 0.3558 0.0338 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.GU.A766.01 4 0.0504 0.8031 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FD.A6TB.01 5 0.1166 0.8368 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.GU.A762.01 4 0.4266 0.0869 0.00 0.04 0.44 0.52 0.00 0.00 0.00
#> TCGA.K4.A3WS.01 4 0.0863 0.7940 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.XF.AAME.01 2 0.3519 0.6581 0.22 0.74 0.00 0.00 0.00 0.00 0.04
#> TCGA.XF.A9T8.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G2.AA3D.01 4 0.4244 0.0383 0.00 0.00 0.00 0.54 0.00 0.04 0.42
#> TCGA.K4.A5RJ.01 4 0.4266 0.0869 0.00 0.04 0.44 0.52 0.00 0.00 0.00
#> TCGA.ZF.A9RG.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A5C0.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9RD.01 3 0.3841 0.3174 0.00 0.04 0.68 0.28 0.00 0.00 0.00
#> TCGA.BT.A20O.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A3SO.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43S.01 2 0.3370 0.7358 0.06 0.78 0.00 0.00 0.16 0.00 0.00
#> TCGA.XF.A8HE.01 5 0.2803 0.7099 0.00 0.06 0.00 0.00 0.84 0.00 0.10
#> TCGA.GC.A3WC.01 5 0.3667 0.5851 0.00 0.06 0.00 0.00 0.74 0.00 0.20
#> TCGA.XF.A9SY.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GD.A2C5.11 5 0.0504 0.8411 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CU.A0YR.01 3 0.3086 0.5546 0.00 0.04 0.80 0.16 0.00 0.00 0.00
#> TCGA.4Z.AA7N.01 2 0.3244 0.7007 0.18 0.78 0.00 0.00 0.04 0.00 0.00
#> TCGA.K4.A54R.11 1 0.0000 0.9193 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WY.01 2 0.2708 0.6707 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA53.01 5 0.3994 -0.2851 0.00 0.48 0.00 0.00 0.50 0.00 0.02
#> TCGA.DK.A1AF.01 2 0.3519 0.6581 0.22 0.74 0.00 0.00 0.00 0.00 0.04
#> TCGA.BT.A20P.11 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BT.A2LA.11 1 0.3370 0.7724 0.78 0.16 0.00 0.00 0.00 0.00 0.06
#> TCGA.DK.AA6T.01 4 0.2421 0.7303 0.00 0.08 0.00 0.88 0.00 0.02 0.02
#> TCGA.ZF.AA58.01 4 0.2376 0.6625 0.00 0.00 0.00 0.86 0.12 0.00 0.02
#> TCGA.BT.A20X.11 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.GC.A6I3.11 2 0.3815 0.5729 0.00 0.62 0.00 0.00 0.36 0.00 0.02
#> TCGA.XF.AAN4.01 2 0.4514 0.0578 0.46 0.48 0.00 0.00 0.00 0.00 0.06
#> TCGA.GD.A3OP.11 1 0.3370 0.7724 0.78 0.16 0.00 0.00 0.00 0.00 0.06
#> TCGA.XF.AAMJ.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMZ.01 3 0.3086 0.5546 0.00 0.04 0.80 0.16 0.00 0.00 0.00
#> TCGA.BT.A20V.11 1 0.0000 0.9193 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BT.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.PQ.A6FN.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20U.01 4 0.4266 0.0869 0.00 0.04 0.44 0.52 0.00 0.00 0.00
#> TCGA.SY.A9G0.01 5 0.0504 0.8493 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.K4.A4AC.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A43U.01 4 0.0000 0.8170 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GC.A3WC.11 1 0.3370 0.7724 0.78 0.16 0.00 0.00 0.00 0.00 0.06
#> TCGA.DK.A3WX.01 2 0.4015 0.6867 0.00 0.68 0.00 0.00 0.26 0.00 0.06
#> TCGA.E7.A85H.01 3 0.3558 0.0338 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.GU.A764.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A2I4.01 4 0.0504 0.8063 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.CU.A0YR.11 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BL.A13I.01 5 0.2708 0.6962 0.00 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.GD.A3OS.01 3 0.1433 0.6518 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.FD.A6TK.01 5 0.1166 0.8368 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.BT.A3PK.01 5 0.1166 0.8368 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.XF.A9SW.01 4 0.4108 0.2657 0.00 0.00 0.00 0.66 0.28 0.00 0.06
#> TCGA.FD.A3B4.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN0.01 3 0.0000 0.7176 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4W.01 5 0.0504 0.8411 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.UY.A9PA.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FJ.A871.01 6 0.6962 0.0000 0.00 0.08 0.26 0.02 0.00 0.36 0.28
#> TCGA.XF.A9SL.01 2 0.3244 0.7007 0.18 0.78 0.00 0.00 0.04 0.00 0.00
#> TCGA.CF.A5UA.01 3 0.3558 0.0338 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.BT.A20R.11 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.R3.A69X.01 5 0.0000 0.8540 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A519.01 7 0.4778 -0.1720 0.00 0.02 0.00 0.34 0.00 0.06 0.58
#> TCGA.CF.A9FM.01 2 0.6295 0.4113 0.02 0.52 0.00 0.00 0.08 0.12 0.26
#> TCGA.XF.AAMR.01 5 0.1433 0.8225 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.BT.A20N.11 1 0.0504 0.9193 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ZF.AA5P.01 2 0.3186 0.6669 0.22 0.76 0.00 0.00 0.00 0.00 0.02
#> TCGA.FD.A3SP.01 4 0.3199 0.5772 0.00 0.00 0.00 0.80 0.14 0.00 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GD.A3OP.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA86.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BL.A13J.11 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.GU.A42Q.01 7 0.3015 0.3258 0.00 0.00 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.FD.A5BU.01 5 0.2650 0.7393 0.00 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.E7.A6MF.01 1 0.0941 0.8827 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.FD.A43P.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.BT.A20W.11 2 0.1341 0.8565 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.UY.A78P.01 2 0.1563 0.8496 0.00 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.DK.AA6X.01 4 0.0941 0.8635 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.K4.A6FZ.01 3 0.3714 0.3925 0.00 0.00 0.54 0.44 0.00 0.02 0.00 0.00
#> TCGA.GC.A3OO.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN5.01 3 0.4765 0.5962 0.00 0.00 0.56 0.22 0.00 0.00 0.00 0.22
#> TCGA.DK.A2I2.01 5 0.2650 0.7393 0.00 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.CF.A1HS.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.4Z.AA7W.01 4 0.2856 0.6364 0.00 0.00 0.00 0.78 0.20 0.00 0.02 0.00
#> TCGA.XF.A9SI.01 2 0.1765 0.8326 0.00 0.88 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.K4.A5RH.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.XF.A9SM.01 5 0.0808 0.9023 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.GC.A3BM.11 1 0.3483 0.7831 0.76 0.04 0.18 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.A3IU.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A7XN.01 5 0.0471 0.9014 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.K4.A5RI.11 2 0.1341 0.8565 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.K4.A3WV.11 1 0.1557 0.8711 0.92 0.00 0.06 0.00 0.00 0.00 0.02 0.00
#> TCGA.FD.A3B3.01 5 0.0471 0.9062 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FD.A6TF.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A3OQ.11 1 0.0941 0.8827 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.FD.A43Y.01 5 0.2534 0.7175 0.00 0.00 0.00 0.00 0.78 0.00 0.22 0.00
#> TCGA.GU.A767.01 4 0.1275 0.8421 0.00 0.00 0.04 0.94 0.00 0.02 0.00 0.00
#> TCGA.CU.A0YN.11 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.YC.A8S6.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CU.A0YO.01 5 0.1557 0.8308 0.00 0.00 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.XF.A9T5.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.FD.A62P.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA74.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20U.11 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A83P.01 2 0.1563 0.8496 0.00 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.XF.AAN8.01 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BT.A42F.01 5 0.0808 0.9057 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.FT.A61P.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.BT.A20J.11 1 0.0471 0.8834 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.FD.A5BS.01 2 0.1341 0.8565 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.XF.A9SX.01 3 0.4765 0.5962 0.00 0.00 0.56 0.22 0.00 0.00 0.00 0.22
#> TCGA.DK.A3IQ.01 5 0.0471 0.9014 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FD.A3B8.01 1 0.3483 0.7831 0.76 0.04 0.18 0.00 0.00 0.02 0.00 0.00
#> TCGA.FD.A3B7.01 5 0.0808 0.9023 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.DK.A1AB.01 7 0.4350 0.3021 0.00 0.06 0.00 0.00 0.30 0.02 0.62 0.00
#> TCGA.K4.A3WU.01 4 0.3922 0.3722 0.00 0.00 0.00 0.64 0.30 0.00 0.06 0.00
#> TCGA.FD.A62N.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A9PB.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9ST.01 8 0.0808 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.GU.A766.01 4 0.1275 0.8462 0.00 0.00 0.00 0.94 0.04 0.00 0.02 0.00
#> TCGA.FD.A6TB.01 5 0.0471 0.9014 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.GU.A762.01 3 0.3714 0.3925 0.00 0.00 0.54 0.44 0.00 0.02 0.00 0.00
#> TCGA.K4.A3WS.01 4 0.1275 0.8421 0.00 0.00 0.04 0.94 0.00 0.02 0.00 0.00
#> TCGA.XF.AAME.01 2 0.1804 0.7999 0.08 0.90 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T8.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.AA3D.01 7 0.4910 0.0655 0.00 0.00 0.00 0.40 0.00 0.16 0.44 0.00
#> TCGA.K4.A5RJ.01 3 0.3714 0.3925 0.00 0.00 0.54 0.44 0.00 0.02 0.00 0.00
#> TCGA.ZF.A9RG.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5C0.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.ZF.A9RD.01 3 0.4757 0.5854 0.00 0.00 0.56 0.24 0.00 0.00 0.00 0.20
#> TCGA.BT.A20O.01 5 0.0808 0.9023 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.FD.A3SO.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.FD.A43S.01 2 0.1341 0.8565 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.XF.A8HE.01 5 0.3444 0.7241 0.00 0.06 0.00 0.00 0.78 0.02 0.14 0.00
#> TCGA.GC.A3WC.01 5 0.4096 0.5609 0.00 0.06 0.00 0.00 0.68 0.02 0.24 0.00
#> TCGA.XF.A9SY.01 5 0.0808 0.9023 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.GD.A2C5.11 5 0.0808 0.9023 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.CU.A0YR.01 3 0.5180 0.5890 0.00 0.00 0.54 0.22 0.00 0.02 0.00 0.22
#> TCGA.4Z.AA7N.01 2 0.1607 0.8423 0.04 0.92 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.K4.A54R.11 1 0.0941 0.8827 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.DK.A3WY.01 2 0.1341 0.8069 0.08 0.92 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA53.01 2 0.4077 0.3087 0.00 0.56 0.00 0.00 0.40 0.02 0.02 0.00
#> TCGA.DK.A1AF.01 2 0.2132 0.7867 0.08 0.88 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20P.11 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BT.A2LA.11 1 0.3483 0.7831 0.76 0.04 0.18 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.AA6T.01 4 0.4280 0.5825 0.00 0.00 0.12 0.72 0.00 0.10 0.06 0.00
#> TCGA.ZF.AA58.01 4 0.2856 0.6364 0.00 0.00 0.00 0.78 0.20 0.00 0.02 0.00
#> TCGA.BT.A20X.11 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.GC.A6I3.11 2 0.1765 0.8326 0.00 0.88 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.XF.AAN4.01 1 0.5342 0.2927 0.46 0.34 0.18 0.00 0.00 0.02 0.00 0.00
#> TCGA.GD.A3OP.11 1 0.3483 0.7831 0.76 0.04 0.18 0.00 0.00 0.02 0.00 0.00
#> TCGA.XF.AAMJ.01 4 0.0471 0.8777 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.XF.AAMZ.01 3 0.4765 0.5962 0.00 0.00 0.56 0.22 0.00 0.00 0.00 0.22
#> TCGA.BT.A20V.11 1 0.0941 0.8827 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.FD.A5BT.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.PQ.A6FN.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20U.01 3 0.3714 0.3925 0.00 0.00 0.54 0.44 0.00 0.02 0.00 0.00
#> TCGA.SY.A9G0.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A4AC.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43U.01 4 0.0000 0.8893 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3WC.11 1 0.3483 0.7831 0.76 0.04 0.18 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.A3WX.01 2 0.2864 0.8162 0.00 0.84 0.00 0.00 0.08 0.02 0.06 0.00
#> TCGA.E7.A85H.01 8 0.0808 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.GU.A764.01 5 0.0471 0.9062 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DK.A2I4.01 4 0.0471 0.8752 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YR.11 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BL.A13I.01 5 0.2650 0.7393 0.00 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.GD.A3OS.01 3 0.4619 0.5035 0.00 0.02 0.48 0.00 0.00 0.06 0.00 0.44
#> TCGA.FD.A6TK.01 5 0.0471 0.9014 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BT.A3PK.01 5 0.0471 0.9014 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.XF.A9SW.01 4 0.3449 0.4007 0.00 0.00 0.00 0.66 0.32 0.00 0.02 0.00
#> TCGA.FD.A3B4.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.XF.AAN0.01 3 0.3329 0.5678 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.ZF.AA4W.01 5 0.1607 0.8664 0.00 0.04 0.00 0.00 0.92 0.00 0.04 0.00
#> TCGA.UY.A9PA.01 5 0.0808 0.9023 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.FJ.A871.01 6 0.2404 0.0000 0.00 0.00 0.14 0.00 0.00 0.84 0.02 0.00
#> TCGA.XF.A9SL.01 2 0.1607 0.8423 0.04 0.92 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.CF.A5UA.01 8 0.0808 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.BT.A20R.11 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.R3.A69X.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A519.01 7 0.4644 0.0279 0.00 0.00 0.00 0.18 0.02 0.16 0.64 0.00
#> TCGA.CF.A9FM.01 2 0.5838 -0.1729 0.00 0.38 0.28 0.00 0.00 0.04 0.30 0.00
#> TCGA.XF.AAMR.01 5 0.1091 0.8743 0.00 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.BT.A20N.11 1 0.0471 0.8840 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.ZF.AA5P.01 2 0.1804 0.7999 0.08 0.90 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SP.01 4 0.2856 0.6364 0.00 0.00 0.00 0.78 0.20 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-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 34 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 0.1150 0.886 0.886
#> 3 3 0.556 0.859 0.862 3.2212 0.545 0.487
#> 4 4 0.879 0.971 0.922 0.3488 0.872 0.702
#> 5 5 0.942 0.909 0.984 0.0643 0.998 0.994
#> 6 6 0.881 0.791 0.932 0.0362 0.988 0.959
#> 7 7 0.749 0.680 0.862 0.0622 0.979 0.926
#> 8 8 0.759 0.560 0.846 0.0363 0.925 0.732
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.BL.A13J.11 2 0 1 0 1
#> TCGA.E7.A6MF.01 1 0 1 1 0
#> TCGA.BT.A20W.11 2 0 1 0 1
#> TCGA.UY.A78P.01 2 0 1 0 1
#> TCGA.GC.A3BM.11 2 0 1 0 1
#> TCGA.K4.A5RI.11 2 0 1 0 1
#> TCGA.K4.A3WV.11 2 0 1 0 1
#> TCGA.GD.A3OQ.11 2 0 1 0 1
#> TCGA.CU.A0YN.11 2 0 1 0 1
#> TCGA.K4.A83P.01 2 0 1 0 1
#> TCGA.XF.AAN8.01 2 0 1 0 1
#> TCGA.BT.A20J.11 2 0 1 0 1
#> TCGA.FD.A5BS.01 2 0 1 0 1
#> TCGA.FD.A3B8.01 2 0 1 0 1
#> TCGA.XF.AAME.01 2 0 1 0 1
#> TCGA.FD.A43S.01 2 0 1 0 1
#> TCGA.4Z.AA7N.01 2 0 1 0 1
#> TCGA.K4.A54R.11 2 0 1 0 1
#> TCGA.DK.A3WY.01 2 0 1 0 1
#> TCGA.DK.A1AF.01 2 0 1 0 1
#> TCGA.BT.A20P.11 2 0 1 0 1
#> TCGA.BT.A2LA.11 2 0 1 0 1
#> TCGA.BT.A20X.11 2 0 1 0 1
#> TCGA.XF.AAN4.01 2 0 1 0 1
#> TCGA.GD.A3OP.11 2 0 1 0 1
#> TCGA.BT.A20V.11 2 0 1 0 1
#> TCGA.GC.A3WC.11 2 0 1 0 1
#> TCGA.DK.A3WX.01 2 0 1 0 1
#> TCGA.CU.A0YR.11 2 0 1 0 1
#> TCGA.XF.A9SL.01 2 0 1 0 1
#> TCGA.BT.A20R.11 2 0 1 0 1
#> TCGA.CF.A9FM.01 1 0 1 1 0
#> TCGA.BT.A20N.11 2 0 1 0 1
#> TCGA.ZF.AA5P.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BL.A13J.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.E7.A6MF.01 1 0.0892 0.993 0.98 0.00 0.02
#> TCGA.BT.A20W.11 2 0.0892 0.788 0.00 0.98 0.02
#> TCGA.UY.A78P.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.GC.A3BM.11 2 0.6045 0.559 0.00 0.62 0.38
#> TCGA.K4.A5RI.11 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.K4.A3WV.11 2 0.6045 0.559 0.00 0.62 0.38
#> TCGA.GD.A3OQ.11 2 0.6045 0.559 0.00 0.62 0.38
#> TCGA.CU.A0YN.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.K4.A83P.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.XF.AAN8.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.BT.A20J.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.FD.A5BS.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.FD.A3B8.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.XF.AAME.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.FD.A43S.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.4Z.AA7N.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.K4.A54R.11 2 0.6045 0.559 0.00 0.62 0.38
#> TCGA.DK.A3WY.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.DK.A1AF.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.BT.A20P.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.BT.A2LA.11 2 0.6045 0.559 0.00 0.62 0.38
#> TCGA.BT.A20X.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.XF.AAN4.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.GD.A3OP.11 2 0.2066 0.780 0.00 0.94 0.06
#> TCGA.BT.A20V.11 2 0.2959 0.767 0.00 0.90 0.10
#> TCGA.GC.A3WC.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.DK.A3WX.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.CU.A0YR.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.XF.A9SL.01 3 0.6126 1.000 0.00 0.40 0.60
#> TCGA.BT.A20R.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.CF.A9FM.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.BT.A20N.11 2 0.0000 0.788 0.00 1.00 0.00
#> TCGA.ZF.AA5P.01 3 0.6126 1.000 0.00 0.40 0.60
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BL.A13J.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.E7.A6MF.01 1 0.0000 0.880 1.00 0.00 0.00 0.00
#> TCGA.BT.A20W.11 4 0.3400 0.724 0.00 0.00 0.18 0.82
#> TCGA.UY.A78P.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.GC.A3BM.11 4 0.0000 0.941 0.00 0.00 0.00 1.00
#> TCGA.K4.A5RI.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.K4.A3WV.11 4 0.0000 0.941 0.00 0.00 0.00 1.00
#> TCGA.GD.A3OQ.11 4 0.0000 0.941 0.00 0.00 0.00 1.00
#> TCGA.CU.A0YN.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.K4.A83P.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.XF.AAN8.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BT.A20J.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.FD.A5BS.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FD.A3B8.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.XF.AAME.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FD.A43S.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.4Z.AA7N.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.K4.A54R.11 4 0.0000 0.941 0.00 0.00 0.00 1.00
#> TCGA.DK.A3WY.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DK.A1AF.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BT.A20P.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.BT.A2LA.11 4 0.0000 0.941 0.00 0.00 0.00 1.00
#> TCGA.BT.A20X.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.XF.AAN4.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.GD.A3OP.11 4 0.1637 0.890 0.00 0.00 0.06 0.94
#> TCGA.BT.A20V.11 4 0.0707 0.929 0.00 0.00 0.02 0.98
#> TCGA.GC.A3WC.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.DK.A3WX.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.CU.A0YR.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.XF.A9SL.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BT.A20R.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.CF.A9FM.01 1 0.4134 0.880 0.74 0.26 0.00 0.00
#> TCGA.BT.A20N.11 2 0.4939 1.000 0.00 0.74 0.04 0.22
#> TCGA.ZF.AA5P.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BL.A13J.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.E7.A6MF.01 1 0.0000 0.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20W.11 4 0.4653 0.677 0.00 0.06 0.16 0.76 0.02
#> TCGA.UY.A78P.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.GC.A3BM.11 4 0.0000 0.919 0.00 0.00 0.00 1.00 0.00
#> TCGA.K4.A5RI.11 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A3WV.11 4 0.0000 0.919 0.00 0.00 0.00 1.00 0.00
#> TCGA.GD.A3OQ.11 4 0.0000 0.919 0.00 0.00 0.00 1.00 0.00
#> TCGA.CU.A0YN.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A83P.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.AAN8.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20J.11 2 0.0609 0.977 0.00 0.98 0.00 0.00 0.02
#> TCGA.FD.A5BS.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A3B8.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.XF.AAME.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A43S.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7N.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.K4.A54R.11 4 0.0000 0.919 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A3WY.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A1AF.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20P.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A2LA.11 4 0.1043 0.899 0.00 0.00 0.00 0.96 0.04
#> TCGA.BT.A20X.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN4.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.GD.A3OP.11 4 0.2249 0.886 0.00 0.04 0.02 0.92 0.02
#> TCGA.BT.A20V.11 4 0.2331 0.860 0.00 0.08 0.00 0.90 0.02
#> TCGA.GC.A3WC.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YR.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SL.01 3 0.0000 0.998 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20R.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A9FM.01 5 0.1410 0.000 0.06 0.00 0.00 0.00 0.94
#> TCGA.BT.A20N.11 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA5P.01 3 0.0609 0.978 0.00 0.00 0.98 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.BL.A13J.11 2 0.0000 0.933 0 1.00 0.00 0.00 0.00 0.0
#> TCGA.E7.A6MF.01 1 0.0000 0.000 1 0.00 0.00 0.00 0.00 0.0
#> TCGA.BT.A20W.11 4 0.1556 0.610 0 0.00 0.08 0.92 0.00 0.0
#> TCGA.UY.A78P.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.GC.A3BM.11 4 0.3409 0.719 0 0.00 0.00 0.70 0.30 0.0
#> TCGA.K4.A5RI.11 3 0.1267 0.946 0 0.00 0.94 0.06 0.00 0.0
#> TCGA.K4.A3WV.11 4 0.3309 0.721 0 0.00 0.00 0.72 0.28 0.0
#> TCGA.GD.A3OQ.11 4 0.3409 0.719 0 0.00 0.00 0.70 0.30 0.0
#> TCGA.CU.A0YN.11 2 0.0000 0.933 0 1.00 0.00 0.00 0.00 0.0
#> TCGA.K4.A83P.01 3 0.0937 0.955 0 0.00 0.96 0.04 0.00 0.0
#> TCGA.XF.AAN8.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.BT.A20J.11 2 0.3076 0.722 0 0.76 0.00 0.24 0.00 0.0
#> TCGA.FD.A5BS.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.FD.A3B8.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.XF.AAME.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.FD.A43S.01 3 0.1267 0.946 0 0.00 0.94 0.06 0.00 0.0
#> TCGA.4Z.AA7N.01 3 0.0937 0.955 0 0.00 0.96 0.04 0.00 0.0
#> TCGA.K4.A54R.11 4 0.3409 0.719 0 0.00 0.00 0.70 0.30 0.0
#> TCGA.DK.A3WY.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.DK.A1AF.01 3 0.0937 0.955 0 0.00 0.96 0.04 0.00 0.0
#> TCGA.BT.A20P.11 2 0.0000 0.933 0 1.00 0.00 0.00 0.00 0.0
#> TCGA.BT.A2LA.11 6 0.3409 0.000 0 0.00 0.00 0.00 0.30 0.7
#> TCGA.BT.A20X.11 2 0.0000 0.933 0 1.00 0.00 0.00 0.00 0.0
#> TCGA.XF.AAN4.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.GD.A3OP.11 4 0.1556 0.610 0 0.00 0.08 0.92 0.00 0.0
#> TCGA.BT.A20V.11 4 0.0000 0.654 0 0.00 0.00 1.00 0.00 0.0
#> TCGA.GC.A3WC.11 2 0.2941 0.745 0 0.78 0.00 0.22 0.00 0.0
#> TCGA.DK.A3WX.01 3 0.0000 0.961 0 0.00 1.00 0.00 0.00 0.0
#> TCGA.CU.A0YR.11 2 0.0000 0.933 0 1.00 0.00 0.00 0.00 0.0
#> TCGA.XF.A9SL.01 3 0.1267 0.946 0 0.00 0.94 0.06 0.00 0.0
#> TCGA.BT.A20R.11 2 0.0000 0.933 0 1.00 0.00 0.00 0.00 0.0
#> TCGA.CF.A9FM.01 5 0.3409 0.000 0 0.00 0.00 0.00 0.70 0.3
#> TCGA.BT.A20N.11 2 0.0000 0.933 0 1.00 0.00 0.00 0.00 0.0
#> TCGA.ZF.AA5P.01 3 0.2941 0.761 0 0.00 0.78 0.22 0.00 0.0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BL.A13J.11 2 0.0000 0.891 0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.E7.A6MF.01 1 0.0000 0.000 1 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.BT.A20W.11 7 0.2803 0.651 0 0.00 0.06 0.10 0 0.00 0.84
#> TCGA.UY.A78P.01 3 0.2376 0.675 0 0.00 0.86 0.00 0 0.02 0.12
#> TCGA.GC.A3BM.11 4 0.0000 0.881 0 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.K4.A5RI.11 3 0.3927 0.715 0 0.00 0.66 0.00 0 0.04 0.30
#> TCGA.K4.A3WV.11 4 0.3526 0.654 0 0.00 0.00 0.76 0 0.06 0.18
#> TCGA.GD.A3OQ.11 4 0.0504 0.881 0 0.00 0.00 0.98 0 0.00 0.02
#> TCGA.CU.A0YN.11 2 0.0000 0.891 0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.K4.A83P.01 3 0.3841 0.734 0 0.00 0.68 0.00 0 0.04 0.28
#> TCGA.XF.AAN8.01 3 0.0504 0.777 0 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.BT.A20J.11 2 0.3496 0.354 0 0.58 0.00 0.00 0 0.00 0.42
#> TCGA.FD.A5BS.01 3 0.1718 0.787 0 0.00 0.92 0.00 0 0.04 0.04
#> TCGA.FD.A3B8.01 3 0.0504 0.777 0 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.XF.AAME.01 3 0.0863 0.786 0 0.00 0.96 0.00 0 0.00 0.04
#> TCGA.FD.A43S.01 3 0.3841 0.734 0 0.00 0.68 0.00 0 0.04 0.28
#> TCGA.4Z.AA7N.01 3 0.3637 0.753 0 0.00 0.72 0.00 0 0.04 0.24
#> TCGA.K4.A54R.11 4 0.0504 0.868 0 0.00 0.00 0.98 0 0.02 0.00
#> TCGA.DK.A3WY.01 3 0.0504 0.777 0 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.DK.A1AF.01 3 0.3911 0.755 0 0.00 0.70 0.00 0 0.06 0.24
#> TCGA.BT.A20P.11 2 0.0000 0.891 0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.BT.A2LA.11 6 0.2081 0.000 0 0.00 0.00 0.14 0 0.86 0.00
#> TCGA.BT.A20X.11 2 0.0000 0.891 0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.XF.AAN4.01 3 0.0504 0.777 0 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.GD.A3OP.11 7 0.3386 0.718 0 0.00 0.02 0.18 0 0.02 0.78
#> TCGA.BT.A20V.11 7 0.3867 0.437 0 0.00 0.00 0.38 0 0.02 0.60
#> TCGA.GC.A3WC.11 2 0.4070 0.509 0 0.66 0.02 0.00 0 0.02 0.30
#> TCGA.DK.A3WX.01 3 0.2016 0.724 0 0.00 0.90 0.00 0 0.04 0.06
#> TCGA.CU.A0YR.11 2 0.0000 0.891 0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.XF.A9SL.01 3 0.3841 0.734 0 0.00 0.68 0.00 0 0.04 0.28
#> TCGA.BT.A20R.11 2 0.0000 0.891 0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.CF.A9FM.01 5 0.0000 0.000 0 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.BT.A20N.11 2 0.0000 0.891 0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.ZF.AA5P.01 3 0.4283 0.413 0 0.00 0.48 0.00 0 0.04 0.48
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BL.A13J.11 2 0.0000 0.9209 0 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.E7.A6MF.01 1 0.0000 0.0000 1 0.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.BT.A20W.11 7 0.0471 0.5373 0 0.00 0.00 0.00 0 0 0.98 0.02
#> TCGA.UY.A78P.01 8 0.2267 0.0000 0 0.00 0.18 0.00 0 0 0.00 0.82
#> TCGA.GC.A3BM.11 4 0.2114 0.8505 0 0.00 0.00 0.84 0 0 0.16 0.00
#> TCGA.K4.A5RI.11 3 0.3514 0.4589 0 0.00 0.64 0.00 0 0 0.34 0.02
#> TCGA.K4.A3WV.11 4 0.3073 0.5867 0 0.00 0.00 0.80 0 0 0.10 0.10
#> TCGA.GD.A3OQ.11 4 0.2981 0.8072 0 0.00 0.00 0.76 0 0 0.22 0.02
#> TCGA.CU.A0YN.11 2 0.0000 0.9209 0 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.K4.A83P.01 3 0.3170 0.6629 0 0.00 0.76 0.00 0 0 0.20 0.04
#> TCGA.XF.AAN8.01 3 0.1765 0.6754 0 0.00 0.88 0.00 0 0 0.00 0.12
#> TCGA.BT.A20J.11 2 0.3729 0.0924 0 0.52 0.00 0.00 0 0 0.46 0.02
#> TCGA.FD.A5BS.01 3 0.1341 0.6955 0 0.00 0.92 0.00 0 0 0.00 0.08
#> TCGA.FD.A3B8.01 3 0.1765 0.6754 0 0.00 0.88 0.00 0 0 0.00 0.12
#> TCGA.XF.AAME.01 3 0.1091 0.6993 0 0.00 0.94 0.00 0 0 0.00 0.06
#> TCGA.FD.A43S.01 3 0.3095 0.6331 0 0.00 0.74 0.00 0 0 0.24 0.02
#> TCGA.4Z.AA7N.01 3 0.2719 0.6812 0 0.00 0.80 0.00 0 0 0.18 0.02
#> TCGA.K4.A54R.11 4 0.2114 0.8505 0 0.00 0.00 0.84 0 0 0.16 0.00
#> TCGA.DK.A3WY.01 3 0.1765 0.6754 0 0.00 0.88 0.00 0 0 0.00 0.12
#> TCGA.DK.A1AF.01 3 0.2852 0.6066 0 0.00 0.72 0.00 0 0 0.28 0.00
#> TCGA.BT.A20P.11 2 0.0000 0.9209 0 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.BT.A2LA.11 6 0.0000 0.0000 0 0.00 0.00 0.00 0 1 0.00 0.00
#> TCGA.BT.A20X.11 2 0.0000 0.9209 0 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.XF.AAN4.01 3 0.1341 0.6958 0 0.00 0.92 0.00 0 0 0.00 0.08
#> TCGA.GD.A3OP.11 7 0.2348 0.5415 0 0.00 0.04 0.06 0 0 0.88 0.02
#> TCGA.BT.A20V.11 7 0.1804 0.4362 0 0.00 0.00 0.08 0 0 0.90 0.02
#> TCGA.GC.A3WC.11 7 0.4794 0.1261 0 0.42 0.08 0.00 0 0 0.48 0.02
#> TCGA.DK.A3WX.01 3 0.3272 0.0423 0 0.00 0.58 0.00 0 0 0.00 0.42
#> TCGA.CU.A0YR.11 2 0.0000 0.9209 0 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.XF.A9SL.01 3 0.2856 0.6689 0 0.00 0.78 0.00 0 0 0.20 0.02
#> TCGA.BT.A20R.11 2 0.0000 0.9209 0 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.CF.A9FM.01 5 0.0000 0.0000 0 0.00 0.00 0.00 1 0 0.00 0.00
#> TCGA.BT.A20N.11 2 0.0000 0.9209 0 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.ZF.AA5P.01 7 0.4216 -0.1166 0 0.00 0.44 0.00 0 0 0.50 0.06
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0213"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 15 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 0.5148 0.486 0.486
#> 3 3 0.667 0.323 0.736 0.2444 0.867 0.725
#> 4 4 0.600 0.802 0.792 0.1083 0.810 0.556
#> 5 5 0.629 0.436 0.753 0.0918 0.905 0.697
#> 6 6 0.676 0.626 0.823 0.0713 0.876 0.500
#> 7 7 0.790 0.528 0.847 0.0516 0.971 0.812
#> 8 8 0.819 0.361 0.793 0.0284 0.943 0.571
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.UY.A78P.01 2 0 1 0 1
#> TCGA.K4.A5RI.11 2 0 1 0 1
#> TCGA.K4.A83P.01 1 0 1 1 0
#> TCGA.XF.AAN8.01 2 0 1 0 1
#> TCGA.FD.A5BS.01 1 0 1 1 0
#> TCGA.FD.A3B8.01 1 0 1 1 0
#> TCGA.XF.AAME.01 2 0 1 0 1
#> TCGA.FD.A43S.01 2 0 1 0 1
#> TCGA.4Z.AA7N.01 1 0 1 1 0
#> TCGA.DK.A3WY.01 2 0 1 0 1
#> TCGA.DK.A1AF.01 2 0 1 0 1
#> TCGA.XF.AAN4.01 2 0 1 0 1
#> TCGA.DK.A3WX.01 2 0 1 0 1
#> TCGA.XF.A9SL.01 1 0 1 1 0
#> TCGA.ZF.AA5P.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.UY.A78P.01 3 0.522 0.3408 0.00 0.26 0.74
#> TCGA.K4.A5RI.11 2 0.000 0.3734 0.00 1.00 0.00
#> TCGA.K4.A83P.01 1 0.000 0.9160 1.00 0.00 0.00
#> TCGA.XF.AAN8.01 3 0.631 -0.0926 0.00 0.50 0.50
#> TCGA.FD.A5BS.01 1 0.400 0.8857 0.84 0.00 0.16
#> TCGA.FD.A3B8.01 1 0.296 0.9133 0.90 0.00 0.10
#> TCGA.XF.AAME.01 2 0.631 -0.5277 0.00 0.50 0.50
#> TCGA.FD.A43S.01 2 0.000 0.3734 0.00 1.00 0.00
#> TCGA.4Z.AA7N.01 1 0.153 0.9173 0.96 0.00 0.04
#> TCGA.DK.A3WY.01 2 0.000 0.3734 0.00 1.00 0.00
#> TCGA.DK.A1AF.01 2 0.631 -0.5277 0.00 0.50 0.50
#> TCGA.XF.AAN4.01 2 0.631 -0.5277 0.00 0.50 0.50
#> TCGA.DK.A3WX.01 2 0.624 -0.3725 0.00 0.56 0.44
#> TCGA.XF.A9SL.01 1 0.254 0.9171 0.92 0.00 0.08
#> TCGA.ZF.AA5P.01 1 0.522 0.8829 0.74 0.00 0.26
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.UY.A78P.01 4 0.754 0.317 0.00 0.20 0.34 0.46
#> TCGA.K4.A5RI.11 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.K4.A83P.01 1 0.234 0.782 0.90 0.00 0.00 0.10
#> TCGA.XF.AAN8.01 4 0.462 0.846 0.00 0.34 0.00 0.66
#> TCGA.FD.A5BS.01 1 0.526 0.742 0.70 0.00 0.26 0.04
#> TCGA.FD.A3B8.01 1 0.588 0.754 0.64 0.00 0.30 0.06
#> TCGA.XF.AAME.01 4 0.462 0.846 0.00 0.34 0.00 0.66
#> TCGA.FD.A43S.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA7N.01 1 0.283 0.790 0.90 0.00 0.04 0.06
#> TCGA.DK.A3WY.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DK.A1AF.01 4 0.462 0.846 0.00 0.34 0.00 0.66
#> TCGA.XF.AAN4.01 4 0.462 0.846 0.00 0.34 0.00 0.66
#> TCGA.DK.A3WX.01 4 0.657 0.747 0.00 0.32 0.10 0.58
#> TCGA.XF.A9SL.01 1 0.385 0.785 0.82 0.00 0.16 0.02
#> TCGA.ZF.AA5P.01 1 0.500 0.720 0.50 0.00 0.50 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.UY.A78P.01 5 0.311 0.0000 0.00 0.00 0.00 0.20 0.80
#> TCGA.K4.A5RI.11 2 0.273 1.0000 0.00 0.84 0.00 0.16 0.00
#> TCGA.K4.A83P.01 1 0.651 0.0397 0.60 0.06 0.24 0.00 0.10
#> TCGA.XF.AAN8.01 4 0.000 0.8530 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A5BS.01 1 0.000 0.3047 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B8.01 3 0.513 0.0000 0.42 0.04 0.54 0.00 0.00
#> TCGA.XF.AAME.01 4 0.000 0.8530 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A43S.01 2 0.273 1.0000 0.00 0.84 0.00 0.16 0.00
#> TCGA.4Z.AA7N.01 1 0.501 0.2501 0.74 0.02 0.14 0.00 0.10
#> TCGA.DK.A3WY.01 2 0.273 1.0000 0.00 0.84 0.00 0.16 0.00
#> TCGA.DK.A1AF.01 4 0.000 0.8530 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.AAN4.01 4 0.000 0.8530 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.A3WX.01 4 0.593 0.1903 0.00 0.06 0.40 0.52 0.02
#> TCGA.XF.A9SL.01 1 0.569 -0.5949 0.48 0.02 0.46 0.00 0.04
#> TCGA.ZF.AA5P.01 1 0.342 -0.0594 0.76 0.00 0.24 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.UY.A78P.01 5 0.2048 0.000 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.K4.A5RI.11 2 0.1814 1.000 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.K4.A83P.01 1 0.7006 0.390 0.50 0.04 0.24 0.00 0.04 0.18
#> TCGA.XF.AAN8.01 4 0.1267 0.914 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.FD.A5BS.01 6 0.1556 0.590 0.08 0.00 0.00 0.00 0.00 0.92
#> TCGA.FD.A3B8.01 1 0.3997 0.388 0.78 0.02 0.14 0.00 0.06 0.00
#> TCGA.XF.AAME.01 4 0.0937 0.926 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.FD.A43S.01 2 0.1814 1.000 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.4Z.AA7N.01 1 0.6835 0.253 0.46 0.06 0.08 0.00 0.04 0.36
#> TCGA.DK.A3WY.01 2 0.1814 1.000 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.DK.A1AF.01 4 0.0547 0.931 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.XF.AAN4.01 4 0.0547 0.931 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DK.A3WX.01 3 0.4199 0.000 0.00 0.02 0.60 0.38 0.00 0.00
#> TCGA.XF.A9SL.01 1 0.0547 0.499 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZF.AA5P.01 6 0.4962 0.570 0.28 0.00 0.06 0.00 0.02 0.64
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.UY.A78P.01 5 0.0504 0.0000 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.K4.A5RI.11 2 0.0504 1.0000 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.K4.A83P.01 7 0.4848 0.0000 0.40 0.00 0.00 0.00 0.00 0.10 0.50
#> TCGA.XF.AAN8.01 4 0.3667 0.7832 0.00 0.00 0.00 0.74 0.00 0.06 0.20
#> TCGA.FD.A5BS.01 6 0.1671 0.6306 0.10 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.FD.A3B8.01 1 0.5397 0.2389 0.66 0.02 0.06 0.00 0.02 0.04 0.20
#> TCGA.XF.AAME.01 4 0.2945 0.7832 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.FD.A43S.01 2 0.0504 1.0000 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.4Z.AA7N.01 1 0.5680 -0.0407 0.52 0.00 0.04 0.00 0.00 0.30 0.14
#> TCGA.DK.A3WY.01 2 0.0504 1.0000 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DK.A1AF.01 4 0.0000 0.8277 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN4.01 4 0.0000 0.8277 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 3 0.1671 0.0000 0.00 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.XF.A9SL.01 1 0.0000 0.2675 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA5P.01 6 0.3991 0.6078 0.22 0.00 0.02 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.UY.A78P.01 5 0.0471 0.000 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.K4.A5RI.11 2 0.1887 0.910 0.04 0.90 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.K4.A83P.01 7 0.1275 0.252 0.04 0.00 0.00 0.00 0.00 0.02 0.94 0.00
#> TCGA.XF.AAN8.01 8 0.3737 0.000 0.00 0.02 0.00 0.48 0.00 0.00 0.00 0.50
#> TCGA.FD.A5BS.01 6 0.2569 0.484 0.02 0.00 0.00 0.00 0.00 0.82 0.16 0.00
#> TCGA.FD.A3B8.01 1 0.1563 0.465 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.XF.AAME.01 4 0.5843 -0.552 0.04 0.02 0.00 0.44 0.00 0.08 0.02 0.40
#> TCGA.FD.A43S.01 2 0.0000 0.942 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7N.01 7 0.5962 0.221 0.10 0.00 0.00 0.00 0.00 0.14 0.40 0.36
#> TCGA.DK.A3WY.01 2 0.0941 0.938 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.DK.A1AF.01 4 0.0471 0.468 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN4.01 4 0.0471 0.468 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WX.01 3 0.1091 0.000 0.00 0.00 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SL.01 1 0.6479 0.341 0.50 0.00 0.04 0.02 0.02 0.04 0.28 0.10
#> TCGA.ZF.AA5P.01 6 0.3942 0.473 0.34 0.00 0.02 0.00 0.00 0.62 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-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 59 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 0.4027 0.598 0.598
#> 3 3 0.619 0.793 0.816 0.5518 0.731 0.550
#> 4 4 0.676 0.742 0.815 0.1733 0.863 0.613
#> 5 5 0.711 0.699 0.793 0.0641 0.972 0.890
#> 6 6 0.700 0.545 0.798 0.0487 0.906 0.638
#> 7 7 0.725 0.657 0.761 0.0288 0.959 0.783
#> 8 8 0.754 0.555 0.677 0.0156 0.943 0.674
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.GD.A3OP.01 1 0 1 1 0
#> TCGA.4Z.AA86.01 2 0 1 0 1
#> TCGA.GU.A42Q.01 2 0 1 0 1
#> TCGA.FD.A5BU.01 1 0 1 1 0
#> TCGA.DK.AA6X.01 2 0 1 0 1
#> TCGA.GC.A3OO.01 2 0 1 0 1
#> TCGA.DK.A2I2.01 1 0 1 1 0
#> TCGA.4Z.AA7W.01 2 0 1 0 1
#> TCGA.XF.A9SI.01 1 0 1 1 0
#> TCGA.XF.A9SM.01 2 0 1 0 1
#> TCGA.DK.A3IU.01 2 0 1 0 1
#> TCGA.E7.A7XN.01 2 0 1 0 1
#> TCGA.FD.A3B3.01 1 0 1 1 0
#> TCGA.FD.A6TF.01 1 0 1 1 0
#> TCGA.FD.A43Y.01 2 0 1 0 1
#> TCGA.YC.A8S6.01 2 0 1 0 1
#> TCGA.CU.A0YO.01 2 0 1 0 1
#> TCGA.FD.A62P.01 2 0 1 0 1
#> TCGA.DK.AA74.01 2 0 1 0 1
#> TCGA.BT.A20U.11 1 0 1 1 0
#> TCGA.BT.A42F.01 2 0 1 0 1
#> TCGA.DK.A3IQ.01 2 0 1 0 1
#> TCGA.FD.A3B7.01 2 0 1 0 1
#> TCGA.DK.A1AB.01 1 0 1 1 0
#> TCGA.K4.A3WU.01 2 0 1 0 1
#> TCGA.FD.A62N.01 2 0 1 0 1
#> TCGA.UY.A9PB.01 2 0 1 0 1
#> TCGA.GU.A766.01 2 0 1 0 1
#> TCGA.FD.A6TB.01 2 0 1 0 1
#> TCGA.XF.A9T8.01 2 0 1 0 1
#> TCGA.G2.AA3D.01 2 0 1 0 1
#> TCGA.ZF.A9RG.01 1 0 1 1 0
#> TCGA.BT.A20O.01 2 0 1 0 1
#> TCGA.XF.A8HE.01 2 0 1 0 1
#> TCGA.GC.A3WC.01 1 0 1 1 0
#> TCGA.XF.A9SY.01 1 0 1 1 0
#> TCGA.GD.A2C5.11 1 0 1 1 0
#> TCGA.ZF.AA53.01 2 0 1 0 1
#> TCGA.DK.AA6T.01 2 0 1 0 1
#> TCGA.ZF.AA58.01 1 0 1 1 0
#> TCGA.GC.A6I3.11 1 0 1 1 0
#> TCGA.XF.AAMJ.01 2 0 1 0 1
#> TCGA.FD.A5BT.01 2 0 1 0 1
#> TCGA.PQ.A6FN.01 1 0 1 1 0
#> TCGA.SY.A9G0.01 2 0 1 0 1
#> TCGA.K4.A4AC.01 2 0 1 0 1
#> TCGA.FD.A43U.01 2 0 1 0 1
#> TCGA.GU.A764.01 2 0 1 0 1
#> TCGA.DK.A2I4.01 2 0 1 0 1
#> TCGA.BL.A13I.01 1 0 1 1 0
#> TCGA.FD.A6TK.01 2 0 1 0 1
#> TCGA.BT.A3PK.01 2 0 1 0 1
#> TCGA.XF.A9SW.01 2 0 1 0 1
#> TCGA.ZF.AA4W.01 2 0 1 0 1
#> TCGA.UY.A9PA.01 2 0 1 0 1
#> TCGA.R3.A69X.01 2 0 1 0 1
#> TCGA.E7.A519.01 2 0 1 0 1
#> TCGA.XF.AAMR.01 2 0 1 0 1
#> TCGA.FD.A3SP.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GD.A3OP.01 1 0.400 0.9290 0.84 0.16 0.00
#> TCGA.4Z.AA86.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.GU.A42Q.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.FD.A5BU.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.DK.AA6X.01 2 0.630 0.2228 0.00 0.52 0.48
#> TCGA.GC.A3OO.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.DK.A2I2.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.4Z.AA7W.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.XF.A9SI.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.XF.A9SM.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.DK.A3IU.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.E7.A7XN.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.FD.A3B3.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.FD.A6TF.01 1 0.400 0.9290 0.84 0.16 0.00
#> TCGA.FD.A43Y.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.YC.A8S6.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.CU.A0YO.01 3 0.624 0.0365 0.00 0.44 0.56
#> TCGA.FD.A62P.01 2 0.455 0.9160 0.00 0.80 0.20
#> TCGA.DK.AA74.01 2 0.480 0.8916 0.00 0.78 0.22
#> TCGA.BT.A20U.11 1 0.369 0.9342 0.86 0.14 0.00
#> TCGA.BT.A42F.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.DK.A3IQ.01 2 0.522 0.8289 0.00 0.74 0.26
#> TCGA.FD.A3B7.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.DK.A1AB.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.K4.A3WU.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.FD.A62N.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.UY.A9PB.01 3 0.613 0.1885 0.00 0.40 0.60
#> TCGA.GU.A766.01 2 0.429 0.9351 0.00 0.82 0.18
#> TCGA.FD.A6TB.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.XF.A9T8.01 3 0.630 -0.0765 0.00 0.48 0.52
#> TCGA.G2.AA3D.01 3 0.624 0.0365 0.00 0.44 0.56
#> TCGA.ZF.A9RG.01 1 0.400 0.9290 0.84 0.16 0.00
#> TCGA.BT.A20O.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.XF.A8HE.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.GC.A3WC.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.XF.A9SY.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.GD.A2C5.11 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.ZF.AA53.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.DK.AA6T.01 3 0.254 0.7284 0.00 0.08 0.92
#> TCGA.ZF.AA58.01 1 0.400 0.9290 0.84 0.16 0.00
#> TCGA.GC.A6I3.11 1 0.369 0.9342 0.86 0.14 0.00
#> TCGA.XF.AAMJ.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.FD.A5BT.01 2 0.480 0.8916 0.00 0.78 0.22
#> TCGA.PQ.A6FN.01 1 0.369 0.9342 0.86 0.14 0.00
#> TCGA.SY.A9G0.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.K4.A4AC.01 2 0.502 0.8435 0.00 0.76 0.24
#> TCGA.FD.A43U.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.GU.A764.01 3 0.613 0.1885 0.00 0.40 0.60
#> TCGA.DK.A2I4.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.BL.A13I.01 1 0.000 0.9497 1.00 0.00 0.00
#> TCGA.FD.A6TK.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.BT.A3PK.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.XF.A9SW.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.ZF.AA4W.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.UY.A9PA.01 3 0.000 0.7873 0.00 0.00 1.00
#> TCGA.R3.A69X.01 2 0.400 0.9515 0.00 0.84 0.16
#> TCGA.E7.A519.01 3 0.624 0.0365 0.00 0.44 0.56
#> TCGA.XF.AAMR.01 3 0.571 0.3648 0.00 0.32 0.68
#> TCGA.FD.A3SP.01 2 0.400 0.9515 0.00 0.84 0.16
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GD.A3OP.01 1 0.1211 0.8449 0.96 0.04 0.00 0.00
#> TCGA.4Z.AA86.01 3 0.1211 0.8058 0.00 0.00 0.96 0.04
#> TCGA.GU.A42Q.01 2 0.4907 0.8626 0.00 0.58 0.00 0.42
#> TCGA.FD.A5BU.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.DK.AA6X.01 4 0.3400 0.6926 0.00 0.00 0.18 0.82
#> TCGA.GC.A3OO.01 3 0.1637 0.8053 0.00 0.00 0.94 0.06
#> TCGA.DK.A2I2.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.4Z.AA7W.01 2 0.4855 0.8666 0.00 0.60 0.00 0.40
#> TCGA.XF.A9SI.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.XF.A9SM.01 2 0.6299 0.7141 0.00 0.60 0.08 0.32
#> TCGA.DK.A3IU.01 3 0.2011 0.7791 0.00 0.08 0.92 0.00
#> TCGA.E7.A7XN.01 2 0.4855 0.8666 0.00 0.60 0.00 0.40
#> TCGA.FD.A3B3.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.FD.A6TF.01 1 0.1211 0.8449 0.96 0.04 0.00 0.00
#> TCGA.FD.A43Y.01 2 0.4907 0.8626 0.00 0.58 0.00 0.42
#> TCGA.YC.A8S6.01 3 0.4624 0.4330 0.00 0.00 0.66 0.34
#> TCGA.CU.A0YO.01 4 0.3801 0.6647 0.00 0.00 0.22 0.78
#> TCGA.FD.A62P.01 4 0.4841 0.4247 0.00 0.14 0.08 0.78
#> TCGA.DK.AA74.01 4 0.3606 0.4741 0.00 0.14 0.02 0.84
#> TCGA.BT.A20U.11 1 0.0000 0.8603 1.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 2 0.4855 0.8666 0.00 0.60 0.00 0.40
#> TCGA.DK.A3IQ.01 4 0.1637 0.6553 0.00 0.00 0.06 0.94
#> TCGA.FD.A3B7.01 2 0.4855 0.8666 0.00 0.60 0.00 0.40
#> TCGA.DK.A1AB.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.K4.A3WU.01 3 0.2647 0.7536 0.00 0.12 0.88 0.00
#> TCGA.FD.A62N.01 3 0.1211 0.7938 0.00 0.04 0.96 0.00
#> TCGA.UY.A9PB.01 3 0.7344 0.0194 0.00 0.38 0.46 0.16
#> TCGA.GU.A766.01 4 0.4088 0.4903 0.00 0.14 0.04 0.82
#> TCGA.FD.A6TB.01 2 0.5957 0.7847 0.00 0.54 0.04 0.42
#> TCGA.XF.A9T8.01 2 0.6286 0.6343 0.00 0.66 0.14 0.20
#> TCGA.G2.AA3D.01 4 0.3801 0.6647 0.00 0.00 0.22 0.78
#> TCGA.ZF.A9RG.01 1 0.0707 0.8537 0.98 0.02 0.00 0.00
#> TCGA.BT.A20O.01 2 0.5355 0.8460 0.00 0.62 0.02 0.36
#> TCGA.XF.A8HE.01 2 0.4855 0.8666 0.00 0.60 0.00 0.40
#> TCGA.GC.A3WC.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.XF.A9SY.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.GD.A2C5.11 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.ZF.AA53.01 2 0.4907 0.8626 0.00 0.58 0.00 0.42
#> TCGA.DK.AA6T.01 3 0.4079 0.6631 0.00 0.02 0.80 0.18
#> TCGA.ZF.AA58.01 1 0.0707 0.8537 0.98 0.02 0.00 0.00
#> TCGA.GC.A6I3.11 1 0.0000 0.8603 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMJ.01 3 0.1637 0.8053 0.00 0.00 0.94 0.06
#> TCGA.FD.A5BT.01 4 0.3821 0.4893 0.00 0.12 0.04 0.84
#> TCGA.PQ.A6FN.01 1 0.0000 0.8603 1.00 0.00 0.00 0.00
#> TCGA.SY.A9G0.01 3 0.1637 0.8053 0.00 0.00 0.94 0.06
#> TCGA.K4.A4AC.01 2 0.6881 0.6361 0.00 0.54 0.12 0.34
#> TCGA.FD.A43U.01 3 0.1913 0.7994 0.00 0.04 0.94 0.02
#> TCGA.GU.A764.01 3 0.7344 0.0194 0.00 0.38 0.46 0.16
#> TCGA.DK.A2I4.01 3 0.1211 0.7938 0.00 0.04 0.96 0.00
#> TCGA.BL.A13I.01 1 0.4642 0.8947 0.74 0.24 0.00 0.02
#> TCGA.FD.A6TK.01 2 0.5957 0.7847 0.00 0.54 0.04 0.42
#> TCGA.BT.A3PK.01 2 0.4994 0.8145 0.00 0.52 0.00 0.48
#> TCGA.XF.A9SW.01 3 0.1637 0.8053 0.00 0.00 0.94 0.06
#> TCGA.ZF.AA4W.01 2 0.4855 0.8666 0.00 0.60 0.00 0.40
#> TCGA.UY.A9PA.01 3 0.1637 0.8053 0.00 0.00 0.94 0.06
#> TCGA.R3.A69X.01 4 0.3172 0.4056 0.00 0.16 0.00 0.84
#> TCGA.E7.A519.01 4 0.3801 0.6647 0.00 0.00 0.22 0.78
#> TCGA.XF.AAMR.01 4 0.5173 0.4364 0.00 0.02 0.32 0.66
#> TCGA.FD.A3SP.01 2 0.5957 0.7847 0.00 0.54 0.04 0.42
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GD.A3OP.01 1 0.4262 0.741 0.56 0.00 0.00 0.44 0.00
#> TCGA.4Z.AA86.01 3 0.1410 0.852 0.00 0.00 0.94 0.06 0.00
#> TCGA.GU.A42Q.01 2 0.0609 0.800 0.00 0.98 0.00 0.00 0.02
#> TCGA.FD.A5BU.01 1 0.1043 0.854 0.96 0.00 0.00 0.00 0.04
#> TCGA.DK.AA6X.01 5 0.6929 0.666 0.00 0.14 0.04 0.32 0.50
#> TCGA.GC.A3OO.01 3 0.0000 0.863 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A2I2.01 1 0.1043 0.854 0.96 0.00 0.00 0.00 0.04
#> TCGA.4Z.AA7W.01 2 0.1410 0.778 0.00 0.94 0.00 0.06 0.00
#> TCGA.XF.A9SI.01 1 0.1043 0.852 0.96 0.00 0.00 0.00 0.04
#> TCGA.XF.A9SM.01 2 0.5095 0.539 0.00 0.56 0.00 0.04 0.40
#> TCGA.DK.A3IU.01 3 0.3110 0.817 0.00 0.00 0.86 0.06 0.08
#> TCGA.E7.A7XN.01 2 0.1043 0.787 0.00 0.96 0.00 0.04 0.00
#> TCGA.FD.A3B3.01 1 0.1043 0.854 0.96 0.00 0.00 0.00 0.04
#> TCGA.FD.A6TF.01 1 0.4262 0.741 0.56 0.00 0.00 0.44 0.00
#> TCGA.FD.A43Y.01 2 0.0609 0.800 0.00 0.98 0.00 0.00 0.02
#> TCGA.YC.A8S6.01 3 0.6111 0.228 0.00 0.00 0.56 0.26 0.18
#> TCGA.CU.A0YO.01 5 0.7316 0.648 0.00 0.10 0.10 0.32 0.48
#> TCGA.FD.A62P.01 5 0.3109 0.289 0.00 0.20 0.00 0.00 0.80
#> TCGA.DK.AA74.01 5 0.7222 0.573 0.00 0.30 0.02 0.28 0.40
#> TCGA.BT.A20U.11 1 0.3424 0.822 0.76 0.00 0.00 0.24 0.00
#> TCGA.BT.A42F.01 2 0.1043 0.800 0.00 0.96 0.00 0.00 0.04
#> TCGA.DK.A3IQ.01 5 0.6727 0.661 0.00 0.16 0.02 0.32 0.50
#> TCGA.FD.A3B7.01 2 0.3037 0.730 0.00 0.86 0.00 0.10 0.04
#> TCGA.DK.A1AB.01 1 0.1043 0.852 0.96 0.00 0.00 0.00 0.04
#> TCGA.K4.A3WU.01 3 0.4921 0.530 0.00 0.00 0.62 0.04 0.34
#> TCGA.FD.A62N.01 3 0.2438 0.838 0.00 0.00 0.90 0.06 0.04
#> TCGA.UY.A9PB.01 5 0.7526 -0.231 0.00 0.32 0.26 0.04 0.38
#> TCGA.GU.A766.01 5 0.7179 0.582 0.00 0.28 0.02 0.28 0.42
#> TCGA.FD.A6TB.01 2 0.4060 0.608 0.00 0.64 0.00 0.00 0.36
#> TCGA.XF.A9T8.01 2 0.3034 0.744 0.00 0.88 0.06 0.04 0.02
#> TCGA.G2.AA3D.01 5 0.7259 0.647 0.00 0.10 0.10 0.30 0.50
#> TCGA.ZF.A9RG.01 1 0.4126 0.763 0.62 0.00 0.00 0.38 0.00
#> TCGA.BT.A20O.01 2 0.1732 0.792 0.00 0.92 0.00 0.00 0.08
#> TCGA.XF.A8HE.01 2 0.0609 0.793 0.00 0.98 0.00 0.02 0.00
#> TCGA.GC.A3WC.01 1 0.1043 0.854 0.96 0.00 0.00 0.00 0.04
#> TCGA.XF.A9SY.01 1 0.0000 0.855 1.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.11 1 0.1043 0.854 0.96 0.00 0.00 0.00 0.04
#> TCGA.ZF.AA53.01 2 0.0609 0.797 0.00 0.98 0.00 0.00 0.02
#> TCGA.DK.AA6T.01 3 0.4725 0.669 0.00 0.00 0.72 0.20 0.08
#> TCGA.ZF.AA58.01 1 0.4126 0.763 0.62 0.00 0.00 0.38 0.00
#> TCGA.GC.A6I3.11 1 0.3424 0.822 0.76 0.00 0.00 0.24 0.00
#> TCGA.XF.AAMJ.01 3 0.0609 0.860 0.00 0.00 0.98 0.02 0.00
#> TCGA.FD.A5BT.01 5 0.7179 0.582 0.00 0.28 0.02 0.28 0.42
#> TCGA.PQ.A6FN.01 1 0.3424 0.822 0.76 0.00 0.00 0.24 0.00
#> TCGA.SY.A9G0.01 3 0.0609 0.860 0.00 0.00 0.98 0.02 0.00
#> TCGA.K4.A4AC.01 2 0.5663 0.493 0.00 0.52 0.02 0.04 0.42
#> TCGA.FD.A43U.01 3 0.1216 0.859 0.00 0.00 0.96 0.02 0.02
#> TCGA.GU.A764.01 5 0.7526 -0.231 0.00 0.32 0.26 0.04 0.38
#> TCGA.DK.A2I4.01 3 0.2797 0.827 0.00 0.00 0.88 0.06 0.06
#> TCGA.BL.A13I.01 1 0.1043 0.854 0.96 0.00 0.00 0.00 0.04
#> TCGA.FD.A6TK.01 2 0.4126 0.594 0.00 0.62 0.00 0.00 0.38
#> TCGA.BT.A3PK.01 2 0.1410 0.792 0.00 0.94 0.00 0.00 0.06
#> TCGA.XF.A9SW.01 3 0.0609 0.861 0.00 0.00 0.98 0.02 0.00
#> TCGA.ZF.AA4W.01 2 0.2020 0.747 0.00 0.90 0.00 0.10 0.00
#> TCGA.UY.A9PA.01 3 0.0000 0.863 0.00 0.00 1.00 0.00 0.00
#> TCGA.R3.A69X.01 5 0.6816 0.560 0.00 0.32 0.00 0.32 0.36
#> TCGA.E7.A519.01 5 0.7234 0.631 0.00 0.08 0.12 0.30 0.50
#> TCGA.XF.AAMR.01 5 0.7019 0.579 0.00 0.04 0.16 0.30 0.50
#> TCGA.FD.A3SP.01 2 0.4126 0.594 0.00 0.62 0.00 0.00 0.38
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GD.A3OP.01 1 0.5641 -0.743 0.50 0.00 0.00 0.40 0.04 0.06
#> TCGA.4Z.AA86.01 3 0.2512 0.831 0.00 0.06 0.88 0.06 0.00 0.00
#> TCGA.GU.A42Q.01 2 0.3567 0.804 0.00 0.80 0.00 0.10 0.00 0.10
#> TCGA.FD.A5BU.01 1 0.0000 0.538 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6X.01 5 0.0937 0.729 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.GC.A3OO.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A2I2.01 1 0.0000 0.538 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA7W.01 2 0.1092 0.828 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.XF.A9SI.01 1 0.3321 0.437 0.82 0.00 0.00 0.10 0.00 0.08
#> TCGA.XF.A9SM.01 6 0.2793 0.697 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.DK.A3IU.01 3 0.2260 0.825 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.E7.A7XN.01 2 0.1807 0.817 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.FD.A3B3.01 1 0.0000 0.538 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TF.01 1 0.5641 -0.743 0.50 0.00 0.00 0.40 0.04 0.06
#> TCGA.FD.A43Y.01 2 0.3567 0.804 0.00 0.80 0.00 0.10 0.00 0.10
#> TCGA.YC.A8S6.01 5 0.5260 0.184 0.00 0.02 0.44 0.02 0.50 0.02
#> TCGA.CU.A0YO.01 5 0.1556 0.728 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.FD.A62P.01 6 0.5103 0.655 0.00 0.04 0.00 0.06 0.24 0.66
#> TCGA.DK.AA74.01 5 0.5691 0.553 0.00 0.26 0.00 0.14 0.58 0.02
#> TCGA.BT.A20U.11 1 0.4144 -0.415 0.62 0.00 0.00 0.36 0.00 0.02
#> TCGA.BT.A42F.01 2 0.2350 0.828 0.00 0.88 0.00 0.02 0.00 0.10
#> TCGA.DK.A3IQ.01 5 0.1092 0.721 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.FD.A3B7.01 2 0.4547 0.737 0.00 0.76 0.00 0.08 0.08 0.08
#> TCGA.DK.A1AB.01 1 0.3321 0.437 0.82 0.00 0.00 0.10 0.00 0.08
#> TCGA.K4.A3WU.01 6 0.3756 0.222 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.FD.A62N.01 3 0.1267 0.885 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.UY.A9PB.01 6 0.3544 0.729 0.00 0.08 0.12 0.00 0.00 0.80
#> TCGA.GU.A766.01 5 0.6456 0.473 0.00 0.18 0.00 0.10 0.56 0.16
#> TCGA.FD.A6TB.01 6 0.5392 0.708 0.00 0.18 0.00 0.04 0.12 0.66
#> TCGA.XF.A9T8.01 2 0.2190 0.812 0.00 0.90 0.00 0.06 0.00 0.04
#> TCGA.G2.AA3D.01 5 0.3073 0.714 0.00 0.00 0.08 0.08 0.84 0.00
#> TCGA.ZF.A9RG.01 4 0.3869 0.000 0.50 0.00 0.00 0.50 0.00 0.00
#> TCGA.BT.A20O.01 2 0.2956 0.812 0.00 0.84 0.00 0.04 0.00 0.12
#> TCGA.XF.A8HE.01 2 0.2474 0.829 0.00 0.88 0.00 0.08 0.00 0.04
#> TCGA.GC.A3WC.01 1 0.0000 0.538 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SY.01 1 0.2350 0.469 0.88 0.00 0.00 0.10 0.00 0.02
#> TCGA.GD.A2C5.11 1 0.0937 0.523 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.ZF.AA53.01 2 0.4430 0.778 0.00 0.76 0.00 0.12 0.04 0.08
#> TCGA.DK.AA6T.01 3 0.6806 0.477 0.00 0.14 0.56 0.20 0.04 0.06
#> TCGA.ZF.AA58.01 1 0.4337 -0.945 0.50 0.00 0.00 0.48 0.02 0.00
#> TCGA.GC.A6I3.11 1 0.4144 -0.415 0.62 0.00 0.00 0.36 0.00 0.02
#> TCGA.XF.AAMJ.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BT.01 5 0.5691 0.553 0.00 0.26 0.00 0.14 0.58 0.02
#> TCGA.PQ.A6FN.01 1 0.4144 -0.415 0.62 0.00 0.00 0.36 0.00 0.02
#> TCGA.SY.A9G0.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A4AC.01 6 0.3544 0.758 0.00 0.12 0.00 0.00 0.08 0.80
#> TCGA.FD.A43U.01 3 0.2629 0.858 0.00 0.00 0.88 0.02 0.02 0.08
#> TCGA.GU.A764.01 6 0.3544 0.729 0.00 0.08 0.12 0.00 0.00 0.80
#> TCGA.DK.A2I4.01 3 0.1267 0.885 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.BL.A13I.01 1 0.0000 0.538 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TK.01 6 0.5239 0.726 0.00 0.16 0.00 0.04 0.12 0.68
#> TCGA.BT.A3PK.01 2 0.5636 0.500 0.00 0.62 0.00 0.06 0.08 0.24
#> TCGA.XF.A9SW.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4W.01 2 0.2094 0.815 0.00 0.90 0.00 0.08 0.00 0.02
#> TCGA.UY.A9PA.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 5 0.5310 0.578 0.00 0.22 0.00 0.12 0.64 0.02
#> TCGA.E7.A519.01 5 0.2794 0.720 0.00 0.00 0.08 0.06 0.86 0.00
#> TCGA.XF.AAMR.01 5 0.3073 0.714 0.00 0.00 0.08 0.08 0.84 0.00
#> TCGA.FD.A3SP.01 6 0.5529 0.704 0.00 0.20 0.00 0.04 0.12 0.64
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GD.A3OP.01 4 0.5874 0.772 0.30 0.00 0.02 0.54 0.00 0.08 0.06
#> TCGA.4Z.AA86.01 3 0.3244 0.438 0.00 0.00 0.78 0.04 0.00 0.00 0.18
#> TCGA.GU.A42Q.01 2 0.1166 0.715 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.FD.A5BU.01 1 0.0000 0.848 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6X.01 5 0.0863 0.655 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.GC.A3OO.01 3 0.0504 0.791 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DK.A2I2.01 1 0.0863 0.836 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.4Z.AA7W.01 2 0.3887 0.714 0.00 0.70 0.00 0.02 0.02 0.00 0.26
#> TCGA.XF.A9SI.01 1 0.5287 0.577 0.66 0.00 0.00 0.16 0.02 0.04 0.12
#> TCGA.XF.A9SM.01 6 0.1886 0.718 0.00 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.DK.A3IU.01 3 0.3186 0.578 0.00 0.00 0.76 0.00 0.00 0.22 0.02
#> TCGA.E7.A7XN.01 2 0.5460 0.639 0.00 0.58 0.00 0.14 0.00 0.04 0.24
#> TCGA.FD.A3B3.01 1 0.0000 0.848 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TF.01 4 0.5874 0.772 0.30 0.00 0.02 0.54 0.00 0.08 0.06
#> TCGA.FD.A43Y.01 2 0.1166 0.715 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.YC.A8S6.01 5 0.5293 -0.116 0.00 0.00 0.42 0.02 0.46 0.00 0.10
#> TCGA.CU.A0YO.01 5 0.0863 0.655 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.FD.A62P.01 6 0.5962 0.620 0.00 0.20 0.00 0.06 0.14 0.58 0.02
#> TCGA.DK.AA74.01 5 0.6237 0.422 0.00 0.16 0.00 0.02 0.48 0.04 0.30
#> TCGA.BT.A20U.11 4 0.3413 0.842 0.38 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.BT.A42F.01 2 0.3687 0.676 0.00 0.76 0.00 0.00 0.00 0.12 0.12
#> TCGA.DK.A3IQ.01 5 0.0863 0.652 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.FD.A3B7.01 2 0.5083 0.579 0.00 0.56 0.00 0.00 0.06 0.04 0.34
#> TCGA.DK.A1AB.01 1 0.5302 0.586 0.66 0.00 0.00 0.14 0.02 0.04 0.14
#> TCGA.K4.A3WU.01 6 0.3755 0.265 0.00 0.00 0.34 0.00 0.00 0.64 0.02
#> TCGA.FD.A62N.01 3 0.3315 0.690 0.00 0.00 0.82 0.02 0.00 0.08 0.08
#> TCGA.UY.A9PB.01 6 0.3289 0.661 0.00 0.06 0.10 0.00 0.00 0.82 0.02
#> TCGA.GU.A766.01 5 0.6615 0.407 0.00 0.16 0.00 0.02 0.46 0.08 0.28
#> TCGA.FD.A6TB.01 6 0.4524 0.605 0.00 0.34 0.00 0.02 0.04 0.60 0.00
#> TCGA.XF.A9T8.01 2 0.5922 0.588 0.00 0.52 0.00 0.16 0.00 0.06 0.26
#> TCGA.G2.AA3D.01 5 0.3114 0.626 0.00 0.00 0.04 0.08 0.84 0.00 0.04
#> TCGA.ZF.A9RG.01 4 0.3685 0.856 0.32 0.00 0.00 0.66 0.02 0.00 0.00
#> TCGA.BT.A20O.01 2 0.4177 0.642 0.00 0.70 0.00 0.00 0.00 0.12 0.18
#> TCGA.XF.A8HE.01 2 0.2163 0.738 0.00 0.88 0.00 0.02 0.00 0.00 0.10
#> TCGA.GC.A3WC.01 1 0.0000 0.848 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SY.01 1 0.2081 0.724 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.GD.A2C5.11 1 0.1664 0.821 0.92 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.ZF.AA53.01 2 0.1671 0.738 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DK.AA6T.01 7 0.5390 0.000 0.00 0.00 0.40 0.04 0.04 0.02 0.50
#> TCGA.ZF.AA58.01 4 0.3606 0.851 0.30 0.00 0.00 0.68 0.02 0.00 0.00
#> TCGA.GC.A6I3.11 4 0.3413 0.842 0.38 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.XF.AAMJ.01 3 0.1006 0.774 0.00 0.00 0.96 0.02 0.02 0.00 0.00
#> TCGA.FD.A5BT.01 5 0.6237 0.422 0.00 0.16 0.00 0.02 0.48 0.04 0.30
#> TCGA.PQ.A6FN.01 4 0.3413 0.842 0.38 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.SY.A9G0.01 3 0.0504 0.791 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.K4.A4AC.01 6 0.2569 0.727 0.00 0.14 0.00 0.00 0.02 0.84 0.00
#> TCGA.FD.A43U.01 3 0.3011 0.653 0.00 0.00 0.82 0.00 0.00 0.12 0.06
#> TCGA.GU.A764.01 6 0.2572 0.690 0.00 0.06 0.08 0.00 0.00 0.86 0.00
#> TCGA.DK.A2I4.01 3 0.3744 0.656 0.00 0.00 0.78 0.02 0.00 0.12 0.08
#> TCGA.BL.A13I.01 1 0.0000 0.848 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TK.01 6 0.4479 0.668 0.00 0.26 0.00 0.02 0.06 0.66 0.00
#> TCGA.BT.A3PK.01 2 0.4158 0.606 0.00 0.76 0.00 0.02 0.02 0.14 0.06
#> TCGA.XF.A9SW.01 3 0.1006 0.786 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.ZF.AA4W.01 2 0.3530 0.700 0.00 0.76 0.00 0.02 0.02 0.00 0.20
#> TCGA.UY.A9PA.01 3 0.0504 0.791 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.R3.A69X.01 5 0.5165 0.472 0.00 0.28 0.00 0.02 0.58 0.00 0.12
#> TCGA.E7.A519.01 5 0.2563 0.635 0.00 0.00 0.04 0.04 0.88 0.00 0.04
#> TCGA.XF.AAMR.01 5 0.3114 0.626 0.00 0.00 0.04 0.08 0.84 0.00 0.04
#> TCGA.FD.A3SP.01 6 0.5103 0.635 0.00 0.30 0.00 0.02 0.06 0.60 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.GD.A3OP.01 4 0.3601 0.562 0.00 0.00 0.00 0.76 0.00 0.06 0.16 0.02
#> TCGA.4Z.AA86.01 3 0.4903 0.714 0.12 0.02 0.70 0.00 0.02 0.10 0.04 0.00
#> TCGA.GU.A42Q.01 2 0.5801 0.627 0.02 0.46 0.00 0.00 0.14 0.34 0.00 0.04
#> TCGA.FD.A5BU.01 1 0.3514 0.896 0.64 0.02 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6X.01 5 0.3862 -0.285 0.00 0.00 0.04 0.00 0.60 0.00 0.36 0.00
#> TCGA.GC.A3OO.01 3 0.0000 0.766 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2I2.01 1 0.3514 0.892 0.64 0.00 0.00 0.34 0.00 0.00 0.00 0.02
#> TCGA.4Z.AA7W.01 2 0.1947 0.628 0.00 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.XF.A9SI.01 4 0.4340 -0.398 0.38 0.00 0.00 0.54 0.00 0.08 0.00 0.00
#> TCGA.XF.A9SM.01 8 0.1408 0.726 0.00 0.02 0.00 0.00 0.02 0.02 0.00 0.94
#> TCGA.DK.A3IU.01 3 0.4233 0.516 0.04 0.00 0.60 0.00 0.00 0.02 0.00 0.34
#> TCGA.E7.A7XN.01 2 0.4087 0.516 0.02 0.78 0.00 0.00 0.02 0.06 0.08 0.04
#> TCGA.FD.A3B3.01 1 0.3083 0.898 0.66 0.00 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TF.01 4 0.3601 0.562 0.00 0.00 0.00 0.76 0.00 0.06 0.16 0.02
#> TCGA.FD.A43Y.01 2 0.5801 0.627 0.02 0.46 0.00 0.00 0.14 0.34 0.00 0.04
#> TCGA.YC.A8S6.01 3 0.5088 0.175 0.02 0.00 0.54 0.00 0.34 0.02 0.08 0.00
#> TCGA.CU.A0YO.01 5 0.3943 -0.350 0.00 0.00 0.04 0.00 0.56 0.00 0.40 0.00
#> TCGA.FD.A62P.01 8 0.5032 0.615 0.00 0.00 0.00 0.00 0.26 0.16 0.02 0.56
#> TCGA.DK.AA74.01 5 0.1341 0.478 0.00 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.BT.A20U.11 4 0.0808 0.699 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 2 0.6005 0.607 0.02 0.50 0.00 0.00 0.20 0.22 0.00 0.06
#> TCGA.DK.A3IQ.01 5 0.3193 -0.227 0.00 0.00 0.00 0.00 0.62 0.00 0.38 0.00
#> TCGA.FD.A3B7.01 2 0.4968 0.460 0.02 0.52 0.00 0.00 0.38 0.06 0.00 0.02
#> TCGA.DK.A1AB.01 1 0.5133 0.430 0.40 0.00 0.00 0.38 0.00 0.22 0.00 0.00
#> TCGA.K4.A3WU.01 8 0.2719 0.528 0.02 0.00 0.18 0.00 0.00 0.00 0.00 0.80
#> TCGA.FD.A62N.01 3 0.4720 0.705 0.12 0.00 0.70 0.00 0.00 0.10 0.02 0.06
#> TCGA.UY.A9PB.01 8 0.0941 0.718 0.00 0.02 0.02 0.00 0.00 0.00 0.00 0.96
#> TCGA.GU.A766.01 5 0.2399 0.473 0.00 0.04 0.00 0.00 0.88 0.04 0.00 0.04
#> TCGA.FD.A6TB.01 8 0.5458 0.564 0.00 0.04 0.00 0.00 0.22 0.22 0.00 0.52
#> TCGA.XF.A9T8.01 2 0.4134 0.482 0.02 0.76 0.00 0.00 0.00 0.06 0.08 0.08
#> TCGA.G2.AA3D.01 7 0.4106 0.933 0.00 0.00 0.04 0.00 0.30 0.02 0.64 0.00
#> TCGA.ZF.A9RG.01 4 0.0000 0.700 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20O.01 2 0.6005 0.607 0.02 0.50 0.00 0.00 0.20 0.22 0.00 0.06
#> TCGA.XF.A8HE.01 2 0.3385 0.648 0.00 0.76 0.00 0.00 0.08 0.16 0.00 0.00
#> TCGA.GC.A3WC.01 1 0.3083 0.898 0.66 0.00 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SY.01 4 0.3299 -0.496 0.44 0.00 0.00 0.56 0.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.11 1 0.3449 0.870 0.66 0.00 0.00 0.32 0.00 0.02 0.00 0.00
#> TCGA.ZF.AA53.01 2 0.5423 0.596 0.00 0.52 0.00 0.00 0.26 0.18 0.00 0.04
#> TCGA.DK.AA6T.01 3 0.7673 0.305 0.20 0.04 0.30 0.00 0.20 0.22 0.04 0.00
#> TCGA.ZF.AA58.01 4 0.0000 0.700 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.11 4 0.0808 0.699 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMJ.01 3 0.0941 0.763 0.02 0.00 0.96 0.00 0.00 0.02 0.00 0.00
#> TCGA.FD.A5BT.01 5 0.2482 0.476 0.02 0.06 0.00 0.00 0.88 0.02 0.00 0.02
#> TCGA.PQ.A6FN.01 4 0.0808 0.699 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.SY.A9G0.01 3 0.0941 0.763 0.02 0.00 0.96 0.00 0.00 0.02 0.00 0.00
#> TCGA.K4.A4AC.01 8 0.2484 0.730 0.00 0.02 0.00 0.00 0.02 0.10 0.00 0.86
#> TCGA.FD.A43U.01 3 0.3587 0.726 0.02 0.00 0.80 0.00 0.02 0.02 0.02 0.12
#> TCGA.GU.A764.01 8 0.0941 0.718 0.00 0.02 0.02 0.00 0.00 0.00 0.00 0.96
#> TCGA.DK.A2I4.01 3 0.5133 0.683 0.12 0.00 0.66 0.00 0.00 0.10 0.02 0.10
#> TCGA.BL.A13I.01 1 0.3514 0.896 0.64 0.02 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TK.01 8 0.5019 0.649 0.00 0.04 0.00 0.00 0.22 0.14 0.00 0.60
#> TCGA.BT.A3PK.01 5 0.6129 -0.481 0.00 0.36 0.00 0.00 0.36 0.18 0.00 0.10
#> TCGA.XF.A9SW.01 3 0.0941 0.765 0.00 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.ZF.AA4W.01 2 0.3227 0.635 0.00 0.78 0.00 0.00 0.14 0.08 0.00 0.00
#> TCGA.UY.A9PA.01 3 0.0471 0.766 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.R3.A69X.01 5 0.3314 0.433 0.00 0.10 0.00 0.00 0.80 0.02 0.08 0.00
#> TCGA.E7.A519.01 7 0.3594 0.898 0.00 0.00 0.04 0.00 0.28 0.00 0.68 0.00
#> TCGA.XF.AAMR.01 7 0.4028 0.928 0.00 0.00 0.04 0.00 0.28 0.02 0.66 0.00
#> TCGA.FD.A3SP.01 8 0.5109 0.632 0.00 0.04 0.00 0.00 0.24 0.14 0.00 0.58
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0221"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5005 0.500 0.500
#> 3 3 0.675 0.881 0.605 0.2900 0.792 0.583
#> 4 4 0.650 0.446 0.681 0.1172 0.750 0.348
#> 5 5 0.608 0.763 0.851 0.0753 0.933 0.733
#> 6 6 0.692 0.448 0.776 0.0688 0.992 0.960
#> 7 7 0.783 0.604 0.787 0.0450 0.892 0.480
#> 8 8 0.792 0.504 0.684 0.0237 0.942 0.562
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.GD.A3OP.01 1 0 1 1 0
#> TCGA.FD.A5BU.01 2 0 1 0 1
#> TCGA.DK.A2I2.01 2 0 1 0 1
#> TCGA.XF.A9SI.01 1 0 1 1 0
#> TCGA.FD.A3B3.01 2 0 1 0 1
#> TCGA.FD.A6TF.01 1 0 1 1 0
#> TCGA.BT.A20U.11 1 0 1 1 0
#> TCGA.DK.A1AB.01 1 0 1 1 0
#> TCGA.ZF.A9RG.01 1 0 1 1 0
#> TCGA.GC.A3WC.01 2 0 1 0 1
#> TCGA.XF.A9SY.01 1 0 1 1 0
#> TCGA.GD.A2C5.11 2 0 1 0 1
#> TCGA.ZF.AA58.01 1 0 1 1 0
#> TCGA.GC.A6I3.11 1 0 1 1 0
#> TCGA.PQ.A6FN.01 1 0 1 1 0
#> TCGA.BL.A13I.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GD.A3OP.01 1 0.624 1.000 0.56 0.00 0.44
#> TCGA.FD.A5BU.01 2 0.595 0.868 0.36 0.64 0.00
#> TCGA.DK.A2I2.01 2 0.000 0.749 0.00 1.00 0.00
#> TCGA.XF.A9SI.01 3 0.000 0.866 0.00 0.00 1.00
#> TCGA.FD.A3B3.01 2 0.613 0.873 0.40 0.60 0.00
#> TCGA.FD.A6TF.01 1 0.624 1.000 0.56 0.00 0.44
#> TCGA.BT.A20U.11 3 0.000 0.866 0.00 0.00 1.00
#> TCGA.DK.A1AB.01 1 0.624 1.000 0.56 0.00 0.44
#> TCGA.ZF.A9RG.01 1 0.624 1.000 0.56 0.00 0.44
#> TCGA.GC.A3WC.01 2 0.000 0.749 0.00 1.00 0.00
#> TCGA.XF.A9SY.01 3 0.254 0.779 0.08 0.00 0.92
#> TCGA.GD.A2C5.11 2 0.613 0.873 0.40 0.60 0.00
#> TCGA.ZF.AA58.01 1 0.624 1.000 0.56 0.00 0.44
#> TCGA.GC.A6I3.11 3 0.296 0.803 0.10 0.00 0.90
#> TCGA.PQ.A6FN.01 3 0.296 0.803 0.10 0.00 0.90
#> TCGA.BL.A13I.01 2 0.613 0.873 0.40 0.60 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GD.A3OP.01 1 0.361 1.000 0.80 0.00 0.20 0.00
#> TCGA.FD.A5BU.01 2 0.499 -0.398 0.00 0.52 0.00 0.48
#> TCGA.DK.A2I2.01 2 0.201 0.546 0.08 0.92 0.00 0.00
#> TCGA.XF.A9SI.01 3 0.000 0.697 0.00 0.00 1.00 0.00
#> TCGA.FD.A3B3.01 4 0.495 0.143 0.00 0.44 0.00 0.56
#> TCGA.FD.A6TF.01 1 0.361 1.000 0.80 0.00 0.20 0.00
#> TCGA.BT.A20U.11 3 0.000 0.697 0.00 0.00 1.00 0.00
#> TCGA.DK.A1AB.01 1 0.361 1.000 0.80 0.00 0.20 0.00
#> TCGA.ZF.A9RG.01 3 0.491 0.227 0.42 0.00 0.58 0.00
#> TCGA.GC.A3WC.01 2 0.000 0.555 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SY.01 4 0.704 -0.277 0.12 0.00 0.42 0.46
#> TCGA.GD.A2C5.11 4 0.495 0.143 0.00 0.44 0.00 0.56
#> TCGA.ZF.AA58.01 3 0.491 0.227 0.42 0.00 0.58 0.00
#> TCGA.GC.A6I3.11 3 0.234 0.720 0.10 0.00 0.90 0.00
#> TCGA.PQ.A6FN.01 3 0.234 0.720 0.10 0.00 0.90 0.00
#> TCGA.BL.A13I.01 4 0.495 0.143 0.00 0.44 0.00 0.56
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GD.A3OP.01 1 0.2020 0.915 0.90 0.00 0.10 0.00 0.00
#> TCGA.FD.A5BU.01 4 0.3697 0.716 0.10 0.08 0.00 0.82 0.00
#> TCGA.DK.A2I2.01 2 0.5487 0.810 0.00 0.62 0.00 0.28 0.10
#> TCGA.XF.A9SI.01 3 0.0000 0.794 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A3B3.01 4 0.0000 0.918 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TF.01 1 0.2020 0.915 0.90 0.00 0.10 0.00 0.00
#> TCGA.BT.A20U.11 3 0.2929 0.655 0.00 0.18 0.82 0.00 0.00
#> TCGA.DK.A1AB.01 1 0.5295 0.819 0.74 0.10 0.10 0.00 0.06
#> TCGA.ZF.A9RG.01 3 0.4588 0.711 0.22 0.06 0.72 0.00 0.00
#> TCGA.GC.A3WC.01 2 0.5245 0.803 0.08 0.64 0.00 0.28 0.00
#> TCGA.XF.A9SY.01 5 0.2732 0.000 0.00 0.00 0.16 0.00 0.84
#> TCGA.GD.A2C5.11 4 0.0000 0.918 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA58.01 3 0.4588 0.711 0.22 0.06 0.72 0.00 0.00
#> TCGA.GC.A6I3.11 3 0.2012 0.805 0.02 0.06 0.92 0.00 0.00
#> TCGA.PQ.A6FN.01 3 0.0609 0.805 0.02 0.00 0.98 0.00 0.00
#> TCGA.BL.A13I.01 4 0.0000 0.918 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GD.A3OP.01 1 0.0547 0.8890 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.FD.A5BU.01 4 0.4328 -0.0611 0.02 0.00 0.00 0.52 0.00 0.46
#> TCGA.DK.A2I2.01 2 0.5555 0.0000 0.00 0.48 0.00 0.14 0.00 0.38
#> TCGA.XF.A9SI.01 3 0.3409 0.5225 0.00 0.30 0.70 0.00 0.00 0.00
#> TCGA.FD.A3B3.01 4 0.0000 0.7677 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TF.01 1 0.0547 0.8890 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BT.A20U.11 3 0.4282 0.4001 0.00 0.42 0.56 0.00 0.02 0.00
#> TCGA.DK.A1AB.01 1 0.4502 0.7602 0.74 0.10 0.02 0.00 0.00 0.14
#> TCGA.ZF.A9RG.01 3 0.3706 0.2200 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.GC.A3WC.01 6 0.2260 0.0000 0.00 0.00 0.00 0.14 0.00 0.86
#> TCGA.XF.A9SY.01 5 0.1814 0.0000 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.GD.A2C5.11 4 0.0000 0.7677 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA58.01 3 0.3706 0.2200 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.GC.A6I3.11 3 0.0937 0.5190 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.PQ.A6FN.01 3 0.4265 0.5466 0.04 0.30 0.66 0.00 0.00 0.00
#> TCGA.BL.A13I.01 4 0.1814 0.7350 0.00 0.00 0.00 0.90 0.10 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GD.A3OP.01 1 0.000 0.820 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BU.01 6 0.458 0.398 0.00 0.00 0.04 0.36 0.02 0.58 0.00
#> TCGA.DK.A2I2.01 2 0.419 0.000 0.00 0.64 0.00 0.06 0.00 0.30 0.00
#> TCGA.XF.A9SI.01 3 0.356 0.729 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.FD.A3B3.01 4 0.000 0.902 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A6TF.01 1 0.000 0.820 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20U.11 3 0.496 0.533 0.00 0.06 0.64 0.00 0.00 0.06 0.24
#> TCGA.DK.A1AB.01 1 0.465 0.599 0.62 0.30 0.06 0.00 0.02 0.00 0.00
#> TCGA.ZF.A9RG.01 7 0.226 0.820 0.16 0.00 0.00 0.00 0.00 0.00 0.84
#> TCGA.GC.A3WC.01 6 0.117 0.268 0.00 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.XF.A9SY.01 5 0.101 0.000 0.00 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.GD.A2C5.11 4 0.000 0.902 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA58.01 7 0.226 0.820 0.16 0.00 0.00 0.00 0.00 0.00 0.84
#> TCGA.GC.A6I3.11 7 0.117 0.539 0.00 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.PQ.A6FN.01 3 0.356 0.729 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.BL.A13I.01 4 0.242 0.793 0.00 0.00 0.18 0.82 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.GD.A3OP.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BU.01 6 0.3083 0.3360 0.00 0.00 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.DK.A2I2.01 2 0.1341 0.0000 0.00 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SI.01 3 0.0000 0.5836 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B3.01 4 0.0808 0.7901 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.FD.A6TF.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20U.11 3 0.5723 0.2773 0.00 0.00 0.44 0.00 0.00 0.34 0.06 0.16
#> TCGA.DK.A1AB.01 8 0.3237 0.0000 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.ZF.A9RG.01 7 0.4213 1.0000 0.16 0.00 0.18 0.00 0.00 0.00 0.66 0.00
#> TCGA.GC.A3WC.01 6 0.6569 0.2274 0.00 0.26 0.00 0.08 0.02 0.48 0.04 0.12
#> TCGA.XF.A9SY.01 5 0.0471 0.0000 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.GD.A2C5.11 4 0.0000 0.7901 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA58.01 7 0.4213 1.0000 0.16 0.00 0.18 0.00 0.00 0.00 0.66 0.00
#> TCGA.GC.A6I3.11 3 0.3237 -0.0966 0.00 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.PQ.A6FN.01 3 0.1804 0.5810 0.00 0.08 0.90 0.00 0.00 0.00 0.00 0.02
#> TCGA.BL.A13I.01 4 0.4073 0.5830 0.00 0.00 0.00 0.66 0.00 0.00 0.24 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: Node022. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-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 43 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 0.4789 0.522 0.522
#> 3 3 1.000 0.957 0.982 0.4224 0.739 0.525
#> 4 4 0.876 0.905 0.943 0.0981 0.910 0.727
#> 5 5 0.849 0.731 0.874 0.0363 0.956 0.827
#> 6 6 0.894 0.852 0.939 0.0230 0.972 0.879
#> 7 7 0.822 0.756 0.862 0.0298 0.958 0.809
#> 8 8 0.785 0.602 0.822 0.0259 0.963 0.819
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.4Z.AA86.01 1 0 1 1 0
#> TCGA.GU.A42Q.01 1 0 1 1 0
#> TCGA.DK.AA6X.01 2 0 1 0 1
#> TCGA.GC.A3OO.01 2 0 1 0 1
#> TCGA.4Z.AA7W.01 1 0 1 1 0
#> TCGA.XF.A9SM.01 1 0 1 1 0
#> TCGA.DK.A3IU.01 1 0 1 1 0
#> TCGA.E7.A7XN.01 1 0 1 1 0
#> TCGA.FD.A43Y.01 1 0 1 1 0
#> TCGA.YC.A8S6.01 2 0 1 0 1
#> TCGA.CU.A0YO.01 2 0 1 0 1
#> TCGA.FD.A62P.01 2 0 1 0 1
#> TCGA.DK.AA74.01 1 0 1 1 0
#> TCGA.BT.A42F.01 1 0 1 1 0
#> TCGA.DK.A3IQ.01 2 0 1 0 1
#> TCGA.FD.A3B7.01 1 0 1 1 0
#> TCGA.K4.A3WU.01 2 0 1 0 1
#> TCGA.FD.A62N.01 1 0 1 1 0
#> TCGA.UY.A9PB.01 1 0 1 1 0
#> TCGA.GU.A766.01 1 0 1 1 0
#> TCGA.FD.A6TB.01 1 0 1 1 0
#> TCGA.XF.A9T8.01 1 0 1 1 0
#> TCGA.G2.AA3D.01 2 0 1 0 1
#> TCGA.BT.A20O.01 1 0 1 1 0
#> TCGA.XF.A8HE.01 1 0 1 1 0
#> TCGA.ZF.AA53.01 1 0 1 1 0
#> TCGA.DK.AA6T.01 1 0 1 1 0
#> TCGA.XF.AAMJ.01 2 0 1 0 1
#> TCGA.FD.A5BT.01 1 0 1 1 0
#> TCGA.SY.A9G0.01 2 0 1 0 1
#> TCGA.K4.A4AC.01 1 0 1 1 0
#> TCGA.FD.A43U.01 2 0 1 0 1
#> TCGA.GU.A764.01 1 0 1 1 0
#> TCGA.DK.A2I4.01 1 0 1 1 0
#> TCGA.FD.A6TK.01 1 0 1 1 0
#> TCGA.BT.A3PK.01 1 0 1 1 0
#> TCGA.XF.A9SW.01 2 0 1 0 1
#> TCGA.ZF.AA4W.01 1 0 1 1 0
#> TCGA.UY.A9PA.01 2 0 1 0 1
#> TCGA.R3.A69X.01 2 0 1 0 1
#> TCGA.E7.A519.01 2 0 1 0 1
#> TCGA.XF.AAMR.01 2 0 1 0 1
#> TCGA.FD.A3SP.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.4Z.AA86.01 3 0.1529 0.964 0.04 0.00 0.96
#> TCGA.GU.A42Q.01 1 0.2537 0.918 0.92 0.00 0.08
#> TCGA.DK.AA6X.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.GC.A3OO.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.4Z.AA7W.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.XF.A9SM.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DK.A3IU.01 3 0.1529 0.964 0.04 0.00 0.96
#> TCGA.E7.A7XN.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FD.A43Y.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.YC.A8S6.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.CU.A0YO.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.FD.A62P.01 3 0.2066 0.929 0.00 0.06 0.94
#> TCGA.DK.AA74.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.BT.A42F.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DK.A3IQ.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.FD.A3B7.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.K4.A3WU.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.FD.A62N.01 3 0.0892 0.974 0.02 0.00 0.98
#> TCGA.UY.A9PB.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.GU.A766.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.FD.A6TB.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.XF.A9T8.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.G2.AA3D.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.BT.A20O.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.XF.A8HE.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.ZF.AA53.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DK.AA6T.01 3 0.2066 0.947 0.06 0.00 0.94
#> TCGA.XF.AAMJ.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.FD.A5BT.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.SY.A9G0.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.K4.A4AC.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FD.A43U.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.GU.A764.01 3 0.1529 0.964 0.04 0.00 0.96
#> TCGA.DK.A2I4.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.FD.A6TK.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.BT.A3PK.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.XF.A9SW.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.ZF.AA4W.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.R3.A69X.01 2 0.6244 0.213 0.00 0.56 0.44
#> TCGA.E7.A519.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.XF.AAMR.01 2 0.0000 0.965 0.00 1.00 0.00
#> TCGA.FD.A3SP.01 3 0.0000 0.980 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.4Z.AA86.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.GU.A42Q.01 1 0.5784 0.623 0.70 0.00 0.10 0.20
#> TCGA.DK.AA6X.01 4 0.4277 0.757 0.00 0.28 0.00 0.72
#> TCGA.GC.A3OO.01 2 0.2647 0.869 0.00 0.88 0.00 0.12
#> TCGA.4Z.AA7W.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SM.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IU.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.E7.A7XN.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.FD.A43Y.01 3 0.3610 0.813 0.00 0.00 0.80 0.20
#> TCGA.YC.A8S6.01 4 0.3975 0.797 0.00 0.24 0.00 0.76
#> TCGA.CU.A0YO.01 4 0.4134 0.782 0.00 0.26 0.00 0.74
#> TCGA.FD.A62P.01 4 0.1211 0.774 0.00 0.00 0.04 0.96
#> TCGA.DK.AA74.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.BT.A42F.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IQ.01 2 0.0000 0.946 0.00 1.00 0.00 0.00
#> TCGA.FD.A3B7.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.K4.A3WU.01 4 0.3975 0.797 0.00 0.24 0.00 0.76
#> TCGA.FD.A62N.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.UY.A9PB.01 1 0.0707 0.956 0.98 0.00 0.02 0.00
#> TCGA.GU.A766.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TB.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.XF.A9T8.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.G2.AA3D.01 2 0.0000 0.946 0.00 1.00 0.00 0.00
#> TCGA.BT.A20O.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.XF.A8HE.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA53.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.DK.AA6T.01 3 0.1211 0.919 0.00 0.00 0.96 0.04
#> TCGA.XF.AAMJ.01 2 0.0000 0.946 0.00 1.00 0.00 0.00
#> TCGA.FD.A5BT.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.SY.A9G0.01 2 0.2345 0.887 0.00 0.90 0.00 0.10
#> TCGA.K4.A4AC.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.FD.A43U.01 4 0.1211 0.774 0.00 0.00 0.04 0.96
#> TCGA.GU.A764.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.DK.A2I4.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TK.01 3 0.3610 0.813 0.00 0.00 0.80 0.20
#> TCGA.BT.A3PK.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SW.01 2 0.2647 0.869 0.00 0.88 0.00 0.12
#> TCGA.ZF.AA4W.01 1 0.0000 0.975 1.00 0.00 0.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.946 0.00 1.00 0.00 0.00
#> TCGA.R3.A69X.01 4 0.1411 0.783 0.00 0.02 0.02 0.96
#> TCGA.E7.A519.01 2 0.0000 0.946 0.00 1.00 0.00 0.00
#> TCGA.XF.AAMR.01 2 0.0000 0.946 0.00 1.00 0.00 0.00
#> TCGA.FD.A3SP.01 3 0.3610 0.813 0.00 0.00 0.80 0.20
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.4Z.AA86.01 3 0.0000 0.859 0.00 0.00 1.00 0.00 0.00
#> TCGA.GU.A42Q.01 5 0.5783 -0.162 0.10 0.00 0.36 0.00 0.54
#> TCGA.DK.AA6X.01 4 0.6723 0.622 0.00 0.28 0.00 0.42 0.30
#> TCGA.GC.A3OO.01 2 0.2754 0.877 0.00 0.88 0.00 0.08 0.04
#> TCGA.4Z.AA7W.01 1 0.0609 0.976 0.98 0.00 0.00 0.02 0.00
#> TCGA.XF.A9SM.01 1 0.0609 0.976 0.98 0.00 0.00 0.02 0.00
#> TCGA.DK.A3IU.01 3 0.0000 0.859 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A7XN.01 1 0.0609 0.976 0.98 0.00 0.00 0.02 0.00
#> TCGA.FD.A43Y.01 5 0.4287 -0.320 0.00 0.00 0.46 0.00 0.54
#> TCGA.YC.A8S6.01 4 0.5173 0.735 0.00 0.04 0.00 0.50 0.46
#> TCGA.CU.A0YO.01 4 0.6593 0.686 0.00 0.22 0.00 0.44 0.34
#> TCGA.FD.A62P.01 5 0.4307 -0.781 0.00 0.00 0.00 0.50 0.50
#> TCGA.DK.AA74.01 3 0.0000 0.859 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A42F.01 1 0.0609 0.976 0.98 0.00 0.00 0.02 0.00
#> TCGA.DK.A3IQ.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A3B7.01 1 0.0000 0.978 1.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A3WU.01 4 0.5173 0.735 0.00 0.04 0.00 0.50 0.46
#> TCGA.FD.A62N.01 3 0.0000 0.859 0.00 0.00 1.00 0.00 0.00
#> TCGA.UY.A9PB.01 1 0.1732 0.918 0.92 0.00 0.00 0.00 0.08
#> TCGA.GU.A766.01 3 0.0609 0.852 0.00 0.00 0.98 0.00 0.02
#> TCGA.FD.A6TB.01 3 0.2280 0.795 0.00 0.00 0.88 0.00 0.12
#> TCGA.XF.A9T8.01 1 0.0000 0.978 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.AA3D.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20O.01 1 0.0609 0.976 0.98 0.00 0.00 0.02 0.00
#> TCGA.XF.A8HE.01 1 0.0000 0.978 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA53.01 1 0.0000 0.978 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6T.01 3 0.4307 0.254 0.00 0.00 0.50 0.50 0.00
#> TCGA.XF.AAMJ.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BT.01 3 0.0000 0.859 0.00 0.00 1.00 0.00 0.00
#> TCGA.SY.A9G0.01 2 0.2754 0.877 0.00 0.88 0.00 0.08 0.04
#> TCGA.K4.A4AC.01 1 0.1732 0.918 0.92 0.00 0.00 0.00 0.08
#> TCGA.FD.A43U.01 4 0.4829 0.659 0.00 0.00 0.02 0.50 0.48
#> TCGA.GU.A764.01 3 0.1732 0.822 0.00 0.00 0.92 0.00 0.08
#> TCGA.DK.A2I4.01 3 0.0000 0.859 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TK.01 3 0.3684 0.631 0.00 0.00 0.72 0.00 0.28
#> TCGA.BT.A3PK.01 1 0.0000 0.978 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SW.01 2 0.2754 0.877 0.00 0.88 0.00 0.08 0.04
#> TCGA.ZF.AA4W.01 1 0.0000 0.978 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 5 0.4307 -0.781 0.00 0.00 0.00 0.50 0.50
#> TCGA.E7.A519.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMR.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A3SP.01 3 0.3684 0.631 0.00 0.00 0.72 0.00 0.28
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.4Z.AA86.01 3 0.1267 0.899 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.GU.A42Q.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.AA6X.01 4 0.4199 0.330 0.00 0.38 0.00 0.60 0.00 0.02
#> TCGA.GC.A3OO.01 2 0.3156 0.785 0.00 0.80 0.00 0.18 0.00 0.02
#> TCGA.4Z.AA7W.01 1 0.0547 0.964 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.XF.A9SM.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IU.01 3 0.1267 0.899 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.E7.A7XN.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A43Y.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.YC.A8S6.01 4 0.1092 0.802 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.CU.A0YO.01 4 0.3592 0.630 0.00 0.24 0.00 0.74 0.00 0.02
#> TCGA.FD.A62P.01 4 0.0937 0.786 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.DK.AA74.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A42F.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IQ.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B7.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A3WU.01 4 0.0000 0.808 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A62N.01 3 0.1267 0.899 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.UY.A9PB.01 1 0.3045 0.831 0.86 0.00 0.06 0.00 0.06 0.02
#> TCGA.GU.A766.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A6TB.01 3 0.1807 0.876 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.XF.A9T8.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.AA3D.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20O.01 1 0.0547 0.964 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.XF.A8HE.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA53.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.AA6T.01 6 0.0937 0.000 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.XF.AAMJ.01 2 0.0547 0.893 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.FD.A5BT.01 3 0.0000 0.906 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.SY.A9G0.01 2 0.3315 0.765 0.00 0.78 0.00 0.20 0.00 0.02
#> TCGA.K4.A4AC.01 1 0.1807 0.904 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.FD.A43U.01 4 0.1267 0.763 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.GU.A764.01 3 0.2512 0.882 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.DK.A2I4.01 3 0.0937 0.903 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.FD.A6TK.01 3 0.3156 0.781 0.00 0.00 0.80 0.00 0.18 0.02
#> TCGA.BT.A3PK.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SW.01 2 0.3315 0.765 0.00 0.78 0.00 0.20 0.00 0.02
#> TCGA.ZF.AA4W.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 4 0.0000 0.808 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A519.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMR.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SP.01 3 0.3592 0.711 0.00 0.00 0.74 0.00 0.24 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.4Z.AA86.01 3 0.0863 0.8447 0.00 0.00 0.96 0.00 0.00 0 0.04
#> TCGA.GU.A42Q.01 5 0.0000 0.8861 0.00 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.DK.AA6X.01 7 0.5055 0.6744 0.00 0.18 0.00 0.26 0.00 0 0.56
#> TCGA.GC.A3OO.01 7 0.4615 0.7767 0.00 0.30 0.00 0.10 0.00 0 0.60
#> TCGA.4Z.AA7W.01 1 0.0504 0.9220 0.98 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.XF.A9SM.01 1 0.0000 0.9321 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.DK.A3IU.01 3 0.1166 0.8443 0.00 0.00 0.94 0.00 0.00 0 0.06
#> TCGA.E7.A7XN.01 1 0.0000 0.9321 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.FD.A43Y.01 5 0.1860 0.8883 0.00 0.00 0.02 0.02 0.92 0 0.04
#> TCGA.YC.A8S6.01 4 0.3546 0.0452 0.00 0.00 0.00 0.54 0.00 0 0.46
#> TCGA.CU.A0YO.01 7 0.4939 0.5949 0.00 0.14 0.00 0.30 0.00 0 0.56
#> TCGA.FD.A62P.01 4 0.0000 0.7906 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.DK.AA74.01 3 0.1860 0.8307 0.00 0.00 0.92 0.04 0.02 0 0.02
#> TCGA.BT.A42F.01 1 0.0000 0.9321 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.DK.A3IQ.01 2 0.3139 0.3970 0.00 0.70 0.00 0.00 0.00 0 0.30
#> TCGA.FD.A3B7.01 1 0.0504 0.9335 0.98 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.K4.A3WU.01 4 0.1671 0.7686 0.00 0.00 0.00 0.90 0.00 0 0.10
#> TCGA.FD.A62N.01 3 0.0504 0.8362 0.00 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.UY.A9PB.01 1 0.5023 0.4955 0.62 0.00 0.08 0.00 0.04 0 0.26
#> TCGA.GU.A766.01 3 0.1006 0.8417 0.00 0.00 0.96 0.00 0.02 0 0.02
#> TCGA.FD.A6TB.01 3 0.3263 0.7996 0.00 0.00 0.80 0.00 0.08 0 0.12
#> TCGA.XF.A9T8.01 1 0.0504 0.9335 0.98 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.G2.AA3D.01 2 0.0000 0.8155 0.00 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.BT.A20O.01 1 0.0000 0.9321 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.XF.A8HE.01 1 0.0504 0.9335 0.98 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.ZF.AA53.01 1 0.0504 0.9335 0.98 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.DK.AA6T.01 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.XF.AAMJ.01 7 0.3985 0.4459 0.00 0.46 0.00 0.02 0.00 0 0.52
#> TCGA.FD.A5BT.01 3 0.1006 0.8349 0.00 0.00 0.96 0.02 0.00 0 0.02
#> TCGA.SY.A9G0.01 7 0.4487 0.7560 0.00 0.32 0.00 0.08 0.00 0 0.60
#> TCGA.K4.A4AC.01 1 0.3863 0.6831 0.74 0.00 0.02 0.00 0.04 0 0.20
#> TCGA.FD.A43U.01 4 0.0504 0.7704 0.00 0.00 0.02 0.98 0.00 0 0.00
#> TCGA.GU.A764.01 3 0.3667 0.7663 0.00 0.00 0.74 0.00 0.06 0 0.20
#> TCGA.DK.A2I4.01 3 0.1664 0.8449 0.00 0.00 0.92 0.00 0.02 0 0.06
#> TCGA.FD.A6TK.01 3 0.5218 0.6304 0.00 0.00 0.60 0.02 0.18 0 0.20
#> TCGA.BT.A3PK.01 1 0.0504 0.9335 0.98 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.XF.A9SW.01 7 0.4615 0.7767 0.00 0.30 0.00 0.10 0.00 0 0.60
#> TCGA.ZF.AA4W.01 1 0.0504 0.9335 0.98 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.UY.A9PA.01 2 0.2081 0.7356 0.00 0.86 0.00 0.00 0.00 0 0.14
#> TCGA.R3.A69X.01 4 0.0504 0.7961 0.00 0.00 0.00 0.98 0.00 0 0.02
#> TCGA.E7.A519.01 2 0.0863 0.7871 0.00 0.96 0.00 0.00 0.00 0 0.04
#> TCGA.XF.AAMR.01 2 0.0504 0.8180 0.00 0.98 0.00 0.00 0.00 0 0.02
#> TCGA.FD.A3SP.01 3 0.5604 0.4746 0.00 0.00 0.52 0.02 0.26 0 0.20
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.4Z.AA86.01 3 0.1341 0.814 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.GU.A42Q.01 5 0.0000 0.819 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.AA6X.01 7 0.2547 0.642 0.00 0.00 0.00 0.12 0.00 0.00 0.84 0.04
#> TCGA.GC.A3OO.01 7 0.0000 0.686 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.4Z.AA7W.01 1 0.1275 0.644 0.94 0.02 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.XF.A9SM.01 1 0.0808 0.659 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DK.A3IU.01 3 0.0471 0.819 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.E7.A7XN.01 1 0.0471 0.677 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.FD.A43Y.01 5 0.2569 0.822 0.00 0.00 0.00 0.02 0.82 0.00 0.00 0.16
#> TCGA.YC.A8S6.01 7 0.3862 0.139 0.00 0.00 0.00 0.36 0.00 0.00 0.60 0.04
#> TCGA.CU.A0YO.01 7 0.2888 0.593 0.00 0.00 0.00 0.16 0.00 0.00 0.80 0.04
#> TCGA.FD.A62P.01 4 0.2224 0.876 0.00 0.00 0.00 0.86 0.00 0.00 0.12 0.02
#> TCGA.DK.AA74.01 3 0.3218 0.789 0.00 0.06 0.82 0.06 0.00 0.00 0.00 0.06
#> TCGA.BT.A42F.01 1 0.0471 0.671 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DK.A3IQ.01 7 0.4004 -0.492 0.00 0.46 0.00 0.00 0.00 0.00 0.50 0.04
#> TCGA.FD.A3B7.01 1 0.2569 0.677 0.82 0.00 0.00 0.02 0.00 0.00 0.00 0.16
#> TCGA.K4.A3WU.01 4 0.3095 0.760 0.00 0.00 0.00 0.74 0.00 0.00 0.24 0.02
#> TCGA.FD.A62N.01 3 0.1341 0.804 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.UY.A9PB.01 8 0.5026 0.000 0.38 0.00 0.08 0.00 0.04 0.00 0.00 0.50
#> TCGA.GU.A766.01 3 0.3663 0.764 0.00 0.06 0.78 0.06 0.00 0.00 0.00 0.10
#> TCGA.FD.A6TB.01 3 0.3454 0.783 0.00 0.02 0.80 0.02 0.04 0.00 0.00 0.12
#> TCGA.XF.A9T8.01 1 0.3907 0.314 0.58 0.00 0.00 0.04 0.00 0.00 0.00 0.38
#> TCGA.G2.AA3D.01 2 0.2534 0.813 0.00 0.78 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.BT.A20O.01 1 0.1275 0.644 0.94 0.02 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.XF.A8HE.01 1 0.2859 0.682 0.82 0.00 0.00 0.02 0.00 0.02 0.00 0.14
#> TCGA.ZF.AA53.01 1 0.3169 0.664 0.78 0.00 0.00 0.02 0.00 0.02 0.00 0.18
#> TCGA.DK.AA6T.01 6 0.0471 0.000 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.XF.AAMJ.01 7 0.2406 0.377 0.00 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.FD.A5BT.01 3 0.1887 0.814 0.00 0.06 0.90 0.04 0.00 0.00 0.00 0.00
#> TCGA.SY.A9G0.01 7 0.0000 0.686 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.K4.A4AC.01 1 0.4077 -0.464 0.56 0.00 0.02 0.00 0.02 0.00 0.00 0.40
#> TCGA.FD.A43U.01 4 0.1741 0.790 0.00 0.02 0.00 0.92 0.00 0.00 0.04 0.02
#> TCGA.GU.A764.01 3 0.2888 0.762 0.00 0.00 0.80 0.00 0.04 0.00 0.00 0.16
#> TCGA.DK.A2I4.01 3 0.1091 0.809 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.FD.A6TK.01 3 0.5003 0.638 0.00 0.02 0.62 0.02 0.12 0.00 0.00 0.22
#> TCGA.BT.A3PK.01 1 0.3169 0.664 0.78 0.00 0.00 0.02 0.00 0.02 0.00 0.18
#> TCGA.XF.A9SW.01 7 0.0000 0.686 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA4W.01 1 0.3303 0.656 0.76 0.00 0.00 0.02 0.00 0.02 0.00 0.20
#> TCGA.UY.A9PA.01 2 0.3318 0.449 0.00 0.54 0.00 0.00 0.00 0.00 0.46 0.00
#> TCGA.R3.A69X.01 4 0.1765 0.877 0.00 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.E7.A519.01 2 0.1341 0.688 0.00 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.XF.AAMR.01 2 0.2534 0.813 0.00 0.78 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.FD.A3SP.01 3 0.4904 0.576 0.00 0.00 0.58 0.02 0.14 0.00 0.00 0.26
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0222. Child nodes: Node022221-leaf , Node022222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02222"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 14 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 8.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3633 0.637 0.637
#> 3 3 0.549 0.820 0.874 0.6369 0.736 0.586
#> 4 4 0.736 0.883 0.973 0.1055 0.978 0.941
#> 5 5 0.989 0.909 0.987 0.1892 0.758 0.405
#> 6 6 0.846 0.838 0.930 0.0902 0.912 0.600
#> 7 7 0.923 0.528 0.844 0.0376 0.956 0.714
#> 8 8 0.901 0.613 0.921 0.0204 0.967 0.750
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 5 7
There is also optional best \(k\) = 2 5 7 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.DK.AA6X.01 1 0 1 1 0
#> TCGA.GC.A3OO.01 1 0 1 1 0
#> TCGA.YC.A8S6.01 1 0 1 1 0
#> TCGA.CU.A0YO.01 1 0 1 1 0
#> TCGA.DK.A3IQ.01 1 0 1 1 0
#> TCGA.K4.A3WU.01 1 0 1 1 0
#> TCGA.G2.AA3D.01 2 0 1 0 1
#> TCGA.XF.AAMJ.01 1 0 1 1 0
#> TCGA.SY.A9G0.01 1 0 1 1 0
#> TCGA.XF.A9SW.01 1 0 1 1 0
#> TCGA.UY.A9PA.01 2 0 1 0 1
#> TCGA.R3.A69X.01 1 0 1 1 0
#> TCGA.E7.A519.01 2 0 1 0 1
#> TCGA.XF.AAMR.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DK.AA6X.01 1 0.0000 0.815 1.00 0.00 0.00
#> TCGA.GC.A3OO.01 1 0.5397 0.590 0.72 0.00 0.28
#> TCGA.YC.A8S6.01 1 0.0000 0.815 1.00 0.00 0.00
#> TCGA.CU.A0YO.01 1 0.0892 0.796 0.98 0.02 0.00
#> TCGA.DK.A3IQ.01 1 0.5560 0.550 0.70 0.00 0.30
#> TCGA.K4.A3WU.01 1 0.5397 0.590 0.72 0.00 0.28
#> TCGA.G2.AA3D.01 2 0.0000 0.926 0.00 1.00 0.00
#> TCGA.XF.AAMJ.01 3 0.4796 1.000 0.22 0.00 0.78
#> TCGA.SY.A9G0.01 3 0.4796 1.000 0.22 0.00 0.78
#> TCGA.XF.A9SW.01 3 0.4796 1.000 0.22 0.00 0.78
#> TCGA.UY.A9PA.01 2 0.0000 0.926 0.00 1.00 0.00
#> TCGA.R3.A69X.01 1 0.0000 0.815 1.00 0.00 0.00
#> TCGA.E7.A519.01 2 0.4796 0.847 0.00 0.78 0.22
#> TCGA.XF.AAMR.01 1 0.0000 0.815 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.DK.AA6X.01 1 0.000 0.939 1.00 0 0.00 0
#> TCGA.GC.A3OO.01 1 0.265 0.895 0.88 0 0.12 0
#> TCGA.YC.A8S6.01 1 0.000 0.939 1.00 0 0.00 0
#> TCGA.CU.A0YO.01 1 0.000 0.939 1.00 0 0.00 0
#> TCGA.DK.A3IQ.01 1 0.292 0.879 0.86 0 0.14 0
#> TCGA.K4.A3WU.01 1 0.265 0.895 0.88 0 0.12 0
#> TCGA.G2.AA3D.01 2 0.000 1.000 0.00 1 0.00 0
#> TCGA.XF.AAMJ.01 3 0.000 1.000 0.00 0 1.00 0
#> TCGA.SY.A9G0.01 3 0.000 1.000 0.00 0 1.00 0
#> TCGA.XF.A9SW.01 3 0.000 1.000 0.00 0 1.00 0
#> TCGA.UY.A9PA.01 2 0.000 1.000 0.00 1 0.00 0
#> TCGA.R3.A69X.01 1 0.000 0.939 1.00 0 0.00 0
#> TCGA.E7.A519.01 4 0.000 0.000 0.00 0 0.00 1
#> TCGA.XF.AAMR.01 1 0.000 0.939 1.00 0 0.00 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DK.AA6X.01 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.GC.A3OO.01 1 0.0000 0.973 1.00 0.00 0.00 0 0.00
#> TCGA.YC.A8S6.01 1 0.1043 0.952 0.96 0.00 0.00 0 0.04
#> TCGA.CU.A0YO.01 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.DK.A3IQ.01 1 0.0000 0.973 1.00 0.00 0.00 0 0.00
#> TCGA.K4.A3WU.01 1 0.0000 0.973 1.00 0.00 0.00 0 0.00
#> TCGA.G2.AA3D.01 2 0.0000 0.984 0.00 1.00 0.00 0 0.00
#> TCGA.XF.AAMJ.01 1 0.1410 0.928 0.94 0.00 0.06 0 0.00
#> TCGA.SY.A9G0.01 3 0.0609 1.000 0.02 0.00 0.98 0 0.00
#> TCGA.XF.A9SW.01 3 0.0609 1.000 0.02 0.00 0.98 0 0.00
#> TCGA.UY.A9PA.01 2 0.0609 0.984 0.00 0.98 0.02 0 0.00
#> TCGA.R3.A69X.01 1 0.0609 0.965 0.98 0.00 0.00 0 0.02
#> TCGA.E7.A519.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00
#> TCGA.XF.AAMR.01 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DK.AA6X.01 5 0.0000 0.946 0.00 0.0 0.00 0 1.00 0.00
#> TCGA.GC.A3OO.01 1 0.0000 0.961 1.00 0.0 0.00 0 0.00 0.00
#> TCGA.YC.A8S6.01 1 0.1267 0.905 0.94 0.0 0.00 0 0.06 0.00
#> TCGA.CU.A0YO.01 5 0.2048 0.888 0.00 0.0 0.00 0 0.88 0.12
#> TCGA.DK.A3IQ.01 6 0.3198 0.910 0.26 0.0 0.00 0 0.00 0.74
#> TCGA.K4.A3WU.01 1 0.0547 0.947 0.98 0.0 0.00 0 0.00 0.02
#> TCGA.G2.AA3D.01 2 0.1814 0.916 0.00 0.9 0.00 0 0.00 0.10
#> TCGA.XF.AAMJ.01 6 0.3315 0.906 0.20 0.0 0.02 0 0.00 0.78
#> TCGA.SY.A9G0.01 3 0.2793 0.768 0.00 0.0 0.80 0 0.00 0.20
#> TCGA.XF.A9SW.01 3 0.0000 0.765 0.00 0.0 1.00 0 0.00 0.00
#> TCGA.UY.A9PA.01 2 0.0000 0.916 0.00 1.0 0.00 0 0.00 0.00
#> TCGA.R3.A69X.01 1 0.0000 0.961 1.00 0.0 0.00 0 0.00 0.00
#> TCGA.E7.A519.01 4 0.0000 0.000 0.00 0.0 0.00 1 0.00 0.00
#> TCGA.XF.AAMR.01 5 0.0000 0.946 0.00 0.0 0.00 0 1.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DK.AA6X.01 5 0.3558 0.758 0.00 0.00 0.00 0 0.52 0.48 0.00
#> TCGA.GC.A3OO.01 1 0.0000 0.966 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.YC.A8S6.01 1 0.0504 0.955 0.98 0.00 0.00 0 0.00 0.02 0.00
#> TCGA.CU.A0YO.01 5 0.0000 0.472 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DK.A3IQ.01 3 0.5293 -0.337 0.02 0.00 0.46 0 0.00 0.42 0.10
#> TCGA.K4.A3WU.01 1 0.1664 0.919 0.92 0.00 0.02 0 0.00 0.06 0.00
#> TCGA.G2.AA3D.01 2 0.1664 0.933 0.00 0.92 0.02 0 0.00 0.06 0.00
#> TCGA.XF.AAMJ.01 7 0.3985 0.149 0.02 0.00 0.46 0 0.00 0.00 0.52
#> TCGA.SY.A9G0.01 7 0.0000 0.153 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.XF.A9SW.01 3 0.3558 -0.227 0.00 0.00 0.52 0 0.00 0.00 0.48
#> TCGA.UY.A9PA.01 2 0.0000 0.933 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.R3.A69X.01 1 0.0000 0.966 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.E7.A519.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.XF.AAMR.01 5 0.3562 0.753 0.00 0.00 0.00 0 0.50 0.50 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.DK.AA6X.01 5 0.0000 0.913 0.00 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.GC.A3OO.01 1 0.0000 0.921 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.YC.A8S6.01 1 0.0000 0.921 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YO.01 6 0.2534 0.000 0.00 0.00 0.00 0 0.22 0.78 0.00 0.00
#> TCGA.DK.A3IQ.01 3 0.1607 0.000 0.04 0.00 0.92 0 0.00 0.00 0.04 0.00
#> TCGA.K4.A3WU.01 1 0.3941 0.734 0.76 0.00 0.04 0 0.00 0.14 0.02 0.04
#> TCGA.G2.AA3D.01 2 0.2674 0.880 0.00 0.86 0.04 0 0.00 0.04 0.00 0.06
#> TCGA.XF.AAMJ.01 7 0.2725 0.745 0.00 0.00 0.14 0 0.00 0.04 0.82 0.00
#> TCGA.SY.A9G0.01 7 0.0471 0.753 0.00 0.00 0.00 0 0.00 0.00 0.98 0.02
#> TCGA.XF.A9SW.01 8 0.1947 0.000 0.00 0.00 0.00 0 0.00 0.00 0.14 0.86
#> TCGA.UY.A9PA.01 2 0.0000 0.880 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.R3.A69X.01 1 0.0000 0.921 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.E7.A519.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMR.01 5 0.1607 0.913 0.00 0.00 0.04 0 0.92 0.00 0.00 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-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 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 0.997 0.998 0.1405 0.930 0.860
#> 4 4 0.913 0.932 0.944 0.2784 0.833 0.612
#> 5 5 0.846 0.841 0.921 0.0628 0.953 0.827
#> 6 6 0.755 0.711 0.856 0.0322 0.973 0.887
#> 7 7 0.806 0.710 0.886 0.0515 0.847 0.425
#> 8 8 0.802 0.737 0.878 0.0295 0.960 0.755
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.FD.A43P.01 2 0 1 0 1
#> TCGA.K4.A6FZ.01 1 0 1 1 0
#> TCGA.XF.AAN5.01 1 0 1 1 0
#> TCGA.CF.A1HS.01 1 0 1 1 0
#> TCGA.K4.A5RH.01 1 0 1 1 0
#> TCGA.GU.A767.01 2 0 1 0 1
#> TCGA.XF.A9T5.01 1 0 1 1 0
#> TCGA.FT.A61P.01 1 0 1 1 0
#> TCGA.XF.A9SX.01 1 0 1 1 0
#> TCGA.XF.A9ST.01 2 0 1 0 1
#> TCGA.GU.A762.01 1 0 1 1 0
#> TCGA.K4.A3WS.01 2 0 1 0 1
#> TCGA.K4.A5RJ.01 1 0 1 1 0
#> TCGA.FD.A5C0.01 2 0 1 0 1
#> TCGA.ZF.A9RD.01 1 0 1 1 0
#> TCGA.FD.A3SO.01 1 0 1 1 0
#> TCGA.CU.A0YR.01 2 0 1 0 1
#> TCGA.XF.AAMZ.01 2 0 1 0 1
#> TCGA.BT.A20U.01 1 0 1 1 0
#> TCGA.E7.A85H.01 2 0 1 0 1
#> TCGA.GD.A3OS.01 1 0 1 1 0
#> TCGA.FD.A3B4.01 1 0 1 1 0
#> TCGA.XF.AAN0.01 2 0 1 0 1
#> TCGA.FJ.A871.01 1 0 1 1 0
#> TCGA.CF.A5UA.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FD.A43P.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.K4.A6FZ.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.XF.AAN5.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CF.A1HS.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.K4.A5RH.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.GU.A767.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.XF.A9T5.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.FT.A61P.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.XF.A9SX.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.XF.A9ST.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.GU.A762.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.K4.A3WS.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.K4.A5RJ.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.FD.A5C0.01 2 0.153 0.958 0 0.96 0.04
#> TCGA.ZF.A9RD.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.FD.A3SO.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CU.A0YR.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.XF.AAMZ.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.BT.A20U.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E7.A85H.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.GD.A3OS.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.FD.A3B4.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.XF.AAN0.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.FJ.A871.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CF.A5UA.01 3 0.000 1.000 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FD.A43P.01 2 0.0000 0.977 0.00 1.00 0.00 0.00
#> TCGA.K4.A6FZ.01 1 0.0000 0.903 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN5.01 1 0.0000 0.903 1.00 0.00 0.00 0.00
#> TCGA.CF.A1HS.01 1 0.4134 0.716 0.74 0.00 0.00 0.26
#> TCGA.K4.A5RH.01 4 0.2011 1.000 0.08 0.00 0.00 0.92
#> TCGA.GU.A767.01 2 0.0000 0.977 0.00 1.00 0.00 0.00
#> TCGA.XF.A9T5.01 4 0.2011 1.000 0.08 0.00 0.00 0.92
#> TCGA.FT.A61P.01 1 0.0000 0.903 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SX.01 1 0.0000 0.903 1.00 0.00 0.00 0.00
#> TCGA.XF.A9ST.01 3 0.2011 0.939 0.00 0.00 0.92 0.08
#> TCGA.GU.A762.01 1 0.3172 0.839 0.84 0.00 0.00 0.16
#> TCGA.K4.A3WS.01 2 0.0000 0.977 0.00 1.00 0.00 0.00
#> TCGA.K4.A5RJ.01 4 0.2011 1.000 0.08 0.00 0.00 0.92
#> TCGA.FD.A5C0.01 2 0.2011 0.942 0.00 0.92 0.00 0.08
#> TCGA.ZF.A9RD.01 1 0.3400 0.822 0.82 0.00 0.00 0.18
#> TCGA.FD.A3SO.01 1 0.0000 0.903 1.00 0.00 0.00 0.00
#> TCGA.CU.A0YR.01 2 0.0000 0.977 0.00 1.00 0.00 0.00
#> TCGA.XF.AAMZ.01 2 0.0707 0.973 0.00 0.98 0.00 0.02
#> TCGA.BT.A20U.01 1 0.0000 0.903 1.00 0.00 0.00 0.00
#> TCGA.E7.A85H.01 3 0.0000 0.970 0.00 0.00 1.00 0.00
#> TCGA.GD.A3OS.01 4 0.2011 1.000 0.08 0.00 0.00 0.92
#> TCGA.FD.A3B4.01 1 0.3172 0.839 0.84 0.00 0.00 0.16
#> TCGA.XF.AAN0.01 2 0.1637 0.955 0.00 0.94 0.00 0.06
#> TCGA.FJ.A871.01 4 0.2011 1.000 0.08 0.00 0.00 0.92
#> TCGA.CF.A5UA.01 3 0.0000 0.970 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FD.A43P.01 2 0.0000 0.894 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A6FZ.01 1 0.0000 0.826 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN5.01 1 0.0000 0.826 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A1HS.01 1 0.3983 0.650 0.66 0.00 0.00 0.34 0.00
#> TCGA.K4.A5RH.01 4 0.0000 0.989 0.00 0.00 0.00 1.00 0.00
#> TCGA.GU.A767.01 2 0.0000 0.894 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T5.01 4 0.0000 0.989 0.00 0.00 0.00 1.00 0.00
#> TCGA.FT.A61P.01 1 0.0609 0.822 0.98 0.00 0.00 0.00 0.02
#> TCGA.XF.A9SX.01 1 0.0609 0.822 0.98 0.00 0.00 0.00 0.02
#> TCGA.XF.A9ST.01 5 0.1410 0.836 0.00 0.00 0.06 0.00 0.94
#> TCGA.GU.A762.01 1 0.3796 0.705 0.70 0.00 0.00 0.30 0.00
#> TCGA.K4.A3WS.01 2 0.0000 0.894 0.00 1.00 0.00 0.00 0.00
#> TCGA.K4.A5RJ.01 4 0.0000 0.989 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A5C0.01 5 0.1043 0.870 0.00 0.04 0.00 0.00 0.96
#> TCGA.ZF.A9RD.01 1 0.3796 0.705 0.70 0.00 0.00 0.30 0.00
#> TCGA.FD.A3SO.01 1 0.0609 0.822 0.98 0.00 0.00 0.00 0.02
#> TCGA.CU.A0YR.01 2 0.0000 0.894 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMZ.01 2 0.4060 0.343 0.00 0.64 0.00 0.00 0.36
#> TCGA.BT.A20U.01 1 0.0000 0.826 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A85H.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.GD.A3OS.01 4 0.0609 0.983 0.00 0.00 0.00 0.98 0.02
#> TCGA.FD.A3B4.01 1 0.3796 0.705 0.70 0.00 0.00 0.30 0.00
#> TCGA.XF.AAN0.01 5 0.2929 0.772 0.00 0.18 0.00 0.00 0.82
#> TCGA.FJ.A871.01 4 0.0609 0.983 0.00 0.00 0.00 0.98 0.02
#> TCGA.CF.A5UA.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FD.A43P.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.K4.A6FZ.01 1 0.0937 0.679 0.96 0.00 0 0.00 0.00 0.04
#> TCGA.XF.AAN5.01 1 0.2190 0.681 0.90 0.00 0 0.06 0.00 0.04
#> TCGA.CF.A1HS.01 1 0.4609 0.497 0.54 0.00 0 0.42 0.00 0.04
#> TCGA.K4.A5RH.01 4 0.0547 0.861 0.02 0.00 0 0.98 0.00 0.00
#> TCGA.GU.A767.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.XF.A9T5.01 4 0.0547 0.861 0.02 0.00 0 0.98 0.00 0.00
#> TCGA.FT.A61P.01 1 0.2094 0.661 0.90 0.00 0 0.00 0.02 0.08
#> TCGA.XF.A9SX.01 1 0.2094 0.661 0.90 0.00 0 0.00 0.02 0.08
#> TCGA.XF.A9ST.01 6 0.3499 0.000 0.00 0.00 0 0.00 0.32 0.68
#> TCGA.GU.A762.01 1 0.4609 0.497 0.54 0.00 0 0.42 0.00 0.04
#> TCGA.K4.A3WS.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.K4.A5RJ.01 4 0.1092 0.864 0.02 0.00 0 0.96 0.00 0.02
#> TCGA.FD.A5C0.01 5 0.0547 0.514 0.00 0.02 0 0.00 0.98 0.00
#> TCGA.ZF.A9RD.01 1 0.4609 0.497 0.54 0.00 0 0.42 0.00 0.04
#> TCGA.FD.A3SO.01 1 0.2094 0.661 0.90 0.00 0 0.00 0.02 0.08
#> TCGA.CU.A0YR.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.XF.AAMZ.01 5 0.3756 0.451 0.00 0.40 0 0.00 0.60 0.00
#> TCGA.BT.A20U.01 1 0.0547 0.687 0.98 0.00 0 0.02 0.00 0.00
#> TCGA.E7.A85H.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.GD.A3OS.01 4 0.2793 0.790 0.00 0.00 0 0.80 0.00 0.20
#> TCGA.FD.A3B4.01 1 0.4609 0.497 0.54 0.00 0 0.42 0.00 0.04
#> TCGA.XF.AAN0.01 5 0.2048 0.631 0.00 0.12 0 0.00 0.88 0.00
#> TCGA.FJ.A871.01 4 0.2793 0.790 0.00 0.00 0 0.80 0.00 0.20
#> TCGA.CF.A5UA.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FD.A43P.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A6FZ.01 1 0.1166 0.8572 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.XF.AAN5.01 4 0.3525 -0.0103 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.CF.A1HS.01 4 0.1433 0.6794 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.K4.A5RH.01 4 0.3459 0.3410 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.GU.A767.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T5.01 4 0.3459 0.3247 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.FT.A61P.01 1 0.0000 0.8812 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SX.01 1 0.0000 0.8812 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9ST.01 6 0.0504 0.0000 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.GU.A762.01 4 0.1886 0.6710 0.12 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.K4.A3WS.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RJ.01 4 0.3525 0.2811 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.FD.A5C0.01 5 0.0863 0.7609 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.ZF.A9RD.01 4 0.1671 0.6793 0.10 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.FD.A3SO.01 1 0.0000 0.8812 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YR.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMZ.01 5 0.3517 0.5997 0.00 0.28 0.00 0.02 0.70 0.00 0.00
#> TCGA.BT.A20U.01 1 0.3139 0.5399 0.70 0.00 0.00 0.30 0.00 0.00 0.00
#> TCGA.E7.A85H.01 3 0.1006 0.9669 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.GD.A3OS.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FD.A3B4.01 4 0.1886 0.6710 0.12 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.XF.AAN0.01 5 0.0504 0.7768 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.FJ.A871.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CF.A5UA.01 3 0.0000 0.9669 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FD.A43P.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.K4.A6FZ.01 1 0.2650 0.694 0.76 0.00 0.00 0.24 0.00 0 0.00 0.00
#> TCGA.XF.AAN5.01 4 0.1947 0.677 0.14 0.00 0.00 0.86 0.00 0 0.00 0.00
#> TCGA.CF.A1HS.01 4 0.2719 0.646 0.02 0.00 0.00 0.80 0.00 0 0.00 0.18
#> TCGA.K4.A5RH.01 4 0.3907 -0.108 0.00 0.00 0.00 0.58 0.00 0 0.04 0.38
#> TCGA.GU.A767.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.XF.A9T5.01 8 0.1765 0.744 0.00 0.00 0.00 0.12 0.00 0 0.00 0.88
#> TCGA.FT.A61P.01 1 0.0471 0.743 0.98 0.00 0.00 0.00 0.00 0 0.00 0.02
#> TCGA.XF.A9SX.01 1 0.0471 0.743 0.98 0.00 0.00 0.00 0.00 0 0.00 0.02
#> TCGA.XF.A9ST.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.GU.A762.01 4 0.0000 0.791 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.K4.A3WS.01 2 0.0471 0.980 0.00 0.98 0.00 0.00 0.00 0 0.02 0.00
#> TCGA.K4.A5RJ.01 8 0.3404 0.754 0.00 0.00 0.00 0.24 0.00 0 0.04 0.72
#> TCGA.FD.A5C0.01 5 0.2350 0.757 0.00 0.00 0.00 0.00 0.86 0 0.10 0.04
#> TCGA.ZF.A9RD.01 4 0.0000 0.791 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FD.A3SO.01 1 0.1091 0.759 0.94 0.00 0.00 0.06 0.00 0 0.00 0.00
#> TCGA.CU.A0YR.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.XF.AAMZ.01 5 0.3830 0.671 0.00 0.16 0.00 0.00 0.74 0 0.08 0.02
#> TCGA.BT.A20U.01 1 0.3943 0.384 0.56 0.00 0.00 0.40 0.00 0 0.00 0.04
#> TCGA.E7.A85H.01 3 0.1557 0.933 0.00 0.00 0.92 0.00 0.00 0 0.06 0.02
#> TCGA.GD.A3OS.01 7 0.2852 1.000 0.00 0.00 0.00 0.00 0.00 0 0.72 0.28
#> TCGA.FD.A3B4.01 4 0.0000 0.791 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.XF.AAN0.01 5 0.1275 0.757 0.00 0.00 0.00 0.00 0.94 0 0.04 0.02
#> TCGA.FJ.A871.01 7 0.2852 1.000 0.00 0.00 0.00 0.00 0.00 0 0.72 0.28
#> TCGA.CF.A5UA.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node023. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-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 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 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 0.2484 0.752 0.752
#> 3 3 1.000 0.994 0.973 1.2729 0.657 0.544
#> 4 4 0.771 0.782 0.853 0.2060 1.000 1.000
#> 5 5 0.762 0.900 0.877 0.0951 0.790 0.488
#> 6 6 0.810 0.832 0.941 0.0553 0.990 0.952
#> 7 7 0.810 0.676 0.908 0.0495 0.981 0.900
#> 8 8 0.829 0.585 0.873 0.0396 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.K4.A6FZ.01 2 0 1 0 1
#> TCGA.XF.AAN5.01 2 0 1 0 1
#> TCGA.CF.A1HS.01 2 0 1 0 1
#> TCGA.K4.A5RH.01 2 0 1 0 1
#> TCGA.XF.A9T5.01 2 0 1 0 1
#> TCGA.FT.A61P.01 2 0 1 0 1
#> TCGA.XF.A9SX.01 2 0 1 0 1
#> TCGA.GU.A762.01 2 0 1 0 1
#> TCGA.K4.A5RJ.01 2 0 1 0 1
#> TCGA.ZF.A9RD.01 2 0 1 0 1
#> TCGA.FD.A3SO.01 2 0 1 0 1
#> TCGA.BT.A20U.01 2 0 1 0 1
#> TCGA.GD.A3OS.01 1 0 1 1 0
#> TCGA.FD.A3B4.01 2 0 1 0 1
#> TCGA.FJ.A871.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.K4.A6FZ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.XF.AAN5.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CF.A1HS.01 3 0.254 1.000 0.00 0.08 0.92
#> TCGA.K4.A5RH.01 3 0.254 1.000 0.00 0.08 0.92
#> TCGA.XF.A9T5.01 3 0.254 1.000 0.00 0.08 0.92
#> TCGA.FT.A61P.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.XF.A9SX.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.GU.A762.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.K4.A5RJ.01 3 0.254 1.000 0.00 0.08 0.92
#> TCGA.ZF.A9RD.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FD.A3SO.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BT.A20U.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.GD.A3OS.01 1 0.000 0.953 1.00 0.00 0.00
#> TCGA.FD.A3B4.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FJ.A871.01 1 0.254 0.953 0.92 0.00 0.08
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.K4.A6FZ.01 2 0.491 0.841 0.0 0.58 0.42 0.00
#> TCGA.XF.AAN5.01 2 0.491 0.841 0.0 0.58 0.42 0.00
#> TCGA.CF.A1HS.01 4 0.471 0.733 0.0 0.00 0.36 0.64
#> TCGA.K4.A5RH.01 4 0.000 0.751 0.0 0.00 0.00 1.00
#> TCGA.XF.A9T5.01 4 0.499 0.677 0.0 0.00 0.48 0.52
#> TCGA.FT.A61P.01 2 0.000 0.638 0.0 1.00 0.00 0.00
#> TCGA.XF.A9SX.01 2 0.491 0.841 0.0 0.58 0.42 0.00
#> TCGA.GU.A762.01 2 0.491 0.841 0.0 0.58 0.42 0.00
#> TCGA.K4.A5RJ.01 4 0.000 0.751 0.0 0.00 0.00 1.00
#> TCGA.ZF.A9RD.01 2 0.491 0.841 0.0 0.58 0.42 0.00
#> TCGA.FD.A3SO.01 2 0.000 0.638 0.0 1.00 0.00 0.00
#> TCGA.BT.A20U.01 2 0.000 0.638 0.0 1.00 0.00 0.00
#> TCGA.GD.A3OS.01 1 0.000 0.932 1.0 0.00 0.00 0.00
#> TCGA.FD.A3B4.01 2 0.491 0.841 0.0 0.58 0.42 0.00
#> TCGA.FJ.A871.01 1 0.234 0.932 0.9 0.00 0.10 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.K4.A6FZ.01 2 0.104 0.964 0.00 0.96 0.04 0.00 0.00
#> TCGA.XF.AAN5.01 2 0.000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.CF.A1HS.01 4 0.548 0.469 0.00 0.00 0.12 0.64 0.24
#> TCGA.K4.A5RH.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.XF.A9T5.01 4 0.473 0.539 0.00 0.00 0.20 0.72 0.08
#> TCGA.FT.A61P.01 3 0.380 1.000 0.00 0.30 0.70 0.00 0.00
#> TCGA.XF.A9SX.01 2 0.104 0.964 0.00 0.96 0.04 0.00 0.00
#> TCGA.GU.A762.01 2 0.104 0.964 0.00 0.96 0.04 0.00 0.00
#> TCGA.K4.A5RJ.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZF.A9RD.01 2 0.000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A3SO.01 3 0.380 1.000 0.00 0.30 0.70 0.00 0.00
#> TCGA.BT.A20U.01 3 0.380 1.000 0.00 0.30 0.70 0.00 0.00
#> TCGA.GD.A3OS.01 1 0.000 0.854 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B4.01 2 0.000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.FJ.A871.01 1 0.370 0.854 0.82 0.00 0.10 0.08 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.K4.A6FZ.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAN5.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A1HS.01 4 0.279 0.000 0.00 0.00 0.02 0.84 0.00 0.14
#> TCGA.K4.A5RH.01 5 0.000 0.950 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XF.A9T5.01 6 0.000 0.000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FT.A61P.01 3 0.226 1.000 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.XF.A9SX.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GU.A762.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.K4.A5RJ.01 5 0.127 0.950 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.ZF.A9RD.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SO.01 3 0.226 1.000 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.BT.A20U.01 3 0.226 1.000 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.GD.A3OS.01 1 0.393 0.789 0.76 0.00 0.08 0.16 0.00 0.00
#> TCGA.FD.A3B4.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FJ.A871.01 1 0.000 0.789 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.K4.A6FZ.01 2 0.2512 0.901 0.00 0.86 0.04 0 0.00 0 0.10
#> TCGA.XF.AAN5.01 2 0.0000 0.904 0.00 1.00 0.00 0 0.00 0 0.00
#> TCGA.CF.A1HS.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0 0.00
#> TCGA.K4.A5RH.01 5 0.0000 0.862 0.00 0.00 0.00 0 1.00 0 0.00
#> TCGA.XF.A9T5.01 6 0.0000 0.000 0.00 0.00 0.00 0 0.00 1 0.00
#> TCGA.FT.A61P.01 3 0.2163 0.718 0.00 0.02 0.88 0 0.00 0 0.10
#> TCGA.XF.A9SX.01 2 0.2512 0.901 0.00 0.86 0.04 0 0.00 0 0.10
#> TCGA.GU.A762.01 2 0.2512 0.901 0.00 0.86 0.04 0 0.00 0 0.10
#> TCGA.K4.A5RJ.01 5 0.2569 0.862 0.00 0.00 0.02 0 0.84 0 0.14
#> TCGA.ZF.A9RD.01 2 0.0000 0.904 0.00 1.00 0.00 0 0.00 0 0.00
#> TCGA.FD.A3SO.01 3 0.0504 0.740 0.00 0.02 0.98 0 0.00 0 0.00
#> TCGA.BT.A20U.01 7 0.3867 0.000 0.00 0.02 0.38 0 0.00 0 0.60
#> TCGA.GD.A3OS.01 1 0.2945 0.770 0.74 0.00 0.00 0 0.00 0 0.26
#> TCGA.FD.A3B4.01 2 0.0000 0.904 0.00 1.00 0.00 0 0.00 0 0.00
#> TCGA.FJ.A871.01 1 0.0000 0.770 1.00 0.00 0.00 0 0.00 0 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.K4.A6FZ.01 2 0.3744 0.778 0.00 0.74 0.02 0 0.0 0 0.18 0.06
#> TCGA.XF.AAN5.01 2 0.0000 0.800 0.00 1.00 0.00 0 0.0 0 0.00 0.00
#> TCGA.CF.A1HS.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.0 0 0.00 0.00
#> TCGA.K4.A5RH.01 5 0.0000 0.916 0.00 0.00 0.00 0 1.0 0 0.00 0.00
#> TCGA.XF.A9T5.01 6 0.0000 0.000 0.00 0.00 0.00 0 0.0 1 0.00 0.00
#> TCGA.FT.A61P.01 3 0.4050 0.526 0.00 0.00 0.60 0 0.0 0 0.34 0.06
#> TCGA.XF.A9SX.01 2 0.3744 0.778 0.00 0.74 0.02 0 0.0 0 0.18 0.06
#> TCGA.GU.A762.01 2 0.4191 0.740 0.00 0.66 0.02 0 0.0 0 0.26 0.06
#> TCGA.K4.A5RJ.01 5 0.1804 0.916 0.00 0.00 0.00 0 0.9 0 0.08 0.02
#> TCGA.ZF.A9RD.01 2 0.1091 0.788 0.00 0.94 0.00 0 0.0 0 0.06 0.00
#> TCGA.FD.A3SO.01 3 0.0000 0.533 0.00 0.00 1.00 0 0.0 0 0.00 0.00
#> TCGA.BT.A20U.01 8 0.0471 0.000 0.00 0.00 0.02 0 0.0 0 0.00 0.98
#> TCGA.GD.A3OS.01 1 0.0000 0.611 1.00 0.00 0.00 0 0.0 0 0.00 0.00
#> TCGA.FD.A3B4.01 2 0.0808 0.784 0.00 0.96 0.00 0 0.0 0 0.04 0.00
#> TCGA.FJ.A871.01 1 0.3272 0.611 0.58 0.00 0.00 0 0.0 0 0.42 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 , Node021 , Node022 , Node023 , Node031-leaf , Node032 , Node033 .
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 176 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 0.812 0.895 0.956 0.4939 0.497 0.497
#> 3 3 0.992 0.966 0.985 0.3462 0.696 0.465
#> 4 4 0.725 0.668 0.846 0.1161 0.761 0.423
#> 5 5 0.736 0.756 0.830 0.0634 0.855 0.522
#> 6 6 0.816 0.705 0.853 0.0421 0.921 0.656
#> 7 7 0.788 0.745 0.838 0.0184 0.954 0.759
#> 8 8 0.813 0.656 0.824 0.0173 0.965 0.807
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.2F.A9KO.01 1 0.000 0.994 1.00 0.00
#> TCGA.HQ.A5NE.01 1 0.000 0.994 1.00 0.00
#> TCGA.PQ.A6FI.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A3SL.01 2 0.000 0.911 0.00 1.00
#> TCGA.UY.A9PE.01 2 0.995 0.290 0.46 0.54
#> TCGA.CU.A3YL.01 2 0.000 0.911 0.00 1.00
#> TCGA.ZF.AA52.01 2 0.000 0.911 0.00 1.00
#> TCGA.E7.A541.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A6TI.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A9SZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.C4.A0EZ.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A3SJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.AA56.01 1 0.000 0.994 1.00 0.00
#> TCGA.XF.AAMH.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A3NA.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A3IK.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.A9RF.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A3PJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.YC.A9TC.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.A9R7.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A1A7.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A2LB.01 1 0.000 0.994 1.00 0.00
#> TCGA.GV.A3QF.01 2 0.000 0.911 0.00 1.00
#> TCGA.ZF.A9R9.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A8HB.01 2 0.000 0.911 0.00 1.00
#> TCGA.E7.A97P.01 2 0.995 0.290 0.46 0.54
#> TCGA.ZF.AA4V.01 2 0.000 0.911 0.00 1.00
#> TCGA.CU.A5W6.01 1 0.000 0.994 1.00 0.00
#> TCGA.C4.A0F7.01 2 0.000 0.911 0.00 1.00
#> TCGA.4Z.AA7Q.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.AA6S.01 1 0.000 0.994 1.00 0.00
#> TCGA.XF.A8HD.01 2 0.000 0.911 0.00 1.00
#> TCGA.KQ.A41S.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.AAMW.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A0YX.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A6TC.01 2 0.981 0.380 0.42 0.58
#> TCGA.GC.A3I6.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A9SK.01 1 0.904 0.444 0.68 0.32
#> TCGA.GU.AATP.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A20T.01 2 0.995 0.290 0.46 0.54
#> TCGA.UY.A9PH.01 1 0.000 0.994 1.00 0.00
#> TCGA.UY.A78K.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A20W.01 2 0.995 0.290 0.46 0.54
#> TCGA.E7.A7DV.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A20R.01 1 0.000 0.994 1.00 0.00
#> TCGA.E7.A6MD.01 2 0.990 0.337 0.44 0.56
#> TCGA.ZF.A9RC.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A6B2.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A6B6.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.AA6M.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A3IN.01 1 0.000 0.994 1.00 0.00
#> TCGA.XF.A9T3.01 1 0.000 0.994 1.00 0.00
#> TCGA.CF.A47Y.01 1 0.000 0.994 1.00 0.00
#> TCGA.BL.A13J.01 2 0.000 0.911 0.00 1.00
#> TCGA.GD.A2C5.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A9SP.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A3SR.01 2 0.000 0.911 0.00 1.00
#> TCGA.G2.A2EO.01 2 0.000 0.911 0.00 1.00
#> TCGA.ZF.AA5N.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A6B0.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A20N.01 2 0.000 0.911 0.00 1.00
#> TCGA.ZF.AA5H.01 1 0.000 0.994 1.00 0.00
#> TCGA.G2.A2EJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A3SN.01 2 0.000 0.911 0.00 1.00
#> TCGA.G2.A2EF.01 2 0.000 0.911 0.00 1.00
#> TCGA.GV.A3QK.01 2 0.000 0.911 0.00 1.00
#> TCGA.LT.A5Z6.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A5C1.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A8HH.01 1 0.000 0.994 1.00 0.00
#> TCGA.LC.A66R.01 2 0.995 0.290 0.46 0.54
#> TCGA.BT.A2LA.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.AA54.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.AA6R.01 1 0.000 0.994 1.00 0.00
#> TCGA.FT.A3EE.01 2 0.995 0.290 0.46 0.54
#> TCGA.ZF.AA4T.01 1 0.000 0.994 1.00 0.00
#> TCGA.2F.A9KW.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.A9R1.01 1 0.000 0.994 1.00 0.00
#> TCGA.CF.A47S.01 1 0.000 0.994 1.00 0.00
#> TCGA.E7.A3X6.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A6TG.01 2 0.995 0.290 0.46 0.54
#> TCGA.CF.A47V.01 2 0.000 0.911 0.00 1.00
#> TCGA.ZF.AA4X.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A5BZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.UY.A9PF.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A1A5.01 2 0.000 0.911 0.00 1.00
#> TCGA.UY.A78L.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A6TA.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A3X1.01 1 0.000 0.994 1.00 0.00
#> TCGA.YC.A89H.01 1 0.000 0.994 1.00 0.00
#> TCGA.XF.AAMY.01 1 0.000 0.994 1.00 0.00
#> TCGA.4Z.AA81.01 2 0.000 0.911 0.00 1.00
#> TCGA.UY.A8OC.01 2 0.000 0.911 0.00 1.00
#> TCGA.BT.A20Q.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A3SS.01 2 0.000 0.911 0.00 1.00
#> TCGA.E7.A6ME.01 1 0.000 0.994 1.00 0.00
#> TCGA.G2.A2EK.01 1 0.000 0.994 1.00 0.00
#> TCGA.SY.A9G5.01 2 0.000 0.911 0.00 1.00
#> TCGA.ZF.A9RM.01 2 0.995 0.290 0.46 0.54
#> TCGA.FD.A5BR.01 1 0.000 0.994 1.00 0.00
#> TCGA.G2.A2EC.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A9T4.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A62S.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A6B5.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.AA51.01 2 0.000 0.911 0.00 1.00
#> TCGA.BT.A42B.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A3WW.01 1 0.000 0.994 1.00 0.00
#> TCGA.GV.A40E.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A1A6.06 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A2I1.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A2HX.01 2 0.000 0.911 0.00 1.00
#> TCGA.BL.A3JM.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A9SU.01 1 0.000 0.994 1.00 0.00
#> TCGA.GD.A76B.01 2 0.995 0.290 0.46 0.54
#> TCGA.BT.A20J.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.AA71.01 2 0.000 0.911 0.00 1.00
#> TCGA.GC.A3RC.01 2 0.000 0.911 0.00 1.00
#> TCGA.GC.A3YS.01 2 0.000 0.911 0.00 1.00
#> TCGA.CF.A47W.01 1 0.000 0.994 1.00 0.00
#> TCGA.XF.AAN3.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.AAN2.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A3IV.01 2 0.000 0.911 0.00 1.00
#> TCGA.XF.A9SJ.01 2 0.000 0.911 0.00 1.00
#> TCGA.C4.A0F0.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.AA4R.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A3SQ.01 2 0.995 0.290 0.46 0.54
#> TCGA.K4.AAQO.01 1 0.000 0.994 1.00 0.00
#> TCGA.GC.A6I3.01 1 0.000 0.994 1.00 0.00
#> TCGA.XF.AAMT.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A3IM.01 2 0.995 0.290 0.46 0.54
#> TCGA.S5.A6DX.01 2 0.000 0.911 0.00 1.00
#> TCGA.ZF.A9R0.01 2 0.000 0.911 0.00 1.00
#> TCGA.BT.A0S7.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A42E.01 2 0.000 0.911 0.00 1.00
#> TCGA.GU.A42R.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A3SM.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZF.AA4N.01 2 0.402 0.847 0.08 0.92
#> TCGA.CF.A1HR.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A5BY.01 2 0.000 0.911 0.00 1.00
#> TCGA.GV.A3QH.01 1 0.000 0.994 1.00 0.00
#> TCGA.BL.A5ZZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.G2.A3IE.01 1 0.000 0.994 1.00 0.00
#> TCGA.UY.A8OD.01 2 0.995 0.290 0.46 0.54
#> TCGA.DK.A1A3.01 1 0.000 0.994 1.00 0.00
#> TCGA.H4.A2HO.01 1 0.000 0.994 1.00 0.00
#> TCGA.4Z.AA84.01 2 0.995 0.290 0.46 0.54
#> TCGA.XF.A9SG.01 1 0.000 0.994 1.00 0.00
#> TCGA.GC.A4ZW.01 2 0.000 0.911 0.00 1.00
#> TCGA.BT.A2LD.01 1 0.000 0.994 1.00 0.00
#> TCGA.GV.A3JV.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A1AC.01 1 0.000 0.994 1.00 0.00
#> TCGA.G2.A2ES.01 2 0.000 0.911 0.00 1.00
#> TCGA.HQ.A2OF.01 2 0.000 0.911 0.00 1.00
#> TCGA.GU.AATO.01 2 0.000 0.911 0.00 1.00
#> TCGA.C4.A0F1.01 1 0.000 0.994 1.00 0.00
#> TCGA.E7.A8O7.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.AA6Q.01 2 0.000 0.911 0.00 1.00
#> TCGA.GV.A3QG.01 1 0.000 0.994 1.00 0.00
#> TCGA.K4.A54R.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A6TD.01 2 0.000 0.911 0.00 1.00
#> TCGA.2F.A9KT.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.A6AV.01 1 0.000 0.994 1.00 0.00
#> TCGA.K4.A3WV.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A20P.01 2 0.000 0.911 0.00 1.00
#> TCGA.DK.A3IT.01 1 0.000 0.994 1.00 0.00
#> TCGA.DK.AA6W.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A3N5.01 2 0.000 0.911 0.00 1.00
#> TCGA.BT.A20X.01 1 0.000 0.994 1.00 0.00
#> TCGA.G2.AA3C.01 1 0.000 0.994 1.00 0.00
#> TCGA.CU.A0YN.01 2 0.000 0.911 0.00 1.00
#> TCGA.FJ.A3Z7.01 1 0.000 0.994 1.00 0.00
#> TCGA.GV.A3QI.01 2 0.000 0.911 0.00 1.00
#> TCGA.4Z.AA82.01 1 0.529 0.841 0.88 0.12
#> TCGA.GC.A6I1.01 2 0.000 0.911 0.00 1.00
#> TCGA.FD.A5BX.01 1 0.000 0.994 1.00 0.00
#> TCGA.FD.A3B6.01 1 0.000 0.994 1.00 0.00
#> TCGA.BT.A20V.01 2 0.881 0.593 0.30 0.70
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.2F.A9KO.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.HQ.A5NE.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.PQ.A6FI.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FD.A3SL.01 2 0.2959 0.884 0.00 0.90 0.10
#> TCGA.UY.A9PE.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.CU.A3YL.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.ZF.AA52.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.E7.A541.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.FD.A6TI.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.XF.A9SZ.01 1 0.5216 0.639 0.74 0.00 0.26
#> TCGA.C4.A0EZ.01 2 0.2537 0.903 0.00 0.92 0.08
#> TCGA.FD.A3SJ.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZF.AA56.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.XF.AAMH.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FD.A3NA.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A3IK.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZF.A9RF.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A3PJ.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.YC.A9TC.01 3 0.5948 0.444 0.36 0.00 0.64
#> TCGA.ZF.A9R7.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.DK.A1A7.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A2LB.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.GV.A3QF.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.ZF.A9R9.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.XF.A8HB.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.E7.A97P.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.ZF.AA4V.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.CU.A5W6.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C4.A0F7.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.4Z.AA7Q.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.AA6S.01 3 0.4002 0.805 0.16 0.00 0.84
#> TCGA.XF.A8HD.01 2 0.5016 0.712 0.00 0.76 0.24
#> TCGA.KQ.A41S.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.XF.AAMW.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A0YX.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FD.A6TC.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.GC.A3I6.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.XF.A9SK.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.GU.AATP.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BT.A20T.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.UY.A9PH.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.UY.A78K.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A20W.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.E7.A7DV.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BT.A20R.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.ZF.A9RC.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A6B2.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A6B6.01 3 0.1529 0.944 0.00 0.04 0.96
#> TCGA.DK.AA6M.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.DK.A3IN.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.XF.A9T3.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.CF.A47Y.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BL.A13J.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.GD.A2C5.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.XF.A9SP.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FD.A3SR.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.G2.A2EO.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.ZF.AA5N.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.DK.A6B0.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BT.A20N.01 2 0.6045 0.437 0.00 0.62 0.38
#> TCGA.ZF.AA5H.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.G2.A2EJ.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FD.A3SN.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.G2.A2EF.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.GV.A3QK.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.LT.A5Z6.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.FD.A5C1.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.XF.A8HH.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.LC.A66R.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A2LA.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZF.AA54.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.AA6R.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FT.A3EE.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.ZF.AA4T.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.2F.A9KW.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZF.A9R1.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.CF.A47S.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.E7.A3X6.01 3 0.5706 0.534 0.32 0.00 0.68
#> TCGA.FD.A6TG.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.CF.A47V.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.ZF.AA4X.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.FD.A5BZ.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.UY.A9PF.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A1A5.01 2 0.5216 0.680 0.00 0.74 0.26
#> TCGA.UY.A78L.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FD.A6TA.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.DK.A3X1.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.YC.A89H.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.XF.AAMY.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.4Z.AA81.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.UY.A8OC.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.BT.A20Q.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FD.A3SS.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.E7.A6ME.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.G2.A2EK.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.SY.A9G5.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.ZF.A9RM.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FD.A5BR.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.G2.A2EC.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.XF.A9T4.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.FD.A62S.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A6B5.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZF.AA51.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A42B.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.DK.A3WW.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.GV.A40E.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.DK.A2I1.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A2HX.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.BL.A3JM.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.XF.A9SU.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.GD.A76B.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A20J.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.DK.AA71.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.GC.A3RC.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.GC.A3YS.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.CF.A47W.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.XF.AAN3.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.XF.AAN2.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.DK.A3IV.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.XF.A9SJ.01 2 0.4796 0.741 0.00 0.78 0.22
#> TCGA.C4.A0F0.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZF.AA4R.01 2 0.4291 0.795 0.00 0.82 0.18
#> TCGA.FD.A3SQ.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.K4.AAQO.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.GC.A6I3.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.XF.AAMT.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A3IM.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.S5.A6DX.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.ZF.A9R0.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A0S7.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BT.A42E.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.GU.A42R.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FD.A3SM.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZF.AA4N.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.CF.A1HR.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FD.A5BY.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.GV.A3QH.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BL.A5ZZ.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.G2.A3IE.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.UY.A8OD.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.DK.A1A3.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.H4.A2HO.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.XF.A9SG.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.GC.A4ZW.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.BT.A2LD.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.GV.A3JV.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.DK.A1AC.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.G2.A2ES.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.HQ.A2OF.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.GU.AATO.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.C4.A0F1.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.E7.A8O7.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.DK.AA6Q.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.GV.A3QG.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.K4.A54R.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.FD.A6TD.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.2F.A9KT.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DK.A6AV.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.K4.A3WV.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BT.A20P.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.DK.A3IT.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.DK.AA6W.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FD.A3N5.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.BT.A20X.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.G2.AA3C.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FJ.A3Z7.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.GV.A3QI.01 2 0.0000 0.970 0.00 1.00 0.00
#> TCGA.4Z.AA82.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.GC.A6I1.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.FD.A5BX.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FD.A3B6.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.BT.A20V.01 3 0.0000 0.985 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.2F.A9KO.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.HQ.A5NE.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.PQ.A6FI.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.UY.A9PE.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.CU.A3YL.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA52.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.E7.A541.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.FD.A6TI.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.XF.A9SZ.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.C4.A0EZ.01 3 0.0707 0.6784 0.00 0.02 0.98 0.00
#> TCGA.FD.A3SJ.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA56.01 4 0.4713 0.5039 0.36 0.00 0.00 0.64
#> TCGA.XF.AAMH.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.FD.A3NA.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IK.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.ZF.A9RF.01 4 0.4277 0.3175 0.00 0.00 0.28 0.72
#> TCGA.BT.A3PJ.01 4 0.4406 0.2759 0.00 0.00 0.30 0.70
#> TCGA.YC.A9TC.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.ZF.A9R7.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.DK.A1A7.01 4 0.4522 0.2241 0.00 0.00 0.32 0.68
#> TCGA.BT.A2LB.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.GV.A3QF.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.ZF.A9R9.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.XF.A8HB.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.E7.A97P.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.ZF.AA4V.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.CU.A5W6.01 4 0.4624 0.5247 0.34 0.00 0.00 0.66
#> TCGA.C4.A0F7.01 2 0.4994 0.4314 0.00 0.52 0.48 0.00
#> TCGA.4Z.AA7Q.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.DK.AA6S.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.XF.A8HD.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.KQ.A41S.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.XF.AAMW.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.BT.A0YX.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.FD.A6TC.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.GC.A3I6.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SK.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.GU.AATP.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.BT.A20T.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.UY.A9PH.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.UY.A78K.01 4 0.4855 -0.0151 0.00 0.00 0.40 0.60
#> TCGA.BT.A20W.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.E7.A7DV.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.ZF.A9RC.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.DK.A6B2.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.DK.A6B6.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.DK.AA6M.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.DK.A3IN.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.XF.A9T3.01 4 0.3801 0.6234 0.22 0.00 0.00 0.78
#> TCGA.CF.A47Y.01 4 0.4855 0.4429 0.40 0.00 0.00 0.60
#> TCGA.BL.A13J.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.GD.A2C5.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.XF.A9SP.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.FD.A3SR.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.G2.A2EO.01 3 0.4713 -0.0123 0.00 0.36 0.64 0.00
#> TCGA.ZF.AA5N.01 3 0.4994 -0.3640 0.00 0.48 0.52 0.00
#> TCGA.DK.A6B0.01 1 0.1211 0.9487 0.96 0.00 0.00 0.04
#> TCGA.BT.A20N.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA5H.01 4 0.4624 0.1761 0.00 0.00 0.34 0.66
#> TCGA.G2.A2EJ.01 4 0.3172 0.5177 0.00 0.00 0.16 0.84
#> TCGA.FD.A3SN.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.G2.A2EF.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.GV.A3QK.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.LT.A5Z6.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.FD.A5C1.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.XF.A8HH.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.LC.A66R.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.BT.A2LA.01 4 0.2345 0.6779 0.10 0.00 0.00 0.90
#> TCGA.ZF.AA54.01 4 0.3975 0.6093 0.24 0.00 0.00 0.76
#> TCGA.DK.AA6R.01 4 0.2011 0.6782 0.08 0.00 0.00 0.92
#> TCGA.FT.A3EE.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.ZF.AA4T.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.2F.A9KW.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R1.01 4 0.4855 -0.0151 0.00 0.00 0.40 0.60
#> TCGA.CF.A47S.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.E7.A3X6.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.FD.A6TG.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.CF.A47V.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA4X.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.FD.A5BZ.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.UY.A9PF.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.DK.A1A5.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.UY.A78L.01 4 0.4855 -0.0151 0.00 0.00 0.40 0.60
#> TCGA.FD.A6TA.01 4 0.3172 0.5177 0.00 0.00 0.16 0.84
#> TCGA.DK.A3X1.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.YC.A89H.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.XF.AAMY.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA81.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.UY.A8OC.01 3 0.4713 -0.0123 0.00 0.36 0.64 0.00
#> TCGA.BT.A20Q.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.FD.A3SS.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.E7.A6ME.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.G2.A2EK.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.SY.A9G5.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.ZF.A9RM.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.FD.A5BR.01 4 0.4522 0.2291 0.00 0.00 0.32 0.68
#> TCGA.G2.A2EC.01 3 0.4713 -0.0123 0.00 0.36 0.64 0.00
#> TCGA.XF.A9T4.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.FD.A62S.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.DK.A6B5.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA51.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.BT.A42B.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.DK.A3WW.01 4 0.4277 0.3189 0.00 0.00 0.28 0.72
#> TCGA.GV.A40E.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.DK.A1A6.06 3 0.0707 0.6983 0.00 0.00 0.98 0.02
#> TCGA.DK.A2I1.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 3 0.5000 -0.4119 0.00 0.50 0.50 0.00
#> TCGA.BL.A3JM.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.XF.A9SU.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.GD.A76B.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.BT.A20J.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.DK.AA71.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.GC.A3RC.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.CF.A47W.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.XF.AAN3.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.XF.AAN2.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IV.01 3 0.0707 0.6983 0.00 0.00 0.98 0.02
#> TCGA.XF.A9SJ.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.C4.A0F0.01 4 0.4522 0.5436 0.32 0.00 0.00 0.68
#> TCGA.ZF.AA4R.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.FD.A3SQ.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.K4.AAQO.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.01 4 0.0707 0.6760 0.02 0.00 0.00 0.98
#> TCGA.XF.AAMT.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.S5.A6DX.01 3 0.4624 0.5918 0.00 0.00 0.66 0.34
#> TCGA.ZF.A9R0.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.BT.A0S7.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.BT.A42E.01 3 0.4713 -0.0123 0.00 0.36 0.64 0.00
#> TCGA.GU.A42R.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.FD.A3SM.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.CF.A1HR.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.FD.A5BY.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.GV.A3QH.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.BL.A5ZZ.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.G2.A3IE.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.DK.A1A3.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.H4.A2HO.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.XF.A9SG.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.GC.A4ZW.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.BT.A2LD.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.GV.A3JV.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.DK.A1AC.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.G2.A2ES.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.HQ.A2OF.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.GU.AATO.01 2 0.4790 0.6223 0.00 0.62 0.38 0.00
#> TCGA.C4.A0F1.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.E7.A8O7.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.DK.AA6Q.01 3 0.4855 -0.1434 0.00 0.40 0.60 0.00
#> TCGA.GV.A3QG.01 4 0.4522 0.2283 0.00 0.00 0.32 0.68
#> TCGA.K4.A54R.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TD.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.2F.A9KT.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.K4.A3WV.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.BT.A20P.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IT.01 4 0.2647 0.5673 0.00 0.00 0.12 0.88
#> TCGA.DK.AA6W.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.FD.A3N5.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.BT.A20X.01 4 0.4790 0.4810 0.38 0.00 0.00 0.62
#> TCGA.G2.AA3C.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.0000 0.6976 0.00 0.00 1.00 0.00
#> TCGA.FJ.A3Z7.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.GV.A3QI.01 2 0.0000 0.8683 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA82.01 3 0.4855 0.5441 0.00 0.00 0.60 0.40
#> TCGA.GC.A6I1.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
#> TCGA.FD.A5BX.01 1 0.0000 0.9986 1.00 0.00 0.00 0.00
#> TCGA.FD.A3B6.01 4 0.0000 0.6738 0.00 0.00 0.00 1.00
#> TCGA.BT.A20V.01 3 0.4790 0.5748 0.00 0.00 0.62 0.38
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.2F.A9KO.01 4 0.2280 0.834 0.12 0.00 0.00 0.88 0.00
#> TCGA.HQ.A5NE.01 1 0.4540 0.503 0.64 0.02 0.00 0.34 0.00
#> TCGA.PQ.A6FI.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 5 0.5425 0.674 0.00 0.08 0.32 0.00 0.60
#> TCGA.UY.A9PE.01 3 0.1410 0.708 0.00 0.06 0.94 0.00 0.00
#> TCGA.CU.A3YL.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.ZF.AA52.01 5 0.4227 0.607 0.00 0.00 0.42 0.00 0.58
#> TCGA.E7.A541.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.FD.A6TI.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.XF.A9SZ.01 4 0.1648 0.862 0.00 0.02 0.04 0.94 0.00
#> TCGA.C4.A0EZ.01 5 0.6336 0.658 0.00 0.14 0.26 0.02 0.58
#> TCGA.FD.A3SJ.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA56.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.XF.AAMH.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3NA.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IK.01 4 0.1043 0.877 0.04 0.00 0.00 0.96 0.00
#> TCGA.ZF.A9RF.01 3 0.4728 0.580 0.00 0.06 0.70 0.24 0.00
#> TCGA.BT.A3PJ.01 3 0.4728 0.580 0.00 0.06 0.70 0.24 0.00
#> TCGA.YC.A9TC.01 4 0.2754 0.827 0.00 0.08 0.04 0.88 0.00
#> TCGA.ZF.A9R7.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.DK.A1A7.01 3 0.5659 0.580 0.00 0.32 0.58 0.10 0.00
#> TCGA.BT.A2LB.01 3 0.5783 0.337 0.00 0.10 0.54 0.36 0.00
#> TCGA.GV.A3QF.01 3 0.3684 0.304 0.00 0.00 0.72 0.00 0.28
#> TCGA.ZF.A9R9.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.XF.A8HB.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.E7.A97P.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA4V.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.CU.A5W6.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.C4.A0F7.01 5 0.4748 0.674 0.00 0.14 0.08 0.02 0.76
#> TCGA.4Z.AA7Q.01 4 0.2077 0.871 0.04 0.04 0.00 0.92 0.00
#> TCGA.DK.AA6S.01 4 0.3291 0.830 0.00 0.12 0.04 0.84 0.00
#> TCGA.XF.A8HD.01 5 0.4182 0.633 0.00 0.00 0.40 0.00 0.60
#> TCGA.KQ.A41S.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.XF.AAMW.01 3 0.5727 0.385 0.00 0.10 0.56 0.34 0.00
#> TCGA.BT.A0YX.01 4 0.2797 0.857 0.06 0.06 0.00 0.88 0.00
#> TCGA.FD.A6TC.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.GC.A3I6.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.XF.A9SK.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.GU.AATP.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.BT.A20T.01 3 0.4252 0.639 0.00 0.28 0.70 0.02 0.00
#> TCGA.UY.A9PH.01 1 0.2732 0.838 0.84 0.00 0.00 0.16 0.00
#> TCGA.UY.A78K.01 3 0.4588 0.604 0.00 0.06 0.72 0.22 0.00
#> TCGA.BT.A20W.01 3 0.4252 0.639 0.00 0.28 0.70 0.02 0.00
#> TCGA.E7.A7DV.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.1043 0.708 0.00 0.04 0.96 0.00 0.00
#> TCGA.ZF.A9RC.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B2.01 4 0.1043 0.877 0.04 0.00 0.00 0.96 0.00
#> TCGA.DK.A6B6.01 5 0.5232 0.667 0.00 0.06 0.34 0.00 0.60
#> TCGA.DK.AA6M.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.DK.A3IN.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T3.01 4 0.2610 0.864 0.02 0.06 0.02 0.90 0.00
#> TCGA.CF.A47Y.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.BL.A13J.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.GD.A2C5.01 3 0.3684 0.304 0.00 0.00 0.72 0.00 0.28
#> TCGA.XF.A9SP.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SR.01 5 0.4287 0.535 0.00 0.00 0.46 0.00 0.54
#> TCGA.G2.A2EO.01 5 0.3796 0.719 0.00 0.00 0.30 0.00 0.70
#> TCGA.ZF.AA5N.01 5 0.2929 0.729 0.00 0.00 0.18 0.00 0.82
#> TCGA.DK.A6B0.01 1 0.2929 0.816 0.82 0.00 0.00 0.18 0.00
#> TCGA.BT.A20N.01 5 0.5232 0.667 0.00 0.06 0.34 0.00 0.60
#> TCGA.ZF.AA5H.01 3 0.4588 0.604 0.00 0.06 0.72 0.22 0.00
#> TCGA.G2.A2EJ.01 3 0.5599 0.517 0.00 0.12 0.62 0.26 0.00
#> TCGA.FD.A3SN.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.G2.A2EF.01 5 0.4182 0.633 0.00 0.00 0.40 0.00 0.60
#> TCGA.GV.A3QK.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.LT.A5Z6.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.FD.A5C1.01 3 0.3684 0.304 0.00 0.00 0.72 0.00 0.28
#> TCGA.XF.A8HH.01 4 0.5979 0.214 0.00 0.12 0.36 0.52 0.00
#> TCGA.LC.A66R.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A2LA.01 4 0.3903 0.825 0.02 0.16 0.02 0.80 0.00
#> TCGA.ZF.AA54.01 4 0.1820 0.873 0.02 0.02 0.02 0.94 0.00
#> TCGA.DK.AA6R.01 4 0.1820 0.873 0.02 0.02 0.02 0.94 0.00
#> TCGA.FT.A3EE.01 3 0.1732 0.707 0.00 0.08 0.92 0.00 0.00
#> TCGA.ZF.AA4T.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KW.01 1 0.0609 0.943 0.98 0.00 0.00 0.02 0.00
#> TCGA.ZF.A9R1.01 3 0.4588 0.604 0.00 0.06 0.72 0.22 0.00
#> TCGA.CF.A47S.01 3 0.5783 0.384 0.00 0.10 0.54 0.36 0.00
#> TCGA.E7.A3X6.01 4 0.1648 0.866 0.00 0.02 0.04 0.94 0.00
#> TCGA.FD.A6TG.01 3 0.1410 0.708 0.00 0.06 0.94 0.00 0.00
#> TCGA.CF.A47V.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.ZF.AA4X.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.FD.A5BZ.01 4 0.2797 0.857 0.06 0.06 0.00 0.88 0.00
#> TCGA.UY.A9PF.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A5.01 5 0.5232 0.667 0.00 0.06 0.34 0.00 0.60
#> TCGA.UY.A78L.01 3 0.4728 0.580 0.00 0.06 0.70 0.24 0.00
#> TCGA.FD.A6TA.01 3 0.5263 0.564 0.00 0.10 0.66 0.24 0.00
#> TCGA.DK.A3X1.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A89H.01 4 0.5382 0.487 0.00 0.10 0.26 0.64 0.00
#> TCGA.XF.AAMY.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA81.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.UY.A8OC.01 5 0.3796 0.719 0.00 0.00 0.30 0.00 0.70
#> TCGA.BT.A20Q.01 3 0.5692 0.261 0.00 0.08 0.64 0.02 0.26
#> TCGA.FD.A3SS.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.E7.A6ME.01 4 0.5892 0.546 0.00 0.18 0.22 0.60 0.00
#> TCGA.G2.A2EK.01 1 0.2280 0.876 0.88 0.00 0.00 0.12 0.00
#> TCGA.SY.A9G5.01 3 0.3684 0.304 0.00 0.00 0.72 0.00 0.28
#> TCGA.ZF.A9RM.01 3 0.5659 0.580 0.00 0.32 0.58 0.10 0.00
#> TCGA.FD.A5BR.01 3 0.5263 0.564 0.00 0.10 0.66 0.24 0.00
#> TCGA.G2.A2EC.01 5 0.3796 0.719 0.00 0.00 0.30 0.00 0.70
#> TCGA.XF.A9T4.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.FD.A62S.01 4 0.2797 0.857 0.06 0.06 0.00 0.88 0.00
#> TCGA.DK.A6B5.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA51.01 5 0.4302 0.491 0.00 0.00 0.48 0.00 0.52
#> TCGA.BT.A42B.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.DK.A3WW.01 3 0.5263 0.564 0.00 0.10 0.66 0.24 0.00
#> TCGA.GV.A40E.01 4 0.2438 0.865 0.04 0.06 0.00 0.90 0.00
#> TCGA.DK.A1A6.06 3 0.1043 0.672 0.00 0.00 0.96 0.00 0.04
#> TCGA.DK.A2I1.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 5 0.2516 0.703 0.00 0.00 0.14 0.00 0.86
#> TCGA.BL.A3JM.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.XF.A9SU.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.GD.A76B.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20J.01 4 0.5341 0.460 0.00 0.08 0.30 0.62 0.00
#> TCGA.DK.AA71.01 2 0.4126 0.978 0.00 0.62 0.00 0.00 0.38
#> TCGA.GC.A3RC.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.GC.A3YS.01 3 0.3684 0.304 0.00 0.00 0.72 0.00 0.28
#> TCGA.CF.A47W.01 1 0.2020 0.891 0.90 0.00 0.00 0.10 0.00
#> TCGA.XF.AAN3.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.XF.AAN2.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.DK.A3IV.01 3 0.1410 0.656 0.00 0.00 0.94 0.00 0.06
#> TCGA.XF.A9SJ.01 5 0.4182 0.633 0.00 0.00 0.40 0.00 0.60
#> TCGA.C4.A0F0.01 4 0.1043 0.877 0.04 0.00 0.00 0.96 0.00
#> TCGA.ZF.AA4R.01 5 0.5232 0.667 0.00 0.06 0.34 0.00 0.60
#> TCGA.FD.A3SQ.01 3 0.1732 0.707 0.00 0.08 0.92 0.00 0.00
#> TCGA.K4.AAQO.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.01 4 0.2438 0.858 0.00 0.06 0.04 0.90 0.00
#> TCGA.XF.AAMT.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 3 0.5425 0.600 0.00 0.32 0.60 0.08 0.00
#> TCGA.S5.A6DX.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9R0.01 3 0.3684 0.304 0.00 0.00 0.72 0.00 0.28
#> TCGA.BT.A0S7.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42E.01 5 0.3274 0.735 0.00 0.00 0.22 0.00 0.78
#> TCGA.GU.A42R.01 4 0.6244 0.438 0.00 0.26 0.20 0.54 0.00
#> TCGA.FD.A3SM.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 3 0.0609 0.706 0.00 0.02 0.98 0.00 0.00
#> TCGA.CF.A1HR.01 4 0.3697 0.767 0.00 0.08 0.10 0.82 0.00
#> TCGA.FD.A5BY.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.GV.A3QH.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.BL.A5ZZ.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.G2.A3IE.01 1 0.2732 0.838 0.84 0.00 0.00 0.16 0.00
#> TCGA.UY.A8OD.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.A1A3.01 1 0.2732 0.838 0.84 0.00 0.00 0.16 0.00
#> TCGA.H4.A2HO.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.1732 0.707 0.00 0.08 0.92 0.00 0.00
#> TCGA.XF.A9SG.01 4 0.2797 0.857 0.06 0.06 0.00 0.88 0.00
#> TCGA.GC.A4ZW.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.BT.A2LD.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JV.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.DK.A1AC.01 1 0.2280 0.877 0.88 0.00 0.00 0.12 0.00
#> TCGA.G2.A2ES.01 5 0.0609 0.592 0.00 0.00 0.02 0.00 0.98
#> TCGA.HQ.A2OF.01 2 0.4126 0.978 0.00 0.62 0.00 0.00 0.38
#> TCGA.GU.AATO.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00
#> TCGA.C4.A0F1.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A8O7.01 3 0.3690 0.664 0.00 0.20 0.78 0.02 0.00
#> TCGA.DK.AA6Q.01 5 0.3109 0.736 0.00 0.00 0.20 0.00 0.80
#> TCGA.GV.A3QG.01 3 0.4588 0.604 0.00 0.06 0.72 0.22 0.00
#> TCGA.K4.A54R.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.FD.A6TD.01 3 0.3684 0.304 0.00 0.00 0.72 0.00 0.28
#> TCGA.2F.A9KT.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 4 0.4818 0.650 0.00 0.10 0.18 0.72 0.00
#> TCGA.K4.A3WV.01 4 0.3521 0.830 0.04 0.14 0.00 0.82 0.00
#> TCGA.BT.A20P.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.DK.A3IT.01 3 0.5579 0.467 0.00 0.10 0.60 0.30 0.00
#> TCGA.DK.AA6W.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3N5.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.BT.A20X.01 4 0.1648 0.875 0.04 0.02 0.00 0.94 0.00
#> TCGA.G2.AA3C.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.3109 0.473 0.00 0.00 0.80 0.00 0.20
#> TCGA.FJ.A3Z7.01 4 0.3731 0.819 0.00 0.16 0.04 0.80 0.00
#> TCGA.GV.A3QI.01 2 0.4182 0.998 0.00 0.60 0.00 0.00 0.40
#> TCGA.4Z.AA82.01 3 0.5659 0.580 0.00 0.32 0.58 0.10 0.00
#> TCGA.GC.A6I1.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A5BX.01 1 0.2516 0.859 0.86 0.00 0.00 0.14 0.00
#> TCGA.FD.A3B6.01 4 0.2797 0.847 0.00 0.06 0.06 0.88 0.00
#> TCGA.BT.A20V.01 3 0.0000 0.702 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.2F.A9KO.01 4 0.0547 0.7979 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.HQ.A5NE.01 4 0.4195 0.6687 0.20 0.00 0.04 0.74 0.00 0.02
#> TCGA.PQ.A6FI.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 5 0.0547 0.9281 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.UY.A9PE.01 3 0.4310 -0.1980 0.00 0.00 0.54 0.00 0.02 0.44
#> TCGA.CU.A3YL.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA52.01 5 0.3578 0.4686 0.00 0.00 0.34 0.00 0.66 0.00
#> TCGA.E7.A541.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.FD.A6TI.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.XF.A9SZ.01 4 0.1092 0.7866 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.C4.A0EZ.01 5 0.2629 0.8650 0.00 0.00 0.02 0.02 0.88 0.08
#> TCGA.FD.A3SJ.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA56.01 4 0.0547 0.7932 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.XF.AAMH.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3NA.01 1 0.0547 0.9325 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.A3IK.01 4 0.0547 0.7979 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.ZF.A9RF.01 3 0.2190 0.5635 0.00 0.00 0.90 0.04 0.00 0.06
#> TCGA.BT.A3PJ.01 3 0.2190 0.5635 0.00 0.00 0.90 0.04 0.00 0.06
#> TCGA.YC.A9TC.01 4 0.4420 0.2485 0.00 0.00 0.04 0.62 0.00 0.34
#> TCGA.ZF.A9R7.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.DK.A1A7.01 6 0.2981 0.7082 0.00 0.00 0.16 0.00 0.02 0.82
#> TCGA.BT.A2LB.01 6 0.5555 0.5626 0.00 0.00 0.38 0.14 0.00 0.48
#> TCGA.GV.A3QF.01 3 0.3309 0.5385 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.ZF.A9R9.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HB.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A97P.01 3 0.2581 0.5677 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.ZF.AA4V.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.CU.A5W6.01 4 0.0547 0.7945 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.C4.A0F7.01 5 0.2882 0.8450 0.00 0.02 0.00 0.02 0.86 0.10
#> TCGA.4Z.AA7Q.01 4 0.0547 0.7979 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DK.AA6S.01 4 0.4042 0.6958 0.00 0.00 0.04 0.76 0.02 0.18
#> TCGA.XF.A8HD.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.KQ.A41S.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.XF.AAMW.01 6 0.4873 0.6799 0.00 0.00 0.32 0.08 0.00 0.60
#> TCGA.BT.A0YX.01 4 0.2725 0.7824 0.02 0.00 0.06 0.88 0.00 0.04
#> TCGA.FD.A6TC.01 3 0.2094 0.6045 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.GC.A3I6.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SK.01 3 0.2350 0.5990 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.GU.AATP.01 4 0.1092 0.7970 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.BT.A20T.01 6 0.3076 0.7367 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.UY.A9PH.01 4 0.3851 0.1719 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.UY.A78K.01 3 0.1865 0.5722 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.BT.A20W.01 6 0.3076 0.7367 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.E7.A7DV.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.4246 -0.0630 0.00 0.00 0.58 0.00 0.02 0.40
#> TCGA.ZF.A9RC.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B2.01 4 0.0547 0.7979 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DK.A6B6.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.DK.AA6M.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.DK.A3IN.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T3.01 4 0.2956 0.7541 0.00 0.00 0.12 0.84 0.00 0.04
#> TCGA.CF.A47Y.01 4 0.1092 0.7963 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.BL.A13J.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.01 3 0.3409 0.5232 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.XF.A9SP.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SR.01 5 0.3828 0.1744 0.00 0.00 0.44 0.00 0.56 0.00
#> TCGA.G2.A2EO.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.ZF.AA5N.01 5 0.1092 0.9311 0.00 0.02 0.02 0.00 0.96 0.00
#> TCGA.DK.A6B0.01 4 0.4282 0.2497 0.42 0.00 0.00 0.56 0.00 0.02
#> TCGA.BT.A20N.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.ZF.AA5H.01 3 0.1865 0.5722 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.G2.A2EJ.01 6 0.4576 0.5521 0.00 0.00 0.40 0.04 0.00 0.56
#> TCGA.FD.A3SN.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EF.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.GV.A3QK.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LT.A5Z6.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5C1.01 3 0.3409 0.5232 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.XF.A8HH.01 3 0.4247 0.2485 0.00 0.00 0.70 0.24 0.00 0.06
#> TCGA.LC.A66R.01 3 0.2094 0.6045 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.BT.A2LA.01 4 0.4754 0.6772 0.00 0.00 0.08 0.70 0.02 0.20
#> TCGA.ZF.AA54.01 4 0.0547 0.7932 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.DK.AA6R.01 4 0.0547 0.7932 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.FT.A3EE.01 3 0.4144 0.0716 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.ZF.AA4T.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KW.01 1 0.2793 0.6905 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.ZF.A9R1.01 3 0.1865 0.5722 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.CF.A47S.01 6 0.4121 0.7416 0.00 0.00 0.22 0.06 0.00 0.72
#> TCGA.E7.A3X6.01 4 0.0937 0.7902 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.FD.A6TG.01 3 0.4246 -0.0630 0.00 0.00 0.58 0.00 0.02 0.40
#> TCGA.CF.A47V.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4X.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BZ.01 4 0.2725 0.7824 0.02 0.00 0.06 0.88 0.00 0.04
#> TCGA.UY.A9PF.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A5.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.UY.A78L.01 3 0.2190 0.5635 0.00 0.00 0.90 0.04 0.00 0.06
#> TCGA.FD.A6TA.01 3 0.4310 -0.2198 0.00 0.00 0.54 0.02 0.00 0.44
#> TCGA.DK.A3X1.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A89H.01 6 0.5992 0.5123 0.00 0.00 0.34 0.24 0.00 0.42
#> TCGA.XF.AAMY.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA81.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.UY.A8OC.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.BT.A20Q.01 3 0.5712 0.3555 0.00 0.00 0.52 0.00 0.26 0.22
#> TCGA.FD.A3SS.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6ME.01 6 0.4834 0.6052 0.00 0.00 0.10 0.26 0.00 0.64
#> TCGA.G2.A2EK.01 1 0.3864 -0.0482 0.52 0.00 0.00 0.48 0.00 0.00
#> TCGA.SY.A9G5.01 3 0.3409 0.5232 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.ZF.A9RM.01 6 0.2941 0.7378 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.FD.A5BR.01 3 0.4337 -0.3440 0.00 0.00 0.50 0.02 0.00 0.48
#> TCGA.G2.A2EC.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.XF.A9T4.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A62S.01 4 0.3007 0.7743 0.02 0.00 0.08 0.86 0.00 0.04
#> TCGA.DK.A6B5.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA51.01 3 0.3828 0.1482 0.00 0.00 0.56 0.00 0.44 0.00
#> TCGA.BT.A42B.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WW.01 3 0.4310 -0.2198 0.00 0.00 0.54 0.02 0.00 0.44
#> TCGA.GV.A40E.01 4 0.2725 0.7824 0.02 0.00 0.06 0.88 0.00 0.04
#> TCGA.DK.A1A6.06 3 0.2474 0.6055 0.00 0.00 0.88 0.00 0.04 0.08
#> TCGA.DK.A2I1.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 5 0.1092 0.9311 0.00 0.02 0.02 0.00 0.96 0.00
#> TCGA.BL.A3JM.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SU.01 4 0.0547 0.7979 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.GD.A76B.01 3 0.2094 0.6045 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.BT.A20J.01 6 0.5922 0.5698 0.00 0.00 0.34 0.22 0.00 0.44
#> TCGA.DK.AA71.01 2 0.0547 0.9807 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.GC.A3RC.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.3309 0.5385 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.CF.A47W.01 4 0.4337 0.0778 0.48 0.00 0.00 0.50 0.00 0.02
#> TCGA.XF.AAN3.01 5 0.0937 0.9263 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.XF.AAN2.01 2 0.0547 0.9773 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DK.A3IV.01 3 0.2512 0.6080 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.XF.A9SJ.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.C4.A0F0.01 4 0.0547 0.7932 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.ZF.AA4R.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.FD.A3SQ.01 3 0.4310 -0.1980 0.00 0.00 0.54 0.00 0.02 0.44
#> TCGA.K4.AAQO.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.01 4 0.3045 0.7597 0.00 0.00 0.10 0.84 0.00 0.06
#> TCGA.XF.AAMT.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 6 0.2941 0.7378 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.S5.A6DX.01 3 0.3592 0.3862 0.00 0.00 0.74 0.00 0.02 0.24
#> TCGA.ZF.A9R0.01 3 0.3409 0.5232 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.BT.A0S7.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42E.01 5 0.0937 0.9299 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.GU.A42R.01 6 0.3321 0.6607 0.00 0.00 0.08 0.10 0.00 0.82
#> TCGA.FD.A3SM.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 3 0.2350 0.5898 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.CF.A1HR.01 4 0.5432 -0.3415 0.00 0.00 0.12 0.48 0.00 0.40
#> TCGA.FD.A5BY.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QH.01 4 0.1480 0.7931 0.02 0.00 0.00 0.94 0.00 0.04
#> TCGA.BL.A5ZZ.01 4 0.1480 0.7931 0.02 0.00 0.00 0.94 0.00 0.04
#> TCGA.G2.A3IE.01 4 0.3851 0.1719 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.UY.A8OD.01 3 0.2094 0.6045 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.DK.A1A3.01 4 0.3851 0.1719 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.H4.A2HO.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.4282 -0.1336 0.00 0.00 0.56 0.00 0.02 0.42
#> TCGA.XF.A9SG.01 4 0.2725 0.7824 0.02 0.00 0.06 0.88 0.00 0.04
#> TCGA.GC.A4ZW.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A2LD.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JV.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AC.01 1 0.3797 0.1694 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.G2.A2ES.01 5 0.0937 0.9263 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.HQ.A2OF.01 2 0.0547 0.9807 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.GU.AATO.01 5 0.1267 0.9187 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.C4.A0F1.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A8O7.01 6 0.3499 0.6802 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.DK.AA6Q.01 5 0.1092 0.9311 0.00 0.02 0.02 0.00 0.96 0.00
#> TCGA.GV.A3QG.01 3 0.1865 0.5722 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.K4.A54R.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TD.01 3 0.3198 0.5541 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.2F.A9KT.01 1 0.0547 0.9325 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.A6AV.01 6 0.5798 0.5448 0.00 0.00 0.20 0.32 0.00 0.48
#> TCGA.K4.A3WV.01 4 0.3678 0.7123 0.00 0.00 0.02 0.78 0.02 0.18
#> TCGA.BT.A20P.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IT.01 6 0.4700 0.6557 0.00 0.00 0.34 0.06 0.00 0.60
#> TCGA.DK.AA6W.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3N5.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20X.01 4 0.0547 0.7979 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.G2.AA3C.01 1 0.0000 0.9498 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.3076 0.5595 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.FJ.A3Z7.01 4 0.4982 0.6510 0.00 0.00 0.10 0.68 0.02 0.20
#> TCGA.GV.A3QI.01 2 0.0000 0.9974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA82.01 6 0.2941 0.7378 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.GC.A6I1.01 3 0.2094 0.6045 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.FD.A5BX.01 4 0.3864 0.1163 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.FD.A3B6.01 4 0.4902 0.1824 0.00 0.00 0.46 0.48 0.00 0.06
#> TCGA.BT.A20V.01 3 0.2350 0.5898 0.00 0.00 0.88 0.00 0.02 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.2F.A9KO.01 4 0.1664 0.7957 0.02 0.00 0.00 0.92 0.00 0.06 0.00
#> TCGA.HQ.A5NE.01 4 0.3526 0.7284 0.18 0.00 0.00 0.76 0.00 0.06 0.00
#> TCGA.PQ.A6FI.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 5 0.2259 0.8550 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.UY.A9PE.01 7 0.3358 0.4380 0.00 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.CU.A3YL.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA52.01 3 0.3546 0.0205 0.00 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.E7.A541.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.FD.A6TI.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.XF.A9SZ.01 4 0.0863 0.7885 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.C4.A0EZ.01 5 0.5361 0.5949 0.00 0.00 0.08 0.00 0.58 0.28 0.06
#> TCGA.FD.A3SJ.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA56.01 4 0.0504 0.7938 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.XF.AAMH.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3NA.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IK.01 4 0.0863 0.7923 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.ZF.A9RF.01 3 0.3386 0.5869 0.00 0.00 0.78 0.00 0.02 0.18 0.02
#> TCGA.BT.A3PJ.01 3 0.3386 0.5869 0.00 0.00 0.78 0.00 0.02 0.18 0.02
#> TCGA.YC.A9TC.01 4 0.3841 0.3807 0.00 0.00 0.00 0.68 0.00 0.04 0.28
#> TCGA.ZF.A9R7.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.DK.A1A7.01 7 0.2832 0.6548 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.BT.A2LB.01 7 0.4121 0.6989 0.00 0.00 0.10 0.20 0.00 0.00 0.70
#> TCGA.GV.A3QF.01 3 0.1166 0.6771 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.ZF.A9R9.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.XF.A8HB.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E7.A97P.01 3 0.2945 0.5817 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.ZF.AA4V.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.CU.A5W6.01 4 0.0863 0.7851 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.C4.A0F7.01 5 0.5107 0.5951 0.00 0.04 0.00 0.00 0.60 0.28 0.08
#> TCGA.4Z.AA7Q.01 4 0.1166 0.7947 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.DK.AA6S.01 4 0.3685 0.6807 0.00 0.00 0.02 0.66 0.00 0.32 0.00
#> TCGA.XF.A8HD.01 5 0.2259 0.8550 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.KQ.A41S.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.XF.AAMW.01 7 0.3263 0.7307 0.00 0.00 0.08 0.12 0.00 0.00 0.80
#> TCGA.BT.A0YX.01 4 0.3055 0.7669 0.00 0.00 0.02 0.82 0.02 0.14 0.00
#> TCGA.FD.A6TC.01 3 0.2708 0.6280 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.GC.A3I6.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SK.01 3 0.2708 0.6280 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.GU.AATP.01 4 0.1433 0.7884 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.BT.A20T.01 7 0.2512 0.7121 0.00 0.00 0.04 0.00 0.00 0.10 0.86
#> TCGA.UY.A9PH.01 4 0.4070 0.5276 0.34 0.00 0.00 0.62 0.00 0.04 0.00
#> TCGA.UY.A78K.01 3 0.3386 0.5869 0.00 0.00 0.78 0.00 0.02 0.18 0.02
#> TCGA.BT.A20W.01 7 0.2512 0.7121 0.00 0.00 0.04 0.00 0.00 0.10 0.86
#> TCGA.E7.A7DV.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 7 0.3558 0.0815 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.ZF.A9RC.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B2.01 4 0.1166 0.7963 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.DK.A6B6.01 5 0.3055 0.8492 0.00 0.00 0.14 0.00 0.82 0.02 0.02
#> TCGA.DK.AA6M.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.DK.A3IN.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T3.01 4 0.4993 0.6063 0.00 0.00 0.12 0.62 0.02 0.24 0.00
#> TCGA.CF.A47Y.01 4 0.1928 0.7661 0.00 0.00 0.00 0.90 0.02 0.08 0.00
#> TCGA.BL.A13J.01 2 0.1363 0.9523 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.GD.A2C5.01 3 0.2259 0.6555 0.00 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.XF.A9SP.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SR.01 3 0.3459 0.2394 0.00 0.00 0.60 0.00 0.40 0.00 0.00
#> TCGA.G2.A2EO.01 5 0.1886 0.8695 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.ZF.AA5N.01 5 0.2163 0.8724 0.00 0.02 0.10 0.00 0.88 0.00 0.00
#> TCGA.DK.A6B0.01 4 0.4872 0.5343 0.30 0.00 0.00 0.60 0.02 0.08 0.00
#> TCGA.BT.A20N.01 5 0.2259 0.8550 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.ZF.AA5H.01 3 0.3386 0.5869 0.00 0.00 0.78 0.00 0.02 0.18 0.02
#> TCGA.G2.A2EJ.01 7 0.4162 0.7164 0.00 0.00 0.12 0.12 0.00 0.02 0.74
#> TCGA.FD.A3SN.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EF.01 5 0.2832 0.7608 0.00 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.GV.A3QK.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LT.A5Z6.01 2 0.1363 0.9523 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.FD.A5C1.01 3 0.2422 0.6334 0.00 0.00 0.82 0.00 0.18 0.00 0.00
#> TCGA.XF.A8HH.01 3 0.5986 0.3358 0.00 0.00 0.58 0.18 0.02 0.16 0.06
#> TCGA.LC.A66R.01 3 0.2708 0.6280 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.BT.A2LA.01 4 0.4244 0.6038 0.00 0.00 0.00 0.54 0.04 0.42 0.00
#> TCGA.ZF.AA54.01 4 0.0504 0.7884 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DK.AA6R.01 4 0.0000 0.7903 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 3 0.3558 0.0203 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.ZF.AA4T.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KW.01 1 0.4328 0.2261 0.60 0.00 0.00 0.34 0.00 0.06 0.00
#> TCGA.ZF.A9R1.01 3 0.3722 0.5676 0.00 0.00 0.76 0.00 0.02 0.18 0.04
#> TCGA.CF.A47S.01 7 0.3404 0.7308 0.00 0.00 0.04 0.08 0.00 0.06 0.82
#> TCGA.E7.A3X6.01 4 0.0863 0.7939 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.FD.A6TG.01 3 0.3562 -0.0628 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.CF.A47V.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.ZF.AA4X.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BZ.01 4 0.2376 0.7820 0.00 0.00 0.02 0.86 0.00 0.12 0.00
#> TCGA.UY.A9PF.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A5.01 5 0.2259 0.8550 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.UY.A78L.01 3 0.3386 0.5869 0.00 0.00 0.78 0.00 0.02 0.18 0.02
#> TCGA.FD.A6TA.01 7 0.4177 0.6788 0.00 0.00 0.18 0.12 0.00 0.00 0.70
#> TCGA.DK.A3X1.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A89H.01 7 0.6652 0.5251 0.00 0.00 0.16 0.20 0.02 0.12 0.50
#> TCGA.XF.AAMY.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA81.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.UY.A8OC.01 5 0.1886 0.8695 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.BT.A20Q.01 3 0.5652 0.4792 0.00 0.00 0.58 0.00 0.16 0.06 0.20
#> TCGA.FD.A3SS.01 2 0.1363 0.9523 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.E7.A6ME.01 7 0.4594 0.6688 0.00 0.00 0.00 0.22 0.00 0.14 0.64
#> TCGA.G2.A2EK.01 4 0.3413 0.4808 0.38 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.SY.A9G5.01 3 0.2422 0.6334 0.00 0.00 0.82 0.00 0.18 0.00 0.00
#> TCGA.ZF.A9RM.01 7 0.1433 0.6994 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.FD.A5BR.01 7 0.4177 0.6788 0.00 0.00 0.18 0.12 0.00 0.00 0.70
#> TCGA.G2.A2EC.01 5 0.1886 0.8695 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.XF.A9T4.01 2 0.1363 0.9523 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.FD.A62S.01 4 0.3396 0.7578 0.00 0.00 0.04 0.80 0.02 0.14 0.00
#> TCGA.DK.A6B5.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA51.01 3 0.2708 0.5746 0.00 0.00 0.78 0.00 0.22 0.00 0.00
#> TCGA.BT.A42B.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DK.A3WW.01 7 0.4177 0.6788 0.00 0.00 0.18 0.12 0.00 0.00 0.70
#> TCGA.GV.A40E.01 4 0.2745 0.7727 0.00 0.00 0.02 0.82 0.00 0.16 0.00
#> TCGA.DK.A1A6.06 3 0.2422 0.6411 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.DK.A2I1.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 5 0.2804 0.8686 0.00 0.06 0.06 0.00 0.86 0.02 0.00
#> TCGA.BL.A3JM.01 2 0.1363 0.9523 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.XF.A9SU.01 4 0.0504 0.7884 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.GD.A76B.01 3 0.2708 0.6280 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.BT.A20J.01 7 0.4702 0.6977 0.00 0.00 0.08 0.20 0.00 0.04 0.68
#> TCGA.DK.AA71.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3RC.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.1886 0.6633 0.00 0.00 0.88 0.00 0.12 0.00 0.00
#> TCGA.CF.A47W.01 4 0.5077 0.3896 0.38 0.00 0.00 0.52 0.02 0.08 0.00
#> TCGA.XF.AAN3.01 5 0.2654 0.8615 0.00 0.10 0.02 0.00 0.86 0.02 0.00
#> TCGA.XF.AAN2.01 2 0.2163 0.8904 0.00 0.88 0.00 0.00 0.10 0.02 0.00
#> TCGA.DK.A3IV.01 3 0.2745 0.6494 0.00 0.00 0.82 0.00 0.02 0.00 0.16
#> TCGA.XF.A9SJ.01 5 0.2259 0.8550 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.C4.A0F0.01 4 0.0000 0.7903 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 5 0.2259 0.8550 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.FD.A3SQ.01 7 0.3294 0.4734 0.00 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.K4.AAQO.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.01 4 0.2906 0.7642 0.00 0.00 0.02 0.80 0.00 0.18 0.00
#> TCGA.XF.AAMT.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 7 0.1433 0.6994 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.S5.A6DX.01 3 0.3459 0.2512 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.ZF.A9R0.01 3 0.1886 0.6694 0.00 0.00 0.88 0.00 0.12 0.00 0.00
#> TCGA.BT.A0S7.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42E.01 5 0.1886 0.8695 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.GU.A42R.01 7 0.2376 0.7074 0.00 0.00 0.00 0.02 0.00 0.12 0.86
#> TCGA.FD.A3SM.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 3 0.2945 0.5835 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.CF.A1HR.01 7 0.4266 0.4178 0.00 0.00 0.04 0.44 0.00 0.00 0.52
#> TCGA.FD.A5BY.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QH.01 4 0.1166 0.7894 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.BL.A5ZZ.01 4 0.1433 0.7840 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.G2.A3IE.01 4 0.4328 0.5121 0.34 0.00 0.00 0.60 0.00 0.06 0.00
#> TCGA.UY.A8OD.01 3 0.2708 0.6280 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.DK.A1A3.01 4 0.4070 0.5276 0.34 0.00 0.00 0.62 0.00 0.04 0.00
#> TCGA.H4.A2HO.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 7 0.3459 0.3478 0.00 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.XF.A9SG.01 4 0.1886 0.7868 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.GC.A4ZW.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BT.A2LD.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JV.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DK.A1AC.01 4 0.4669 0.4049 0.40 0.00 0.00 0.52 0.00 0.08 0.00
#> TCGA.G2.A2ES.01 5 0.2654 0.8615 0.00 0.10 0.02 0.00 0.86 0.02 0.00
#> TCGA.HQ.A2OF.01 2 0.0000 0.9728 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GU.AATO.01 5 0.2376 0.8538 0.00 0.12 0.00 0.00 0.86 0.02 0.00
#> TCGA.C4.A0F1.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A8O7.01 7 0.0863 0.7101 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.DK.AA6Q.01 5 0.1886 0.8695 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.GV.A3QG.01 3 0.3386 0.5869 0.00 0.00 0.78 0.00 0.02 0.18 0.02
#> TCGA.K4.A54R.01 2 0.1363 0.9523 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.FD.A6TD.01 3 0.2422 0.6334 0.00 0.00 0.82 0.00 0.18 0.00 0.00
#> TCGA.2F.A9KT.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 7 0.6196 0.5658 0.00 0.00 0.12 0.26 0.00 0.12 0.50
#> TCGA.K4.A3WV.01 4 0.4175 0.6362 0.00 0.00 0.00 0.58 0.04 0.38 0.00
#> TCGA.BT.A20P.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DK.A3IT.01 7 0.3263 0.7307 0.00 0.00 0.08 0.12 0.00 0.00 0.80
#> TCGA.DK.AA6W.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3N5.01 2 0.1363 0.9523 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.BT.A20X.01 4 0.0504 0.7884 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.G2.AA3C.01 1 0.0000 0.9819 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.1166 0.6771 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.FJ.A3Z7.01 4 0.5438 0.4680 0.00 0.00 0.12 0.44 0.02 0.42 0.00
#> TCGA.GV.A3QI.01 2 0.0504 0.9704 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.4Z.AA82.01 7 0.1433 0.6994 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.GC.A6I1.01 3 0.2708 0.6280 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.FD.A5BX.01 4 0.3815 0.5056 0.36 0.00 0.00 0.62 0.00 0.02 0.00
#> TCGA.FD.A3B6.01 3 0.6057 0.2577 0.00 0.00 0.50 0.22 0.02 0.24 0.02
#> TCGA.BT.A20V.01 3 0.2832 0.6083 0.00 0.00 0.76 0.00 0.00 0.00 0.24
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.2F.A9KO.01 4 0.1563 0.6521 0.00 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.HQ.A5NE.01 4 0.3675 0.4942 0.04 0.00 0.00 0.66 0.00 0.30 0.00 0.00
#> TCGA.PQ.A6FI.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SL.01 5 0.1408 0.7936 0.00 0.00 0.02 0.00 0.94 0.02 0.00 0.02
#> TCGA.UY.A9PE.01 3 0.3193 0.1573 0.00 0.00 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.CU.A3YL.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA52.01 5 0.3992 0.0367 0.00 0.00 0.44 0.00 0.52 0.04 0.00 0.00
#> TCGA.E7.A541.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.FD.A6TI.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.XF.A9SZ.01 4 0.3630 0.5279 0.00 0.00 0.00 0.78 0.00 0.08 0.10 0.04
#> TCGA.C4.A0EZ.01 8 0.4125 0.0000 0.00 0.00 0.00 0.00 0.44 0.02 0.02 0.52
#> TCGA.FD.A3SJ.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA56.01 4 0.1563 0.6521 0.00 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.XF.AAMH.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3NA.01 1 0.0471 0.9422 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IK.01 4 0.2888 0.5872 0.00 0.00 0.00 0.80 0.00 0.16 0.00 0.04
#> TCGA.ZF.A9RF.01 3 0.3808 0.4419 0.00 0.00 0.62 0.00 0.00 0.34 0.04 0.00
#> TCGA.BT.A3PJ.01 3 0.3746 0.4719 0.00 0.00 0.64 0.00 0.00 0.32 0.04 0.00
#> TCGA.YC.A9TC.01 4 0.5564 0.0945 0.00 0.00 0.00 0.52 0.00 0.10 0.28 0.10
#> TCGA.ZF.A9R7.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DK.A1A7.01 7 0.5243 0.3556 0.00 0.00 0.02 0.00 0.02 0.24 0.58 0.14
#> TCGA.BT.A2LB.01 7 0.5046 0.5938 0.00 0.00 0.26 0.12 0.00 0.00 0.58 0.04
#> TCGA.GV.A3QF.01 3 0.2862 0.6386 0.00 0.00 0.82 0.00 0.08 0.10 0.00 0.00
#> TCGA.ZF.A9R9.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HB.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A97P.01 3 0.1947 0.6050 0.00 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.ZF.AA4V.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.CU.A5W6.01 4 0.2071 0.6305 0.00 0.00 0.00 0.90 0.00 0.02 0.04 0.04
#> TCGA.C4.A0F7.01 5 0.4407 -0.9339 0.00 0.00 0.00 0.00 0.48 0.04 0.02 0.46
#> TCGA.4Z.AA7Q.01 4 0.1563 0.6521 0.00 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.DK.AA6S.01 6 0.4756 0.4692 0.00 0.00 0.00 0.34 0.00 0.56 0.06 0.04
#> TCGA.XF.A8HD.01 5 0.1607 0.7828 0.00 0.00 0.04 0.00 0.92 0.04 0.00 0.00
#> TCGA.KQ.A41S.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 7 0.4467 0.6264 0.00 0.00 0.20 0.12 0.00 0.00 0.66 0.02
#> TCGA.BT.A0YX.01 4 0.3083 0.4383 0.00 0.00 0.00 0.66 0.00 0.34 0.00 0.00
#> TCGA.FD.A6TC.01 3 0.1947 0.5956 0.00 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.GC.A3I6.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SK.01 3 0.1765 0.6186 0.00 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.GU.AATP.01 4 0.3630 0.5194 0.00 0.00 0.00 0.78 0.00 0.10 0.04 0.08
#> TCGA.BT.A20T.01 7 0.3710 0.6199 0.00 0.00 0.12 0.00 0.02 0.00 0.76 0.10
#> TCGA.UY.A9PH.01 4 0.3337 0.5641 0.16 0.00 0.00 0.78 0.00 0.04 0.00 0.02
#> TCGA.UY.A78K.01 3 0.3594 0.5201 0.00 0.00 0.68 0.00 0.00 0.28 0.04 0.00
#> TCGA.BT.A20W.01 7 0.3710 0.6199 0.00 0.00 0.12 0.00 0.02 0.00 0.76 0.10
#> TCGA.E7.A7DV.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20R.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 3 0.3083 0.2594 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.ZF.A9RC.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6B2.01 4 0.0808 0.6596 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.DK.A6B6.01 5 0.2071 0.7497 0.00 0.00 0.04 0.00 0.90 0.04 0.00 0.02
#> TCGA.DK.AA6M.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DK.A3IN.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9T3.01 4 0.3329 0.1117 0.00 0.00 0.00 0.52 0.00 0.48 0.00 0.00
#> TCGA.CF.A47Y.01 4 0.2914 0.5968 0.00 0.00 0.00 0.84 0.00 0.04 0.04 0.08
#> TCGA.BL.A13J.01 2 0.1275 0.9499 0.00 0.94 0.00 0.00 0.04 0.02 0.00 0.00
#> TCGA.GD.A2C5.01 3 0.2818 0.6293 0.00 0.00 0.82 0.00 0.12 0.06 0.00 0.00
#> TCGA.XF.A9SP.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SR.01 3 0.4174 0.3432 0.00 0.00 0.62 0.00 0.32 0.04 0.00 0.02
#> TCGA.G2.A2EO.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.ZF.AA5N.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.DK.A6B0.01 4 0.4262 0.5391 0.12 0.00 0.00 0.74 0.00 0.04 0.02 0.08
#> TCGA.BT.A20N.01 5 0.2071 0.7497 0.00 0.00 0.04 0.00 0.90 0.04 0.00 0.02
#> TCGA.ZF.AA5H.01 3 0.3675 0.4991 0.00 0.00 0.66 0.00 0.00 0.30 0.04 0.00
#> TCGA.G2.A2EJ.01 7 0.4199 0.5372 0.00 0.00 0.32 0.08 0.00 0.00 0.60 0.00
#> TCGA.FD.A3SN.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EF.01 5 0.3293 0.4099 0.00 0.00 0.22 0.00 0.74 0.04 0.00 0.00
#> TCGA.GV.A3QK.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LT.A5Z6.01 2 0.0941 0.9630 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.FD.A5C1.01 3 0.3154 0.5947 0.00 0.00 0.78 0.00 0.16 0.06 0.00 0.00
#> TCGA.XF.A8HH.01 3 0.5716 0.0941 0.00 0.00 0.42 0.08 0.00 0.38 0.12 0.00
#> TCGA.LC.A66R.01 3 0.1091 0.6394 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.BT.A2LA.01 6 0.4862 0.6121 0.00 0.00 0.00 0.16 0.00 0.60 0.02 0.22
#> TCGA.ZF.AA54.01 4 0.1887 0.6313 0.00 0.00 0.00 0.90 0.00 0.00 0.06 0.04
#> TCGA.DK.AA6R.01 4 0.2020 0.6407 0.00 0.00 0.00 0.90 0.00 0.02 0.06 0.02
#> TCGA.FT.A3EE.01 3 0.2938 0.3630 0.00 0.00 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.ZF.AA4T.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2F.A9KW.01 1 0.4644 0.4545 0.64 0.00 0.00 0.24 0.00 0.06 0.00 0.06
#> TCGA.ZF.A9R1.01 3 0.3808 0.4419 0.00 0.00 0.62 0.00 0.00 0.34 0.04 0.00
#> TCGA.CF.A47S.01 7 0.3879 0.6185 0.00 0.00 0.10 0.02 0.00 0.00 0.74 0.14
#> TCGA.E7.A3X6.01 4 0.3537 0.5092 0.00 0.00 0.00 0.72 0.00 0.24 0.02 0.02
#> TCGA.FD.A6TG.01 3 0.2938 0.3592 0.00 0.00 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.CF.A47V.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4X.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BZ.01 4 0.3083 0.4383 0.00 0.00 0.00 0.66 0.00 0.34 0.00 0.00
#> TCGA.UY.A9PF.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A5.01 5 0.1741 0.7741 0.00 0.00 0.02 0.00 0.92 0.04 0.00 0.02
#> TCGA.UY.A78L.01 3 0.3808 0.4419 0.00 0.00 0.62 0.00 0.00 0.34 0.04 0.00
#> TCGA.FD.A6TA.01 7 0.4800 0.4908 0.00 0.00 0.36 0.06 0.00 0.00 0.54 0.04
#> TCGA.DK.A3X1.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A89H.01 7 0.6099 0.2819 0.00 0.00 0.14 0.14 0.00 0.28 0.44 0.00
#> TCGA.XF.AAMY.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA81.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.UY.A8OC.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.BT.A20Q.01 3 0.6184 0.3399 0.00 0.00 0.50 0.00 0.18 0.04 0.22 0.06
#> TCGA.FD.A3SS.01 2 0.1275 0.9499 0.00 0.94 0.00 0.00 0.04 0.02 0.00 0.00
#> TCGA.E7.A6ME.01 7 0.5879 0.3830 0.00 0.00 0.04 0.16 0.00 0.12 0.58 0.10
#> TCGA.G2.A2EK.01 4 0.3293 0.5323 0.22 0.00 0.00 0.74 0.00 0.04 0.00 0.00
#> TCGA.SY.A9G5.01 3 0.3154 0.5947 0.00 0.00 0.78 0.00 0.16 0.06 0.00 0.00
#> TCGA.ZF.A9RM.01 7 0.3169 0.5474 0.00 0.00 0.02 0.00 0.02 0.00 0.78 0.18
#> TCGA.FD.A5BR.01 7 0.4050 0.5131 0.00 0.00 0.34 0.06 0.00 0.00 0.60 0.00
#> TCGA.G2.A2EC.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.XF.A9T4.01 2 0.0808 0.9556 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.FD.A62S.01 4 0.3142 0.3993 0.00 0.00 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.DK.A6B5.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA51.01 3 0.3975 0.4239 0.00 0.00 0.66 0.00 0.26 0.08 0.00 0.00
#> TCGA.BT.A42B.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WW.01 7 0.3862 0.4815 0.00 0.00 0.36 0.04 0.00 0.00 0.60 0.00
#> TCGA.GV.A40E.01 4 0.3299 0.2754 0.00 0.00 0.00 0.56 0.00 0.44 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.2132 0.6317 0.00 0.00 0.88 0.00 0.00 0.04 0.08 0.00
#> TCGA.DK.A2I1.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.BL.A3JM.01 2 0.1275 0.9499 0.00 0.94 0.00 0.00 0.04 0.02 0.00 0.00
#> TCGA.XF.A9SU.01 4 0.0471 0.6601 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.GD.A76B.01 3 0.1091 0.6387 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.BT.A20J.01 7 0.6155 0.5521 0.00 0.00 0.24 0.16 0.00 0.06 0.50 0.04
#> TCGA.DK.AA71.01 2 0.0941 0.9597 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.GC.A3RC.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 3 0.3263 0.6169 0.00 0.00 0.78 0.00 0.12 0.10 0.00 0.00
#> TCGA.CF.A47W.01 4 0.4276 0.4947 0.18 0.00 0.00 0.70 0.00 0.04 0.00 0.08
#> TCGA.XF.AAN3.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.XF.AAN2.01 2 0.2114 0.7951 0.00 0.84 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.DK.A3IV.01 3 0.1275 0.6469 0.00 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.XF.A9SJ.01 5 0.1607 0.7828 0.00 0.00 0.04 0.00 0.92 0.04 0.00 0.00
#> TCGA.C4.A0F0.01 4 0.1563 0.6521 0.00 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.ZF.AA4R.01 5 0.1741 0.7741 0.00 0.00 0.02 0.00 0.92 0.04 0.00 0.02
#> TCGA.FD.A3SQ.01 3 0.3329 -0.1629 0.00 0.00 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.K4.AAQO.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I3.01 4 0.3329 0.1746 0.00 0.00 0.00 0.52 0.00 0.48 0.00 0.00
#> TCGA.XF.AAMT.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 7 0.3483 0.5576 0.00 0.00 0.04 0.00 0.02 0.00 0.76 0.18
#> TCGA.S5.A6DX.01 3 0.2650 0.4729 0.00 0.00 0.76 0.00 0.00 0.00 0.24 0.00
#> TCGA.ZF.A9R0.01 3 0.2648 0.6416 0.00 0.00 0.84 0.00 0.08 0.08 0.00 0.00
#> TCGA.BT.A0S7.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42E.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.GU.A42R.01 7 0.3170 0.4758 0.00 0.00 0.00 0.00 0.00 0.04 0.76 0.20
#> TCGA.FD.A3SM.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 3 0.2267 0.5566 0.00 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.CF.A1HR.01 7 0.5126 0.3564 0.00 0.00 0.10 0.34 0.00 0.00 0.52 0.04
#> TCGA.FD.A5BY.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QH.01 4 0.4022 0.5137 0.00 0.00 0.00 0.74 0.00 0.12 0.04 0.10
#> TCGA.BL.A5ZZ.01 4 0.4280 0.4873 0.00 0.00 0.00 0.72 0.00 0.12 0.06 0.10
#> TCGA.G2.A3IE.01 4 0.3337 0.5641 0.16 0.00 0.00 0.78 0.00 0.04 0.00 0.02
#> TCGA.UY.A8OD.01 3 0.1563 0.6212 0.00 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.DK.A1A3.01 4 0.3337 0.5641 0.16 0.00 0.00 0.78 0.00 0.04 0.00 0.02
#> TCGA.H4.A2HO.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 3 0.3237 0.0872 0.00 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.XF.A9SG.01 4 0.2756 0.5452 0.00 0.00 0.00 0.74 0.00 0.26 0.00 0.00
#> TCGA.GC.A4ZW.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A2LD.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3JV.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1AC.01 1 0.4680 -0.1092 0.48 0.00 0.00 0.40 0.00 0.12 0.00 0.00
#> TCGA.G2.A2ES.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.HQ.A2OF.01 2 0.0808 0.9604 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.GU.AATO.01 5 0.0808 0.8275 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.C4.A0F1.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A8O7.01 7 0.4371 0.6143 0.00 0.00 0.14 0.00 0.02 0.00 0.68 0.16
#> TCGA.DK.AA6Q.01 5 0.0941 0.8390 0.00 0.02 0.02 0.00 0.96 0.00 0.00 0.00
#> TCGA.GV.A3QG.01 3 0.3594 0.5216 0.00 0.00 0.68 0.00 0.00 0.28 0.04 0.00
#> TCGA.K4.A54R.01 2 0.0808 0.9556 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.FD.A6TD.01 3 0.3154 0.5947 0.00 0.00 0.78 0.00 0.16 0.06 0.00 0.00
#> TCGA.2F.A9KT.01 1 0.0471 0.9422 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 7 0.5955 0.4078 0.00 0.00 0.10 0.14 0.00 0.20 0.54 0.02
#> TCGA.K4.A3WV.01 6 0.5171 0.5474 0.00 0.00 0.00 0.24 0.00 0.54 0.02 0.20
#> TCGA.BT.A20P.01 2 0.0471 0.9686 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DK.A3IT.01 7 0.4504 0.6101 0.00 0.00 0.24 0.10 0.00 0.00 0.64 0.02
#> TCGA.DK.AA6W.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3N5.01 2 0.0471 0.9678 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BT.A20X.01 4 0.0941 0.6500 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.G2.AA3C.01 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 3 0.2862 0.6386 0.00 0.00 0.82 0.00 0.08 0.10 0.00 0.00
#> TCGA.FJ.A3Z7.01 6 0.4053 0.6022 0.00 0.00 0.00 0.18 0.00 0.72 0.06 0.04
#> TCGA.GV.A3QI.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA82.01 7 0.3169 0.5474 0.00 0.00 0.02 0.00 0.02 0.00 0.78 0.18
#> TCGA.GC.A6I1.01 3 0.0808 0.6436 0.00 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.FD.A5BX.01 4 0.2856 0.5533 0.20 0.00 0.00 0.78 0.00 0.02 0.00 0.00
#> TCGA.FD.A3B6.01 6 0.5401 0.1774 0.00 0.00 0.34 0.14 0.00 0.48 0.04 0.00
#> TCGA.BT.A20V.01 3 0.1563 0.6222 0.00 0.00 0.90 0.00 0.00 0.00 0.10 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-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 50 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 0.968 0.988 0.5091 0.491 0.491
#> 3 3 1.000 0.982 0.992 0.2864 0.769 0.567
#> 4 4 0.759 0.717 0.862 0.1130 0.948 0.853
#> 5 5 0.725 0.662 0.792 0.0720 0.873 0.604
#> 6 6 0.722 0.598 0.730 0.0327 0.924 0.676
#> 7 7 0.729 0.535 0.736 0.0414 0.949 0.758
#> 8 8 0.754 0.486 0.693 0.0171 0.932 0.656
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.FD.A3SL.01 2 0.000 0.983 0.00 1.00
#> TCGA.CU.A3YL.01 2 0.000 0.983 0.00 1.00
#> TCGA.E7.A541.01 1 0.000 0.990 1.00 0.00
#> TCGA.FD.A6TI.01 1 0.000 0.990 1.00 0.00
#> TCGA.C4.A0EZ.01 2 0.000 0.983 0.00 1.00
#> TCGA.ZF.A9R7.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZF.A9R9.01 1 0.000 0.990 1.00 0.00
#> TCGA.XF.A8HB.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZF.AA4V.01 1 0.000 0.990 1.00 0.00
#> TCGA.C4.A0F7.01 2 0.000 0.983 0.00 1.00
#> TCGA.XF.A8HD.01 2 0.000 0.983 0.00 1.00
#> TCGA.KQ.A41S.01 2 0.000 0.983 0.00 1.00
#> TCGA.GC.A3I6.01 1 0.000 0.990 1.00 0.00
#> TCGA.DK.AA6M.01 1 0.000 0.990 1.00 0.00
#> TCGA.BL.A13J.01 2 0.000 0.983 0.00 1.00
#> TCGA.G2.A2EO.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZF.AA5N.01 1 0.000 0.990 1.00 0.00
#> TCGA.BT.A20N.01 2 0.000 0.983 0.00 1.00
#> TCGA.FD.A3SN.01 1 0.000 0.990 1.00 0.00
#> TCGA.GV.A3QK.01 1 0.000 0.990 1.00 0.00
#> TCGA.LT.A5Z6.01 2 0.000 0.983 0.00 1.00
#> TCGA.CF.A47V.01 2 0.000 0.983 0.00 1.00
#> TCGA.ZF.AA4X.01 2 0.000 0.983 0.00 1.00
#> TCGA.DK.A1A5.01 1 0.000 0.990 1.00 0.00
#> TCGA.4Z.AA81.01 1 0.000 0.990 1.00 0.00
#> TCGA.UY.A8OC.01 1 0.000 0.990 1.00 0.00
#> TCGA.FD.A3SS.01 2 0.000 0.983 0.00 1.00
#> TCGA.G2.A2EC.01 2 0.958 0.372 0.38 0.62
#> TCGA.XF.A9T4.01 1 0.000 0.990 1.00 0.00
#> TCGA.BT.A42B.01 1 0.000 0.990 1.00 0.00
#> TCGA.DK.A2HX.01 2 0.000 0.983 0.00 1.00
#> TCGA.BL.A3JM.01 2 0.000 0.983 0.00 1.00
#> TCGA.DK.AA71.01 2 0.000 0.983 0.00 1.00
#> TCGA.GC.A3RC.01 1 0.000 0.990 1.00 0.00
#> TCGA.XF.AAN3.01 1 0.000 0.990 1.00 0.00
#> TCGA.XF.AAN2.01 2 0.000 0.983 0.00 1.00
#> TCGA.XF.A9SJ.01 2 0.000 0.983 0.00 1.00
#> TCGA.ZF.AA4R.01 2 0.000 0.983 0.00 1.00
#> TCGA.BT.A42E.01 1 0.000 0.990 1.00 0.00
#> TCGA.FD.A5BY.01 1 0.000 0.990 1.00 0.00
#> TCGA.GC.A4ZW.01 2 0.000 0.983 0.00 1.00
#> TCGA.GV.A3JV.01 1 0.000 0.990 1.00 0.00
#> TCGA.G2.A2ES.01 1 0.000 0.990 1.00 0.00
#> TCGA.HQ.A2OF.01 2 0.000 0.983 0.00 1.00
#> TCGA.GU.AATO.01 2 0.000 0.983 0.00 1.00
#> TCGA.DK.AA6Q.01 1 0.000 0.990 1.00 0.00
#> TCGA.K4.A54R.01 1 0.795 0.674 0.76 0.24
#> TCGA.BT.A20P.01 2 0.000 0.983 0.00 1.00
#> TCGA.FD.A3N5.01 1 0.000 0.990 1.00 0.00
#> TCGA.GV.A3QI.01 2 0.000 0.983 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FD.A3SL.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.CU.A3YL.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.E7.A541.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FD.A6TI.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.C4.A0EZ.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.ZF.A9R7.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.ZF.A9R9.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.XF.A8HB.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.ZF.AA4V.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.C4.A0F7.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.XF.A8HD.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.KQ.A41S.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.GC.A3I6.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DK.AA6M.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.BL.A13J.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.G2.A2EO.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.ZF.AA5N.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BT.A20N.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.FD.A3SN.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.GV.A3QK.01 2 0.207 0.921 0.06 0.94 0.00
#> TCGA.LT.A5Z6.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.CF.A47V.01 2 0.369 0.835 0.00 0.86 0.14
#> TCGA.ZF.AA4X.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.DK.A1A5.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.4Z.AA81.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.UY.A8OC.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FD.A3SS.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.G2.A2EC.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.XF.A9T4.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BT.A42B.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DK.A2HX.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.BL.A3JM.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.DK.AA71.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.GC.A3RC.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.XF.AAN3.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.XF.AAN2.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.XF.A9SJ.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.ZF.AA4R.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.BT.A42E.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FD.A5BY.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.GC.A4ZW.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.GV.A3JV.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.G2.A2ES.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.HQ.A2OF.01 3 0.455 0.744 0.00 0.20 0.80
#> TCGA.GU.AATO.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.DK.AA6Q.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.K4.A54R.01 2 0.000 0.986 0.00 1.00 0.00
#> TCGA.BT.A20P.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.FD.A3N5.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.GV.A3QI.01 3 0.000 0.979 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.FD.A3SL.01 2 0.1913 0.847 0.00 0.94 0.04 0.02
#> TCGA.CU.A3YL.01 2 0.4907 0.283 0.00 0.58 0.42 0.00
#> TCGA.E7.A541.01 1 0.4332 0.729 0.80 0.04 0.00 0.16
#> TCGA.FD.A6TI.01 1 0.4855 0.490 0.60 0.00 0.00 0.40
#> TCGA.C4.A0EZ.01 3 0.4907 0.809 0.00 0.00 0.58 0.42
#> TCGA.ZF.A9R7.01 1 0.2345 0.811 0.90 0.00 0.00 0.10
#> TCGA.ZF.A9R9.01 1 0.4713 0.501 0.64 0.00 0.00 0.36
#> TCGA.XF.A8HB.01 1 0.4713 0.501 0.64 0.00 0.00 0.36
#> TCGA.ZF.AA4V.01 1 0.3853 0.750 0.82 0.02 0.00 0.16
#> TCGA.C4.A0F7.01 3 0.4977 0.830 0.00 0.00 0.54 0.46
#> TCGA.XF.A8HD.01 2 0.0707 0.851 0.00 0.98 0.00 0.02
#> TCGA.KQ.A41S.01 2 0.1913 0.847 0.00 0.94 0.04 0.02
#> TCGA.GC.A3I6.01 1 0.3853 0.750 0.82 0.02 0.00 0.16
#> TCGA.DK.AA6M.01 2 0.5383 0.551 0.10 0.74 0.00 0.16
#> TCGA.BL.A13J.01 2 0.1211 0.850 0.00 0.96 0.04 0.00
#> TCGA.G2.A2EO.01 2 0.2921 0.733 0.00 0.86 0.00 0.14
#> TCGA.ZF.AA5N.01 1 0.2345 0.811 0.90 0.00 0.00 0.10
#> TCGA.BT.A20N.01 2 0.0000 0.854 0.00 1.00 0.00 0.00
#> TCGA.FD.A3SN.01 1 0.2011 0.813 0.92 0.00 0.00 0.08
#> TCGA.GV.A3QK.01 4 0.7499 0.668 0.00 0.18 0.40 0.42
#> TCGA.LT.A5Z6.01 3 0.4977 0.828 0.00 0.00 0.54 0.46
#> TCGA.CF.A47V.01 3 0.5570 -0.421 0.00 0.44 0.54 0.02
#> TCGA.ZF.AA4X.01 2 0.1211 0.845 0.00 0.96 0.04 0.00
#> TCGA.DK.A1A5.01 1 0.2921 0.772 0.86 0.00 0.00 0.14
#> TCGA.4Z.AA81.01 1 0.2345 0.811 0.90 0.00 0.00 0.10
#> TCGA.UY.A8OC.01 1 0.2345 0.811 0.90 0.00 0.00 0.10
#> TCGA.FD.A3SS.01 2 0.1411 0.851 0.00 0.96 0.02 0.02
#> TCGA.G2.A2EC.01 2 0.4855 0.280 0.00 0.60 0.40 0.00
#> TCGA.XF.A9T4.01 1 0.2345 0.811 0.90 0.00 0.00 0.10
#> TCGA.BT.A42B.01 1 0.2345 0.811 0.90 0.00 0.00 0.10
#> TCGA.DK.A2HX.01 3 0.4977 0.828 0.00 0.00 0.54 0.46
#> TCGA.BL.A3JM.01 2 0.2011 0.836 0.00 0.92 0.08 0.00
#> TCGA.DK.AA71.01 3 0.4977 0.830 0.00 0.00 0.54 0.46
#> TCGA.GC.A3RC.01 1 0.2647 0.782 0.88 0.00 0.00 0.12
#> TCGA.XF.AAN3.01 1 0.0707 0.810 0.98 0.00 0.00 0.02
#> TCGA.XF.AAN2.01 2 0.1411 0.853 0.00 0.96 0.02 0.02
#> TCGA.XF.A9SJ.01 2 0.0707 0.851 0.00 0.98 0.00 0.02
#> TCGA.ZF.AA4R.01 3 0.4977 0.828 0.00 0.00 0.54 0.46
#> TCGA.BT.A42E.01 1 0.3853 0.750 0.82 0.02 0.00 0.16
#> TCGA.FD.A5BY.01 1 0.2345 0.811 0.90 0.00 0.00 0.10
#> TCGA.GC.A4ZW.01 3 0.4977 0.830 0.00 0.00 0.54 0.46
#> TCGA.GV.A3JV.01 4 0.7593 0.696 0.12 0.02 0.38 0.48
#> TCGA.G2.A2ES.01 1 0.3853 0.750 0.82 0.02 0.00 0.16
#> TCGA.HQ.A2OF.01 3 0.3400 -0.205 0.00 0.18 0.82 0.00
#> TCGA.GU.AATO.01 3 0.4977 0.828 0.00 0.00 0.54 0.46
#> TCGA.DK.AA6Q.01 1 0.1637 0.804 0.94 0.00 0.00 0.06
#> TCGA.K4.A54R.01 2 0.1211 0.840 0.00 0.96 0.00 0.04
#> TCGA.BT.A20P.01 3 0.4977 0.830 0.00 0.00 0.54 0.46
#> TCGA.FD.A3N5.01 1 0.0707 0.808 0.98 0.00 0.00 0.02
#> TCGA.GV.A3QI.01 3 0.4977 0.830 0.00 0.00 0.54 0.46
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FD.A3SL.01 2 0.5355 0.564 0.00 0.66 0.22 0.12 0.00
#> TCGA.CU.A3YL.01 4 0.3690 0.693 0.00 0.20 0.02 0.78 0.00
#> TCGA.E7.A541.01 5 0.4767 0.930 0.42 0.02 0.00 0.00 0.56
#> TCGA.FD.A6TI.01 1 0.5444 0.473 0.66 0.00 0.00 0.16 0.18
#> TCGA.C4.A0EZ.01 3 0.2249 0.800 0.00 0.02 0.92 0.02 0.04
#> TCGA.ZF.A9R7.01 1 0.0000 0.695 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R9.01 1 0.5273 0.485 0.68 0.00 0.00 0.16 0.16
#> TCGA.XF.A8HB.01 1 0.5273 0.487 0.68 0.00 0.00 0.16 0.16
#> TCGA.ZF.AA4V.01 5 0.4262 0.960 0.44 0.00 0.00 0.00 0.56
#> TCGA.C4.A0F7.01 3 0.3690 0.837 0.00 0.00 0.78 0.02 0.20
#> TCGA.XF.A8HD.01 2 0.0000 0.788 0.00 1.00 0.00 0.00 0.00
#> TCGA.KQ.A41S.01 2 0.5355 0.564 0.00 0.66 0.22 0.12 0.00
#> TCGA.GC.A3I6.01 5 0.4818 0.927 0.46 0.00 0.00 0.02 0.52
#> TCGA.DK.AA6M.01 2 0.4307 0.200 0.00 0.50 0.00 0.00 0.50
#> TCGA.BL.A13J.01 2 0.0000 0.788 0.00 1.00 0.00 0.00 0.00
#> TCGA.G2.A2EO.01 2 0.2929 0.665 0.00 0.82 0.00 0.00 0.18
#> TCGA.ZF.AA5N.01 1 0.0609 0.682 0.98 0.00 0.00 0.00 0.02
#> TCGA.BT.A20N.01 2 0.0000 0.788 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A3SN.01 1 0.0609 0.682 0.98 0.00 0.00 0.00 0.02
#> TCGA.GV.A3QK.01 4 0.4096 0.689 0.00 0.04 0.00 0.76 0.20
#> TCGA.LT.A5Z6.01 3 0.1043 0.823 0.00 0.04 0.96 0.00 0.00
#> TCGA.CF.A47V.01 4 0.4290 0.726 0.00 0.12 0.04 0.80 0.04
#> TCGA.ZF.AA4X.01 2 0.4360 0.460 0.00 0.68 0.00 0.30 0.02
#> TCGA.DK.A1A5.01 5 0.4302 0.913 0.48 0.00 0.00 0.00 0.52
#> TCGA.4Z.AA81.01 1 0.0000 0.695 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OC.01 1 0.0000 0.695 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SS.01 2 0.3274 0.659 0.00 0.78 0.22 0.00 0.00
#> TCGA.G2.A2EC.01 4 0.4252 0.605 0.00 0.28 0.00 0.70 0.02
#> TCGA.XF.A9T4.01 1 0.0000 0.695 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42B.01 1 0.0000 0.695 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 3 0.2020 0.771 0.00 0.10 0.90 0.00 0.00
#> TCGA.BL.A3JM.01 2 0.2249 0.757 0.00 0.92 0.02 0.02 0.04
#> TCGA.DK.AA71.01 3 0.3690 0.837 0.00 0.00 0.78 0.02 0.20
#> TCGA.GC.A3RC.01 5 0.4287 0.942 0.46 0.00 0.00 0.00 0.54
#> TCGA.XF.AAN3.01 1 0.3796 -0.214 0.70 0.00 0.00 0.00 0.30
#> TCGA.XF.AAN2.01 2 0.0000 0.788 0.00 1.00 0.00 0.00 0.00
#> TCGA.XF.A9SJ.01 2 0.0000 0.788 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 3 0.1043 0.823 0.00 0.04 0.96 0.00 0.00
#> TCGA.BT.A42E.01 5 0.4262 0.960 0.44 0.00 0.00 0.00 0.56
#> TCGA.FD.A5BY.01 1 0.0609 0.685 0.98 0.00 0.00 0.02 0.00
#> TCGA.GC.A4ZW.01 3 0.3690 0.837 0.00 0.00 0.78 0.02 0.20
#> TCGA.GV.A3JV.01 4 0.4433 0.659 0.06 0.00 0.00 0.74 0.20
#> TCGA.G2.A2ES.01 5 0.4262 0.960 0.44 0.00 0.00 0.00 0.56
#> TCGA.HQ.A2OF.01 4 0.4948 0.636 0.00 0.02 0.16 0.74 0.08
#> TCGA.GU.AATO.01 3 0.1043 0.823 0.00 0.04 0.96 0.00 0.00
#> TCGA.DK.AA6Q.01 1 0.3983 -0.379 0.66 0.00 0.00 0.00 0.34
#> TCGA.K4.A54R.01 2 0.1410 0.759 0.00 0.94 0.00 0.00 0.06
#> TCGA.BT.A20P.01 3 0.3690 0.837 0.00 0.00 0.78 0.02 0.20
#> TCGA.FD.A3N5.01 1 0.4227 -0.682 0.58 0.00 0.00 0.00 0.42
#> TCGA.GV.A3QI.01 3 0.3690 0.837 0.00 0.00 0.78 0.02 0.20
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FD.A3SL.01 2 0.6480 0.3255 0.00 0.48 0.06 0.14 0.00 0.32
#> TCGA.CU.A3YL.01 4 0.3795 0.6227 0.00 0.06 0.12 0.80 0.00 0.02
#> TCGA.E7.A541.01 5 0.0937 0.7091 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.FD.A6TI.01 1 0.3746 0.4482 0.78 0.00 0.00 0.08 0.14 0.00
#> TCGA.C4.A0EZ.01 6 0.3007 0.6706 0.04 0.02 0.08 0.00 0.00 0.86
#> TCGA.ZF.A9R7.01 1 0.5555 0.7454 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.ZF.A9R9.01 1 0.3544 0.4373 0.80 0.00 0.00 0.08 0.12 0.00
#> TCGA.XF.A8HB.01 1 0.4667 0.3991 0.74 0.00 0.10 0.04 0.12 0.00
#> TCGA.ZF.AA4V.01 5 0.2048 0.7077 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.C4.A0F7.01 6 0.3499 0.7303 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.XF.A8HD.01 2 0.0000 0.7462 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41S.01 2 0.6480 0.3255 0.00 0.48 0.06 0.14 0.00 0.32
#> TCGA.GC.A3I6.01 5 0.1814 0.7090 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.DK.AA6M.01 5 0.5366 -0.1934 0.00 0.46 0.02 0.06 0.46 0.00
#> TCGA.BL.A13J.01 2 0.0000 0.7462 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EO.01 2 0.5840 0.2865 0.00 0.56 0.02 0.16 0.26 0.00
#> TCGA.ZF.AA5N.01 1 0.5555 0.7454 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.BT.A20N.01 2 0.0547 0.7409 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.FD.A3SN.01 1 0.5575 0.7140 0.46 0.00 0.14 0.00 0.40 0.00
#> TCGA.GV.A3QK.01 4 0.3647 0.5659 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.LT.A5Z6.01 6 0.1556 0.7027 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.CF.A47V.01 4 0.3688 0.6251 0.00 0.04 0.14 0.80 0.00 0.02
#> TCGA.ZF.AA4X.01 4 0.4246 0.2151 0.00 0.40 0.02 0.58 0.00 0.00
#> TCGA.DK.A1A5.01 5 0.0547 0.7239 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.4Z.AA81.01 1 0.5555 0.7454 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.UY.A8OC.01 1 0.5555 0.7454 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.FD.A3SS.01 2 0.3309 0.5543 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.G2.A2EC.01 4 0.3309 0.4679 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.XF.A9T4.01 1 0.5555 0.7454 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.BT.A42B.01 1 0.5555 0.7454 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.DK.A2HX.01 6 0.3076 0.4882 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.BL.A3JM.01 2 0.2474 0.6802 0.04 0.88 0.08 0.00 0.00 0.00
#> TCGA.DK.AA71.01 6 0.3578 0.7258 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.GC.A3RC.01 5 0.1480 0.7116 0.02 0.00 0.04 0.00 0.94 0.00
#> TCGA.XF.AAN3.01 5 0.4810 0.0704 0.22 0.00 0.12 0.00 0.66 0.00
#> TCGA.XF.AAN2.01 2 0.0000 0.7462 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SJ.01 2 0.0000 0.7462 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 6 0.1556 0.7027 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.BT.A42E.01 5 0.0547 0.7275 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.FD.A5BY.01 1 0.5432 0.7225 0.48 0.00 0.12 0.00 0.40 0.00
#> TCGA.GC.A4ZW.01 6 0.3499 0.7303 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.GV.A3JV.01 4 0.3647 0.5659 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.G2.A2ES.01 5 0.0547 0.7281 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.HQ.A2OF.01 4 0.6029 0.5006 0.10 0.00 0.28 0.56 0.00 0.06
#> TCGA.GU.AATO.01 6 0.1556 0.7027 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.DK.AA6Q.01 5 0.4536 0.2698 0.18 0.00 0.12 0.00 0.70 0.00
#> TCGA.K4.A54R.01 2 0.2581 0.6288 0.00 0.86 0.00 0.12 0.02 0.00
#> TCGA.BT.A20P.01 6 0.3578 0.7258 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.FD.A3N5.01 5 0.3351 0.5402 0.04 0.00 0.16 0.00 0.80 0.00
#> TCGA.GV.A3QI.01 6 0.3578 0.7258 0.00 0.00 0.34 0.00 0.00 0.66
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FD.A3SL.01 6 0.7012 -0.1600 0.00 0.36 0.16 0.04 0.02 0.38 0.04
#> TCGA.CU.A3YL.01 3 0.4211 0.1818 0.00 0.04 0.68 0.00 0.02 0.00 0.26
#> TCGA.E7.A541.01 5 0.3546 0.7235 0.08 0.02 0.00 0.02 0.82 0.00 0.06
#> TCGA.FD.A6TI.01 1 0.4870 0.5302 0.58 0.00 0.14 0.28 0.00 0.00 0.00
#> TCGA.C4.A0EZ.01 6 0.4609 0.4136 0.00 0.02 0.00 0.06 0.02 0.70 0.20
#> TCGA.ZF.A9R7.01 1 0.0504 0.7958 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.ZF.A9R9.01 1 0.5317 0.5060 0.56 0.00 0.14 0.28 0.02 0.00 0.00
#> TCGA.XF.A8HB.01 1 0.6315 0.3887 0.48 0.00 0.12 0.32 0.04 0.00 0.04
#> TCGA.ZF.AA4V.01 5 0.3833 0.7575 0.12 0.00 0.00 0.04 0.78 0.00 0.06
#> TCGA.C4.A0F7.01 6 0.3459 0.5426 0.00 0.00 0.00 0.40 0.00 0.60 0.00
#> TCGA.XF.A8HD.01 2 0.0000 0.7328 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41S.01 6 0.6511 -0.1311 0.00 0.38 0.14 0.04 0.00 0.40 0.04
#> TCGA.GC.A3I6.01 5 0.3630 0.7070 0.10 0.00 0.00 0.06 0.80 0.00 0.04
#> TCGA.DK.AA6M.01 2 0.6433 0.3390 0.00 0.46 0.06 0.04 0.34 0.00 0.10
#> TCGA.BL.A13J.01 2 0.1363 0.7269 0.00 0.94 0.04 0.00 0.02 0.00 0.00
#> TCGA.G2.A2EO.01 2 0.7040 0.3710 0.00 0.46 0.18 0.06 0.22 0.00 0.08
#> TCGA.ZF.AA5N.01 1 0.1860 0.7519 0.92 0.00 0.00 0.02 0.04 0.00 0.02
#> TCGA.BT.A20N.01 2 0.2278 0.7061 0.00 0.88 0.08 0.04 0.00 0.00 0.00
#> TCGA.FD.A3SN.01 1 0.1860 0.7519 0.92 0.00 0.00 0.02 0.04 0.00 0.02
#> TCGA.GV.A3QK.01 3 0.2832 0.3801 0.00 0.00 0.76 0.24 0.00 0.00 0.00
#> TCGA.LT.A5Z6.01 6 0.1166 0.5470 0.00 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.CF.A47V.01 3 0.3927 0.0879 0.00 0.00 0.66 0.04 0.00 0.00 0.30
#> TCGA.ZF.AA4X.01 3 0.5411 0.1866 0.00 0.30 0.58 0.06 0.04 0.00 0.02
#> TCGA.DK.A1A5.01 5 0.3680 0.7679 0.14 0.00 0.00 0.02 0.78 0.00 0.06
#> TCGA.4Z.AA81.01 1 0.0504 0.7886 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.UY.A8OC.01 1 0.0000 0.7959 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SS.01 2 0.3047 0.4514 0.00 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.G2.A2EC.01 3 0.3208 0.3770 0.00 0.12 0.82 0.00 0.04 0.00 0.02
#> TCGA.XF.A9T4.01 1 0.0000 0.7959 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A42B.01 1 0.0504 0.7958 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 6 0.2572 0.4484 0.00 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.BL.A3JM.01 2 0.3863 0.5463 0.00 0.74 0.00 0.02 0.04 0.00 0.20
#> TCGA.DK.AA71.01 6 0.3867 0.5403 0.00 0.00 0.00 0.38 0.00 0.60 0.02
#> TCGA.GC.A3RC.01 5 0.4969 0.7275 0.20 0.00 0.00 0.06 0.66 0.00 0.08
#> TCGA.XF.AAN3.01 5 0.3994 0.4299 0.48 0.00 0.00 0.02 0.50 0.00 0.00
#> TCGA.XF.AAN2.01 2 0.0000 0.7328 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.A9SJ.01 2 0.0000 0.7328 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 6 0.2016 0.5532 0.00 0.06 0.00 0.04 0.00 0.90 0.00
#> TCGA.BT.A42E.01 5 0.3055 0.7772 0.14 0.00 0.00 0.02 0.82 0.00 0.02
#> TCGA.FD.A5BY.01 1 0.1664 0.7551 0.92 0.00 0.00 0.02 0.06 0.00 0.00
#> TCGA.GC.A4ZW.01 6 0.3459 0.5426 0.00 0.00 0.00 0.40 0.00 0.60 0.00
#> TCGA.GV.A3JV.01 3 0.2945 0.3674 0.00 0.00 0.74 0.26 0.00 0.00 0.00
#> TCGA.G2.A2ES.01 5 0.2912 0.7738 0.14 0.00 0.00 0.04 0.82 0.00 0.00
#> TCGA.HQ.A2OF.01 7 0.3186 0.0000 0.00 0.00 0.22 0.00 0.00 0.02 0.76
#> TCGA.GU.AATO.01 6 0.1166 0.5470 0.00 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.DK.AA6Q.01 5 0.3968 0.5045 0.44 0.00 0.00 0.02 0.54 0.00 0.00
#> TCGA.K4.A54R.01 2 0.5394 0.5801 0.00 0.68 0.12 0.04 0.08 0.00 0.08
#> TCGA.BT.A20P.01 6 0.3867 0.5403 0.00 0.00 0.00 0.38 0.00 0.60 0.02
#> TCGA.FD.A3N5.01 5 0.5429 0.5176 0.40 0.00 0.00 0.06 0.48 0.00 0.06
#> TCGA.GV.A3QI.01 6 0.3867 0.5403 0.00 0.00 0.00 0.38 0.00 0.60 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.FD.A3SL.01 6 0.3594 0.3963 0.00 0.28 0.00 0.04 0.00 0.68 0.00 0.00
#> TCGA.CU.A3YL.01 3 0.5448 -0.5267 0.00 0.00 0.44 0.04 0.00 0.14 0.38 0.00
#> TCGA.E7.A541.01 5 0.3941 0.6197 0.04 0.02 0.00 0.14 0.76 0.04 0.00 0.00
#> TCGA.FD.A6TI.01 1 0.4004 -0.4362 0.50 0.00 0.46 0.04 0.00 0.00 0.00 0.00
#> TCGA.C4.A0EZ.01 6 0.5575 0.4592 0.00 0.00 0.00 0.20 0.00 0.48 0.04 0.28
#> TCGA.ZF.A9R7.01 1 0.0808 0.7471 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R9.01 3 0.4407 -0.6242 0.46 0.00 0.46 0.08 0.00 0.00 0.00 0.00
#> TCGA.XF.A8HB.01 4 0.5116 0.0000 0.26 0.00 0.28 0.46 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4V.01 5 0.4827 0.6094 0.06 0.00 0.00 0.12 0.70 0.08 0.04 0.00
#> TCGA.C4.A0F7.01 8 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.XF.A8HD.01 2 0.0000 0.7180 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KQ.A41S.01 6 0.2756 0.4589 0.00 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.GC.A3I6.01 5 0.3670 0.6274 0.06 0.00 0.00 0.06 0.80 0.06 0.02 0.00
#> TCGA.DK.AA6M.01 2 0.5618 0.3784 0.00 0.50 0.00 0.10 0.30 0.10 0.00 0.00
#> TCGA.BL.A13J.01 2 0.1741 0.7108 0.00 0.92 0.00 0.00 0.02 0.04 0.02 0.00
#> TCGA.G2.A2EO.01 2 0.6340 0.4035 0.00 0.50 0.06 0.10 0.24 0.10 0.00 0.00
#> TCGA.ZF.AA5N.01 1 0.0941 0.7615 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.BT.A20N.01 2 0.1557 0.7058 0.00 0.92 0.00 0.02 0.00 0.06 0.00 0.00
#> TCGA.FD.A3SN.01 1 0.0941 0.7615 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.GV.A3QK.01 3 0.0000 0.2533 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LT.A5Z6.01 6 0.3690 0.6083 0.00 0.02 0.00 0.00 0.00 0.56 0.00 0.42
#> TCGA.CF.A47V.01 7 0.5839 0.1515 0.00 0.00 0.38 0.04 0.02 0.14 0.42 0.00
#> TCGA.ZF.AA4X.01 3 0.6103 0.0717 0.00 0.26 0.40 0.08 0.00 0.26 0.00 0.00
#> TCGA.DK.A1A5.01 5 0.4593 0.5771 0.26 0.00 0.00 0.10 0.62 0.02 0.00 0.00
#> TCGA.4Z.AA81.01 1 0.0471 0.7669 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.UY.A8OC.01 1 0.0000 0.7662 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3SS.01 2 0.3729 -0.2376 0.00 0.52 0.00 0.00 0.00 0.46 0.02 0.00
#> TCGA.G2.A2EC.01 3 0.5584 0.0961 0.00 0.16 0.54 0.08 0.00 0.22 0.00 0.00
#> TCGA.XF.A9T4.01 1 0.0471 0.7669 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BT.A42B.01 1 0.0808 0.7471 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.DK.A2HX.01 6 0.4730 0.6399 0.00 0.18 0.00 0.00 0.00 0.56 0.00 0.26
#> TCGA.BL.A3JM.01 2 0.5046 0.5333 0.00 0.66 0.00 0.18 0.04 0.06 0.06 0.00
#> TCGA.DK.AA71.01 8 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.GC.A3RC.01 5 0.5882 0.5244 0.26 0.00 0.00 0.14 0.52 0.04 0.04 0.00
#> TCGA.XF.AAN3.01 5 0.3737 0.1894 0.48 0.00 0.00 0.00 0.50 0.02 0.00 0.00
#> TCGA.XF.AAN2.01 2 0.0941 0.7096 0.00 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.XF.A9SJ.01 2 0.0000 0.7180 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4R.01 6 0.3690 0.6083 0.00 0.02 0.00 0.00 0.00 0.56 0.00 0.42
#> TCGA.BT.A42E.01 5 0.3763 0.6708 0.08 0.00 0.00 0.10 0.78 0.02 0.02 0.00
#> TCGA.FD.A5BY.01 1 0.2591 0.6451 0.86 0.00 0.00 0.04 0.08 0.02 0.00 0.00
#> TCGA.GC.A4ZW.01 8 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.GV.A3JV.01 3 0.0000 0.2533 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2ES.01 5 0.1341 0.6765 0.08 0.00 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.HQ.A2OF.01 7 0.1557 0.3780 0.00 0.00 0.02 0.00 0.00 0.06 0.92 0.00
#> TCGA.GU.AATO.01 6 0.3690 0.6083 0.00 0.02 0.00 0.00 0.00 0.56 0.00 0.42
#> TCGA.DK.AA6Q.01 5 0.4077 0.3641 0.40 0.00 0.00 0.00 0.56 0.02 0.02 0.00
#> TCGA.K4.A54R.01 2 0.4604 0.5923 0.00 0.72 0.04 0.06 0.06 0.12 0.00 0.00
#> TCGA.BT.A20P.01 8 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FD.A3N5.01 1 0.5866 -0.1631 0.50 0.00 0.00 0.12 0.30 0.04 0.04 0.00
#> TCGA.GV.A3QI.01 8 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111 , Node0112 , Node0113-leaf , Node0121 , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132 , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222 , Node0231 , Node0232-leaf , Node0233-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf , Node0331 , Node0332 , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["033"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 66 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 0.992 0.997 0.4799 0.522 0.522
#> 3 3 1.000 0.986 0.994 0.3161 0.821 0.666
#> 4 4 0.929 0.893 0.950 0.1242 0.896 0.727
#> 5 5 0.736 0.770 0.877 0.0998 0.878 0.607
#> 6 6 0.696 0.576 0.788 0.0342 0.924 0.681
#> 7 7 0.689 0.556 0.739 0.0110 0.897 0.586
#> 8 8 0.680 0.545 0.748 0.0200 0.918 0.639
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.UY.A9PE.01 2 0.00 0.994 0.00 1.00
#> TCGA.ZF.AA52.01 2 0.00 0.994 0.00 1.00
#> TCGA.ZF.A9RF.01 1 0.00 1.000 1.00 0.00
#> TCGA.BT.A3PJ.01 1 0.00 1.000 1.00 0.00
#> TCGA.YC.A9TC.01 1 0.00 1.000 1.00 0.00
#> TCGA.DK.A1A7.01 2 0.00 0.994 0.00 1.00
#> TCGA.BT.A2LB.01 2 0.00 0.994 0.00 1.00
#> TCGA.GV.A3QF.01 2 0.00 0.994 0.00 1.00
#> TCGA.E7.A97P.01 1 0.00 1.000 1.00 0.00
#> TCGA.DK.AA6S.01 2 0.76 0.718 0.22 0.78
#> TCGA.XF.AAMW.01 1 0.00 1.000 1.00 0.00
#> TCGA.FD.A6TC.01 2 0.00 0.994 0.00 1.00
#> TCGA.XF.A9SK.01 2 0.00 0.994 0.00 1.00
#> TCGA.BT.A20T.01 2 0.00 0.994 0.00 1.00
#> TCGA.UY.A78K.01 2 0.00 0.994 0.00 1.00
#> TCGA.BT.A20W.01 2 0.00 0.994 0.00 1.00
#> TCGA.E7.A6MD.01 2 0.00 0.994 0.00 1.00
#> TCGA.DK.A6B6.01 2 0.00 0.994 0.00 1.00
#> TCGA.GD.A2C5.01 2 0.00 0.994 0.00 1.00
#> TCGA.FD.A3SR.01 2 0.00 0.994 0.00 1.00
#> TCGA.ZF.AA5H.01 1 0.00 1.000 1.00 0.00
#> TCGA.G2.A2EJ.01 1 0.00 1.000 1.00 0.00
#> TCGA.G2.A2EF.01 1 0.00 1.000 1.00 0.00
#> TCGA.FD.A5C1.01 1 0.00 1.000 1.00 0.00
#> TCGA.XF.A8HH.01 2 0.00 0.994 0.00 1.00
#> TCGA.LC.A66R.01 1 0.00 1.000 1.00 0.00
#> TCGA.FT.A3EE.01 2 0.00 0.994 0.00 1.00
#> TCGA.ZF.A9R1.01 2 0.00 0.994 0.00 1.00
#> TCGA.CF.A47S.01 2 0.00 0.994 0.00 1.00
#> TCGA.E7.A3X6.01 2 0.00 0.994 0.00 1.00
#> TCGA.FD.A6TG.01 2 0.00 0.994 0.00 1.00
#> TCGA.UY.A78L.01 1 0.00 1.000 1.00 0.00
#> TCGA.FD.A6TA.01 2 0.00 0.994 0.00 1.00
#> TCGA.YC.A89H.01 2 0.00 0.994 0.00 1.00
#> TCGA.BT.A20Q.01 2 0.00 0.994 0.00 1.00
#> TCGA.E7.A6ME.01 2 0.00 0.994 0.00 1.00
#> TCGA.SY.A9G5.01 1 0.00 1.000 1.00 0.00
#> TCGA.ZF.A9RM.01 2 0.00 0.994 0.00 1.00
#> TCGA.FD.A5BR.01 2 0.00 0.994 0.00 1.00
#> TCGA.ZF.AA51.01 2 0.00 0.994 0.00 1.00
#> TCGA.DK.A3WW.01 1 0.00 1.000 1.00 0.00
#> TCGA.DK.A1A6.06 2 0.00 0.994 0.00 1.00
#> TCGA.GD.A76B.01 2 0.00 0.994 0.00 1.00
#> TCGA.BT.A20J.01 1 0.00 1.000 1.00 0.00
#> TCGA.GC.A3YS.01 1 0.00 1.000 1.00 0.00
#> TCGA.DK.A3IV.01 2 0.00 0.994 0.00 1.00
#> TCGA.FD.A3SQ.01 2 0.00 0.994 0.00 1.00
#> TCGA.DK.A3IM.01 1 0.00 1.000 1.00 0.00
#> TCGA.S5.A6DX.01 2 0.00 0.994 0.00 1.00
#> TCGA.ZF.A9R0.01 2 0.00 0.994 0.00 1.00
#> TCGA.GU.A42R.01 2 0.00 0.994 0.00 1.00
#> TCGA.ZF.AA4N.01 1 0.00 1.000 1.00 0.00
#> TCGA.CF.A1HR.01 2 0.00 0.994 0.00 1.00
#> TCGA.UY.A8OD.01 2 0.00 0.994 0.00 1.00
#> TCGA.4Z.AA84.01 1 0.00 1.000 1.00 0.00
#> TCGA.E7.A8O7.01 2 0.00 0.994 0.00 1.00
#> TCGA.GV.A3QG.01 1 0.00 1.000 1.00 0.00
#> TCGA.FD.A6TD.01 1 0.00 1.000 1.00 0.00
#> TCGA.DK.A6AV.01 2 0.00 0.994 0.00 1.00
#> TCGA.DK.A3IT.01 2 0.00 0.994 0.00 1.00
#> TCGA.CU.A0YN.01 1 0.00 1.000 1.00 0.00
#> TCGA.FJ.A3Z7.01 2 0.00 0.994 0.00 1.00
#> TCGA.4Z.AA82.01 1 0.00 1.000 1.00 0.00
#> TCGA.GC.A6I1.01 1 0.00 1.000 1.00 0.00
#> TCGA.FD.A3B6.01 1 0.00 1.000 1.00 0.00
#> TCGA.BT.A20V.01 1 0.00 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.UY.A9PE.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.ZF.AA52.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.ZF.A9RF.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BT.A3PJ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.YC.A9TC.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DK.A1A7.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BT.A2LB.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.GV.A3QF.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.E7.A97P.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DK.AA6S.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.XF.AAMW.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FD.A6TC.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.XF.A9SK.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.BT.A20T.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.UY.A78K.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.BT.A20W.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E7.A6MD.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.DK.A6B6.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.GD.A2C5.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.FD.A3SR.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.ZF.AA5H.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.G2.A2EJ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.G2.A2EF.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FD.A5C1.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.XF.A8HH.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.LC.A66R.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FT.A3EE.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.ZF.A9R1.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CF.A47S.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E7.A3X6.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.FD.A6TG.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.UY.A78L.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FD.A6TA.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.YC.A89H.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.BT.A20Q.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E7.A6ME.01 2 0.2066 0.930 0.00 0.94 0.06
#> TCGA.SY.A9G5.01 1 0.0892 0.975 0.98 0.02 0.00
#> TCGA.ZF.A9RM.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FD.A5BR.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.ZF.AA51.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.DK.A3WW.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DK.A1A6.06 2 0.4002 0.812 0.00 0.84 0.16
#> TCGA.GD.A76B.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.BT.A20J.01 2 0.4291 0.767 0.18 0.82 0.00
#> TCGA.GC.A3YS.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DK.A3IV.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.FD.A3SQ.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.DK.A3IM.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.S5.A6DX.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.ZF.A9R0.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.GU.A42R.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZF.AA4N.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.CF.A1HR.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.UY.A8OD.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.4Z.AA84.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.E7.A8O7.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.GV.A3QG.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FD.A6TD.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DK.A6AV.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.DK.A3IT.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.CU.A0YN.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FJ.A3Z7.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.4Z.AA82.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.GC.A6I1.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FD.A3B6.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BT.A20V.01 1 0.0000 0.999 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.UY.A9PE.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA52.01 4 0.4948 0.259 0.00 0.44 0.00 0.56
#> TCGA.ZF.A9RF.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.BT.A3PJ.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.YC.A9TC.01 4 0.0000 0.827 0.00 0.00 0.00 1.00
#> TCGA.DK.A1A7.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.BT.A2LB.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.GV.A3QF.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.E7.A97P.01 1 0.4624 0.667 0.66 0.00 0.00 0.34
#> TCGA.DK.AA6S.01 4 0.0000 0.827 0.00 0.00 0.00 1.00
#> TCGA.XF.AAMW.01 1 0.4624 0.667 0.66 0.00 0.00 0.34
#> TCGA.FD.A6TC.01 2 0.0707 0.978 0.00 0.98 0.00 0.02
#> TCGA.XF.A9SK.01 4 0.4713 0.447 0.00 0.36 0.00 0.64
#> TCGA.BT.A20T.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.UY.A78K.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.BT.A20W.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.E7.A6MD.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.DK.A6B6.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.GD.A2C5.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.FD.A3SR.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA5H.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.G2.A2EJ.01 1 0.4624 0.667 0.66 0.00 0.00 0.34
#> TCGA.G2.A2EF.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.FD.A5C1.01 1 0.4277 0.729 0.72 0.00 0.00 0.28
#> TCGA.XF.A8HH.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.LC.A66R.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 2 0.0707 0.978 0.00 0.98 0.00 0.02
#> TCGA.ZF.A9R1.01 3 0.3801 0.664 0.00 0.22 0.78 0.00
#> TCGA.CF.A47S.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.E7.A3X6.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.FD.A6TG.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.UY.A78L.01 1 0.2647 0.832 0.88 0.00 0.00 0.12
#> TCGA.FD.A6TA.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.YC.A89H.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.BT.A20Q.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.E7.A6ME.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.SY.A9G5.01 4 0.0000 0.827 0.00 0.00 0.00 1.00
#> TCGA.ZF.A9RM.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.FD.A5BR.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.ZF.AA51.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.DK.A3WW.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.06 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.GD.A76B.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.BT.A20J.01 4 0.0000 0.827 0.00 0.00 0.00 1.00
#> TCGA.GC.A3YS.01 1 0.4277 0.729 0.72 0.00 0.00 0.28
#> TCGA.DK.A3IV.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.FD.A3SQ.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IM.01 4 0.0000 0.827 0.00 0.00 0.00 1.00
#> TCGA.S5.A6DX.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.ZF.A9R0.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.GU.A42R.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.ZF.AA4N.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.CF.A1HR.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.UY.A8OD.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA84.01 1 0.4522 0.688 0.68 0.00 0.00 0.32
#> TCGA.E7.A8O7.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.GV.A3QG.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.FD.A6TD.01 1 0.1637 0.858 0.94 0.00 0.00 0.06
#> TCGA.DK.A6AV.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IT.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YN.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.FJ.A3Z7.01 3 0.1211 0.922 0.00 0.04 0.96 0.00
#> TCGA.4Z.AA82.01 4 0.0000 0.827 0.00 0.00 0.00 1.00
#> TCGA.GC.A6I1.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.FD.A3B6.01 1 0.0000 0.877 1.00 0.00 0.00 0.00
#> TCGA.BT.A20V.01 4 0.2921 0.651 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.UY.A9PE.01 5 0.3561 0.713 0.00 0.26 0.00 0.00 0.74
#> TCGA.ZF.AA52.01 5 0.1648 0.677 0.00 0.02 0.00 0.04 0.94
#> TCGA.ZF.A9RF.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A3PJ.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A9TC.01 4 0.0609 0.909 0.00 0.00 0.00 0.98 0.02
#> TCGA.DK.A1A7.01 3 0.0000 0.926 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A2LB.01 5 0.4262 0.434 0.00 0.44 0.00 0.00 0.56
#> TCGA.GV.A3QF.01 5 0.1732 0.745 0.00 0.08 0.00 0.00 0.92
#> TCGA.E7.A97P.01 1 0.4302 0.342 0.52 0.00 0.00 0.48 0.00
#> TCGA.DK.AA6S.01 4 0.1410 0.905 0.00 0.00 0.00 0.94 0.06
#> TCGA.XF.AAMW.01 1 0.4302 0.342 0.52 0.00 0.00 0.48 0.00
#> TCGA.FD.A6TC.01 5 0.0609 0.692 0.00 0.02 0.00 0.00 0.98
#> TCGA.XF.A9SK.01 5 0.3852 0.441 0.00 0.02 0.00 0.22 0.76
#> TCGA.BT.A20T.01 3 0.2020 0.942 0.00 0.10 0.90 0.00 0.00
#> TCGA.UY.A78K.01 5 0.4060 0.635 0.00 0.36 0.00 0.00 0.64
#> TCGA.BT.A20W.01 3 0.2020 0.942 0.00 0.10 0.90 0.00 0.00
#> TCGA.E7.A6MD.01 2 0.1043 0.852 0.00 0.96 0.00 0.00 0.04
#> TCGA.DK.A6B6.01 3 0.2020 0.942 0.00 0.10 0.90 0.00 0.00
#> TCGA.GD.A2C5.01 5 0.3109 0.744 0.00 0.20 0.00 0.00 0.80
#> TCGA.FD.A3SR.01 2 0.0000 0.868 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EJ.01 1 0.4302 0.342 0.52 0.00 0.00 0.48 0.00
#> TCGA.G2.A2EF.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5C1.01 1 0.3424 0.708 0.76 0.00 0.00 0.24 0.00
#> TCGA.XF.A8HH.01 2 0.2020 0.821 0.00 0.90 0.00 0.00 0.10
#> TCGA.LC.A66R.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 5 0.1732 0.754 0.00 0.08 0.00 0.00 0.92
#> TCGA.ZF.A9R1.01 2 0.1410 0.820 0.00 0.94 0.06 0.00 0.00
#> TCGA.CF.A47S.01 3 0.0000 0.926 0.00 0.00 1.00 0.00 0.00
#> TCGA.E7.A3X6.01 5 0.2516 0.747 0.00 0.14 0.00 0.00 0.86
#> TCGA.FD.A6TG.01 2 0.0000 0.868 0.00 1.00 0.00 0.00 0.00
#> TCGA.UY.A78L.01 1 0.2732 0.771 0.84 0.00 0.00 0.16 0.00
#> TCGA.FD.A6TA.01 2 0.3796 0.445 0.00 0.70 0.00 0.00 0.30
#> TCGA.YC.A89H.01 2 0.0609 0.863 0.00 0.98 0.00 0.00 0.02
#> TCGA.BT.A20Q.01 3 0.2020 0.942 0.00 0.10 0.90 0.00 0.00
#> TCGA.E7.A6ME.01 2 0.0000 0.868 0.00 1.00 0.00 0.00 0.00
#> TCGA.SY.A9G5.01 4 0.2732 0.866 0.00 0.00 0.00 0.84 0.16
#> TCGA.ZF.A9RM.01 3 0.0000 0.926 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A5BR.01 5 0.4126 0.611 0.00 0.38 0.00 0.00 0.62
#> TCGA.ZF.AA51.01 2 0.0609 0.863 0.00 0.98 0.00 0.00 0.02
#> TCGA.DK.A3WW.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.06 2 0.0609 0.863 0.00 0.98 0.00 0.00 0.02
#> TCGA.GD.A76B.01 2 0.3983 0.314 0.00 0.66 0.00 0.00 0.34
#> TCGA.BT.A20J.01 4 0.3109 0.826 0.00 0.00 0.00 0.80 0.20
#> TCGA.GC.A3YS.01 1 0.3796 0.654 0.70 0.00 0.00 0.30 0.00
#> TCGA.DK.A3IV.01 5 0.4182 0.574 0.00 0.40 0.00 0.00 0.60
#> TCGA.FD.A3SQ.01 2 0.0000 0.868 0.00 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 4 0.0000 0.906 0.00 0.00 0.00 1.00 0.00
#> TCGA.S5.A6DX.01 2 0.0000 0.868 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R0.01 2 0.3109 0.703 0.00 0.80 0.00 0.00 0.20
#> TCGA.GU.A42R.01 3 0.2020 0.942 0.00 0.10 0.90 0.00 0.00
#> TCGA.ZF.AA4N.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A1HR.01 2 0.0000 0.868 0.00 1.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 5 0.3424 0.723 0.00 0.24 0.00 0.00 0.76
#> TCGA.4Z.AA84.01 1 0.3983 0.592 0.66 0.00 0.00 0.34 0.00
#> TCGA.E7.A8O7.01 3 0.0000 0.926 0.00 0.00 1.00 0.00 0.00
#> TCGA.GV.A3QG.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TD.01 1 0.1732 0.815 0.92 0.00 0.00 0.08 0.00
#> TCGA.DK.A6AV.01 2 0.3109 0.703 0.00 0.80 0.00 0.00 0.20
#> TCGA.DK.A3IT.01 2 0.1732 0.822 0.00 0.92 0.00 0.00 0.08
#> TCGA.CU.A0YN.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.FJ.A3Z7.01 2 0.3109 0.641 0.00 0.80 0.20 0.00 0.00
#> TCGA.4Z.AA82.01 4 0.0000 0.906 0.00 0.00 0.00 1.00 0.00
#> TCGA.GC.A6I1.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B6.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20V.01 4 0.2280 0.770 0.12 0.00 0.00 0.88 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.UY.A9PE.01 5 0.2631 0.64798 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.ZF.AA52.01 5 0.5405 -0.23103 0.00 0.04 0.00 0.04 0.50 0.42
#> TCGA.ZF.A9RF.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A3PJ.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A9TC.01 4 0.4632 0.07921 0.00 0.00 0.00 0.52 0.04 0.44
#> TCGA.DK.A1A7.01 3 0.0547 0.87746 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BT.A2LB.01 5 0.3198 0.61025 0.00 0.26 0.00 0.00 0.74 0.00
#> TCGA.GV.A3QF.01 5 0.3270 0.54124 0.00 0.06 0.00 0.00 0.82 0.12
#> TCGA.E7.A97P.01 4 0.4002 0.49280 0.32 0.00 0.00 0.66 0.00 0.02
#> TCGA.DK.AA6S.01 4 0.4078 -0.17818 0.00 0.00 0.00 0.64 0.02 0.34
#> TCGA.XF.AAMW.01 4 0.4002 0.49280 0.32 0.00 0.00 0.66 0.00 0.02
#> TCGA.FD.A6TC.01 5 0.4121 0.45481 0.00 0.06 0.00 0.00 0.72 0.22
#> TCGA.XF.A9SK.01 6 0.5371 0.39231 0.00 0.00 0.00 0.12 0.36 0.52
#> TCGA.BT.A20T.01 3 0.2260 0.90444 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.UY.A78K.01 5 0.5509 0.58827 0.00 0.30 0.00 0.00 0.54 0.16
#> TCGA.BT.A20W.01 3 0.2260 0.90444 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 2 0.1556 0.75813 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.DK.A6B6.01 3 0.2260 0.90444 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.GD.A2C5.01 5 0.3351 0.63377 0.00 0.16 0.00 0.00 0.80 0.04
#> TCGA.FD.A3SR.01 2 0.1635 0.76367 0.00 0.94 0.02 0.00 0.02 0.02
#> TCGA.ZF.AA5H.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EJ.01 4 0.4002 0.49280 0.32 0.00 0.00 0.66 0.00 0.02
#> TCGA.G2.A2EF.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5C1.01 4 0.4801 0.18304 0.46 0.00 0.00 0.50 0.02 0.02
#> TCGA.XF.A8HH.01 2 0.2454 0.71019 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.LC.A66R.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 5 0.3985 0.54709 0.00 0.10 0.00 0.00 0.76 0.14
#> TCGA.ZF.A9R1.01 2 0.2260 0.66820 0.00 0.86 0.14 0.00 0.00 0.00
#> TCGA.CF.A47S.01 3 0.0547 0.87746 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.E7.A3X6.01 5 0.4926 0.48563 0.00 0.12 0.00 0.00 0.64 0.24
#> TCGA.FD.A6TG.01 2 0.0547 0.77183 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.UY.A78L.01 1 0.5020 0.12197 0.56 0.00 0.00 0.38 0.02 0.04
#> TCGA.FD.A6TA.01 2 0.4632 -0.10219 0.00 0.52 0.00 0.00 0.44 0.04
#> TCGA.YC.A89H.01 2 0.1814 0.75501 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.BT.A20Q.01 3 0.2260 0.90444 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.E7.A6ME.01 2 0.1092 0.76602 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.SY.A9G5.01 4 0.4328 -0.35384 0.00 0.00 0.00 0.52 0.02 0.46
#> TCGA.ZF.A9RM.01 3 0.0547 0.87746 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FD.A5BR.01 5 0.5012 0.61258 0.00 0.30 0.00 0.00 0.60 0.10
#> TCGA.ZF.AA51.01 2 0.0547 0.77183 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DK.A3WW.01 1 0.0937 0.87697 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DK.A1A6.06 2 0.2048 0.74418 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.GD.A76B.01 2 0.4806 -0.00773 0.00 0.56 0.00 0.00 0.38 0.06
#> TCGA.BT.A20J.01 6 0.5406 0.41036 0.00 0.00 0.00 0.38 0.12 0.50
#> TCGA.GC.A3YS.01 4 0.4731 0.32569 0.40 0.00 0.00 0.56 0.02 0.02
#> TCGA.DK.A3IV.01 5 0.5324 0.55111 0.00 0.34 0.00 0.00 0.54 0.12
#> TCGA.FD.A3SQ.01 2 0.0547 0.77183 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 4 0.2454 0.27126 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.S5.A6DX.01 2 0.2190 0.73194 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.ZF.A9R0.01 2 0.3869 -0.07810 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.GU.A42R.01 3 0.2260 0.90444 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CF.A1HR.01 2 0.0000 0.77368 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 5 0.4810 0.57522 0.00 0.22 0.00 0.00 0.66 0.12
#> TCGA.4Z.AA84.01 4 0.5106 0.21265 0.44 0.00 0.00 0.50 0.02 0.04
#> TCGA.E7.A8O7.01 3 0.0547 0.87746 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.GV.A3QG.01 1 0.3483 0.74192 0.82 0.00 0.00 0.12 0.02 0.04
#> TCGA.FD.A6TD.01 1 0.3976 0.59630 0.74 0.00 0.00 0.22 0.02 0.02
#> TCGA.DK.A6AV.01 5 0.3869 -0.03047 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.DK.A3IT.01 2 0.2581 0.71233 0.00 0.86 0.00 0.00 0.12 0.02
#> TCGA.CU.A0YN.01 1 0.0937 0.87697 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.FJ.A3Z7.01 2 0.3592 0.52243 0.00 0.74 0.24 0.00 0.00 0.02
#> TCGA.4Z.AA82.01 4 0.1814 0.30377 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.GC.A6I1.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A3B6.01 1 0.0000 0.89708 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A20V.01 4 0.3795 0.42436 0.06 0.00 0.00 0.80 0.02 0.12
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.UY.A9PE.01 5 0.2422 0.6725 0.00 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.ZF.AA52.01 5 0.4630 0.3356 0.26 0.00 0.00 0.12 0.62 0.00 0.00
#> TCGA.ZF.A9RF.01 7 0.3139 0.6150 0.00 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.BT.A3PJ.01 7 0.3139 0.6150 0.00 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.YC.A9TC.01 6 0.5959 0.0000 0.32 0.00 0.00 0.26 0.00 0.40 0.02
#> TCGA.DK.A1A7.01 3 0.1006 0.8065 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.BT.A2LB.01 5 0.3139 0.5986 0.00 0.30 0.00 0.00 0.70 0.00 0.00
#> TCGA.GV.A3QF.01 5 0.2829 0.6419 0.08 0.08 0.00 0.00 0.84 0.00 0.00
#> TCGA.E7.A97P.01 7 0.4848 0.1157 0.00 0.00 0.00 0.40 0.00 0.10 0.50
#> TCGA.DK.AA6S.01 4 0.2803 0.5284 0.10 0.00 0.00 0.84 0.06 0.00 0.00
#> TCGA.XF.AAMW.01 7 0.4820 0.1663 0.00 0.00 0.00 0.38 0.00 0.10 0.52
#> TCGA.FD.A6TC.01 5 0.2708 0.5317 0.22 0.00 0.00 0.00 0.78 0.00 0.00
#> TCGA.XF.A9SK.01 5 0.5247 0.0693 0.40 0.00 0.00 0.16 0.44 0.00 0.00
#> TCGA.BT.A20T.01 3 0.2422 0.8466 0.00 0.18 0.82 0.00 0.00 0.00 0.00
#> TCGA.UY.A78K.01 5 0.4328 0.5583 0.06 0.34 0.00 0.00 0.60 0.00 0.00
#> TCGA.BT.A20W.01 3 0.2422 0.8466 0.00 0.18 0.82 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 2 0.1928 0.7272 0.02 0.90 0.00 0.00 0.08 0.00 0.00
#> TCGA.DK.A6B6.01 3 0.2422 0.8466 0.00 0.18 0.82 0.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.01 5 0.3055 0.6693 0.02 0.14 0.00 0.00 0.82 0.02 0.00
#> TCGA.FD.A3SR.01 2 0.0504 0.7969 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 7 0.3139 0.6150 0.00 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.G2.A2EJ.01 7 0.5002 0.0856 0.00 0.00 0.00 0.40 0.00 0.12 0.48
#> TCGA.G2.A2EF.01 7 0.3047 0.6208 0.00 0.00 0.00 0.00 0.00 0.28 0.72
#> TCGA.FD.A5C1.01 7 0.4338 0.3710 0.00 0.00 0.00 0.28 0.00 0.08 0.64
#> TCGA.XF.A8HH.01 2 0.3530 0.5891 0.02 0.76 0.00 0.00 0.20 0.02 0.00
#> TCGA.LC.A66R.01 7 0.2832 0.6292 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.FT.A3EE.01 5 0.3911 0.5773 0.24 0.06 0.00 0.00 0.70 0.00 0.00
#> TCGA.ZF.A9R1.01 2 0.2081 0.6901 0.00 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.CF.A47S.01 3 0.1006 0.8065 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.E7.A3X6.01 5 0.4594 0.5751 0.22 0.14 0.00 0.00 0.64 0.00 0.00
#> TCGA.FD.A6TG.01 2 0.0000 0.7990 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78L.01 7 0.3388 0.4769 0.00 0.00 0.00 0.20 0.00 0.04 0.76
#> TCGA.FD.A6TA.01 5 0.3525 0.3586 0.00 0.44 0.00 0.00 0.56 0.00 0.00
#> TCGA.YC.A89H.01 2 0.1363 0.7738 0.02 0.94 0.00 0.00 0.04 0.00 0.00
#> TCGA.BT.A20Q.01 3 0.2422 0.8466 0.00 0.18 0.82 0.00 0.00 0.00 0.00
#> TCGA.E7.A6ME.01 2 0.0863 0.7905 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.SY.A9G5.01 4 0.4610 0.4853 0.24 0.00 0.00 0.66 0.08 0.00 0.02
#> TCGA.ZF.A9RM.01 3 0.1006 0.8065 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.FD.A5BR.01 5 0.3307 0.6511 0.02 0.24 0.00 0.00 0.74 0.00 0.00
#> TCGA.ZF.AA51.01 2 0.0863 0.7905 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WW.01 7 0.1886 0.6268 0.00 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.DK.A1A6.06 2 0.0504 0.7979 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.GD.A76B.01 2 0.3985 -0.2479 0.02 0.52 0.00 0.00 0.46 0.00 0.00
#> TCGA.BT.A20J.01 4 0.4795 0.4083 0.28 0.00 0.00 0.62 0.08 0.00 0.02
#> TCGA.GC.A3YS.01 7 0.4538 0.3494 0.00 0.00 0.00 0.28 0.00 0.10 0.62
#> TCGA.DK.A3IV.01 5 0.3685 0.5925 0.02 0.32 0.00 0.00 0.66 0.00 0.00
#> TCGA.FD.A3SQ.01 2 0.0504 0.7978 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 4 0.0504 0.5351 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.S5.A6DX.01 2 0.0504 0.7932 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.A9R0.01 5 0.4425 0.1018 0.02 0.48 0.00 0.00 0.48 0.02 0.00
#> TCGA.GU.A42R.01 3 0.2259 0.8479 0.00 0.16 0.84 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 7 0.3047 0.6256 0.00 0.00 0.00 0.00 0.00 0.28 0.72
#> TCGA.CF.A1HR.01 2 0.0000 0.7990 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 5 0.5091 0.5697 0.16 0.12 0.00 0.00 0.66 0.06 0.00
#> TCGA.4Z.AA84.01 7 0.4960 0.2779 0.06 0.00 0.00 0.30 0.00 0.04 0.60
#> TCGA.E7.A8O7.01 3 0.1006 0.8065 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.GV.A3QG.01 7 0.2163 0.6095 0.00 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.FD.A6TD.01 7 0.2278 0.5643 0.00 0.00 0.00 0.08 0.00 0.04 0.88
#> TCGA.DK.A6AV.01 2 0.4356 0.0833 0.02 0.56 0.00 0.00 0.40 0.02 0.00
#> TCGA.DK.A3IT.01 2 0.3244 0.5739 0.04 0.78 0.00 0.00 0.18 0.00 0.00
#> TCGA.CU.A0YN.01 7 0.1433 0.6272 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.FJ.A3Z7.01 2 0.3139 0.3906 0.00 0.70 0.30 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA82.01 4 0.0504 0.5392 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.GC.A6I1.01 7 0.3139 0.6150 0.00 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.FD.A3B6.01 7 0.3139 0.6150 0.00 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.BT.A20V.01 4 0.5984 0.0739 0.04 0.00 0.00 0.48 0.00 0.22 0.26
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.UY.A9PE.01 5 0.3843 0.5519 0.24 0.04 0.00 0.00 0.70 0.02 0.00 0.00
#> TCGA.ZF.AA52.01 5 0.6011 -0.1445 0.00 0.18 0.00 0.36 0.40 0.04 0.00 0.02
#> TCGA.ZF.A9RF.01 7 0.0000 0.8902 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A3PJ.01 7 0.0000 0.8902 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.YC.A9TC.01 6 0.2132 0.0000 0.00 0.00 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.DK.A1A7.01 3 0.0000 0.6579 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BT.A2LB.01 5 0.3977 0.5272 0.24 0.02 0.00 0.00 0.70 0.02 0.00 0.02
#> TCGA.GV.A3QF.01 5 0.1563 0.5213 0.00 0.10 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.E7.A97P.01 8 0.3154 0.6605 0.00 0.00 0.00 0.06 0.00 0.00 0.16 0.78
#> TCGA.DK.AA6S.01 4 0.3337 0.4161 0.00 0.02 0.00 0.78 0.00 0.04 0.00 0.16
#> TCGA.XF.AAMW.01 8 0.3154 0.6605 0.00 0.00 0.00 0.06 0.00 0.00 0.16 0.78
#> TCGA.FD.A6TC.01 5 0.4939 0.3234 0.04 0.16 0.00 0.18 0.62 0.00 0.00 0.00
#> TCGA.XF.A9SK.01 4 0.5273 0.1375 0.00 0.16 0.00 0.46 0.36 0.02 0.00 0.00
#> TCGA.BT.A20T.01 3 0.4437 0.7293 0.22 0.16 0.62 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78K.01 5 0.4963 0.5674 0.18 0.08 0.00 0.06 0.66 0.02 0.00 0.00
#> TCGA.BT.A20W.01 3 0.4614 0.7012 0.26 0.16 0.58 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 1 0.3426 0.5218 0.74 0.02 0.00 0.00 0.22 0.00 0.00 0.02
#> TCGA.DK.A6B6.01 3 0.4614 0.7012 0.26 0.16 0.58 0.00 0.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.01 5 0.3830 0.5802 0.08 0.16 0.00 0.00 0.74 0.02 0.00 0.00
#> TCGA.FD.A3SR.01 1 0.1887 0.6825 0.90 0.06 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 7 0.0000 0.8902 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G2.A2EJ.01 8 0.3154 0.6605 0.00 0.00 0.00 0.06 0.00 0.00 0.16 0.78
#> TCGA.G2.A2EF.01 7 0.0471 0.8867 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.FD.A5C1.01 8 0.3845 0.6759 0.00 0.00 0.00 0.06 0.00 0.00 0.28 0.66
#> TCGA.XF.A8HH.01 1 0.3808 0.4261 0.66 0.00 0.00 0.00 0.30 0.02 0.00 0.02
#> TCGA.LC.A66R.01 7 0.0808 0.8794 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.FT.A3EE.01 5 0.5239 0.4932 0.10 0.16 0.00 0.08 0.64 0.02 0.00 0.00
#> TCGA.ZF.A9R1.01 1 0.3879 0.5206 0.74 0.14 0.10 0.00 0.00 0.00 0.00 0.02
#> TCGA.CF.A47S.01 3 0.0000 0.6579 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A3X6.01 5 0.5444 0.4421 0.08 0.18 0.00 0.04 0.64 0.02 0.00 0.04
#> TCGA.FD.A6TG.01 1 0.0000 0.6875 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A78L.01 8 0.4370 0.5044 0.00 0.00 0.00 0.08 0.00 0.00 0.40 0.52
#> TCGA.FD.A6TA.01 1 0.4619 -0.1694 0.48 0.06 0.00 0.00 0.44 0.02 0.00 0.00
#> TCGA.YC.A89H.01 1 0.2025 0.6599 0.88 0.02 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.BT.A20Q.01 3 0.4437 0.7293 0.22 0.16 0.62 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6ME.01 1 0.1947 0.6607 0.86 0.14 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SY.A9G5.01 4 0.4185 0.4028 0.00 0.08 0.00 0.76 0.04 0.04 0.00 0.08
#> TCGA.ZF.A9RM.01 3 0.0000 0.6579 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FD.A5BR.01 5 0.2756 0.5609 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.ZF.AA51.01 1 0.2114 0.6504 0.84 0.16 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3WW.01 7 0.2267 0.7326 0.00 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.DK.A1A6.06 1 0.2591 0.6772 0.86 0.04 0.00 0.00 0.08 0.00 0.00 0.02
#> TCGA.GD.A76B.01 5 0.4358 0.2680 0.40 0.04 0.00 0.00 0.54 0.02 0.00 0.00
#> TCGA.BT.A20J.01 4 0.5700 0.3596 0.00 0.12 0.00 0.62 0.08 0.08 0.00 0.10
#> TCGA.GC.A3YS.01 8 0.3291 0.6861 0.00 0.00 0.00 0.02 0.00 0.00 0.28 0.70
#> TCGA.DK.A3IV.01 5 0.4754 0.5085 0.28 0.04 0.00 0.04 0.62 0.02 0.00 0.00
#> TCGA.FD.A3SQ.01 1 0.1765 0.6606 0.88 0.12 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IM.01 4 0.3746 0.3836 0.00 0.00 0.00 0.64 0.00 0.04 0.00 0.32
#> TCGA.S5.A6DX.01 1 0.2569 0.5941 0.82 0.02 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.ZF.A9R0.01 5 0.5159 0.2242 0.38 0.08 0.00 0.00 0.50 0.02 0.00 0.02
#> TCGA.GU.A42R.01 3 0.4213 0.7294 0.18 0.16 0.66 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 7 0.1091 0.8668 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.CF.A1HR.01 1 0.0471 0.6851 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 5 0.5683 0.4063 0.16 0.38 0.00 0.02 0.42 0.02 0.00 0.00
#> TCGA.4Z.AA84.01 8 0.5369 0.5376 0.00 0.04 0.00 0.20 0.00 0.00 0.22 0.54
#> TCGA.E7.A8O7.01 3 0.0000 0.6579 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GV.A3QG.01 7 0.4276 0.2689 0.00 0.00 0.00 0.06 0.00 0.02 0.64 0.28
#> TCGA.FD.A6TD.01 8 0.3992 0.4396 0.00 0.00 0.00 0.04 0.00 0.00 0.44 0.52
#> TCGA.DK.A6AV.01 1 0.4137 -0.0126 0.50 0.00 0.00 0.00 0.46 0.02 0.00 0.02
#> TCGA.DK.A3IT.01 1 0.2852 0.4473 0.72 0.00 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.CU.A0YN.01 7 0.1947 0.7794 0.00 0.00 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.FJ.A3Z7.01 1 0.4213 0.3407 0.66 0.18 0.16 0.00 0.00 0.00 0.00 0.00
#> TCGA.4Z.AA82.01 4 0.3570 0.3681 0.00 0.02 0.00 0.62 0.00 0.00 0.00 0.36
#> TCGA.GC.A6I1.01 7 0.0000 0.8902 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FD.A3B6.01 7 0.0000 0.8902 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BT.A20V.01 8 0.5758 0.1066 0.00 0.16 0.00 0.20 0.00 0.04 0.04 0.56
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: Node033. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0331"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 24 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4896 0.511 0.511
#> 3 3 1.000 1.000 1.000 0.3992 0.804 0.617
#> 4 4 0.900 0.940 0.895 0.0822 0.928 0.770
#> 5 5 0.797 0.740 0.798 0.0527 0.935 0.731
#> 6 6 0.762 0.710 0.844 0.0405 0.949 0.770
#> 7 7 0.808 0.658 0.849 0.0394 0.960 0.814
#> 8 8 0.810 0.502 0.772 0.0255 0.978 0.878
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.ZF.A9RF.01 2 0 1 0 1
#> TCGA.BT.A3PJ.01 2 0 1 0 1
#> TCGA.YC.A9TC.01 1 0 1 1 0
#> TCGA.E7.A97P.01 1 0 1 1 0
#> TCGA.XF.AAMW.01 1 0 1 1 0
#> TCGA.ZF.AA5H.01 2 0 1 0 1
#> TCGA.G2.A2EJ.01 1 0 1 1 0
#> TCGA.G2.A2EF.01 2 0 1 0 1
#> TCGA.FD.A5C1.01 2 0 1 0 1
#> TCGA.LC.A66R.01 2 0 1 0 1
#> TCGA.UY.A78L.01 2 0 1 0 1
#> TCGA.SY.A9G5.01 2 0 1 0 1
#> TCGA.DK.A3WW.01 1 0 1 1 0
#> TCGA.GC.A3YS.01 2 0 1 0 1
#> TCGA.DK.A3IM.01 1 0 1 1 0
#> TCGA.ZF.AA4N.01 1 0 1 1 0
#> TCGA.4Z.AA84.01 2 0 1 0 1
#> TCGA.GV.A3QG.01 2 0 1 0 1
#> TCGA.FD.A6TD.01 2 0 1 0 1
#> TCGA.CU.A0YN.01 2 0 1 0 1
#> TCGA.4Z.AA82.01 1 0 1 1 0
#> TCGA.GC.A6I1.01 2 0 1 0 1
#> TCGA.FD.A3B6.01 2 0 1 0 1
#> TCGA.BT.A20V.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.ZF.A9RF.01 3 0 1 0 0 1
#> TCGA.BT.A3PJ.01 3 0 1 0 0 1
#> TCGA.YC.A9TC.01 1 0 1 1 0 0
#> TCGA.E7.A97P.01 1 0 1 1 0 0
#> TCGA.XF.AAMW.01 1 0 1 1 0 0
#> TCGA.ZF.AA5H.01 3 0 1 0 0 1
#> TCGA.G2.A2EJ.01 1 0 1 1 0 0
#> TCGA.G2.A2EF.01 2 0 1 0 1 0
#> TCGA.FD.A5C1.01 2 0 1 0 1 0
#> TCGA.LC.A66R.01 2 0 1 0 1 0
#> TCGA.UY.A78L.01 3 0 1 0 0 1
#> TCGA.SY.A9G5.01 2 0 1 0 1 0
#> TCGA.DK.A3WW.01 1 0 1 1 0 0
#> TCGA.GC.A3YS.01 2 0 1 0 1 0
#> TCGA.DK.A3IM.01 1 0 1 1 0 0
#> TCGA.ZF.AA4N.01 1 0 1 1 0 0
#> TCGA.4Z.AA84.01 2 0 1 0 1 0
#> TCGA.GV.A3QG.01 3 0 1 0 0 1
#> TCGA.FD.A6TD.01 2 0 1 0 1 0
#> TCGA.CU.A0YN.01 2 0 1 0 1 0
#> TCGA.4Z.AA82.01 1 0 1 1 0 0
#> TCGA.GC.A6I1.01 2 0 1 0 1 0
#> TCGA.FD.A3B6.01 3 0 1 0 0 1
#> TCGA.BT.A20V.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.ZF.A9RF.01 3 0.0707 0.985 0.00 0.00 0.98 0.02
#> TCGA.BT.A3PJ.01 3 0.1211 0.981 0.00 0.00 0.96 0.04
#> TCGA.YC.A9TC.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.E7.A97P.01 1 0.0000 0.923 1.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 1 0.0000 0.923 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 3 0.1211 0.981 0.00 0.00 0.96 0.04
#> TCGA.G2.A2EJ.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.G2.A2EF.01 2 0.4277 0.775 0.00 0.72 0.00 0.28
#> TCGA.FD.A5C1.01 2 0.0000 0.949 0.00 1.00 0.00 0.00
#> TCGA.LC.A66R.01 2 0.0000 0.949 0.00 1.00 0.00 0.00
#> TCGA.UY.A78L.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.SY.A9G5.01 2 0.0000 0.949 0.00 1.00 0.00 0.00
#> TCGA.DK.A3WW.01 1 0.0000 0.923 1.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 2 0.3801 0.820 0.00 0.78 0.00 0.22
#> TCGA.DK.A3IM.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.ZF.AA4N.01 1 0.0000 0.923 1.00 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 2 0.0000 0.949 0.00 1.00 0.00 0.00
#> TCGA.GV.A3QG.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FD.A6TD.01 2 0.0000 0.949 0.00 1.00 0.00 0.00
#> TCGA.CU.A0YN.01 2 0.0000 0.949 0.00 1.00 0.00 0.00
#> TCGA.4Z.AA82.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.GC.A6I1.01 2 0.0000 0.949 0.00 1.00 0.00 0.00
#> TCGA.FD.A3B6.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.BT.A20V.01 1 0.3172 0.715 0.84 0.00 0.00 0.16
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.ZF.A9RF.01 3 0.000 0.888 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A3PJ.01 3 0.122 0.880 0.00 0.02 0.96 0.02 0.00
#> TCGA.YC.A9TC.01 4 0.446 0.977 0.32 0.02 0.00 0.66 0.00
#> TCGA.E7.A97P.01 1 0.000 0.848 1.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 1 0.000 0.848 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 3 0.122 0.880 0.00 0.02 0.96 0.02 0.00
#> TCGA.G2.A2EJ.01 4 0.389 0.992 0.32 0.00 0.00 0.68 0.00
#> TCGA.G2.A2EF.01 5 0.104 0.322 0.00 0.00 0.00 0.04 0.96
#> TCGA.FD.A5C1.01 2 0.431 0.629 0.00 0.50 0.00 0.00 0.50
#> TCGA.LC.A66R.01 2 0.413 0.847 0.00 0.62 0.00 0.00 0.38
#> TCGA.UY.A78L.01 3 0.373 0.892 0.00 0.04 0.80 0.16 0.00
#> TCGA.SY.A9G5.01 2 0.406 0.866 0.00 0.64 0.00 0.00 0.36
#> TCGA.DK.A3WW.01 1 0.000 0.848 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 5 0.459 0.239 0.00 0.22 0.00 0.06 0.72
#> TCGA.DK.A3IM.01 4 0.389 0.992 0.32 0.00 0.00 0.68 0.00
#> TCGA.ZF.AA4N.01 1 0.293 0.626 0.82 0.00 0.00 0.18 0.00
#> TCGA.4Z.AA84.01 2 0.406 0.866 0.00 0.64 0.00 0.00 0.36
#> TCGA.GV.A3QG.01 3 0.373 0.892 0.00 0.04 0.80 0.16 0.00
#> TCGA.FD.A6TD.01 2 0.413 0.847 0.00 0.62 0.00 0.00 0.38
#> TCGA.CU.A0YN.01 5 0.431 -0.794 0.00 0.50 0.00 0.00 0.50
#> TCGA.4Z.AA82.01 4 0.389 0.992 0.32 0.00 0.00 0.68 0.00
#> TCGA.GC.A6I1.01 2 0.413 0.849 0.00 0.62 0.00 0.00 0.38
#> TCGA.FD.A3B6.01 3 0.373 0.892 0.00 0.04 0.80 0.16 0.00
#> TCGA.BT.A20V.01 1 0.453 0.643 0.70 0.26 0.00 0.04 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.ZF.A9RF.01 3 0.0000 0.868 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A3PJ.01 3 0.1480 0.852 0.00 0.02 0.94 0.04 0.00 0.00
#> TCGA.YC.A9TC.01 4 0.4863 0.791 0.14 0.20 0.00 0.66 0.00 0.00
#> TCGA.E7.A97P.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 3 0.1480 0.852 0.00 0.02 0.94 0.04 0.00 0.00
#> TCGA.G2.A2EJ.01 4 0.2260 0.936 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.G2.A2EF.01 5 0.2631 0.000 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.FD.A5C1.01 6 0.2956 0.675 0.00 0.04 0.00 0.00 0.12 0.84
#> TCGA.LC.A66R.01 6 0.0000 0.756 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.UY.A78L.01 3 0.3315 0.850 0.00 0.20 0.78 0.02 0.00 0.00
#> TCGA.SY.A9G5.01 6 0.2260 0.735 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.DK.A3WW.01 1 0.0937 0.799 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 6 0.6720 -0.259 0.00 0.16 0.00 0.08 0.28 0.48
#> TCGA.DK.A3IM.01 4 0.2260 0.936 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.ZF.AA4N.01 1 0.3950 0.544 0.72 0.04 0.00 0.24 0.00 0.00
#> TCGA.4Z.AA84.01 6 0.2260 0.735 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.GV.A3QG.01 3 0.2631 0.870 0.00 0.18 0.82 0.00 0.00 0.00
#> TCGA.FD.A6TD.01 6 0.0000 0.756 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CU.A0YN.01 6 0.2956 0.675 0.00 0.04 0.00 0.00 0.12 0.84
#> TCGA.4Z.AA82.01 4 0.2260 0.936 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.GC.A6I1.01 6 0.2790 0.732 0.00 0.14 0.00 0.00 0.02 0.84
#> TCGA.FD.A3B6.01 3 0.2631 0.870 0.00 0.18 0.82 0.00 0.00 0.00
#> TCGA.BT.A20V.01 1 0.5569 0.530 0.54 0.28 0.00 0.00 0.18 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.ZF.A9RF.01 3 0.1886 0.776 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.BT.A3PJ.01 3 0.2906 0.753 0.00 0.18 0.80 0.00 0.00 0.00 0.02
#> TCGA.YC.A9TC.01 4 0.3449 0.775 0.08 0.14 0.00 0.78 0.00 0.00 0.00
#> TCGA.E7.A97P.01 1 0.1671 0.693 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 1 0.1928 0.693 0.90 0.08 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZF.AA5H.01 3 0.2906 0.753 0.00 0.18 0.80 0.00 0.00 0.00 0.02
#> TCGA.G2.A2EJ.01 4 0.0000 0.931 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G2.A2EF.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FD.A5C1.01 6 0.3370 0.668 0.00 0.06 0.00 0.00 0.16 0.78 0.00
#> TCGA.LC.A66R.01 6 0.0504 0.797 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.UY.A78L.01 3 0.2945 0.710 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.SY.A9G5.01 6 0.2572 0.789 0.00 0.08 0.00 0.00 0.00 0.86 0.06
#> TCGA.DK.A3WW.01 1 0.0504 0.672 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.GC.A3YS.01 2 0.5325 0.000 0.00 0.50 0.00 0.00 0.28 0.22 0.00
#> TCGA.DK.A3IM.01 4 0.0000 0.931 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 1 0.2945 0.332 0.74 0.00 0.00 0.26 0.00 0.00 0.00
#> TCGA.4Z.AA84.01 6 0.2829 0.779 0.00 0.08 0.00 0.00 0.00 0.84 0.08
#> TCGA.GV.A3QG.01 3 0.2259 0.775 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.FD.A6TD.01 6 0.0504 0.797 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CU.A0YN.01 6 0.3086 0.676 0.00 0.04 0.00 0.00 0.16 0.80 0.00
#> TCGA.4Z.AA82.01 4 0.0000 0.931 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GC.A6I1.01 6 0.3289 0.783 0.00 0.10 0.00 0.00 0.02 0.82 0.06
#> TCGA.FD.A3B6.01 3 0.2259 0.775 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.BT.A20V.01 7 0.3413 0.000 0.38 0.00 0.00 0.00 0.00 0.00 0.62
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.ZF.A9RF.01 3 0.1563 0.696 0.00 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.BT.A3PJ.01 3 0.0000 0.690 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YC.A9TC.01 4 0.5404 0.493 0.12 0.08 0.00 0.56 0.00 0.00 0.00 0.24
#> TCGA.E7.A97P.01 1 0.2406 0.768 0.80 0.20 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XF.AAMW.01 1 0.2406 0.768 0.80 0.20 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA5H.01 3 0.0000 0.690 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EJ.01 4 0.0000 0.858 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G2.A2EF.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FD.A5C1.01 6 0.3154 0.469 0.00 0.00 0.00 0.00 0.16 0.78 0.06 0.00
#> TCGA.LC.A66R.01 6 0.0471 0.555 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.UY.A78L.01 7 0.4325 -0.519 0.00 0.04 0.38 0.00 0.00 0.00 0.56 0.02
#> TCGA.SY.A9G5.01 6 0.3237 0.581 0.00 0.40 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.DK.A3WW.01 1 0.0471 0.739 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.GC.A3YS.01 8 0.4799 0.000 0.00 0.00 0.00 0.00 0.16 0.32 0.00 0.52
#> TCGA.DK.A3IM.01 4 0.0000 0.858 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZF.AA4N.01 1 0.2856 0.582 0.78 0.00 0.00 0.20 0.00 0.00 0.00 0.02
#> TCGA.4Z.AA84.01 6 0.3318 0.561 0.00 0.46 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.GV.A3QG.01 3 0.3272 0.526 0.00 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.FD.A6TD.01 6 0.0471 0.555 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CU.A0YN.01 6 0.3154 0.469 0.00 0.00 0.00 0.00 0.16 0.78 0.06 0.00
#> TCGA.4Z.AA82.01 4 0.0000 0.858 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GC.A6I1.01 6 0.3272 0.580 0.00 0.42 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.FD.A3B6.01 3 0.3272 0.526 0.00 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.BT.A20V.01 7 0.6604 -0.261 0.24 0.22 0.00 0.00 0.00 0.00 0.32 0.22
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node033. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01321-leaf , Node01322-leaf , Node01323-leaf , Node01324-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02221-leaf , Node02222 , Node02223-leaf , Node02311-leaf , Node02312-leaf , Node03311-leaf , Node03312-leaf , Node03313-leaf , Node03321-leaf , Node03322-leaf , Node03323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0332"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.978 0.990 0.4929 0.510 0.510
#> 3 3 0.978 0.975 0.983 0.3179 0.708 0.491
#> 4 4 0.768 0.907 0.935 0.1145 0.940 0.826
#> 5 5 0.795 0.839 0.908 0.0815 0.845 0.514
#> 6 6 0.820 0.737 0.892 0.0421 0.972 0.862
#> 7 7 0.779 0.670 0.836 0.0173 0.994 0.964
#> 8 8 0.741 0.637 0.826 0.0213 0.961 0.798
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.UY.A9PE.01 1 0.000 0.986 1.00 0.00
#> TCGA.ZF.AA52.01 1 0.000 0.986 1.00 0.00
#> TCGA.BT.A2LB.01 2 0.000 0.994 0.00 1.00
#> TCGA.GV.A3QF.01 1 0.000 0.986 1.00 0.00
#> TCGA.DK.AA6S.01 1 0.795 0.681 0.76 0.24
#> TCGA.FD.A6TC.01 2 0.000 0.994 0.00 1.00
#> TCGA.XF.A9SK.01 1 0.000 0.986 1.00 0.00
#> TCGA.UY.A78K.01 1 0.000 0.986 1.00 0.00
#> TCGA.E7.A6MD.01 1 0.000 0.986 1.00 0.00
#> TCGA.GD.A2C5.01 2 0.000 0.994 0.00 1.00
#> TCGA.FD.A3SR.01 1 0.000 0.986 1.00 0.00
#> TCGA.XF.A8HH.01 2 0.000 0.994 0.00 1.00
#> TCGA.FT.A3EE.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A3X6.01 1 0.000 0.986 1.00 0.00
#> TCGA.FD.A6TG.01 1 0.000 0.986 1.00 0.00
#> TCGA.FD.A6TA.01 1 0.000 0.986 1.00 0.00
#> TCGA.YC.A89H.01 2 0.000 0.994 0.00 1.00
#> TCGA.E7.A6ME.01 1 0.000 0.986 1.00 0.00
#> TCGA.FD.A5BR.01 1 0.000 0.986 1.00 0.00
#> TCGA.ZF.AA51.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A1A6.06 2 0.000 0.994 0.00 1.00
#> TCGA.GD.A76B.01 2 0.000 0.994 0.00 1.00
#> TCGA.BT.A20J.01 1 0.000 0.986 1.00 0.00
#> TCGA.DK.A3IV.01 1 0.000 0.986 1.00 0.00
#> TCGA.FD.A3SQ.01 1 0.000 0.986 1.00 0.00
#> TCGA.S5.A6DX.01 1 0.000 0.986 1.00 0.00
#> TCGA.ZF.A9R0.01 2 0.327 0.935 0.06 0.94
#> TCGA.CF.A1HR.01 1 0.000 0.986 1.00 0.00
#> TCGA.UY.A8OD.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A6AV.01 2 0.000 0.994 0.00 1.00
#> TCGA.DK.A3IT.01 1 0.000 0.986 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.UY.A9PE.01 3 0.3340 0.883 0.12 0.00 0.88
#> TCGA.ZF.AA52.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BT.A2LB.01 3 0.1529 0.934 0.00 0.04 0.96
#> TCGA.GV.A3QF.01 3 0.2537 0.916 0.08 0.00 0.92
#> TCGA.DK.AA6S.01 3 0.2066 0.937 0.06 0.00 0.94
#> TCGA.FD.A6TC.01 3 0.0000 0.940 0.00 0.00 1.00
#> TCGA.XF.A9SK.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.UY.A78K.01 3 0.2066 0.937 0.06 0.00 0.94
#> TCGA.E7.A6MD.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.GD.A2C5.01 3 0.1529 0.934 0.00 0.04 0.96
#> TCGA.FD.A3SR.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.XF.A8HH.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FT.A3EE.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E7.A3X6.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FD.A6TG.01 3 0.2066 0.937 0.06 0.00 0.94
#> TCGA.FD.A6TA.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.YC.A89H.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E7.A6ME.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FD.A5BR.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.ZF.AA51.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DK.A1A6.06 3 0.0892 0.939 0.00 0.02 0.98
#> TCGA.GD.A76B.01 3 0.1529 0.934 0.00 0.04 0.96
#> TCGA.BT.A20J.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DK.A3IV.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FD.A3SQ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.S5.A6DX.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.ZF.A9R0.01 3 0.0000 0.940 0.00 0.00 1.00
#> TCGA.CF.A1HR.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.UY.A8OD.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DK.A6AV.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DK.A3IT.01 1 0.0000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.UY.A9PE.01 3 0.1211 0.913 0.00 0.00 0.96 0.04
#> TCGA.ZF.AA52.01 1 0.4277 0.771 0.72 0.00 0.28 0.00
#> TCGA.BT.A2LB.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.GV.A3QF.01 3 0.3037 0.889 0.02 0.00 0.88 0.10
#> TCGA.DK.AA6S.01 3 0.0707 0.903 0.00 0.00 0.98 0.02
#> TCGA.FD.A6TC.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.XF.A9SK.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.UY.A78K.01 3 0.0707 0.903 0.00 0.00 0.98 0.02
#> TCGA.E7.A6MD.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.GD.A2C5.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.FD.A3SR.01 1 0.4134 0.793 0.74 0.00 0.26 0.00
#> TCGA.XF.A8HH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FT.A3EE.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E7.A3X6.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.FD.A6TG.01 3 0.1211 0.912 0.00 0.00 0.96 0.04
#> TCGA.FD.A6TA.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.YC.A89H.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E7.A6ME.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.FD.A5BR.01 1 0.2647 0.853 0.88 0.00 0.12 0.00
#> TCGA.ZF.AA51.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.3853 0.851 0.00 0.02 0.82 0.16
#> TCGA.GD.A76B.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.BT.A20J.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.DK.A3IV.01 1 0.4134 0.793 0.74 0.00 0.26 0.00
#> TCGA.FD.A3SQ.01 1 0.4134 0.793 0.74 0.00 0.26 0.00
#> TCGA.S5.A6DX.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.ZF.A9R0.01 3 0.2921 0.871 0.00 0.00 0.86 0.14
#> TCGA.CF.A1HR.01 1 0.0000 0.884 1.00 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DK.A6AV.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DK.A3IT.01 1 0.4134 0.793 0.74 0.00 0.26 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.UY.A9PE.01 3 0.4644 0.69094 0.04 0.00 0.68 0 0.28
#> TCGA.ZF.AA52.01 5 0.3274 0.73927 0.22 0.00 0.00 0 0.78
#> TCGA.BT.A2LB.01 4 0.0000 1.00000 0.00 0.00 0.00 1 0.00
#> TCGA.GV.A3QF.01 3 0.2754 0.69347 0.04 0.00 0.88 0 0.08
#> TCGA.DK.AA6S.01 5 0.0609 0.55435 0.00 0.00 0.02 0 0.98
#> TCGA.FD.A6TC.01 4 0.0000 1.00000 0.00 0.00 0.00 1 0.00
#> TCGA.XF.A9SK.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.UY.A78K.01 5 0.0609 0.55435 0.00 0.00 0.02 0 0.98
#> TCGA.E7.A6MD.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.GD.A2C5.01 4 0.0000 1.00000 0.00 0.00 0.00 1 0.00
#> TCGA.FD.A3SR.01 5 0.3561 0.73448 0.26 0.00 0.00 0 0.74
#> TCGA.XF.A8HH.01 2 0.0000 1.00000 0.00 1.00 0.00 0 0.00
#> TCGA.FT.A3EE.01 2 0.0000 1.00000 0.00 1.00 0.00 0 0.00
#> TCGA.E7.A3X6.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.FD.A6TG.01 5 0.3684 -0.00537 0.00 0.00 0.28 0 0.72
#> TCGA.FD.A6TA.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.YC.A89H.01 2 0.0000 1.00000 0.00 1.00 0.00 0 0.00
#> TCGA.E7.A6ME.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.FD.A5BR.01 1 0.2732 0.74606 0.84 0.00 0.00 0 0.16
#> TCGA.ZF.AA51.01 2 0.0000 1.00000 0.00 1.00 0.00 0 0.00
#> TCGA.DK.A1A6.06 3 0.5425 0.67245 0.00 0.08 0.60 0 0.32
#> TCGA.GD.A76B.01 4 0.0000 1.00000 0.00 0.00 0.00 1 0.00
#> TCGA.BT.A20J.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.DK.A3IV.01 5 0.3424 0.74138 0.24 0.00 0.00 0 0.76
#> TCGA.FD.A3SQ.01 5 0.3684 0.72256 0.28 0.00 0.00 0 0.72
#> TCGA.S5.A6DX.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.ZF.A9R0.01 3 0.2732 0.77294 0.00 0.00 0.84 0 0.16
#> TCGA.CF.A1HR.01 1 0.0000 0.97389 1.00 0.00 0.00 0 0.00
#> TCGA.UY.A8OD.01 2 0.0000 1.00000 0.00 1.00 0.00 0 0.00
#> TCGA.DK.A6AV.01 2 0.0000 1.00000 0.00 1.00 0.00 0 0.00
#> TCGA.DK.A3IT.01 5 0.4126 0.59235 0.38 0.00 0.00 0 0.62
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.UY.A9PE.01 3 0.6103 0.1497 0.00 0.00 0.38 0.00 0.30 0.32
#> TCGA.ZF.AA52.01 5 0.0547 0.7801 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BT.A2LB.01 4 0.0000 0.9807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GV.A3QF.01 6 0.3111 0.0000 0.02 0.00 0.12 0.00 0.02 0.84
#> TCGA.DK.AA6S.01 5 0.4078 0.2956 0.00 0.00 0.34 0.00 0.64 0.02
#> TCGA.FD.A6TC.01 4 0.1092 0.9598 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.XF.A9SK.01 1 0.1092 0.8989 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.UY.A78K.01 5 0.3156 0.5915 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.E7.A6MD.01 1 0.1092 0.8979 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.GD.A2C5.01 4 0.0547 0.9721 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.FD.A3SR.01 5 0.1807 0.7934 0.06 0.00 0.00 0.00 0.92 0.02
#> TCGA.XF.A8HH.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A3X6.01 1 0.1267 0.8725 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.FD.A6TG.01 3 0.4310 -0.0173 0.00 0.00 0.54 0.00 0.44 0.02
#> TCGA.FD.A6TA.01 1 0.0547 0.8897 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.YC.A89H.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6ME.01 1 0.1556 0.8948 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.FD.A5BR.01 1 0.4631 0.4550 0.62 0.00 0.00 0.00 0.32 0.06
#> TCGA.ZF.AA51.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.1092 0.2954 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.GD.A76B.01 4 0.0000 0.9807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BT.A20J.01 1 0.1556 0.8948 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.DK.A3IV.01 5 0.1267 0.7918 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.FD.A3SQ.01 5 0.1267 0.7887 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.S5.A6DX.01 1 0.0937 0.9036 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.ZF.A9R0.01 3 0.4067 0.1991 0.00 0.00 0.70 0.00 0.04 0.26
#> TCGA.CF.A1HR.01 1 0.1267 0.9013 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.UY.A8OD.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IT.01 5 0.3163 0.6776 0.14 0.00 0.00 0.00 0.82 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.UY.A9PE.01 7 0.5875 0.0000 0.00 0.00 0.22 0.00 0.18 0.06 0.54
#> TCGA.ZF.AA52.01 5 0.0863 0.6764 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.BT.A2LB.01 4 0.0000 0.9209 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GV.A3QF.01 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DK.AA6S.01 5 0.3413 0.2399 0.00 0.00 0.38 0.00 0.62 0.00 0.00
#> TCGA.FD.A6TC.01 4 0.2163 0.9091 0.00 0.00 0.02 0.88 0.00 0.00 0.10
#> TCGA.XF.A9SK.01 1 0.1166 0.8715 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.UY.A78K.01 5 0.2572 0.5121 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.E7.A6MD.01 1 0.0863 0.8658 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.GD.A2C5.01 4 0.2569 0.8892 0.00 0.00 0.02 0.84 0.00 0.00 0.14
#> TCGA.FD.A3SR.01 5 0.2016 0.6452 0.04 0.00 0.00 0.00 0.90 0.00 0.06
#> TCGA.XF.A8HH.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A3X6.01 1 0.1928 0.8376 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.FD.A6TG.01 3 0.4212 0.0956 0.00 0.00 0.62 0.00 0.34 0.02 0.02
#> TCGA.FD.A6TA.01 1 0.0863 0.8658 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.YC.A89H.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6ME.01 1 0.2803 0.8353 0.84 0.00 0.00 0.00 0.06 0.00 0.10
#> TCGA.FD.A5BR.01 1 0.4795 0.3705 0.62 0.00 0.00 0.00 0.28 0.02 0.08
#> TCGA.ZF.AA51.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.2159 0.2616 0.00 0.02 0.90 0.00 0.02 0.00 0.06
#> TCGA.GD.A76B.01 4 0.0000 0.9209 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BT.A20J.01 1 0.2163 0.8550 0.88 0.00 0.00 0.00 0.02 0.00 0.10
#> TCGA.DK.A3IV.01 5 0.2313 0.6645 0.06 0.00 0.00 0.00 0.88 0.00 0.06
#> TCGA.FD.A3SQ.01 5 0.3370 0.6062 0.16 0.00 0.00 0.00 0.78 0.00 0.06
#> TCGA.S5.A6DX.01 1 0.0504 0.8755 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.ZF.A9R0.01 3 0.4278 -0.2323 0.00 0.00 0.50 0.00 0.00 0.04 0.46
#> TCGA.CF.A1HR.01 1 0.1363 0.8724 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.UY.A8OD.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IT.01 5 0.4698 0.4091 0.24 0.00 0.00 0.00 0.62 0.00 0.14
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.UY.A9PE.01 7 0.5422 0.3497 0.00 0 0.04 0.10 0.22 0.04 0.60 0.00
#> TCGA.ZF.AA52.01 5 0.1887 0.5739 0.06 0 0.00 0.04 0.90 0.00 0.00 0.00
#> TCGA.BT.A2LB.01 8 0.2265 0.8652 0.00 0 0.02 0.08 0.00 0.00 0.02 0.88
#> TCGA.GV.A3QF.01 6 0.0000 0.0000 0.00 0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DK.AA6S.01 5 0.4537 -0.1435 0.00 0 0.40 0.10 0.50 0.00 0.00 0.00
#> TCGA.FD.A6TC.01 8 0.2265 0.8396 0.00 0 0.02 0.08 0.00 0.00 0.02 0.88
#> TCGA.XF.A9SK.01 1 0.2025 0.8130 0.88 0 0.00 0.10 0.02 0.00 0.00 0.00
#> TCGA.UY.A78K.01 5 0.3551 0.3392 0.00 0 0.22 0.06 0.72 0.00 0.00 0.00
#> TCGA.E7.A6MD.01 1 0.2224 0.8096 0.86 0 0.00 0.12 0.02 0.00 0.00 0.00
#> TCGA.GD.A2C5.01 8 0.1741 0.8337 0.00 0 0.00 0.02 0.02 0.00 0.04 0.92
#> TCGA.FD.A3SR.01 5 0.4779 0.4564 0.12 0 0.02 0.18 0.66 0.00 0.02 0.00
#> TCGA.XF.A8HH.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FT.A3EE.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A3X6.01 1 0.3193 0.5768 0.62 0 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.FD.A6TG.01 3 0.3922 0.4180 0.00 0 0.64 0.00 0.30 0.00 0.06 0.00
#> TCGA.FD.A6TA.01 1 0.1947 0.7904 0.86 0 0.00 0.14 0.00 0.00 0.00 0.00
#> TCGA.YC.A89H.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E7.A6ME.01 1 0.3385 0.7193 0.76 0 0.00 0.16 0.08 0.00 0.00 0.00
#> TCGA.FD.A5BR.01 5 0.6501 0.0238 0.34 0 0.00 0.10 0.36 0.02 0.18 0.00
#> TCGA.ZF.AA51.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A1A6.06 3 0.2224 0.3059 0.00 0 0.86 0.00 0.02 0.00 0.12 0.00
#> TCGA.GD.A76B.01 8 0.2404 0.8686 0.00 0 0.00 0.14 0.00 0.00 0.02 0.84
#> TCGA.BT.A20J.01 1 0.2547 0.7848 0.84 0 0.00 0.12 0.04 0.00 0.00 0.00
#> TCGA.DK.A3IV.01 5 0.1557 0.5906 0.06 0 0.00 0.00 0.92 0.00 0.02 0.00
#> TCGA.FD.A3SQ.01 5 0.3002 0.5827 0.12 0 0.00 0.04 0.82 0.00 0.02 0.00
#> TCGA.S5.A6DX.01 1 0.0808 0.8238 0.96 0 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.ZF.A9R0.01 7 0.2756 0.2481 0.00 0 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.CF.A1HR.01 1 0.2165 0.8077 0.88 0 0.00 0.06 0.06 0.00 0.00 0.00
#> TCGA.UY.A8OD.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A6AV.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DK.A3IT.01 5 0.4224 0.4815 0.14 0 0.00 0.02 0.70 0.00 0.14 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6