Date: 2021-07-22 19:04:52 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 376220 rows and 549 columns.
#> Performed in total 96600 partitions.
#> There are 48 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, 549 cols
#> |-- 01, 64 cols, 14470 signatures
#> | |-- 011, 46 cols, 317 signatures (c)
#> | |-- 012, 13 cols, 1258 signatures
#> | | |-- 0121, 6 cols (b)
#> | | |-- 0122, 4 cols (b)
#> | | `-- 0123, 3 cols (b)
#> | `-- 013, 5 cols (b)
#> |-- 02, 193 cols, 15528 signatures
#> | |-- 021, 78 cols, 5112 signatures
#> | | |-- 0211, 26 cols, 730 signatures (c)
#> | | |-- 0212, 33 cols, 1794 signatures
#> | | | |-- 02121, 15 cols, 31 signatures (c)
#> | | | |-- 02122, 8 cols (b)
#> | | | `-- 02123, 10 cols (b)
#> | | `-- 0213, 19 cols, 925 signatures (c)
#> | |-- 022, 43 cols, 6017 signatures
#> | | |-- 0221, 21 cols, 1762 signatures
#> | | | |-- 02211, 3 cols (b)
#> | | | |-- 02212, 12 cols, 498 signatures (c)
#> | | | |-- 02213, 4 cols (b)
#> | | | `-- 02214, 2 cols (b)
#> | | |-- 0222, 9 cols (b)
#> | | `-- 0223, 13 cols, 683 signatures (c)
#> | |-- 023, 42 cols, 6587 signatures
#> | | |-- 0231, 18 cols, 1360 signatures
#> | | | |-- 02311, 6 cols (b)
#> | | | |-- 02312, 10 cols (b)
#> | | | `-- 02313, 2 cols (b)
#> | | |-- 0232, 14 cols, 826 signatures (c)
#> | | `-- 0233, 10 cols (b)
#> | `-- 024, 30 cols, 3076 signatures
#> | |-- 0241, 10 cols (b)
#> | `-- 0242, 20 cols, 290 signatures (c)
#> |-- 03, 50 cols, 2573 signatures
#> | |-- 031, 9 cols (b)
#> | |-- 032, 19 cols, 267 signatures (c)
#> | |-- 033, 15 cols, 128 signatures (c)
#> | `-- 034, 7 cols (b)
#> |-- 04, 155 cols, 11436 signatures
#> | |-- 041, 58 cols, 4238 signatures
#> | | |-- 0411, 11 cols (b)
#> | | |-- 0412, 26 cols, 963 signatures (c)
#> | | `-- 0413, 21 cols, 466 signatures (c)
#> | |-- 042, 26 cols, 5268 signatures
#> | | |-- 0421, 6 cols (b)
#> | | |-- 0422, 11 cols (b)
#> | | `-- 0423, 9 cols (b)
#> | |-- 043, 41 cols, 4059 signatures
#> | | |-- 0431, 16 cols, 140 signatures (c)
#> | | |-- 0432, 16 cols, 231 signatures (c)
#> | | `-- 0433, 9 cols (b)
#> | `-- 044, 30 cols, 5287 signatures
#> | |-- 0441, 6 cols (b)
#> | |-- 0442, 14 cols, 15 signatures (c)
#> | `-- 0443, 10 cols (b)
#> `-- 05, 87 cols, 2221 signatures
#> |-- 051, 42 cols, 3054 signatures
#> | |-- 0511, 24 cols, 2 signatures (c)
#> | |-- 0512, 14 cols, 3130 signatures
#> | | |-- 05121, 9 cols (b)
#> | | |-- 05122, 3 cols (b)
#> | | `-- 05123, 2 cols (b)
#> | `-- 0513, 4 cols (b)
#> |-- 052, 20 cols, 3130 signatures
#> | |-- 0521, 13 cols, 3 signatures (c)
#> | |-- 0522, 4 cols (b)
#> | `-- 0523, 3 cols (b)
#> `-- 053, 25 cols, 698 signatures (c)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 376220 549
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "012" "0121" "0122" "0123" "013" "02" "021" "0211" "0212"
#> [13] "02121" "02122" "02123" "0213" "022" "0221" "02211" "02212" "02213" "02214" "0222" "0223"
#> [25] "023" "0231" "02311" "02312" "02313" "0232" "0233" "024" "0241" "0242" "03" "031"
#> [37] "032" "033" "034" "04" "041" "0411" "0412" "0413" "042" "0421" "0422" "0423"
#> [49] "043" "0431" "0432" "0433" "044" "0441" "0442" "0443" "05" "051" "0511" "0512"
#> [61] "05121" "05122" "05123" "0513" "052" "0521" "0522" "0523" "053"
all_leaves(res_rh)
#> [1] "011" "0121" "0122" "0123" "013" "0211" "02121" "02122" "02123" "0213" "02211" "02212"
#> [13] "02213" "02214" "0222" "0223" "02311" "02312" "02313" "0232" "0233" "0241" "0242" "031"
#> [25] "032" "033" "034" "0411" "0412" "0413" "0421" "0422" "0423" "0431" "0432" "0433"
#> [37] "0441" "0442" "0443" "0511" "05121" "05122" "05123" "0513" "0521" "0522" "0523" "053"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 5 549 33866 9.00e-02 FALSE
#> 2 01 SD:kmeans 2 3 64 14470 3.85e-02 FALSE
#> 3 011 ATC:skmeans 3 3 46 317 8.43e-04 TRUE
#> 4 012 ATC:kmeans 3 3 13 1258 3.34e-03 FALSE
#> 5 0121 not applied 4 NA 6 NA NA TRUE
#> 6 0122 not applied 4 NA 4 NA NA TRUE
#> 7 0123 not applied 4 NA 3 NA NA TRUE
#> 8 013 not applied 3 NA 5 NA NA TRUE
#> 9 02 ATC:kmeans 2 4 193 15528 4.13e-02 FALSE
#> 10 021 SD:kmeans 3 3 78 5112 1.36e-02 FALSE
#> 11 0211 ATC:skmeans 4 3 26 730 1.94e-03 TRUE
#> 12 0212 ATC:kmeans 4 3 33 1794 4.77e-03 FALSE
#> 13 02121 ATC:kmeans 5 2 15 31 8.24e-05 TRUE
#> 14 02122 not applied 5 NA 8 NA NA TRUE
#> 15 02123 not applied 5 NA 10 NA NA TRUE
#> 16 0213 ATC:skmeans 4 2 19 925 2.46e-03 TRUE
#> 17 022 ATC:kmeans 3 3 43 6017 1.60e-02 FALSE
#> 18 0221 ATC:skmeans 4 4 21 1762 4.68e-03 FALSE
#> 19 02211 not applied 5 NA 3 NA NA TRUE
#> 20 02212 ATC:skmeans 5 2 12 498 1.32e-03 TRUE
#> 21 02213 not applied 5 NA 4 NA NA TRUE
#> 22 02214 not applied 5 NA 2 NA NA TRUE
#> 23 0222 not applied 4 NA 9 NA NA TRUE
#> 24 0223 ATC:skmeans 4 2 13 683 1.82e-03 TRUE
#> 25 023 ATC:kmeans 3 3 42 6587 1.75e-02 FALSE
#> 26 0231 ATC:skmeans 4 3 18 1360 3.61e-03 FALSE
#> 27 02311 not applied 5 NA 6 NA NA TRUE
#> 28 02312 not applied 5 NA 10 NA NA TRUE
#> 29 02313 not applied 5 NA 2 NA NA TRUE
#> 30 0232 ATC:kmeans 4 4 14 826 2.20e-03 TRUE
#> 31 0233 not applied 4 NA 10 NA NA TRUE
#> 32 024 ATC:kmeans 3 2 30 3076 8.18e-03 FALSE
#> 33 0241 not applied 4 NA 10 NA NA TRUE
#> 34 0242 ATC:skmeans 4 4 20 290 7.71e-04 TRUE
#> 35 03 ATC:skmeans 2 4 50 2573 6.84e-03 FALSE
#> 36 031 not applied 3 NA 9 NA NA TRUE
#> 37 032 ATC:skmeans 3 2 19 267 7.10e-04 TRUE
#> 38 033 SD:kmeans 3 2 15 128 3.40e-04 TRUE
#> 39 034 not applied 3 NA 7 NA NA TRUE
#> 40 04 ATC:kmeans 2 4 155 11436 3.04e-02 FALSE
#> 41 041 ATC:kmeans 3 3 58 4238 1.13e-02 FALSE
#> 42 0411 not applied 4 NA 11 NA NA TRUE
#> 43 0412 ATC:kmeans 4 2 26 963 2.56e-03 TRUE
#> 44 0413 ATC:kmeans 4 3 21 466 1.24e-03 TRUE
#> 45 042 ATC:kmeans 3 3 26 5268 1.40e-02 FALSE
#> 46 0421 not applied 4 NA 6 NA NA TRUE
#> 47 0422 not applied 4 NA 11 NA NA TRUE
#> 48 0423 not applied 4 NA 9 NA NA TRUE
#> 49 043 ATC:skmeans 3 3 41 4059 1.08e-02 FALSE
#> 50 0431 SD:skmeans 4 2 16 140 3.72e-04 TRUE
#> 51 0432 SD:kmeans 4 2 16 231 6.14e-04 TRUE
#> 52 0433 not applied 4 NA 9 NA NA TRUE
#> 53 044 ATC:kmeans 3 3 30 5287 1.41e-02 FALSE
#> 54 0441 not applied 4 NA 6 NA NA TRUE
#> 55 0442 ATC:kmeans 4 2 14 15 3.99e-05 TRUE
#> 56 0443 not applied 4 NA 10 NA NA TRUE
#> 57 05 ATC:kmeans 2 3 87 2221 5.90e-03 FALSE
#> 58 051 ATC:skmeans 3 3 42 3054 8.12e-03 FALSE
#> 59 0511 ATC:kmeans 4 2 24 2 5.32e-06 TRUE
#> 60 0512 ATC:kmeans 4 3 14 3130 8.32e-03 FALSE
#> 61 05121 not applied 5 NA 9 NA NA TRUE
#> 62 05122 not applied 5 NA 3 NA NA TRUE
#> 63 05123 not applied 5 NA 2 NA NA TRUE
#> 64 0513 not applied 4 NA 4 NA NA TRUE
#> 65 052 ATC:skmeans 3 3 20 3130 8.32e-03 FALSE
#> 66 0521 ATC:skmeans 4 2 13 3 7.97e-06 TRUE
#> 67 0522 not applied 4 NA 4 NA NA TRUE
#> 68 0523 not applied 4 NA 3 NA NA TRUE
#> 69 053 ATC:kmeans 3 3 25 698 1.86e-03 TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:skmeans | 5 | 1.00 | 0.96 | 0.98 | 549 | ** | |
| Node01 | SD:kmeans | 3 | 0.74 | 0.96 | 0.97 | 64 | ||
| Node011-leaf | ATC:skmeans | ✓ (c) | 8 | 0.91 | 0.84 | 0.91 | 46 | * |
| Node012 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 13 | ** | |
| Node0121-leaf | not applied | ✓ (b) | 6 | |||||
| Node0122-leaf | not applied | ✓ (b) | 4 | |||||
| Node0123-leaf | not applied | ✓ (b) | 3 | |||||
| Node013-leaf | not applied | ✓ (b) | 5 | |||||
| Node02 | ATC:kmeans | 4 | 1.00 | 0.99 | 1.00 | 193 | ** | |
| Node021 | SD:kmeans | 3 | 0.97 | 0.97 | 0.97 | 78 | ** | |
| Node0211-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 26 | ** |
| Node0212 | ATC:kmeans | 3 | 1.00 | 0.99 | 0.99 | 33 | ** | |
| Node02121-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 15 | ** |
| Node02122-leaf | not applied | ✓ (b) | 8 | |||||
| Node02123-leaf | not applied | ✓ (b) | 10 | |||||
| Node0213-leaf | ATC:skmeans | ✓ (c) | 4 | 0.46 | 0.84 | 0.92 | 19 | |
| Node022 | ATC:kmeans | 3 | 0.96 | 0.96 | 0.98 | 43 | ** | |
| Node0221 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 21 | ** | |
| Node02211-leaf | not applied | ✓ (b) | 3 | |||||
| Node02212-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 12 | ** |
| Node02213-leaf | not applied | ✓ (b) | 4 | |||||
| Node02214-leaf | not applied | ✓ (b) | 2 | |||||
| Node0222-leaf | not applied | ✓ (b) | 9 | |||||
| Node0223-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 13 | ** |
| Node023 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.99 | 42 | ** | |
| Node0231 | ATC:skmeans | 6 | 0.92 | 0.60 | 0.90 | 18 | * | |
| Node02311-leaf | not applied | ✓ (b) | 6 | |||||
| Node02312-leaf | not applied | ✓ (b) | 10 | |||||
| Node02313-leaf | not applied | ✓ (b) | 2 | |||||
| Node0232-leaf | ATC:kmeans | ✓ (c) | 4 | 0.93 | 0.98 | 0.99 | 14 | * |
| Node0233-leaf | not applied | ✓ (b) | 10 | |||||
| Node024 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 30 | ** | |
| Node0241-leaf | not applied | ✓ (b) | 10 | |||||
| Node0242-leaf | ATC:skmeans | ✓ (c) | 4 | 0.95 | 0.96 | 0.98 | 20 | * |
| Node03 | ATC:skmeans | 4 | 1.00 | 0.98 | 0.99 | 50 | ** | |
| Node031-leaf | not applied | ✓ (b) | 9 | |||||
| Node032-leaf | ATC:skmeans | ✓ (c) | 4 | 1.00 | 0.93 | 0.99 | 19 | ** |
| Node033-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 0.97 | 15 | ** |
| Node034-leaf | not applied | ✓ (b) | 7 | |||||
| Node04 | ATC:kmeans | 4 | 1.00 | 0.97 | 0.99 | 155 | ** | |
| Node041 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 58 | ** | |
| Node0411-leaf | not applied | ✓ (b) | 11 | |||||
| Node0412-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 26 | ** |
| Node0413-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 21 | ** |
| Node042 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 26 | ** | |
| Node0421-leaf | not applied | ✓ (b) | 6 | |||||
| Node0422-leaf | not applied | ✓ (b) | 11 | |||||
| Node0423-leaf | not applied | ✓ (b) | 9 | |||||
| Node043 | ATC:skmeans | 3 | 1.00 | 0.96 | 0.99 | 41 | ** | |
| Node0431-leaf | SD:skmeans | ✓ (c) | 2 | 0.88 | 0.97 | 0.99 | 16 | |
| Node0432-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 16 | ** |
| Node0433-leaf | not applied | ✓ (b) | 9 | |||||
| Node044 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 30 | ** | |
| Node0441-leaf | not applied | ✓ (b) | 6 | |||||
| Node0442-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 1.00 | 14 | ** |
| Node0443-leaf | not applied | ✓ (b) | 10 | |||||
| Node05 | ATC:kmeans | 4 | 0.90 | 0.88 | 0.94 | 87 | * | |
| Node051 | ATC:skmeans | 3 | 1.00 | 0.98 | 0.99 | 42 | ** | |
| Node0511-leaf | ATC:kmeans | ✓ (c) | 2 | 0.48 | 0.98 | 0.94 | 24 | |
| Node0512 | ATC:kmeans | 5 | 1.00 | 0.92 | 0.98 | 14 | ** | |
| Node05121-leaf | not applied | ✓ (b) | 9 | |||||
| Node05122-leaf | not applied | ✓ (b) | 3 | |||||
| Node05123-leaf | not applied | ✓ (b) | 2 | |||||
| Node0513-leaf | not applied | ✓ (b) | 4 | |||||
| Node052 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 20 | ** | |
| Node0521-leaf | ATC:skmeans | ✓ (c) | 8 | 0.95 | 0.50 | 0.97 | 13 | * |
| Node0522-leaf | not applied | ✓ (b) | 4 | |||||
| Node0523-leaf | not applied | ✓ (b) | 3 | |||||
| Node053-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 25 | ** |
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 = 1258))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1360))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1762))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1794))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2221))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2573))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3054))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3076))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3130))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3130))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4059))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4238))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5112))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5268))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5287))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6017))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6587))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11436))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14470))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15528))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 33866))
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 = 1258))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "02311" "0211" "0123" "02121" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "0511" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "0511" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "02121" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "032" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "053"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "053" "0511" "0431" "02312"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "02121" "011" "02212" "0521" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "02213" "0211" "0413" "0432" "0511" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "0511" "05122" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "032" "0511" "0511" "0521" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "0521" "02123" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "02122" "0211" "02121" "0213" "02212"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "0511" "0522" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "02311" "0233" "0242" "011" "053" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "0521" "031" "0412" "0521"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "0121" "05123" "0211" "053" "02121" "033"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "053" "0242" "0211" "0433" "011" "0521"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "0511" "0413" "02212" "02123" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "053" "05121" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "032" "032" "0233" "0511" "05123" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "032" "011" "0511" "02214" "0122" "032"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "033" "0421" "02212" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "0521" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "053" "0413" "02311" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "032" "0423" "011" "033" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "02311" "0442" "02122" "02121" "0511"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "02121" "0423" "0223" "011" "053"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "0511" "0121" "0421" "02122" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "031" "0242" "0213" "0413" "02123"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "053" "0411" "033" "02122" "02212"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "032" "0413" "011" "0522" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "02312" "0413" "053" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "0122" "0432" "0511" "02312" "02312"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "053" "0412" "02214" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "032" "032" "053" "05121" "033" "05121"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "02312" "0232" "0411" "0242" "0233" "0521"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "053" "0121" "0213" "0511"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "02123" "0123" "0211" "02122" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "031" "0232" "0412" "0412" "034" "053"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "0121" "0422" "011" "0431" "02311"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "02312" "032" "05121"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "033" "02121" "0521" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "033" "034" "0242" "0433" "033" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "031"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "0511" "0431" "0523" "0213" "02121"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "0521" "02121" "053" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05121" "0242" "011" "0442" "0421" "02122"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "034" "0233" "0213" "033"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "0511" "034" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "0511" "02123" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "0523" "02311" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "0511" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "02121" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "02211" "0413" "011" "032"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "02123" "0441" "011" "0521" "0411" "0123"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "053" "011" "0442" "02312"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "02312" "02121"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "033"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "0511" "011" "02211" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "034" "0233" "053" "031" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "02122" "033" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "02213" "0442" "053" "0431" "031" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "0511" "0242" "011" "053" "0241" "034"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "032" "02312" "02123" "032" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "0521" "034"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "0513" "053"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "02313" "0242" "02212" "0242" "031"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "0121" "032" "0223" "02212" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05121" "053" "033" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "0122" "05122" "05121" "031" "033" "02313"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05121" "0242" "0431" "02121" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "053" "011" "02213" "0511" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "02312" "0511" "0521" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "02212" "0422" "053" "0122" "0511" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "02212" "05121"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "0522" "0213" "0422" "053" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "02121" "0513" "032" "0443" "0411" "0523"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "0121" "011" "02121" "02123" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "02212" "0422" "032" "0213" "0513"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "02122" "011" "0222" "0522" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "0513" "0433" "033" "011" "0233" "02211"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "032" "0431" "02213" "031" "0232" "02212"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "02212" "0412" "053" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "02123" "02123" "0422" "032" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05122" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "033" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1360))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "02311" "0211" "012" "02121" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "0511" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "0511" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "02121" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "032" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "053"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "053" "0511" "0431" "02312"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "02121" "011" "02212" "0521" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "02213" "0211" "0413" "0432" "0511" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "0511" "05122" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "032" "0511" "0511" "0521" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "0521" "02123" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "02122" "0211" "02121" "0213" "02212"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "0511" "0522" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "02311" "0233" "0242" "011" "053" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "0521" "031" "0412" "0521"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05123" "0211" "053" "02121" "033"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "053" "0242" "0211" "0433" "011" "0521"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "0511" "0413" "02212" "02123" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "053" "05121" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "032" "032" "0233" "0511" "05123" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "032" "011" "0511" "02214" "012" "032"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "033" "0421" "02212" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "0521" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "053" "0413" "02311" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "032" "0423" "011" "033" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "02311" "0442" "02122" "02121" "0511"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "02121" "0423" "0223" "011" "053"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "0511" "012" "0421" "02122" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "031" "0242" "0213" "0413" "02123"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "053" "0411" "033" "02122" "02212"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "032" "0413" "011" "0522" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "02312" "0413" "053" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "0511" "02312" "02312"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "053" "0412" "02214" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "032" "032" "053" "05121" "033" "05121"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "02312" "0232" "0411" "0242" "0233" "0521"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "053" "012" "0213" "0511"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "02123" "012" "0211" "02122" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "031" "0232" "0412" "0412" "034" "053"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "02311"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "02312" "032" "05121"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "033" "02121" "0521" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "033" "034" "0242" "0433" "033" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "031"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "0511" "0431" "0523" "0213" "02121"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "0521" "02121" "053" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05121" "0242" "011" "0442" "0421" "02122"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "034" "0233" "0213" "033"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "0511" "034" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "0511" "02123" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "0523" "02311" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "0511" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "02121" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "02211" "0413" "011" "032"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "02123" "0441" "011" "0521" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "053" "011" "0442" "02312"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "02312" "02121"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "033"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "0511" "011" "02211" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "034" "0233" "053" "031" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "02122" "033" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "02213" "0442" "053" "0431" "031" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "0511" "0242" "011" "053" "0241" "034"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "032" "02312" "02123" "032" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "0521" "034"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "0513" "053"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "02313" "0242" "02212" "0242" "031"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "032" "0223" "02212" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05121" "053" "033" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05122" "05121" "031" "033" "02313"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05121" "0242" "0431" "02121" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "053" "011" "02213" "0511" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "02312" "0511" "0521" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "02212" "0422" "053" "012" "0511" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "02212" "05121"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "0522" "0213" "0422" "053" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "02121" "0513" "032" "0443" "0411" "0523"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "02121" "02123" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "02212" "0422" "032" "0213" "0513"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "02122" "011" "0222" "0522" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "0513" "0433" "033" "011" "0233" "02211"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "032" "0431" "02213" "031" "0232" "02212"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "02212" "0412" "053" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "02123" "02123" "0422" "032" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05122" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "033" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1762))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "02121" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "0511" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "0511" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "02121" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "032" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "053"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "053" "0511" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "02121" "011" "02212" "0521" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "02213" "0211" "0413" "0432" "0511" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "0511" "05122" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "032" "0511" "0511" "0521" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "0521" "02123" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "02122" "0211" "02121" "0213" "02212"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "0511" "0522" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "0242" "011" "053" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "0521" "031" "0412" "0521"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05123" "0211" "053" "02121" "033"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "053" "0242" "0211" "0433" "011" "0521"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "0511" "0413" "02212" "02123" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "053" "05121" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "032" "032" "0233" "0511" "05123" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "032" "011" "0511" "02214" "012" "032"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "033" "0421" "02212" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "0521" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "053" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "032" "0423" "011" "033" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "02122" "02121" "0511"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "02121" "0423" "0223" "011" "053"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "0511" "012" "0421" "02122" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "031" "0242" "0213" "0413" "02123"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "053" "0411" "033" "02122" "02212"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "032" "0413" "011" "0522" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "053" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "0511" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "053" "0412" "02214" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "032" "032" "053" "05121" "033" "05121"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "0242" "0233" "0521"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "053" "012" "0213" "0511"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "02123" "012" "0211" "02122" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "031" "0232" "0412" "0412" "034" "053"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "0231" "032" "05121"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "033" "02121" "0521" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "033" "034" "0242" "0433" "033" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "031"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "0511" "0431" "0523" "0213" "02121"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "0521" "02121" "053" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05121" "0242" "011" "0442" "0421" "02122"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "034" "0233" "0213" "033"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "0511" "034" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "0511" "02123" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "0523" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "0511" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "02121" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "02211" "0413" "011" "032"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "02123" "0441" "011" "0521" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "053" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "02121"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "033"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "0511" "011" "02211" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "034" "0233" "053" "031" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "02122" "033" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "02213" "0442" "053" "0431" "031" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "0511" "0242" "011" "053" "0241" "034"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "032" "0231" "02123" "032" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "0521" "034"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "0513" "053"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "0242" "02212" "0242" "031"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "032" "0223" "02212" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05121" "053" "033" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05122" "05121" "031" "033" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05121" "0242" "0431" "02121" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "053" "011" "02213" "0511" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "0511" "0521" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "02212" "0422" "053" "012" "0511" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "02212" "05121"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "0522" "0213" "0422" "053" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "02121" "0513" "032" "0443" "0411" "0523"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "02121" "02123" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "02212" "0422" "032" "0213" "0513"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "02122" "011" "0222" "0522" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "0513" "0433" "033" "011" "0233" "02211"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "032" "0431" "02213" "031" "0232" "02212"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "02212" "0412" "053" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "02123" "02123" "0422" "032" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05122" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "033" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1794))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "02121" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "0511" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "0511" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "02121" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "032" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "053"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "053" "0511" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "02121" "011" "0221" "0521" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "0511" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "0511" "05122" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "032" "0511" "0511" "0521" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "0521" "02123" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "02122" "0211" "02121" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "0511" "0522" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "0242" "011" "053" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "0521" "031" "0412" "0521"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05123" "0211" "053" "02121" "033"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "053" "0242" "0211" "0433" "011" "0521"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "0511" "0413" "0221" "02123" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "053" "05121" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "032" "032" "0233" "0511" "05123" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "032" "011" "0511" "0221" "012" "032"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "033" "0421" "0221" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "0521" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "053" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "032" "0423" "011" "033" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "02122" "02121" "0511"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "02121" "0423" "0223" "011" "053"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "0511" "012" "0421" "02122" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "031" "0242" "0213" "0413" "02123"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "053" "0411" "033" "02122" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "032" "0413" "011" "0522" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "053" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "0511" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "053" "0412" "0221" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "032" "032" "053" "05121" "033" "05121"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "0242" "0233" "0521"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "053" "012" "0213" "0511"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "02123" "012" "0211" "02122" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "031" "0232" "0412" "0412" "034" "053"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "0231" "032" "05121"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "033" "02121" "0521" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "033" "034" "0242" "0433" "033" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "031"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "0511" "0431" "0523" "0213" "02121"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "0521" "02121" "053" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05121" "0242" "011" "0442" "0421" "02122"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "034" "0233" "0213" "033"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "0511" "034" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "0511" "02123" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "0523" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "0511" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "02121" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "0221" "0413" "011" "032"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "02123" "0441" "011" "0521" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "053" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "02121"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "033"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "0511" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "034" "0233" "053" "031" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "02122" "033" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "053" "0431" "031" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "0511" "0242" "011" "053" "0241" "034"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "032" "0231" "02123" "032" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "0521" "034"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "0513" "053"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "0242" "0221" "0242" "031"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "032" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05121" "053" "033" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05122" "05121" "031" "033" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05121" "0242" "0431" "02121" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "053" "011" "0221" "0511" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "0511" "0521" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "053" "012" "0511" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "0221" "05121"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "0522" "0213" "0422" "053" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "02121" "0513" "032" "0443" "0411" "0523"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "02121" "02123" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "0221" "0422" "032" "0213" "0513"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "02122" "011" "0222" "0522" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "0513" "0433" "033" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "032" "0431" "0221" "031" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "053" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "02123" "02123" "0422" "032" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05122" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "033" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2221))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "0511" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "0511" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "0212" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "032" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "053"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "053" "0511" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "0521" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "0511" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "0511" "05122" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "032" "0511" "0511" "0521" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "0521" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "0511" "0522" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "0242" "011" "053" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "0521" "031" "0412" "0521"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05123" "0211" "053" "0212" "033"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "053" "0242" "0211" "0433" "011" "0521"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "0511" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "053" "05121" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "032" "032" "0233" "0511" "05123" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "032" "011" "0511" "0221" "012" "032"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "033" "0421" "0221" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "0521" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "053" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "032" "0423" "011" "033" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "0511"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "053"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "0511" "012" "0421" "0212" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "031" "0242" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "053" "0411" "033" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "032" "0413" "011" "0522" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "053" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "0511" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "053" "0412" "0221" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "032" "032" "053" "05121" "033" "05121"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "0242" "0233" "0521"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "053" "012" "0213" "0511"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "031" "0232" "0412" "0412" "034" "053"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "0231" "032" "05121"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "033" "0212" "0521" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "033" "034" "0242" "0433" "033" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "031"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "0511" "0431" "0523" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "0521" "0212" "053" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05121" "0242" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "034" "0233" "0213" "033"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "0511" "034" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "0511" "0212" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "0523" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "0511" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "0221" "0413" "011" "032"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "0521" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "053" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "033"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "0511" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "034" "0233" "053" "031" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "033" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "053" "0431" "031" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "0511" "0242" "011" "053" "0241" "034"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "032" "0231" "0212" "032" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "0521" "034"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "0513" "053"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "0242" "0221" "0242" "031"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "032" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05121" "053" "033" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05122" "05121" "031" "033" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05121" "0242" "0431" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "053" "011" "0221" "0511" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "0511" "0521" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "053" "012" "0511" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "0221" "05121"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "0522" "0213" "0422" "053" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "0513" "032" "0443" "0411" "0523"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "0221" "0422" "032" "0213" "0513"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "0522" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "0513" "0433" "033" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "032" "0431" "0221" "031" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "053" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "032" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05122" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "033" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2573))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "0212" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "032" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "05" "05" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05122" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "032" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "0242" "011" "05" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "031" "0412" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05123" "0211" "05" "0212" "033"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "0242" "0211" "0433" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "05" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05121" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "032" "032" "0233" "05" "05123" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "032" "011" "05" "0221" "012" "032"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "033" "0421" "0221" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "05" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "032" "0423" "011" "033" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "05" "012" "0421" "0212" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "031" "0242" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "0411" "033" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "032" "0413" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "0412" "0221" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "032" "032" "05" "05121" "033" "05121"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "0242" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "031" "0232" "0412" "0412" "034" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "0231" "032" "05121"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "033" "0212" "05" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "033" "034" "0242" "0433" "033" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "031"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "0431" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05121" "0242" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "034" "0233" "0213" "033"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "05" "034" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "05" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "05" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "0221" "0413" "011" "032"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "033"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "034" "0233" "05" "031" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "033" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "0431" "031" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "0242" "011" "05" "0241" "034"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "032" "0231" "0212" "032" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "05" "034"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "0242" "0221" "0242" "031"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "032" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05121" "05" "033" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05122" "05121" "031" "033" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05121" "0242" "0431" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "0221" "05121"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "032" "0443" "0411" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "0221" "0422" "032" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "05" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "0433" "033" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "032" "0431" "0221" "031" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "05" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "032" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05122" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "033" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3054))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "0212" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "05" "05" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05122" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "0242" "011" "05" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "03" "0412" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05123" "0211" "05" "0212" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "0242" "0211" "0433" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "05" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05121" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05123" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "05" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "03" "0423" "011" "03" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "05" "012" "0421" "0212" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "0242" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "0411" "03" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "0413" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "0412" "0221" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05121" "03" "05121"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "0242" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "0412" "0412" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "0231" "03" "05121"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "0212" "05" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "0242" "0433" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "0431" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05121" "0242" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "03" "0233" "0213" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "05" "03" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "05" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "05" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "0221" "0413" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "0431" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "0242" "011" "05" "0241" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "0212" "03" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "0242" "0221" "0242" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05121" "05" "03" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05122" "05121" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05121" "0242" "0431" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "0221" "05121"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "03" "0443" "0411" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "0221" "0422" "03" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "05" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "0433" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "0431" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "05" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "03" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05122" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "03" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3076))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "0212" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "0211" "0242" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "05" "05" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "0242" "011" "05" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "03" "0412" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "0211" "05" "0212" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "0242" "0211" "0433" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "0241" "05" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "0242" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "05" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "0242" "03" "0423" "011" "03" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "05" "012" "0421" "0212" "0241"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "0242" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "0411" "03" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "0413" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "0412" "0221" "0413" "0241" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "0242" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "0412" "0412" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "0242" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "0212" "05" "0242" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "0242" "0433" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "0431" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "0241"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "0242" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "0242" "0232" "03" "0233" "0213" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "05" "03" "0242" "0241"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "0242"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "05" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "05" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "0241" "0412" "0221" "0413" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "0242" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "0431" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "0242" "011" "05" "0241" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "0212" "03" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "0242" "0221" "0242" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05" "05" "03" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05" "0242" "0431" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "0241" "011" "011" "0213" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "03" "0443" "0411" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "0241" "0221" "0422" "03" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "05" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "0433" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "0241" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "0431" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "05" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "03" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "0242" "05" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "03" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3130))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "0212" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "0211" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "05" "05" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "03" "0412" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "0211" "05" "0212" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "0211" "0433" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "024" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "05" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "0423" "011" "03" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "05" "012" "0421" "0212" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "024" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "0411" "03" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "0413" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "0412" "0221" "0413" "024" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "0412" "0412" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "0212" "05" "024" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "0433" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "0431" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "0213" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "05" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "05" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "0412" "0221" "0413" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "0431" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "0212" "03" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05" "05" "03" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05" "024" "0431" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "0213" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "03" "0443" "0411" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "0422" "03" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "05" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "0433" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "0431" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "05" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "03" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "024" "05" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "03" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3130))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "0212" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "0211" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "05" "05" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "03" "0412" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "0211" "05" "0212" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "0211" "0433" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "024" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "05" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "0423" "011" "03" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "05" "012" "0421" "0212" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "024" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "0411" "03" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "0413" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "0412" "0221" "0413" "024" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "0412" "0412" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "0212" "05" "024" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "0433" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "0431" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "0213" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "05" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "05" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "0412" "0221" "0413" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "0431" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "0212" "03" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05" "05" "03" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05" "024" "0431" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "0213" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "03" "0443" "0411" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "0422" "03" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "05" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "0433" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "0431" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "05" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "03" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "024" "05" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "03" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4059))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "0433" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "0411" "0432"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "0432" "0212" "0431" "0432" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "0211" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "0432" "0412" "05" "05" "0431" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "0432" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "03" "0412" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "0211" "05" "0212" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "0211" "0433" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "0432"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "024" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "0431" "05" "0213" "0431" "0431" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "0423" "011" "03" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "05" "012" "0421" "0212" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "024" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "0411" "03" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "0413" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "0432" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "0412" "0221" "0413" "024" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "0431" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "0412" "0412" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "0431" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "0212" "05" "024" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "0433" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "0431" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "0432" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "0432" "0441" "0412" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "0213" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "0433" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "05" "0231" "0432" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "0431" "05" "0433" "0432" "0433" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "0432" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "0412" "0221" "0413" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "0433" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "0432" "011" "0223" "0211" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "0431" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "0432" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "0212" "03" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "0433" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05" "05" "03" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05" "024" "0431" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "0432" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "0431"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "0213" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "03" "0443" "0411" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "0422" "03" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "05" "0432"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "0433" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "0431" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "05" "0431" "0232" "0431"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "03" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "024" "05" "011" "0431"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "03" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4238))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "0413" "0413" "0423" "043" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "0411" "043"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "043" "0212" "043" "043" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "0211" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "0412" "0211" "0412" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "043" "0412" "05" "05" "043" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "0413"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "0413" "043" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "0412" "011" "0413" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "0411"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "03" "0412" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "0211" "05" "0212" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "0211" "043" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "0413" "0221" "0212" "0412"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "043"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "024" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "043" "05" "0213" "043" "043" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "0413" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "0423" "011" "03" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "0412" "05" "012" "0421" "0212" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "024" "0213" "0413" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "0411" "03" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "0413" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "0413" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "043" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "0412" "0221" "0413" "024" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "0411" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "043" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "0412" "0212" "012" "0211" "0212" "0411"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "0412" "0412" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "043" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "0212" "05" "024" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "043" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "043" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "043" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "0413" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "0412" "0223" "043" "0441" "0412" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "0213" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "0412" "0232" "043" "0413" "0412" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "0412" "0423" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "0413" "05" "0231" "043" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "043" "05" "043" "043" "043" "0411"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "0413" "043" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "0412" "0221" "0413" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "0411" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "043" "0233" "0412" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "043" "011" "0223" "0211" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "0413" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "0412" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "043" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "0412" "0232" "0413" "043" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "0212" "03" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "0411" "0211" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "043" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "0411" "05" "05" "03" "0413" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "0412" "05" "024" "043" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "043" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "043"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "0213" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "0412" "0412"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "03" "0443" "0411" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "0412" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "0422" "03" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "0413" "0212" "011" "0222" "05" "043"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "043" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "043" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "0412" "05" "043" "0232" "043"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "03" "0413" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "024" "05" "011" "043"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "0411" "03" "0412"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5112))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "0211" "012" "0212" "0211"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "041" "041" "0423" "043" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "041" "043"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "043" "0212" "043" "043" "0223" "0211"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "0211" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "041" "0211" "041" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "043" "041" "05" "05" "043" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "0212" "011" "0221" "05" "0422" "041"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "0211" "041" "043" "05" "0211"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05" "011" "0211"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "041" "011" "041" "05" "0212" "0213"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "0212" "0211" "0212" "0213" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "0213" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "041"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "0211" "05" "03" "041" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "0211" "05" "0212" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "0211" "043" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "041" "0221" "0212" "041"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "043"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "024" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "043" "05" "0213" "043" "043" "0211"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "041" "0231" "013" "0213"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "0423" "011" "03" "0211"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "0212" "0212" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "0212" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "041" "05" "012" "0421" "0212" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "024" "0213" "041" "0212"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "041" "03" "0212" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "041" "011" "05" "0211" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "041" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "043" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "041" "0221" "041" "024" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "041" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "043" "05" "012" "0213" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "041" "0212" "012" "0211" "0212" "041"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "041" "041" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "0211" "012" "0422" "011" "043" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "0213" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "0212" "05" "024" "0213" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "043" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "043" "05" "0213" "0212"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "043" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "041" "05" "0212" "05" "0213" "0211"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "041" "0223" "043" "0441" "041" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "0442" "0421" "0212"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "0213" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "041" "0232" "043" "041" "041" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "041" "0423" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "0213" "05" "0212" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "041" "05" "0231" "043" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "043" "05" "043" "043" "043" "041"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "041" "043" "0212" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "041" "0221" "041" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "0212" "0441" "011" "05" "041" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "043" "0233" "041" "011" "0231" "0212"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "043" "011" "0223" "0211" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "041" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "041" "0211"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "0212" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "043" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "041" "0232" "041" "043" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "0212" "03" "0213"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "0213" "0223" "041" "0211" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "0213" "043" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "0211"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "041" "05" "05" "03" "041" "0211"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "041" "05" "024" "043" "0212" "0211"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "043" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "043"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "0213" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "0213" "0422" "05" "041" "041"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "0212" "05" "03" "0443" "041" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "0212" "0212" "041" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "0422" "03" "0213" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "041" "0212" "011" "0222" "05" "043"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "043" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "0211" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "043" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "041" "05" "043" "0232" "043"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "0212" "0212" "0422" "03" "041" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "0211" "024" "05" "011" "043"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "041" "03" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5268))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "021" "012" "021" "021"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "041" "041" "0423" "043" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "041" "043"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "043" "021" "043" "043" "0223" "021"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "021" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "041" "021" "041" "0422" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "043" "041" "05" "05" "043" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "021" "011" "0221" "05" "0422" "041"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "021" "041" "043" "05" "021"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "0422" "05" "05" "011" "021"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "041" "011" "041" "05" "021" "021"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "021" "021" "021" "021" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "0422" "05" "05" "0223" "021" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "041"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "021" "05" "03" "041" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "021" "05" "021" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "021" "043" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "041" "0221" "021" "041"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "0423"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "043"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "0421" "0221" "024" "0442" "0422"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "043" "05" "021" "043" "043" "021"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "041" "0231" "013" "021"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "0423" "011" "03" "021"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "021" "021" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "021" "0423" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "041" "05" "012" "0421" "021" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "024" "021" "041" "021"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "0423" "05" "041" "03" "021" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "041" "011" "05" "021" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "0421" "0423" "0231" "041" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "043" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "041" "0221" "041" "024" "0422"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "041" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "043" "05" "012" "021" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "041" "021" "012" "021" "021" "041"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "041" "041" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "021" "012" "0422" "011" "043" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "021" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "021" "05" "024" "021" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "043" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "0423" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "043" "05" "021" "021"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "043" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "041" "05" "021" "05" "021" "021"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "041" "0223" "043" "0441" "041" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "0442" "0421" "021"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "021" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "041" "0232" "043" "041" "041" "0421"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "041" "0423" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "021" "05" "021" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "041" "05" "0231" "043" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "043" "05" "043" "043" "043" "041"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "041" "043" "021" "0423" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "041" "0221" "041" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "021" "0441" "011" "05" "041" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "043" "0233" "041" "011" "0231" "021"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "043" "011" "0223" "021" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "041" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "041" "021"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "021" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "043" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "041" "0232" "041" "043" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "021" "03" "021"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "021" "0223" "041" "021" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "021" "043" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "021"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "041" "05" "05" "03" "041" "021"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "041" "05" "024" "043" "021" "021"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "043" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "0422" "05" "012" "05" "043"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "021" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "021" "0422" "05" "041" "041"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "021" "05" "03" "0443" "041" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "021" "021" "041" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "0422" "03" "021" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "041" "021" "011" "0222" "05" "043"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "043" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "0421" "0223" "021" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "043" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "041" "05" "043" "0232" "043"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "021" "021" "0422" "03" "041" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "021" "024" "05" "011" "043"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "041" "03" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5287))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "0443" "0231" "021" "012" "021" "021"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "041" "041" "042" "043" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "0441" "0223" "05" "0222" "041" "043"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "043" "021" "043" "043" "0223" "021"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "0443" "03" "0232" "021" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "041" "021" "041" "042" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "043" "041" "05" "05" "043" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "021" "011" "0221" "05" "042" "041"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "021" "041" "043" "05" "021"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "042" "05" "05" "011" "021"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "0443"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "041" "011" "041" "05" "021" "021"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "0443" "021" "021" "021" "021" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "042" "05" "05" "0223" "021" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "041"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "021" "05" "03" "041" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "021" "05" "021" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "021" "043" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "041" "0221" "021" "041"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "0442" "05" "05" "0233" "042"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "043"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "042" "0221" "024" "0442" "042"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "043" "05" "021" "043" "043" "021"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "041" "0231" "013" "021"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "042" "011" "03" "021"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "0443" "0231" "0442" "021" "021" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "021" "042" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "041" "05" "012" "042" "021" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "0443" "03" "024" "021" "041" "021"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "042" "05" "041" "03" "021" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "041" "011" "05" "021" "0442"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "042" "042" "0231" "041" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "0443" "012" "043" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "041" "0221" "041" "024" "042"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "041" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "043" "05" "012" "021" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "041" "021" "012" "021" "021" "041"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "041" "041" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "021" "012" "042" "011" "043" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "021" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "021" "05" "024" "021" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "043" "03" "0442"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "0442" "011" "011" "0442" "042" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "043" "05" "021" "021"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "043" "011" "0442" "0442" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "041" "05" "021" "05" "021" "021"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "041" "0223" "043" "0441" "041" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "0442" "042" "021"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "021" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "041" "0232" "043" "041" "041" "042"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "041" "042" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "0443" "0441" "021" "05" "021" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "041" "05" "0231" "043" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "043" "05" "043" "043" "043" "041"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "041" "043" "021" "042" "011" "0443"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "041" "0221" "041" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "021" "0441" "011" "05" "041" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "0442" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "043" "0233" "041" "011" "0231" "021"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "043" "011" "0223" "021" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "041" "05" "011" "0221" "0441" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "041" "021"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "021" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "0442" "05" "043" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "041" "0232" "041" "043" "0441" "0442"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "021" "03" "021"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "021" "0223" "041" "021" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "021" "043" "0442" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "021"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "041" "05" "05" "03" "041" "021"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "041" "05" "024" "043" "021" "021"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "043" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "042" "05" "012" "05" "043"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "021" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "021" "042" "05" "041" "041"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "021" "05" "03" "0443" "041" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "021" "021" "041" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "042" "03" "021" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "041" "021" "011" "0222" "05" "043"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "043" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "042" "0223" "021" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "043" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "041" "05" "043" "0232" "043"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "021" "021" "042" "03" "041" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "021" "024" "05" "011" "043"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "041" "03" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6017))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "044" "0231" "021" "012" "021" "021"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "041" "041" "042" "043" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "044" "0223" "05" "0222" "041" "043"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "043" "021" "043" "043" "0223" "021"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "044" "03" "0232" "021" "024" "0223"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "041" "021" "041" "042" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "043" "041" "05" "05" "043" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "021" "011" "0221" "05" "042" "041"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "0221" "021" "041" "043" "05" "021"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "042" "05" "05" "011" "021"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "044"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "041" "011" "041" "05" "021" "021"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "044" "021" "021" "021" "021" "0221"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "042" "05" "05" "0223" "021" "0222"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "041"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "021" "05" "03" "041" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "021" "05" "021" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "021" "043" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "041" "0221" "021" "041"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "044" "05" "05" "0233" "042"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "043"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "0221" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "042" "0221" "024" "044" "042"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "043" "05" "021" "043" "043" "021"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "041" "0231" "013" "021"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "042" "011" "03" "021"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "044" "0231" "044" "021" "021" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "021" "042" "0223" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "041" "05" "012" "042" "021" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "044" "03" "024" "021" "041" "021"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "042" "05" "041" "03" "021" "0221"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "041" "011" "05" "021" "044"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "042" "042" "0231" "041" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "044" "012" "043" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "041" "0221" "041" "024" "042"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "041" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "043" "05" "012" "021" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "041" "021" "012" "021" "021" "041"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "041" "041" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "021" "012" "042" "011" "043" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "021" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "021" "05" "024" "021" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "043" "03" "044"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "044" "011" "011" "044" "042" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "043" "05" "021" "021"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "0222" "043" "011" "044" "044" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "041" "05" "021" "05" "021" "021"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "041" "0223" "043" "044" "041" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "044" "042" "021"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "021" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "041" "0232" "043" "041" "041" "042"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "041" "042" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "044" "044" "021" "05" "021" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "0223" "041" "05" "0231" "043" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "043" "05" "043" "043" "043" "041"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "041" "043" "021" "042" "011" "044"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "041" "0221" "041" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "021" "044" "011" "05" "041" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "0222" "05" "011" "044" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "043" "0233" "041" "011" "0231" "021"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "043" "011" "0223" "021" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "041" "05" "011" "0221" "044" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "041" "021"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "0222" "021" "03" "011" "0222" "0222"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "0221" "044" "05" "043" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "041" "0232" "041" "043" "044" "044"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "021" "03" "021"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "021" "0223" "041" "021" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "021" "043" "044" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "0223" "0231" "024" "0221" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "0223" "0221" "021"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "041" "05" "05" "03" "041" "021"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "041" "05" "024" "043" "021" "021"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "0221" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "043" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "0221" "042" "05" "012" "05" "043"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "021" "0221" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "021" "042" "05" "041" "041"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "021" "05" "03" "044" "041" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "021" "021" "041" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "0221" "042" "03" "021" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "041" "021" "011" "0222" "05" "043"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "043" "03" "011" "0233" "0221"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "042" "0223" "021" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "043" "0221" "03" "0232" "0221"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "0221" "041" "05" "043" "0232" "043"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "021" "021" "042" "03" "041" "0222"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "0223" "021" "024" "05" "011" "043"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "041" "03" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6587))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "044" "0231" "021" "012" "021" "021"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "041" "041" "042" "043" "05" "0232"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "044" "022" "05" "022" "041" "043"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "043" "021" "043" "043" "022" "021"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "044" "03" "0232" "021" "024" "022"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "0233" "041" "021" "041" "042" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "043" "041" "05" "05" "043" "0231"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "021" "011" "022" "05" "042" "041"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "022" "021" "041" "043" "05" "021"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "0232" "042" "05" "05" "011" "021"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "044"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "041" "011" "041" "05" "021" "021"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "044" "021" "021" "021" "021" "022"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "042" "05" "05" "022" "021" "022"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "0231" "0233" "024" "011" "05" "041"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "021" "05" "03" "041" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "021" "05" "021" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "021" "043" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "041" "022" "021" "041"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "044" "05" "05" "0233" "042"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "0233" "05" "05" "043"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "022" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "042" "022" "024" "044" "042"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "043" "05" "021" "043" "043" "021"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "041" "0231" "013" "021"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "042" "011" "03" "021"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "044" "0231" "044" "021" "021" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "021" "042" "022" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "041" "05" "012" "042" "021" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "044" "03" "024" "021" "041" "021"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "042" "05" "041" "03" "021" "022"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "041" "011" "05" "021" "044"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "042" "042" "0231" "041" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "044" "012" "043" "05" "0231" "0231"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "041" "022" "041" "024" "042"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "0231" "0232" "041" "024" "0233" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "0232" "043" "05" "012" "021" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "041" "021" "012" "021" "021" "041"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "0232" "041" "041" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "021" "012" "042" "011" "043" "0231"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "021" "011" "024" "0231" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "021" "05" "024" "021" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "043" "03" "044"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "044" "011" "011" "044" "042" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "043" "05" "021" "021"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "022" "043" "011" "044" "044" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "041" "05" "021" "05" "021" "021"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "041" "022" "043" "044" "041" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "044" "042" "021"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "0232" "03" "0233" "021" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "041" "0232" "043" "041" "041" "042"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "041" "042" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "044" "044" "021" "05" "021" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "022" "041" "05" "0231" "043" "0233"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "043" "05" "043" "043" "043" "041"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "041" "043" "021" "042" "011" "044"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "041" "022" "041" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "021" "044" "011" "05" "041" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "022" "05" "011" "044" "0231"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "043" "0233" "041" "011" "0231" "021"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "043" "011" "022" "021" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "041" "05" "011" "022" "044" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "0233" "05" "03" "041" "021"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "022" "021" "03" "011" "022" "022"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "022" "044" "05" "043" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "041" "0232" "041" "043" "044" "044"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "0231" "021" "03" "021"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "021" "022" "041" "021" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "021" "043" "044" "0232" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "022" "0231" "024" "022" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "022" "022" "021"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "041" "05" "05" "03" "041" "021"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "0231"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "041" "05" "024" "043" "021" "021"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "022" "05" "0232"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "043" "0231" "05" "05" "011" "0232"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "022" "042" "05" "012" "05" "043"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "021" "022" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "021" "042" "05" "041" "041"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "021" "05" "03" "044" "041" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "021" "021" "041" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "022" "042" "03" "021" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "041" "021" "011" "022" "05" "043"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "043" "03" "011" "0233" "022"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "042" "022" "021" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "043" "022" "03" "0232" "022"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "022" "041" "05" "043" "0232" "043"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "021" "021" "042" "03" "041" "022"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "022" "021" "024" "05" "011" "043"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "041" "03" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11436))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "044" "023" "021" "012" "021" "021"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "041" "041" "042" "043" "05" "023"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "044" "022" "05" "022" "041" "043"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "043" "021" "043" "043" "022" "021"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "044" "03" "023" "021" "024" "022"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "023" "041" "021" "041" "042" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "043" "041" "05" "05" "043" "023"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "021" "011" "022" "05" "042" "041"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "022" "021" "041" "043" "05" "021"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "023" "042" "05" "05" "011" "021"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "044"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "041" "011" "041" "05" "021" "021"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "044" "021" "021" "021" "021" "022"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "042" "05" "05" "022" "021" "022"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "023" "023" "024" "011" "05" "041"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "021" "05" "03" "041" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "021" "05" "021" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "021" "043" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "041" "022" "021" "041"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "044" "05" "05" "023" "042"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "023" "05" "05" "043"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "022" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "042" "022" "024" "044" "042"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "043" "05" "021" "043" "043" "021"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "041" "023" "013" "021"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "042" "011" "03" "021"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "044" "023" "044" "021" "021" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "021" "042" "022" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "041" "05" "012" "042" "021" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "044" "03" "024" "021" "041" "021"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "042" "05" "041" "03" "021" "022"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "041" "011" "05" "021" "044"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "042" "042" "023" "041" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "044" "012" "043" "05" "023" "023"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "041" "022" "041" "024" "042"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "023" "023" "041" "024" "023" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "023" "043" "05" "012" "021" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "041" "021" "012" "021" "021" "041"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "023" "041" "041" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "021" "012" "042" "011" "043" "023"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "021" "011" "024" "023" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "021" "05" "024" "021" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "043" "03" "044"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "044" "011" "011" "044" "042" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "043" "05" "021" "021"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "022" "043" "011" "044" "044" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "041" "05" "021" "05" "021" "021"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "041" "022" "043" "044" "041" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "044" "042" "021"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "023" "03" "023" "021" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "041" "023" "043" "041" "041" "042"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "041" "042" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "044" "044" "021" "05" "021" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "022" "041" "05" "023" "043" "023"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "043" "05" "043" "043" "043" "041"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "041" "043" "021" "042" "011" "044"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "041" "022" "041" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "021" "044" "011" "05" "041" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "022" "05" "011" "044" "023"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "043" "023" "041" "011" "023" "021"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "043" "011" "022" "021" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "041" "05" "011" "022" "044" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "023" "05" "03" "041" "021"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "022" "021" "03" "011" "022" "022"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "022" "044" "05" "043" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "041" "023" "041" "043" "044" "044"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "023" "021" "03" "021"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "021" "022" "041" "021" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "021" "043" "044" "023" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "022" "023" "024" "022" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "022" "022" "021"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "041" "05" "05" "03" "041" "021"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "023"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "041" "05" "024" "043" "021" "021"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "022" "05" "023"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "043" "023" "05" "05" "011" "023"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "022" "042" "05" "012" "05" "043"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "021" "022" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "021" "042" "05" "041" "041"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "021" "05" "03" "044" "041" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "021" "021" "041" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "022" "042" "03" "021" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "041" "021" "011" "022" "05" "043"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "043" "03" "011" "023" "022"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "042" "022" "021" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "043" "022" "03" "023" "022"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "022" "041" "05" "043" "023" "043"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "021" "021" "042" "03" "041" "022"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "022" "021" "024" "05" "011" "043"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "041" "03" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14470))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "04" "023" "021" "012" "021" "021"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "04" "04" "04" "04" "05" "023"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "04" "022" "05" "022" "04" "04"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "04" "021" "04" "04" "022" "021"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "04" "03" "023" "021" "024" "022"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "023" "04" "021" "04" "04" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "04" "04" "05" "05" "04" "023"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "021" "011" "022" "05" "04" "04"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "022" "021" "04" "04" "05" "021"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "023" "04" "05" "05" "011" "021"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "011" "03" "05" "05" "05" "04"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "04" "011" "04" "05" "021" "021"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "04" "021" "021" "021" "021" "022"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "04" "05" "05" "022" "021" "022"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "023" "023" "024" "011" "05" "04"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "013" "021" "05" "03" "04" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "012" "05" "021" "05" "021" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "021" "04" "011" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "04" "022" "021" "04"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "011" "04" "05" "05" "023" "04"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "023" "05" "05" "04"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "011" "05" "022" "012" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "04" "022" "024" "04" "04"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "04" "05" "021" "04" "04" "021"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "011" "05" "04" "023" "013" "021"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "04" "011" "03" "021"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "04" "023" "04" "021" "021" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "011" "021" "04" "022" "011" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "04" "05" "012" "04" "021" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "04" "03" "024" "021" "04" "021"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "04" "05" "04" "03" "021" "022"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "04" "011" "05" "021" "04"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "04" "04" "023" "04" "05" "011"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "04" "012" "04" "05" "023" "023"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "04" "022" "04" "024" "04"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "023" "023" "04" "024" "023" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "023" "04" "05" "012" "021" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "04" "021" "012" "021" "021" "04"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "023" "04" "04" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "021" "012" "04" "011" "04" "023"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "021" "011" "024" "023" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "021" "05" "024" "021" "011"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "04" "03" "04"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "04" "011" "011" "04" "04" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "011" "05" "04" "05" "021" "021"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "022" "04" "011" "04" "04" "011"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "04" "05" "021" "05" "021" "021"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "04" "022" "04" "04" "04" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "011" "04" "04" "021"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "023" "03" "023" "021" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "04" "023" "04" "04" "04" "04"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "04" "04" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "04" "04" "021" "05" "021" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "022" "04" "05" "023" "04" "023"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "04" "05" "04" "04" "04" "04"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "04" "04" "021" "04" "011" "04"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "04" "022" "04" "011" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "021" "04" "011" "05" "04" "012"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "022" "05" "011" "04" "023"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "04" "023" "04" "011" "023" "021"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "011" "04" "011" "022" "021" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "04" "05" "011" "022" "04" "011"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "023" "05" "03" "04" "021"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "022" "021" "03" "011" "022" "022"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "022" "04" "05" "04" "03" "011"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "011" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "04" "023" "04" "04" "04" "04"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "013" "03" "023" "021" "03" "021"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "021" "022" "04" "021" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "021" "04" "04" "023" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "022" "023" "024" "022" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "013" "012" "03" "022" "022" "021"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "04" "05" "05" "03" "04" "021"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "012" "05" "05" "03" "03" "023"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "04" "05" "024" "04" "021" "021"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "011" "05" "011" "022" "05" "023"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "04" "023" "05" "05" "011" "023"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "022" "04" "05" "012" "05" "04"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "011" "011" "021" "022" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "021" "04" "05" "04" "04"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "021" "05" "03" "04" "04" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "012" "011" "021" "021" "04" "013"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "022" "04" "03" "021" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "04" "021" "011" "022" "05" "04"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "04" "03" "011" "023" "022"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "04" "022" "021" "024" "011" "011"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "04" "022" "03" "023" "022"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "022" "04" "05" "04" "023" "04"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "021" "021" "04" "03" "04" "022"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "022" "021" "024" "05" "011" "04"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "04" "03" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15528))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "04" "023" "021" "01" "021" "021"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "04" "04" "04" "04" "05" "023"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "04" "022" "05" "022" "04" "04"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "04" "021" "04" "04" "022" "021"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "04" "03" "023" "021" "024" "022"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "023" "04" "021" "04" "04" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "04" "04" "05" "05" "04" "023"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "021" "01" "022" "05" "04" "04"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "022" "021" "04" "04" "05" "021"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "023" "04" "05" "05" "01" "021"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "01" "03" "05" "05" "05" "04"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "04" "01" "04" "05" "021" "021"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "04" "021" "021" "021" "021" "022"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "04" "05" "05" "022" "021" "022"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "023" "023" "024" "01" "05" "04"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "01" "021" "05" "03" "04" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "01" "05" "021" "05" "021" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "024" "021" "04" "01" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "024" "05" "04" "022" "021" "04"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "01" "04" "05" "05" "023" "04"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "023" "05" "05" "04"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "01" "05" "022" "01" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "04" "022" "024" "04" "04"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "04" "05" "021" "04" "04" "021"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "01" "05" "04" "023" "01" "021"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "024" "03" "04" "01" "03" "021"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "04" "023" "04" "021" "021" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "01" "021" "04" "022" "01" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "04" "05" "01" "04" "021" "024"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "04" "03" "024" "021" "04" "021"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "04" "05" "04" "03" "021" "022"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "04" "01" "05" "021" "04"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "04" "04" "023" "04" "05" "01"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "04" "01" "04" "05" "023" "023"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "04" "022" "04" "024" "04"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "023" "023" "04" "024" "023" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "023" "04" "05" "01" "021" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "04" "021" "01" "021" "021" "04"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "023" "04" "04" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "021" "01" "04" "01" "04" "023"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "021" "01" "024" "023" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "021" "05" "024" "021" "01"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "024" "04" "03" "04"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "04" "01" "01" "04" "04" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "01" "05" "04" "05" "021" "021"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "022" "04" "01" "04" "04" "01"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "04" "05" "021" "05" "021" "021"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "04" "022" "04" "04" "04" "024"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "024" "01" "04" "04" "021"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "024" "023" "03" "023" "021" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "04" "023" "04" "04" "04" "04"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "04" "04" "05" "03" "024" "024"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "04" "04" "021" "05" "021" "024"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "022" "04" "05" "023" "04" "023"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "04" "05" "04" "04" "04" "04"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "04" "04" "021" "04" "01" "04"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "024" "04" "022" "04" "01" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "021" "04" "01" "05" "04" "01"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "024" "022" "05" "01" "04" "023"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "04" "023" "04" "01" "023" "021"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "01" "04" "01" "022" "021" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "04" "05" "01" "022" "04" "01"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "023" "05" "03" "04" "021"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "022" "021" "03" "01" "022" "022"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "022" "04" "05" "04" "03" "01"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "024" "01" "05" "024" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "04" "023" "04" "04" "04" "04"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "01" "03" "023" "021" "03" "021"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "021" "022" "04" "021" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "021" "04" "04" "023" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "022" "023" "024" "022" "024" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "01" "01" "03" "022" "022" "021"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "04" "05" "05" "03" "04" "021"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "01" "05" "05" "03" "03" "023"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "04" "05" "024" "04" "021" "021"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "01" "05" "01" "022" "05" "023"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "04" "023" "05" "05" "01" "023"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "022" "04" "05" "01" "05" "04"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "024" "01" "01" "021" "022" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "021" "04" "05" "04" "04"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "021" "05" "03" "04" "04" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "01" "01" "021" "021" "04" "01"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "024" "022" "04" "03" "021" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "04" "021" "01" "022" "05" "04"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "04" "03" "01" "023" "022"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "04" "022" "021" "024" "01" "01"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "04" "022" "03" "023" "022"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "022" "04" "05" "04" "023" "04"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "021" "021" "04" "03" "04" "022"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "022" "021" "024" "05" "01" "04"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "04" "03" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 33866))
#> TCGA.G9.6343.01 TCGA.KK.A8IA.01 TCGA.KK.A6E4.01 TCGA.EJ.AB20.01 TCGA.H9.7775.01 TCGA.XJ.A9DX.01
#> "04" "02" "02" "01" "02" "02"
#> TCGA.KK.A6E6.01 TCGA.G9.6339.01 TCGA.EJ.5509.01 TCGA.EJ.5521.01 TCGA.YL.A8SB.01 TCGA.V1.A9OF.01
#> "04" "04" "04" "04" "05" "02"
#> TCGA.CH.5754.01 TCGA.EJ.7125.01 TCGA.EJ.7797.01 TCGA.YL.A9WI.01 TCGA.EJ.7314.01 TCGA.XA.A8JR.01
#> "04" "02" "05" "02" "04" "04"
#> TCGA.EJ.7781.01 TCGA.QU.A6IN.01 TCGA.CH.5751.01 TCGA.V1.A8WL.01 TCGA.HC.A6AO.01 TCGA.KK.A7B3.01
#> "04" "02" "04" "04" "02" "02"
#> TCGA.XK.AAJT.01 TCGA.EJ.AB27.01 TCGA.CH.5788.01 TCGA.KK.A8I5.01 TCGA.YL.A8S9.01 TCGA.CH.5761.01
#> "04" "03" "02" "02" "02" "02"
#> TCGA.KK.A7AZ.01 TCGA.G9.6366.01 TCGA.HC.7819.01 TCGA.KC.A4BN.01 TCGA.KK.A8IG.01 TCGA.ZG.A8QW.01
#> "02" "04" "02" "04" "04" "05"
#> TCGA.EJ.7786.01 TCGA.J4.A83K.01 TCGA.YL.A8HK.01 TCGA.EJ.5501.01 TCGA.EJ.8470.01 TCGA.J9.A8CL.01
#> "04" "04" "05" "05" "04" "02"
#> TCGA.EJ.A7NF.01 TCGA.CH.5762.11 TCGA.XK.AAJA.01 TCGA.EJ.7330.01 TCGA.VP.AA1N.01 TCGA.EJ.5524.01
#> "02" "01" "02" "05" "04" "04"
#> TCGA.KK.A6E8.01 TCGA.HC.7821.01 TCGA.HC.7209.01 TCGA.HC.7742.01 TCGA.G9.6351.01 TCGA.EJ.8474.01
#> "02" "02" "04" "04" "05" "02"
#> TCGA.HC.7075.01 TCGA.J9.A8CP.01 TCGA.KK.A8IM.01 TCGA.G9.6348.01 TCGA.CH.5789.01 TCGA.KC.A7F6.01
#> "02" "04" "05" "05" "01" "02"
#> TCGA.G9.6333.11 TCGA.KC.A4BL.01 TCGA.J4.A67Q.01 TCGA.2A.A8VL.01 TCGA.V1.A9ZK.01 TCGA.V1.A9O5.01
#> "01" "03" "05" "05" "05" "04"
#> TCGA.VP.A879.01 TCGA.HC.7819.11 TCGA.VN.A88Q.01 TCGA.HC.7737.01 TCGA.V1.A8WS.01 TCGA.HC.8213.01
#> "04" "01" "04" "05" "02" "02"
#> TCGA.M7.A721.01 TCGA.ZG.A9LZ.01 TCGA.CH.5765.01 TCGA.V1.A8WW.01 TCGA.HC.A48F.01 TCGA.V1.A9OQ.01
#> "04" "02" "02" "02" "02" "02"
#> TCGA.EJ.5514.01 TCGA.G9.6384.01 TCGA.V1.A9ZG.01 TCGA.YL.A8HM.01 TCGA.G9.6377.01 TCGA.M7.A722.01
#> "04" "05" "05" "02" "02" "02"
#> TCGA.G9.6361.01 TCGA.EJ.5511.01 TCGA.ZG.A9KY.01 TCGA.EJ.7784.11 TCGA.ZG.A9LN.01 TCGA.EJ.5526.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.HC.7820.11 TCGA.YJ.A8SW.01 TCGA.EJ.7794.01 TCGA.EJ.A46B.01 TCGA.EJ.5542.01 TCGA.YL.A9WJ.01
#> "01" "02" "05" "03" "04" "05"
#> TCGA.EJ.7328.11 TCGA.V1.A9Z8.01 TCGA.EJ.A46F.01 TCGA.YL.A8SK.01 TCGA.MG.AAMC.01 TCGA.X4.A8KS.01
#> "01" "05" "02" "05" "02" "03"
#> TCGA.J4.A67M.01 TCGA.ZG.A9L0.01 TCGA.HC.7077.01 TCGA.CH.5769.01 TCGA.G9.6353.11 TCGA.G9.6499.01
#> "05" "02" "02" "04" "01" "05"
#> TCGA.EJ.5519.01 TCGA.J4.A67T.01 TCGA.HC.7748.01 TCGA.VN.A88R.01 TCGA.H9.A6BY.01 TCGA.G9.6365.01
#> "02" "05" "04" "02" "02" "04"
#> TCGA.EJ.7317.11 TCGA.G9.7510.01 TCGA.KK.A6E3.01 TCGA.G9.6336.01 TCGA.EJ.5517.01 TCGA.V1.A8MG.01
#> "01" "04" "05" "05" "02" "04"
#> TCGA.KC.A7FE.01 TCGA.HC.7817.01 TCGA.J4.AAU2.01 TCGA.V1.A8MJ.01 TCGA.VP.A87C.01 TCGA.EJ.A7NN.01
#> "03" "03" "02" "05" "05" "04"
#> TCGA.HC.A8D0.01 TCGA.EJ.7792.11 TCGA.EJ.5497.01 TCGA.Y6.A9XI.01 TCGA.HC.7752.11 TCGA.SU.A7E7.01
#> "03" "01" "05" "02" "01" "03"
#> TCGA.G9.6342.11 TCGA.HC.8265.01 TCGA.CH.5737.01 TCGA.G9.6338.01 TCGA.KK.A7AV.01 TCGA.EJ.7218.01
#> "03" "04" "02" "02" "04" "04"
#> TCGA.YL.A8SC.01 TCGA.XK.AAJR.01 TCGA.2A.AAYF.01 TCGA.V1.A8X3.01 TCGA.KK.A6DY.01 TCGA.M7.A71Z.01
#> "04" "05" "02" "04" "04" "02"
#> TCGA.EJ.7123.11 TCGA.G9.6363.11 TCGA.KK.A8I8.01 TCGA.KC.A4BV.01 TCGA.G9.6332.11 TCGA.CH.5750.01
#> "01" "05" "04" "02" "01" "02"
#> TCGA.ZG.A9ND.01 TCGA.EJ.A65B.01 TCGA.QU.A6IO.01 TCGA.EJ.5503.01 TCGA.ZG.A9LU.01 TCGA.EJ.8469.01
#> "02" "03" "04" "01" "03" "02"
#> TCGA.XJ.A83H.01 TCGA.EJ.7315.01 TCGA.ZG.A8QY.01 TCGA.YL.A8SP.01 TCGA.CH.5791.01 TCGA.V1.A9OY.01
#> "04" "02" "04" "02" "02" "05"
#> TCGA.KC.A4BO.01 TCGA.HC.A76X.01 TCGA.YL.A8SO.01 TCGA.KK.A8IF.01 TCGA.EJ.A7NK.01 TCGA.ZG.A9L4.01
#> "01" "02" "04" "02" "01" "05"
#> TCGA.EJ.5522.01 TCGA.HC.7747.01 TCGA.EJ.7125.11 TCGA.ZG.A9M4.01 TCGA.EJ.A65D.01 TCGA.HC.A4ZV.01
#> "04" "05" "01" "04" "02" "02"
#> TCGA.G9.A9S0.01 TCGA.EJ.5506.01 TCGA.KK.A7AP.01 TCGA.VP.A87D.01 TCGA.TP.A8TT.01 TCGA.KK.A8II.01
#> "04" "03" "02" "02" "04" "02"
#> TCGA.V1.A9Z9.01 TCGA.ZG.A9LS.01 TCGA.HC.7232.01 TCGA.EJ.A8FO.01 TCGA.J9.A52B.01 TCGA.CH.5767.01
#> "04" "05" "04" "03" "02" "02"
#> TCGA.J4.AATV.01 TCGA.HC.7081.01 TCGA.CH.5743.01 TCGA.V1.A9OH.01 TCGA.CH.5752.01 TCGA.VP.A87H.01
#> "03" "04" "01" "05" "02" "04"
#> TCGA.G9.7521.01 TCGA.YL.A8HO.01 TCGA.YL.A9WK.01 TCGA.J4.A83M.01 TCGA.VP.A878.01 TCGA.CH.5766.11
#> "04" "04" "02" "04" "05" "01"
#> TCGA.HC.7736.01 TCGA.G9.6385.01 TCGA.VN.A88N.01 TCGA.HC.7745.01 TCGA.HC.7078.01 TCGA.FC.A5OB.01
#> "04" "01" "04" "05" "02" "02"
#> TCGA.G9.6379.01 TCGA.QU.A6IP.01 TCGA.J4.AATZ.01 TCGA.V1.A9O9.01 TCGA.V1.A9OL.01 TCGA.HC.7210.01
#> "05" "04" "02" "04" "02" "04"
#> TCGA.KK.A8I7.01 TCGA.EJ.7791.01 TCGA.CH.5762.01 TCGA.EJ.5527.01 TCGA.KK.A8IC.01 TCGA.G9.6356.01
#> "03" "03" "05" "05" "03" "05"
#> TCGA.J9.A52D.01 TCGA.EJ.7788.01 TCGA.ZG.A9LB.01 TCGA.J9.A8CN.01 TCGA.ZG.A9L1.01 TCGA.G9.6333.01
#> "02" "02" "04" "02" "02" "05"
#> TCGA.VP.A875.01 TCGA.EJ.8468.01 TCGA.EJ.5495.01 TCGA.H9.A6BX.01 TCGA.KK.A59Y.01 TCGA.V1.A8WN.01
#> "02" "04" "05" "01" "02" "05"
#> TCGA.KK.A7B1.01 TCGA.G9.6362.11 TCGA.G9.6364.11 TCGA.HC.A631.01 TCGA.YL.A8SA.01 TCGA.HC.8262.01
#> "04" "02" "01" "02" "02" "04"
#> TCGA.CH.5765.11 TCGA.KC.A7FD.01 TCGA.HI.7170.01 TCGA.J4.A67L.01 TCGA.V1.A9O7.01 TCGA.HC.A6AS.01
#> "03" "02" "04" "04" "03" "05"
#> TCGA.EJ.7784.01 TCGA.EJ.7331.11 TCGA.KC.A7F3.01 TCGA.G9.6494.11 TCGA.HC.8256.01 TCGA.J4.A83I.01
#> "02" "01" "04" "01" "04" "02"
#> TCGA.G9.6373.01 TCGA.EJ.7794.11 TCGA.G9.6371.01 TCGA.XQ.A8TA.01 TCGA.EJ.5498.01 TCGA.EJ.7328.01
#> "02" "01" "02" "02" "03" "05"
#> TCGA.EJ.A46D.01 TCGA.ZG.A9L9.01 TCGA.YL.A8SI.01 TCGA.M7.A724.01 TCGA.VN.A88K.01 TCGA.EJ.A8FP.01
#> "03" "02" "05" "02" "02" "01"
#> TCGA.V1.A8MK.01 TCGA.YL.A8HJ.01 TCGA.KK.A8ID.01 TCGA.CH.5769.11 TCGA.G9.6353.01 TCGA.G9.6499.11
#> "03" "03" "02" "04" "03" "04"
#> TCGA.KK.A8I9.01 TCGA.G9.6365.11 TCGA.EJ.A46H.01 TCGA.EJ.7317.01 TCGA.YL.A8S8.01 TCGA.XJ.A9DQ.01
#> "04" "01" "01" "04" "04" "03"
#> TCGA.EJ.7782.11 TCGA.J4.A67O.01 TCGA.Y6.A8TL.01 TCGA.XK.AAIV.01 TCGA.CH.5790.01 TCGA.HC.7231.01
#> "01" "05" "04" "05" "02" "02"
#> TCGA.ZG.A9L5.01 TCGA.V1.A8MF.01 TCGA.EJ.A7NJ.01 TCGA.EJ.A65E.01 TCGA.ZG.A8QX.01 TCGA.G9.6367.01
#> "02" "04" "01" "04" "04" "01"
#> TCGA.G9.6342.01 TCGA.KK.A8IB.01 TCGA.HC.7230.01 TCGA.XK.AAIR.01 TCGA.CH.5741.01 TCGA.KK.A59V.01
#> "04" "05" "02" "05" "02" "02"
#> TCGA.J4.8200.01 TCGA.KK.A7AQ.01 TCGA.EJ.5532.01 TCGA.HI.7168.01 TCGA.HC.7233.01 TCGA.HC.A6AL.01
#> "04" "02" "04" "04" "04" "02"
#> TCGA.EJ.7783.01 TCGA.HC.8264.01 TCGA.EJ.A8FU.01 TCGA.EJ.A65M.01 TCGA.EJ.A8FN.01 TCGA.HI.7171.01
#> "05" "02" "01" "04" "04" "02"
#> TCGA.XK.AAJP.01 TCGA.HC.7212.01 TCGA.ZG.A9MC.01 TCGA.2A.A8VO.01 TCGA.HC.8259.01 TCGA.G9.6378.01
#> "02" "02" "03" "02" "02" "03"
#> TCGA.J4.A83L.01 TCGA.VN.A88P.01 TCGA.EJ.5507.01 TCGA.J9.A8CK.01 TCGA.CH.5744.01 TCGA.ZG.A9N3.01
#> "04" "02" "04" "04" "04" "04"
#> TCGA.G9.6354.01 TCGA.VN.A88O.01 TCGA.EJ.5502.01 TCGA.HC.7079.01 TCGA.G9.6369.01 TCGA.KK.A6E1.01
#> "04" "04" "05" "03" "02" "02"
#> TCGA.HC.7211.01 TCGA.KK.A8I6.01 TCGA.XJ.A83F.01 TCGA.EJ.7785.01 TCGA.G9.A9S4.01 TCGA.VP.A87B.01
#> "04" "04" "02" "05" "02" "02"
#> TCGA.YL.A8SR.01 TCGA.EJ.7327.01 TCGA.4L.AA1F.01 TCGA.KK.A7AY.01 TCGA.EJ.A65G.01 TCGA.2A.AAYU.01
#> "02" "04" "05" "02" "04" "02"
#> TCGA.HC.A76W.01 TCGA.EJ.5516.01 TCGA.G9.A9S7.01 TCGA.HC.8216.01 TCGA.CH.5794.01 TCGA.V1.A9OA.01
#> "04" "05" "04" "04" "04" "04"
#> TCGA.J9.A52E.01 TCGA.HC.7818.01 TCGA.G9.7525.01 TCGA.FC.7961.01 TCGA.CH.5767.11 TCGA.EJ.5504.01
#> "04" "04" "02" "04" "01" "04"
#> TCGA.VP.A87J.01 TCGA.J4.A67S.01 TCGA.KK.A8IK.01 TCGA.HC.A6AQ.01 TCGA.CH.5763.01 TCGA.HC.A8D1.01
#> "02" "04" "02" "04" "01" "03"
#> TCGA.KK.A7AU.01 TCGA.CH.5766.01 TCGA.EJ.7781.11 TCGA.KK.A7B0.01 TCGA.EJ.7321.01 TCGA.G9.6385.11
#> "02" "04" "01" "05" "04" "01"
#> TCGA.VN.A943.01 TCGA.KK.A59X.01 TCGA.KK.A8I4.01 TCGA.G9.6496.11 TCGA.G9.7523.01 TCGA.EJ.5494.01
#> "02" "02" "05" "01" "04" "02"
#> TCGA.2A.A8VT.01 TCGA.HC.7213.01 TCGA.G9.7519.01 TCGA.CH.5764.11 TCGA.CH.5772.01 TCGA.EJ.7325.01
#> "04" "02" "04" "01" "02" "02"
#> TCGA.G9.6356.11 TCGA.ZG.A9LM.01 TCGA.XJ.A9DK.01 TCGA.EJ.7789.01 TCGA.HC.8257.01 TCGA.EJ.A7NG.01
#> "01" "04" "01" "02" "02" "03"
#> TCGA.EJ.7318.01 TCGA.EJ.5512.01 TCGA.EJ.A46E.01 TCGA.FC.A4JI.01 TCGA.J9.A8CM.01 TCGA.CH.5771.11
#> "04" "05" "01" "02" "04" "01"
#> TCGA.KC.A4BR.01 TCGA.2A.AAYO.01 TCGA.2A.A8W3.01 TCGA.CH.5768.11 TCGA.G9.6364.01 TCGA.YL.A8SL.01
#> "03" "02" "05" "03" "04" "02"
#> TCGA.KK.A5A1.01 TCGA.YL.A9WL.01 TCGA.HC.A6HX.01 TCGA.M7.A720.01 TCGA.HC.7080.01 TCGA.V1.A9O5.06
#> "02" "02" "03" "01" "02" "02"
#> TCGA.KC.A7F5.01 TCGA.EJ.7331.01 TCGA.ZG.A9LY.01 TCGA.G9.6494.01 TCGA.M7.A71Y.01 TCGA.FC.A66V.01
#> "02" "04" "05" "04" "03" "01"
#> TCGA.EJ.7793.01 TCGA.EJ.A8FS.01 TCGA.XK.AAJU.01 TCGA.HC.8266.01 TCGA.YL.A8HL.01 TCGA.VN.A88I.01
#> "05" "02" "01" "05" "02" "03"
#> TCGA.HI.7169.01 TCGA.CH.5753.01 TCGA.J4.A67K.01 TCGA.QU.A6IM.01 TCGA.HC.A9TE.01 TCGA.EJ.7115.01
#> "04" "02" "04" "04" "04" "04"
#> TCGA.HC.7745.11 TCGA.EJ.5531.01 TCGA.YL.A8SH.01 TCGA.G9.6362.01 TCGA.HC.8258.01 TCGA.EJ.5530.01
#> "01" "03" "02" "02" "03" "02"
#> TCGA.VN.A88M.01 TCGA.EJ.7782.01 TCGA.YL.A8SF.01 TCGA.KK.A6E2.01 TCGA.CH.5792.01 TCGA.J4.A6G1.01
#> "02" "02" "04" "02" "05" "03"
#> TCGA.J4.A6M7.01 TCGA.VP.A872.01 TCGA.V1.A8ML.01 TCGA.HC.7744.01 TCGA.G9.6347.01 TCGA.EJ.A46I.01
#> "02" "04" "04" "02" "05" "05"
#> TCGA.XK.AAJ3.01 TCGA.HC.A8CY.01 TCGA.KK.A6E0.01 TCGA.XK.AAK1.01 TCGA.XK.AAIW.01 TCGA.HC.8260.01
#> "02" "02" "02" "02" "02" "03"
#> TCGA.HC.7737.11 TCGA.EJ.7786.11 TCGA.HC.7740.01 TCGA.TP.A8TV.01 TCGA.FC.A6HD.01 TCGA.EJ.8472.01
#> "01" "01" "03" "02" "02" "02"
#> TCGA.CH.5745.01 TCGA.EJ.5508.01 TCGA.EJ.A7NH.01 TCGA.KK.A7B2.01 TCGA.CH.5740.01 TCGA.YL.A9WH.01
#> "04" "05" "05" "03" "04" "02"
#> TCGA.FC.A8O0.01 TCGA.J9.A52C.01 TCGA.FC.7708.01 TCGA.HC.7742.11 TCGA.G9.6351.11 TCGA.KK.A7AW.01
#> "01" "05" "05" "03" "03" "02"
#> TCGA.G9.7509.01 TCGA.J4.A67R.01 TCGA.WW.A8ZI.01 TCGA.KK.A8IJ.01 TCGA.J4.A83N.01 TCGA.HC.A6AN.01
#> "04" "05" "02" "04" "02" "02"
#> TCGA.G9.6348.11 TCGA.EJ.5499.01 TCGA.G9.6367.11 TCGA.QU.A6IL.01 TCGA.CH.5738.01 TCGA.V1.A9ZI.01
#> "01" "05" "01" "02" "05" "02"
#> TCGA.CH.5748.01 TCGA.YL.A8SQ.01 TCGA.G9.7522.01 TCGA.HC.A6AP.01 TCGA.EJ.7785.11 TCGA.KK.A7B4.01
#> "04" "02" "05" "05" "01" "02"
#> TCGA.J4.A83J.01 TCGA.V1.A8MU.01 TCGA.EJ.5510.01 TCGA.EJ.7327.11 TCGA.CH.5746.01 TCGA.V1.A9Z7.01
#> "02" "04" "05" "01" "05" "04"
#> TCGA.M7.A725.01 TCGA.G9.6384.11 TCGA.XJ.A9DI.01 TCGA.J4.A67N.01 TCGA.XJ.A83G.01 TCGA.ZG.A8QZ.01
#> "02" "01" "01" "02" "02" "05"
#> TCGA.TK.A8OK.01 TCGA.VP.A876.01 TCGA.KK.A6E5.01 TCGA.X4.A8KQ.01 TCGA.KK.A8IL.01 TCGA.HC.7820.01
#> "05" "02" "04" "05" "04" "04"
#> TCGA.CH.5739.01 TCGA.HC.7750.01 TCGA.YL.A9WX.01 TCGA.EJ.5518.01 TCGA.ZG.A9NI.01 TCGA.YL.A9WY.01
#> "02" "05" "03" "04" "04" "05"
#> TCGA.CH.5763.11 TCGA.EJ.5515.01 TCGA.KK.A8IH.01 TCGA.VP.A87K.01 TCGA.HC.A6HY.01 TCGA.HC.7211.11
#> "01" "01" "02" "02" "04" "01"
#> TCGA.HC.A632.01 TCGA.G9.6496.01 TCGA.EJ.A7NM.01 TCGA.ZG.A9L6.01 TCGA.2A.A8VV.01 TCGA.VP.A87E.01
#> "02" "02" "04" "03" "02" "05"
#> TCGA.CH.5764.01 TCGA.EJ.5525.01 TCGA.CH.5772.11 TCGA.KK.A59Z.01 TCGA.V1.A9ZR.01 TCGA.EJ.A6RC.01
#> "04" "02" "01" "02" "05" "04"
#> TCGA.EJ.7792.01 TCGA.HC.A9TH.01 TCGA.M7.A723.01 TCGA.EJ.7789.11 TCGA.HC.7752.01 TCGA.EJ.A65J.01
#> "05" "04" "03" "01" "02" "02"
#> TCGA.V1.A8WV.01 TCGA.2A.A8VX.01 TCGA.V1.A9OT.01 TCGA.KC.A7FA.01 TCGA.G9.6373.11 TCGA.G9.6370.01
#> "04" "02" "02" "02" "01" "01"
#> TCGA.CH.5771.01 TCGA.YL.A8SJ.01 TCGA.HC.7738.01 TCGA.EJ.A6RA.01 TCGA.J4.8198.01 TCGA.EJ.7123.01
#> "03" "04" "02" "03" "02" "02"
#> TCGA.2A.A8W1.01 TCGA.G9.6363.01 TCGA.ZG.A9L2.01 TCGA.HC.7749.01 TCGA.CH.5768.01 TCGA.KK.A6E7.01
#> "02" "04" "05" "04" "02" "04"
#> TCGA.G9.6332.01 TCGA.EJ.A46G.01 TCGA.V1.A9OX.01 TCGA.J4.A6G3.01 TCGA.VN.A88L.01 TCGA.EJ.7312.01
#> "02" "02" "04" "03" "04" "02"
#> TCGA.V1.A8MM.01 TCGA.EJ.A65F.01 TCGA.G9.6498.01 TCGA.EJ.5505.01 TCGA.CH.5761.11 TCGA.HC.8261.01
#> "02" "02" "02" "05" "01" "04"
#> TCGA.XQ.A8TB.01 TCGA.G9.6329.01 TCGA.EJ.5496.01
#> "04" "03" "04"
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 = 1258),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1258),
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 = 1360),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1360),
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 = 1762),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1762),
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 = 1794),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1794),
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 = 2221),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2221),
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 = 2573),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2573),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3054),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3054),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3076),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3076),
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 = 3130),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3130),
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 = 3130),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3130),
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 = 4059),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4059),
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 = 4238),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4238),
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 = 5112),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5112),
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 = 5268),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5268),
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 = 5287),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5287),
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 = 6017),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6017),
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 = 6587),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6587),
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 = 11436),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 11436),
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 = 14470),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 14470),
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 = 15528),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 15528),
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 = 33866),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 33866),
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 = 1258))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1360))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1762))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1794))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2221))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2573))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3054))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3076))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3130))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3130))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4059))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4238))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5112))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5268))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5287))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6017))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6587))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 11436))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 14470))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 15528))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 33866))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 , Node04 , Node05 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'DownSamplingConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 376220 rows and 500 columns, randomly sampled from 549 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 'DownSamplingConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.990 0.996 0.2942 0.712 0.712
#> 3 3 1.000 0.970 0.989 0.8078 0.718 0.614
#> 4 4 1.000 0.968 0.988 0.2786 0.774 0.556
#> 5 5 0.998 0.961 0.981 0.0881 0.849 0.588
#> 6 6 0.792 0.742 0.849 0.0495 0.832 0.468
#> 7 7 0.775 0.673 0.836 0.0276 0.966 0.845
#> 8 8 0.856 0.718 0.861 0.0321 0.950 0.764
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.
get_classes(res, k = 2)
#> class p
#> TCGA.G9.6343.01 2 0
#> TCGA.KK.A8IA.01 2 0
#> TCGA.KK.A6E4.01 2 0
#> TCGA.EJ.AB20.01 1 0
#> TCGA.H9.7775.01 2 0
#> TCGA.XJ.A9DX.01 2 0
#> TCGA.KK.A6E6.01 2 0
#> TCGA.G9.6339.01 2 0
#> TCGA.EJ.5509.01 2 0
#> TCGA.EJ.5521.01 2 0
#> TCGA.YL.A8SB.01 2 0
#> TCGA.V1.A9OF.01 2 0
#> TCGA.CH.5754.01 2 0
#> TCGA.EJ.7125.01 2 0
#> TCGA.EJ.7797.01 2 0
#> TCGA.YL.A9WI.01 2 0
#> TCGA.EJ.7314.01 2 0
#> TCGA.XA.A8JR.01 2 0
#> TCGA.EJ.7781.01 2 0
#> TCGA.QU.A6IN.01 2 0
#> TCGA.CH.5751.01 2 0
#> TCGA.V1.A8WL.01 2 0
#> TCGA.HC.A6AO.01 2 0
#> TCGA.KK.A7B3.01 2 0
#> TCGA.XK.AAJT.01 2 0
#> TCGA.EJ.AB27.01 1 0
#> TCGA.CH.5788.01 2 0
#> TCGA.KK.A8I5.01 2 0
#> TCGA.YL.A8S9.01 2 0
#> TCGA.CH.5761.01 2 0
#> TCGA.KK.A7AZ.01 2 0
#> TCGA.G9.6366.01 2 0
#> TCGA.HC.7819.01 2 0
#> TCGA.KC.A4BN.01 2 0
#> TCGA.KK.A8IG.01 2 0
#> TCGA.ZG.A8QW.01 2 0
#> TCGA.EJ.7786.01 2 0
#> TCGA.J4.A83K.01 2 0
#> TCGA.YL.A8HK.01 2 0
#> TCGA.EJ.5501.01 2 0
#> TCGA.EJ.8470.01 2 0
#> TCGA.J9.A8CL.01 2 0
#> TCGA.EJ.A7NF.01 2 0
#> TCGA.CH.5762.11 1 0
#> TCGA.XK.AAJA.01 2 0
#> TCGA.EJ.7330.01 2 0
#> TCGA.VP.AA1N.01 2 0
#> TCGA.EJ.5524.01 2 0
#> TCGA.KK.A6E8.01 2 0
#> TCGA.HC.7821.01 2 0
#> TCGA.HC.7209.01 2 0
#> TCGA.HC.7742.01 2 0
#> TCGA.G9.6351.01 2 0
#> TCGA.EJ.8474.01 2 0
#> TCGA.HC.7075.01 2 0
#> TCGA.J9.A8CP.01 2 0
#> TCGA.KK.A8IM.01 2 0
#> TCGA.G9.6348.01 2 0
#> TCGA.CH.5789.01 1 0
#> TCGA.KC.A7F6.01 2 0
#> TCGA.G9.6333.11 1 0
#> TCGA.KC.A4BL.01 1 0
#> TCGA.J4.A67Q.01 2 0
#> TCGA.2A.A8VL.01 2 0
#> TCGA.V1.A9ZK.01 2 0
#> TCGA.V1.A9O5.01 2 0
#> TCGA.VP.A879.01 2 0
#> TCGA.HC.7819.11 1 0
#> TCGA.VN.A88Q.01 2 0
#> TCGA.HC.7737.01 2 0
#> TCGA.V1.A8WS.01 2 0
#> TCGA.HC.8213.01 2 0
#> TCGA.M7.A721.01 2 0
#> TCGA.ZG.A9LZ.01 2 0
#> TCGA.CH.5765.01 2 0
#> TCGA.V1.A8WW.01 2 0
#> TCGA.HC.A48F.01 2 0
#> TCGA.V1.A9OQ.01 2 0
#> TCGA.EJ.5514.01 2 0
#> TCGA.G9.6384.01 2 0
#> TCGA.V1.A9ZG.01 2 0
#> TCGA.YL.A8HM.01 2 0
#> TCGA.G9.6377.01 2 0
#> TCGA.M7.A722.01 2 0
#> TCGA.G9.6361.01 2 0
#> TCGA.EJ.5511.01 2 0
#> TCGA.ZG.A9KY.01 2 0
#> TCGA.EJ.7784.11 1 0
#> TCGA.ZG.A9LN.01 2 0
#> TCGA.EJ.5526.01 2 0
#> TCGA.HC.7820.11 1 0
#> TCGA.YJ.A8SW.01 2 0
#> TCGA.EJ.7794.01 2 0
#> TCGA.EJ.A46B.01 1 0
#> TCGA.EJ.5542.01 2 0
#> TCGA.YL.A9WJ.01 2 0
#> TCGA.EJ.7328.11 1 0
#> TCGA.V1.A9Z8.01 2 0
#> TCGA.EJ.A46F.01 2 0
#> TCGA.YL.A8SK.01 2 0
#> TCGA.MG.AAMC.01 2 0
#> TCGA.X4.A8KS.01 1 0
#> TCGA.J4.A67M.01 2 0
#> TCGA.ZG.A9L0.01 2 0
#> TCGA.HC.7077.01 2 0
#> TCGA.CH.5769.01 2 0
#> TCGA.G9.6353.11 1 0
#> TCGA.G9.6499.01 2 0
#> TCGA.EJ.5519.01 2 0
#> TCGA.J4.A67T.01 2 0
#> TCGA.HC.7748.01 2 0
#> TCGA.VN.A88R.01 2 0
#> TCGA.H9.A6BY.01 2 0
#> TCGA.G9.6365.01 2 0
#> TCGA.EJ.7317.11 1 0
#> TCGA.G9.7510.01 2 0
#> TCGA.KK.A6E3.01 2 0
#> TCGA.G9.6336.01 2 1
#> TCGA.EJ.5517.01 2 0
#> TCGA.V1.A8MG.01 2 0
#> TCGA.KC.A7FE.01 1 0
#> TCGA.HC.7817.01 1 1
#> TCGA.J4.AAU2.01 2 0
#> TCGA.V1.A8MJ.01 2 1
#> TCGA.VP.A87C.01 2 0
#> TCGA.EJ.A7NN.01 2 0
#> TCGA.HC.A8D0.01 1 0
#> TCGA.EJ.7792.11 1 0
#> TCGA.EJ.5497.01 2 0
#> TCGA.Y6.A9XI.01 2 0
#> TCGA.HC.7752.11 1 0
#> TCGA.SU.A7E7.01 2 1
#> TCGA.G9.6342.11 1 0
#> TCGA.HC.8265.01 2 0
#> TCGA.CH.5737.01 2 0
#> TCGA.G9.6338.01 2 0
#> TCGA.KK.A7AV.01 2 0
#> TCGA.EJ.7218.01 2 0
#> TCGA.YL.A8SC.01 2 0
#> TCGA.XK.AAJR.01 2 0
#> TCGA.2A.AAYF.01 2 0
#> TCGA.V1.A8X3.01 2 0
#> TCGA.KK.A6DY.01 2 0
#> TCGA.M7.A71Z.01 2 0
#> TCGA.EJ.7123.11 1 0
#> TCGA.G9.6363.11 2 0
#> TCGA.KK.A8I8.01 2 0
#> TCGA.KC.A4BV.01 2 0
#> TCGA.G9.6332.11 1 0
#> TCGA.CH.5750.01 2 0
#> TCGA.ZG.A9ND.01 2 0
#> TCGA.EJ.A65B.01 1 0
#> TCGA.QU.A6IO.01 2 0
#> TCGA.EJ.5503.01 1 0
#> TCGA.ZG.A9LU.01 1 0
#> TCGA.EJ.8469.01 2 0
#> TCGA.XJ.A83H.01 2 0
#> TCGA.EJ.7315.01 2 0
#> TCGA.ZG.A8QY.01 2 0
#> TCGA.YL.A8SP.01 2 0
#> TCGA.CH.5791.01 2 0
#> TCGA.V1.A9OY.01 2 0
#> TCGA.KC.A4BO.01 1 0
#> TCGA.HC.A76X.01 2 0
#> TCGA.YL.A8SO.01 2 0
#> TCGA.KK.A8IF.01 2 0
#> TCGA.EJ.A7NK.01 1 0
#> TCGA.ZG.A9L4.01 2 0
#> TCGA.EJ.5522.01 2 0
#> TCGA.HC.7747.01 2 0
#> TCGA.EJ.7125.11 1 0
#> TCGA.ZG.A9M4.01 2 0
#> TCGA.EJ.A65D.01 2 0
#> TCGA.HC.A4ZV.01 2 0
#> TCGA.G9.A9S0.01 2 0
#> TCGA.EJ.5506.01 1 0
#> TCGA.KK.A7AP.01 2 0
#> TCGA.VP.A87D.01 2 0
#> TCGA.TP.A8TT.01 2 0
#> TCGA.KK.A8II.01 2 0
#> TCGA.V1.A9Z9.01 2 0
#> TCGA.ZG.A9LS.01 2 0
#> TCGA.HC.7232.01 2 0
#> TCGA.EJ.A8FO.01 1 0
#> TCGA.J9.A52B.01 2 0
#> TCGA.CH.5767.01 2 0
#> TCGA.J4.AATV.01 1 0
#> TCGA.HC.7081.01 2 0
#> TCGA.CH.5743.01 1 0
#> TCGA.V1.A9OH.01 2 0
#> TCGA.CH.5752.01 2 0
#> TCGA.VP.A87H.01 2 0
#> TCGA.G9.7521.01 2 0
#> TCGA.YL.A8HO.01 2 0
#> TCGA.YL.A9WK.01 2 0
#> TCGA.J4.A83M.01 2 0
#> TCGA.VP.A878.01 2 0
#> TCGA.CH.5766.11 1 0
#> TCGA.HC.7736.01 2 0
#> TCGA.G9.6385.01 1 0
#> TCGA.VN.A88N.01 2 0
#> TCGA.HC.7745.01 2 0
#> TCGA.HC.7078.01 2 0
#> TCGA.FC.A5OB.01 2 0
#> TCGA.G9.6379.01 2 0
#> TCGA.QU.A6IP.01 2 0
#> TCGA.J4.AATZ.01 2 0
#> TCGA.V1.A9O9.01 2 0
#> TCGA.V1.A9OL.01 2 0
#> TCGA.HC.7210.01 2 0
#> TCGA.KK.A8I7.01 1 0
#> TCGA.EJ.7791.01 1 0
#> TCGA.CH.5762.01 2 0
#> TCGA.EJ.5527.01 2 0
#> TCGA.KK.A8IC.01 1 0
#> TCGA.G9.6356.01 2 0
#> TCGA.J9.A52D.01 2 0
#> TCGA.EJ.7788.01 2 0
#> TCGA.ZG.A9LB.01 2 0
#> TCGA.J9.A8CN.01 2 0
#> TCGA.ZG.A9L1.01 2 0
#> TCGA.G9.6333.01 2 0
#> TCGA.VP.A875.01 2 0
#> TCGA.EJ.8468.01 2 0
#> TCGA.EJ.5495.01 2 0
#> TCGA.H9.A6BX.01 1 0
#> TCGA.KK.A59Y.01 2 0
#> TCGA.V1.A8WN.01 2 0
#> TCGA.KK.A7B1.01 2 0
#> TCGA.G9.6362.11 2 0
#> TCGA.G9.6364.11 1 0
#> TCGA.HC.A631.01 2 0
#> TCGA.YL.A8SA.01 2 0
#> TCGA.HC.8262.01 2 0
#> TCGA.CH.5765.11 1 0
#> TCGA.KC.A7FD.01 2 0
#> TCGA.HI.7170.01 2 0
#> TCGA.J4.A67L.01 2 0
#> TCGA.V1.A9O7.01 2 1
#> TCGA.HC.A6AS.01 2 0
#> TCGA.EJ.7784.01 2 0
#> TCGA.EJ.7331.11 1 0
#> TCGA.KC.A7F3.01 2 0
#> TCGA.G9.6494.11 1 0
#> TCGA.HC.8256.01 2 0
#> TCGA.J4.A83I.01 2 0
#> TCGA.G9.6373.01 2 0
#> TCGA.EJ.7794.11 1 0
#> TCGA.G9.6371.01 2 0
#> TCGA.XQ.A8TA.01 2 0
#> TCGA.EJ.5498.01 2 1
#> TCGA.EJ.7328.01 2 0
#> TCGA.EJ.A46D.01 1 0
#> TCGA.ZG.A9L9.01 2 0
#> TCGA.YL.A8SI.01 2 0
#> TCGA.M7.A724.01 2 0
#> TCGA.VN.A88K.01 2 0
#> TCGA.EJ.A8FP.01 1 0
#> TCGA.V1.A8MK.01 1 0
#> TCGA.YL.A8HJ.01 2 1
#> TCGA.KK.A8ID.01 2 0
#> TCGA.CH.5769.11 2 0
#> TCGA.G9.6353.01 1 0
#> TCGA.G9.6499.11 2 0
#> TCGA.KK.A8I9.01 2 0
#> TCGA.G9.6365.11 1 0
#> TCGA.EJ.A46H.01 1 0
#> TCGA.EJ.7317.01 2 0
#> TCGA.YL.A8S8.01 2 0
#> TCGA.XJ.A9DQ.01 1 0
#> TCGA.EJ.7782.11 1 0
#> TCGA.J4.A67O.01 2 0
#> TCGA.Y6.A8TL.01 2 0
#> TCGA.XK.AAIV.01 2 0
#> TCGA.CH.5790.01 2 0
#> TCGA.HC.7231.01 2 0
#> TCGA.ZG.A9L5.01 2 0
#> TCGA.V1.A8MF.01 2 0
#> TCGA.EJ.A7NJ.01 1 0
#> TCGA.EJ.A65E.01 2 0
#> TCGA.ZG.A8QX.01 2 0
#> TCGA.G9.6367.01 1 0
#> TCGA.G9.6342.01 2 0
#> TCGA.KK.A8IB.01 2 0
#> TCGA.HC.7230.01 2 0
#> TCGA.XK.AAIR.01 2 0
#> TCGA.CH.5741.01 2 0
#> TCGA.KK.A59V.01 2 0
#> TCGA.J4.8200.01 2 0
#> TCGA.KK.A7AQ.01 2 0
#> TCGA.EJ.5532.01 2 0
#> TCGA.HI.7168.01 2 0
#> TCGA.HC.7233.01 2 0
#> TCGA.HC.A6AL.01 2 0
#> TCGA.EJ.7783.01 2 0
#> TCGA.HC.8264.01 2 0
#> TCGA.EJ.A8FU.01 1 0
#> TCGA.EJ.A65M.01 2 0
#> TCGA.EJ.A8FN.01 2 0
#> TCGA.HI.7171.01 2 0
#> TCGA.XK.AAJP.01 2 0
#> TCGA.HC.7212.01 2 0
#> TCGA.ZG.A9MC.01 1 0
#> TCGA.2A.A8VO.01 2 0
#> TCGA.HC.8259.01 2 0
#> TCGA.G9.6378.01 1 0
#> TCGA.J4.A83L.01 2 0
#> TCGA.VN.A88P.01 2 0
#> TCGA.EJ.5507.01 2 0
#> TCGA.J9.A8CK.01 2 0
#> TCGA.CH.5744.01 2 0
#> TCGA.ZG.A9N3.01 2 0
#> TCGA.G9.6354.01 2 0
#> TCGA.VN.A88O.01 2 0
#> TCGA.EJ.5502.01 2 0
#> TCGA.HC.7079.01 1 0
#> TCGA.G9.6369.01 2 0
#> TCGA.KK.A6E1.01 2 0
#> TCGA.HC.7211.01 2 0
#> TCGA.KK.A8I6.01 2 0
#> TCGA.XJ.A83F.01 2 0
#> TCGA.EJ.7785.01 2 0
#> TCGA.G9.A9S4.01 2 0
#> TCGA.VP.A87B.01 2 0
#> TCGA.YL.A8SR.01 2 0
#> TCGA.EJ.7327.01 2 0
#> TCGA.4L.AA1F.01 2 0
#> TCGA.KK.A7AY.01 2 0
#> TCGA.EJ.A65G.01 2 0
#> TCGA.2A.AAYU.01 2 0
#> TCGA.HC.A76W.01 2 0
#> TCGA.EJ.5516.01 2 0
#> TCGA.G9.A9S7.01 2 0
#> TCGA.HC.8216.01 2 0
#> TCGA.CH.5794.01 2 0
#> TCGA.V1.A9OA.01 2 0
#> TCGA.J9.A52E.01 2 0
#> TCGA.HC.7818.01 2 0
#> TCGA.G9.7525.01 2 0
#> TCGA.FC.7961.01 2 0
#> TCGA.CH.5767.11 1 0
#> TCGA.EJ.5504.01 2 0
#> TCGA.VP.A87J.01 2 0
#> TCGA.J4.A67S.01 2 0
#> TCGA.KK.A8IK.01 2 0
#> TCGA.HC.A6AQ.01 2 0
#> TCGA.CH.5763.01 1 0
#> TCGA.HC.A8D1.01 1 0
#> TCGA.KK.A7AU.01 2 0
#> TCGA.CH.5766.01 2 0
#> TCGA.EJ.7781.11 1 0
#> TCGA.KK.A7B0.01 2 0
#> TCGA.EJ.7321.01 2 0
#> TCGA.G9.6385.11 1 0
#> TCGA.VN.A943.01 2 0
#> TCGA.KK.A59X.01 2 0
#> TCGA.KK.A8I4.01 2 0
#> TCGA.G9.6496.11 1 0
#> TCGA.G9.7523.01 2 0
#> TCGA.EJ.5494.01 2 0
#> TCGA.2A.A8VT.01 2 0
#> TCGA.HC.7213.01 2 0
#> TCGA.G9.7519.01 2 0
#> TCGA.CH.5764.11 1 0
#> TCGA.CH.5772.01 2 0
#> TCGA.EJ.7325.01 2 0
#> TCGA.G9.6356.11 1 0
#> TCGA.ZG.A9LM.01 2 0
#> TCGA.XJ.A9DK.01 1 0
#> TCGA.EJ.7789.01 2 0
#> TCGA.HC.8257.01 2 0
#> TCGA.EJ.A7NG.01 1 0
#> TCGA.EJ.7318.01 2 0
#> TCGA.EJ.5512.01 2 0
#> TCGA.EJ.A46E.01 1 0
#> TCGA.FC.A4JI.01 2 0
#> TCGA.J9.A8CM.01 2 0
#> TCGA.CH.5771.11 1 0
#> TCGA.KC.A4BR.01 1 0
#> TCGA.2A.AAYO.01 2 0
#> TCGA.2A.A8W3.01 2 0
#> TCGA.CH.5768.11 1 0
#> TCGA.G9.6364.01 2 0
#> TCGA.YL.A8SL.01 2 0
#> TCGA.KK.A5A1.01 2 0
#> TCGA.YL.A9WL.01 2 0
#> TCGA.HC.A6HX.01 1 0
#> TCGA.M7.A720.01 1 0
#> TCGA.HC.7080.01 2 0
#> TCGA.V1.A9O5.06 2 0
#> TCGA.KC.A7F5.01 2 0
#> TCGA.EJ.7331.01 2 0
#> TCGA.ZG.A9LY.01 2 0
#> TCGA.G9.6494.01 2 0
#> TCGA.M7.A71Y.01 1 0
#> TCGA.FC.A66V.01 1 0
#> TCGA.EJ.7793.01 2 0
#> TCGA.EJ.A8FS.01 2 0
#> TCGA.XK.AAJU.01 1 0
#> TCGA.HC.8266.01 2 0
#> TCGA.YL.A8HL.01 2 0
#> TCGA.VN.A88I.01 1 0
#> TCGA.HI.7169.01 2 0
#> TCGA.CH.5753.01 2 0
#> TCGA.J4.A67K.01 2 0
#> TCGA.QU.A6IM.01 2 0
#> TCGA.HC.A9TE.01 2 0
#> TCGA.EJ.7115.01 2 0
#> TCGA.HC.7745.11 1 0
#> TCGA.EJ.5531.01 1 0
#> TCGA.YL.A8SH.01 2 0
#> TCGA.G9.6362.01 2 0
#> TCGA.HC.8258.01 1 0
#> TCGA.EJ.5530.01 2 0
#> TCGA.VN.A88M.01 2 0
#> TCGA.EJ.7782.01 2 0
#> TCGA.YL.A8SF.01 2 0
#> TCGA.KK.A6E2.01 2 0
#> TCGA.CH.5792.01 2 0
#> TCGA.J4.A6G1.01 1 0
#> TCGA.J4.A6M7.01 2 0
#> TCGA.VP.A872.01 2 0
#> TCGA.V1.A8ML.01 2 0
#> TCGA.HC.7744.01 2 0
#> TCGA.G9.6347.01 2 0
#> TCGA.EJ.A46I.01 2 1
#> TCGA.XK.AAJ3.01 2 0
#> TCGA.HC.A8CY.01 2 0
#> TCGA.KK.A6E0.01 2 0
#> TCGA.XK.AAK1.01 2 0
#> TCGA.XK.AAIW.01 2 0
#> TCGA.HC.8260.01 1 0
#> TCGA.HC.7737.11 1 0
#> TCGA.EJ.7786.11 1 0
#> TCGA.HC.7740.01 1 0
#> TCGA.TP.A8TV.01 2 0
#> TCGA.FC.A6HD.01 2 0
#> TCGA.EJ.8472.01 2 0
#> TCGA.CH.5745.01 2 0
#> TCGA.EJ.5508.01 2 0
#> TCGA.EJ.A7NH.01 2 1
#> TCGA.KK.A7B2.01 1 0
#> TCGA.CH.5740.01 2 0
#> TCGA.YL.A9WH.01 2 0
#> TCGA.FC.A8O0.01 1 0
#> TCGA.J9.A52C.01 2 0
#> TCGA.FC.7708.01 2 0
#> TCGA.HC.7742.11 1 0
#> TCGA.G9.6351.11 1 0
#> TCGA.KK.A7AW.01 2 0
#> TCGA.G9.7509.01 2 0
#> TCGA.J4.A67R.01 2 0
#> TCGA.WW.A8ZI.01 2 0
#> TCGA.KK.A8IJ.01 2 0
#> TCGA.J4.A83N.01 2 0
#> TCGA.HC.A6AN.01 2 0
#> TCGA.G9.6348.11 1 0
#> TCGA.EJ.5499.01 2 0
#> TCGA.G9.6367.11 1 0
#> TCGA.QU.A6IL.01 2 0
#> TCGA.CH.5738.01 2 0
#> TCGA.V1.A9ZI.01 2 0
#> TCGA.CH.5748.01 2 0
#> TCGA.YL.A8SQ.01 2 0
#> TCGA.G9.7522.01 2 0
#> TCGA.HC.A6AP.01 2 0
#> TCGA.EJ.7785.11 1 0
#> TCGA.KK.A7B4.01 2 0
#> TCGA.J4.A83J.01 2 0
#> TCGA.V1.A8MU.01 2 0
#> TCGA.EJ.5510.01 2 0
#> TCGA.EJ.7327.11 1 0
#> TCGA.CH.5746.01 2 0
#> TCGA.V1.A9Z7.01 2 0
#> TCGA.M7.A725.01 2 0
#> TCGA.G9.6384.11 1 0
#> TCGA.XJ.A9DI.01 1 0
#> TCGA.J4.A67N.01 2 0
#> TCGA.XJ.A83G.01 2 0
#> TCGA.ZG.A8QZ.01 2 0
#> TCGA.TK.A8OK.01 2 0
#> TCGA.VP.A876.01 2 0
#> TCGA.KK.A6E5.01 2 0
#> TCGA.X4.A8KQ.01 2 0
#> TCGA.KK.A8IL.01 2 0
#> TCGA.HC.7820.01 2 0
#> TCGA.CH.5739.01 2 0
#> TCGA.HC.7750.01 2 0
#> TCGA.YL.A9WX.01 1 0
#> TCGA.EJ.5518.01 2 0
#> TCGA.ZG.A9NI.01 2 0
#> TCGA.YL.A9WY.01 2 0
#> TCGA.CH.5763.11 1 0
#> TCGA.EJ.5515.01 1 0
#> TCGA.KK.A8IH.01 2 0
#> TCGA.VP.A87K.01 2 0
#> TCGA.HC.A6HY.01 2 0
#> TCGA.HC.7211.11 1 0
#> TCGA.HC.A632.01 2 0
#> TCGA.G9.6496.01 2 0
#> TCGA.EJ.A7NM.01 2 0
#> TCGA.ZG.A9L6.01 2 1
#> TCGA.2A.A8VV.01 2 0
#> TCGA.VP.A87E.01 1 1
#> TCGA.CH.5764.01 2 0
#> TCGA.EJ.5525.01 2 0
#> TCGA.CH.5772.11 1 0
#> TCGA.KK.A59Z.01 2 0
#> TCGA.V1.A9ZR.01 2 0
#> TCGA.EJ.A6RC.01 2 0
#> TCGA.EJ.7792.01 2 0
#> TCGA.HC.A9TH.01 2 0
#> TCGA.M7.A723.01 1 0
#> TCGA.EJ.7789.11 1 0
#> TCGA.HC.7752.01 2 0
#> TCGA.EJ.A65J.01 2 0
#> TCGA.V1.A8WV.01 2 0
#> TCGA.2A.A8VX.01 2 0
#> TCGA.V1.A9OT.01 2 0
#> TCGA.KC.A7FA.01 2 0
#> TCGA.G9.6373.11 1 0
#> TCGA.G9.6370.01 1 0
#> TCGA.CH.5771.01 2 1
#> TCGA.YL.A8SJ.01 2 0
#> TCGA.HC.7738.01 2 0
#> TCGA.EJ.A6RA.01 1 0
#> TCGA.J4.8198.01 2 0
#> TCGA.EJ.7123.01 2 0
#> TCGA.2A.A8W1.01 2 0
#> TCGA.G9.6363.01 2 0
#> TCGA.ZG.A9L2.01 2 0
#> TCGA.HC.7749.01 2 0
#> TCGA.CH.5768.01 2 0
#> TCGA.KK.A6E7.01 2 0
#> TCGA.G9.6332.01 2 0
#> TCGA.EJ.A46G.01 2 0
#> TCGA.V1.A9OX.01 2 0
#> TCGA.J4.A6G3.01 2 1
#> TCGA.VN.A88L.01 2 0
#> TCGA.EJ.7312.01 2 0
#> TCGA.V1.A8MM.01 2 0
#> TCGA.EJ.A65F.01 2 0
#> TCGA.G9.6498.01 2 0
#> TCGA.EJ.5505.01 2 0
#> TCGA.CH.5761.11 1 0
#> TCGA.HC.8261.01 2 0
#> TCGA.XQ.A8TB.01 2 0
#> TCGA.G9.6329.01 2 1
#> TCGA.EJ.5496.01 2 0
get_classes(res, k = 3)
#> class p
#> TCGA.G9.6343.01 2 0.000
#> TCGA.KK.A8IA.01 2 0.000
#> TCGA.KK.A6E4.01 2 0.000
#> TCGA.EJ.AB20.01 1 0.000
#> TCGA.H9.7775.01 2 0.000
#> TCGA.XJ.A9DX.01 2 0.000
#> TCGA.KK.A6E6.01 2 0.000
#> TCGA.G9.6339.01 2 1.000
#> TCGA.EJ.5509.01 2 0.000
#> TCGA.EJ.5521.01 2 0.000
#> TCGA.YL.A8SB.01 3 0.000
#> TCGA.V1.A9OF.01 2 0.000
#> TCGA.CH.5754.01 2 0.000
#> TCGA.EJ.7125.01 2 0.000
#> TCGA.EJ.7797.01 3 0.000
#> TCGA.YL.A9WI.01 2 0.000
#> TCGA.EJ.7314.01 2 0.000
#> TCGA.XA.A8JR.01 3 1.000
#> TCGA.EJ.7781.01 2 0.000
#> TCGA.QU.A6IN.01 2 0.000
#> TCGA.CH.5751.01 2 0.000
#> TCGA.V1.A8WL.01 2 0.000
#> TCGA.HC.A6AO.01 2 0.000
#> TCGA.KK.A7B3.01 2 0.000
#> TCGA.XK.AAJT.01 2 0.000
#> TCGA.EJ.AB27.01 3 0.000
#> TCGA.CH.5788.01 2 0.000
#> TCGA.KK.A8I5.01 2 0.000
#> TCGA.YL.A8S9.01 2 0.000
#> TCGA.CH.5761.01 2 0.000
#> TCGA.KK.A7AZ.01 2 0.000
#> TCGA.G9.6366.01 2 0.000
#> TCGA.HC.7819.01 2 0.000
#> TCGA.KC.A4BN.01 2 0.000
#> TCGA.KK.A8IG.01 2 0.000
#> TCGA.ZG.A8QW.01 3 0.000
#> TCGA.EJ.7786.01 2 0.000
#> TCGA.J4.A83K.01 2 0.000
#> TCGA.YL.A8HK.01 3 0.000
#> TCGA.EJ.5501.01 3 0.000
#> TCGA.EJ.8470.01 2 1.000
#> TCGA.J9.A8CL.01 2 0.000
#> TCGA.EJ.A7NF.01 2 0.000
#> TCGA.CH.5762.11 1 0.000
#> TCGA.XK.AAJA.01 2 0.000
#> TCGA.EJ.7330.01 3 0.000
#> TCGA.VP.AA1N.01 2 0.000
#> TCGA.EJ.5524.01 2 0.000
#> TCGA.KK.A6E8.01 2 0.000
#> TCGA.HC.7821.01 2 0.000
#> TCGA.HC.7209.01 2 0.751
#> TCGA.HC.7742.01 2 0.000
#> TCGA.G9.6351.01 3 0.000
#> TCGA.EJ.8474.01 2 0.000
#> TCGA.HC.7075.01 2 0.000
#> TCGA.J9.A8CP.01 2 0.000
#> TCGA.KK.A8IM.01 3 0.000
#> TCGA.G9.6348.01 3 0.000
#> TCGA.CH.5789.01 1 0.000
#> TCGA.KC.A7F6.01 2 0.000
#> TCGA.G9.6333.11 1 0.000
#> TCGA.KC.A4BL.01 3 1.000
#> TCGA.J4.A67Q.01 3 0.000
#> TCGA.2A.A8VL.01 3 0.000
#> TCGA.V1.A9ZK.01 3 0.000
#> TCGA.V1.A9O5.01 2 0.000
#> TCGA.VP.A879.01 3 1.000
#> TCGA.HC.7819.11 1 0.000
#> TCGA.VN.A88Q.01 2 0.000
#> TCGA.HC.7737.01 3 0.000
#> TCGA.V1.A8WS.01 2 0.000
#> TCGA.HC.8213.01 2 0.000
#> TCGA.M7.A721.01 2 1.000
#> TCGA.ZG.A9LZ.01 2 0.000
#> TCGA.CH.5765.01 2 0.000
#> TCGA.V1.A8WW.01 2 0.000
#> TCGA.HC.A48F.01 2 0.000
#> TCGA.V1.A9OQ.01 2 0.000
#> TCGA.EJ.5514.01 2 0.000
#> TCGA.G9.6384.01 3 0.000
#> TCGA.V1.A9ZG.01 3 0.000
#> TCGA.YL.A8HM.01 2 0.000
#> TCGA.G9.6377.01 2 0.000
#> TCGA.M7.A722.01 2 0.000
#> TCGA.G9.6361.01 2 0.000
#> TCGA.EJ.5511.01 2 0.000
#> TCGA.ZG.A9KY.01 2 0.000
#> TCGA.EJ.7784.11 1 0.000
#> TCGA.ZG.A9LN.01 3 0.000
#> TCGA.EJ.5526.01 2 0.000
#> TCGA.HC.7820.11 1 0.000
#> TCGA.YJ.A8SW.01 2 0.000
#> TCGA.EJ.7794.01 3 0.000
#> TCGA.EJ.A46B.01 3 0.000
#> TCGA.EJ.5542.01 2 0.000
#> TCGA.YL.A9WJ.01 3 0.000
#> TCGA.EJ.7328.11 1 0.000
#> TCGA.V1.A9Z8.01 3 0.000
#> TCGA.EJ.A46F.01 2 0.000
#> TCGA.YL.A8SK.01 3 0.000
#> TCGA.MG.AAMC.01 2 0.000
#> TCGA.X4.A8KS.01 3 0.000
#> TCGA.J4.A67M.01 3 0.000
#> TCGA.ZG.A9L0.01 2 0.000
#> TCGA.HC.7077.01 2 0.000
#> TCGA.CH.5769.01 2 0.000
#> TCGA.G9.6353.11 1 0.000
#> TCGA.G9.6499.01 3 0.000
#> TCGA.EJ.5519.01 2 0.000
#> TCGA.J4.A67T.01 3 0.000
#> TCGA.HC.7748.01 3 1.000
#> TCGA.VN.A88R.01 2 0.000
#> TCGA.H9.A6BY.01 2 0.000
#> TCGA.G9.6365.01 3 1.000
#> TCGA.EJ.7317.11 1 0.000
#> TCGA.G9.7510.01 3 1.000
#> TCGA.KK.A6E3.01 3 0.000
#> TCGA.G9.6336.01 3 0.000
#> TCGA.EJ.5517.01 2 0.000
#> TCGA.V1.A8MG.01 2 0.000
#> TCGA.KC.A7FE.01 3 0.000
#> TCGA.HC.7817.01 3 0.000
#> TCGA.J4.AAU2.01 2 0.000
#> TCGA.V1.A8MJ.01 3 0.000
#> TCGA.VP.A87C.01 3 0.000
#> TCGA.EJ.A7NN.01 2 0.000
#> TCGA.HC.A8D0.01 3 0.000
#> TCGA.EJ.7792.11 1 0.000
#> TCGA.EJ.5497.01 3 0.000
#> TCGA.Y6.A9XI.01 2 0.000
#> TCGA.HC.7752.11 1 0.000
#> TCGA.SU.A7E7.01 3 0.000
#> TCGA.G9.6342.11 1 0.000
#> TCGA.HC.8265.01 2 0.000
#> TCGA.CH.5737.01 2 0.000
#> TCGA.G9.6338.01 2 0.000
#> TCGA.KK.A7AV.01 3 1.000
#> TCGA.EJ.7218.01 2 0.000
#> TCGA.YL.A8SC.01 2 0.000
#> TCGA.XK.AAJR.01 3 0.000
#> TCGA.2A.AAYF.01 2 0.000
#> TCGA.V1.A8X3.01 2 0.000
#> TCGA.KK.A6DY.01 2 0.000
#> TCGA.M7.A71Z.01 2 0.000
#> TCGA.EJ.7123.11 1 0.000
#> TCGA.G9.6363.11 3 0.000
#> TCGA.KK.A8I8.01 2 0.000
#> TCGA.KC.A4BV.01 2 0.000
#> TCGA.G9.6332.11 1 0.000
#> TCGA.CH.5750.01 2 0.000
#> TCGA.ZG.A9ND.01 2 0.000
#> TCGA.EJ.A65B.01 3 0.000
#> TCGA.QU.A6IO.01 2 0.000
#> TCGA.EJ.5503.01 1 0.000
#> TCGA.ZG.A9LU.01 1 0.000
#> TCGA.EJ.8469.01 2 0.000
#> TCGA.XJ.A83H.01 3 0.751
#> TCGA.EJ.7315.01 2 0.000
#> TCGA.ZG.A8QY.01 2 0.000
#> TCGA.YL.A8SP.01 2 0.000
#> TCGA.CH.5791.01 2 0.000
#> TCGA.V1.A9OY.01 3 0.000
#> TCGA.KC.A4BO.01 1 0.000
#> TCGA.HC.A76X.01 2 0.000
#> TCGA.YL.A8SO.01 3 1.000
#> TCGA.KK.A8IF.01 2 0.000
#> TCGA.EJ.A7NK.01 1 0.000
#> TCGA.ZG.A9L4.01 3 0.000
#> TCGA.EJ.5522.01 3 0.498
#> TCGA.HC.7747.01 3 0.000
#> TCGA.EJ.7125.11 1 0.000
#> TCGA.ZG.A9M4.01 2 0.000
#> TCGA.EJ.A65D.01 2 0.000
#> TCGA.HC.A4ZV.01 2 0.000
#> TCGA.G9.A9S0.01 2 0.000
#> TCGA.EJ.5506.01 1 0.000
#> TCGA.KK.A7AP.01 2 0.000
#> TCGA.VP.A87D.01 2 0.000
#> TCGA.TP.A8TT.01 2 0.000
#> TCGA.KK.A8II.01 2 0.000
#> TCGA.V1.A9Z9.01 2 0.000
#> TCGA.ZG.A9LS.01 3 0.000
#> TCGA.HC.7232.01 2 0.000
#> TCGA.EJ.A8FO.01 3 0.000
#> TCGA.J9.A52B.01 2 0.000
#> TCGA.CH.5767.01 2 0.000
#> TCGA.J4.AATV.01 3 0.000
#> TCGA.HC.7081.01 2 0.000
#> TCGA.CH.5743.01 1 0.000
#> TCGA.V1.A9OH.01 3 0.000
#> TCGA.CH.5752.01 2 0.000
#> TCGA.VP.A87H.01 2 0.000
#> TCGA.G9.7521.01 2 0.000
#> TCGA.YL.A8HO.01 3 1.000
#> TCGA.YL.A9WK.01 2 0.000
#> TCGA.J4.A83M.01 2 0.000
#> TCGA.VP.A878.01 3 0.000
#> TCGA.CH.5766.11 1 0.000
#> TCGA.HC.7736.01 2 0.000
#> TCGA.G9.6385.01 1 0.000
#> TCGA.VN.A88N.01 2 0.000
#> TCGA.HC.7745.01 3 0.000
#> TCGA.HC.7078.01 2 0.000
#> TCGA.FC.A5OB.01 2 0.000
#> TCGA.G9.6379.01 3 0.000
#> TCGA.QU.A6IP.01 3 1.000
#> TCGA.J4.AATZ.01 2 0.000
#> TCGA.V1.A9O9.01 2 0.000
#> TCGA.V1.A9OL.01 2 0.000
#> TCGA.HC.7210.01 3 1.000
#> TCGA.KK.A8I7.01 3 1.000
#> TCGA.EJ.7791.01 3 0.000
#> TCGA.CH.5762.01 3 0.000
#> TCGA.EJ.5527.01 3 0.000
#> TCGA.KK.A8IC.01 3 0.000
#> TCGA.G9.6356.01 3 0.000
#> TCGA.J9.A52D.01 2 0.000
#> TCGA.EJ.7788.01 2 0.000
#> TCGA.ZG.A9LB.01 2 0.000
#> TCGA.J9.A8CN.01 2 0.000
#> TCGA.ZG.A9L1.01 2 0.000
#> TCGA.G9.6333.01 3 0.000
#> TCGA.VP.A875.01 2 0.000
#> TCGA.EJ.8468.01 2 0.000
#> TCGA.EJ.5495.01 3 0.000
#> TCGA.H9.A6BX.01 1 0.000
#> TCGA.KK.A59Y.01 2 0.000
#> TCGA.V1.A8WN.01 3 0.000
#> TCGA.KK.A7B1.01 2 0.249
#> TCGA.G9.6362.11 2 0.000
#> TCGA.G9.6364.11 1 0.000
#> TCGA.HC.A631.01 2 0.000
#> TCGA.YL.A8SA.01 2 0.000
#> TCGA.HC.8262.01 2 0.000
#> TCGA.CH.5765.11 1 0.000
#> TCGA.KC.A7FD.01 2 0.000
#> TCGA.HI.7170.01 2 0.249
#> TCGA.J4.A67L.01 3 1.000
#> TCGA.V1.A9O7.01 3 0.000
#> TCGA.HC.A6AS.01 3 0.000
#> TCGA.EJ.7784.01 2 0.000
#> TCGA.EJ.7331.11 1 0.000
#> TCGA.KC.A7F3.01 3 1.000
#> TCGA.G9.6494.11 1 0.000
#> TCGA.HC.8256.01 2 0.000
#> TCGA.J4.A83I.01 2 0.000
#> TCGA.G9.6373.01 2 0.000
#> TCGA.EJ.7794.11 1 0.000
#> TCGA.G9.6371.01 2 0.000
#> TCGA.XQ.A8TA.01 2 0.000
#> TCGA.EJ.5498.01 3 0.000
#> TCGA.EJ.7328.01 3 0.000
#> TCGA.EJ.A46D.01 3 0.000
#> TCGA.ZG.A9L9.01 2 0.000
#> TCGA.YL.A8SI.01 3 0.000
#> TCGA.M7.A724.01 2 0.000
#> TCGA.VN.A88K.01 2 0.000
#> TCGA.EJ.A8FP.01 1 0.000
#> TCGA.V1.A8MK.01 3 0.000
#> TCGA.YL.A8HJ.01 3 0.000
#> TCGA.KK.A8ID.01 2 0.000
#> TCGA.CH.5769.11 3 1.000
#> TCGA.G9.6353.01 3 1.000
#> TCGA.G9.6499.11 2 0.000
#> TCGA.KK.A8I9.01 2 1.000
#> TCGA.G9.6365.11 1 0.000
#> TCGA.EJ.A46H.01 1 0.000
#> TCGA.EJ.7317.01 2 0.000
#> TCGA.YL.A8S8.01 2 0.000
#> TCGA.XJ.A9DQ.01 1 0.000
#> TCGA.EJ.7782.11 1 0.000
#> TCGA.J4.A67O.01 3 0.000
#> TCGA.Y6.A8TL.01 2 0.000
#> TCGA.XK.AAIV.01 3 0.000
#> TCGA.CH.5790.01 2 0.000
#> TCGA.HC.7231.01 2 0.000
#> TCGA.ZG.A9L5.01 2 0.000
#> TCGA.V1.A8MF.01 2 0.000
#> TCGA.EJ.A7NJ.01 1 0.000
#> TCGA.EJ.A65E.01 2 0.000
#> TCGA.ZG.A8QX.01 2 0.000
#> TCGA.G9.6367.01 1 0.000
#> TCGA.G9.6342.01 2 1.000
#> TCGA.KK.A8IB.01 3 0.000
#> TCGA.HC.7230.01 2 0.000
#> TCGA.XK.AAIR.01 3 0.000
#> TCGA.CH.5741.01 2 0.000
#> TCGA.KK.A59V.01 2 0.000
#> TCGA.J4.8200.01 2 0.000
#> TCGA.KK.A7AQ.01 2 0.000
#> TCGA.EJ.5532.01 2 0.000
#> TCGA.HI.7168.01 2 0.000
#> TCGA.HC.7233.01 2 0.000
#> TCGA.HC.A6AL.01 2 0.000
#> TCGA.EJ.7783.01 3 0.000
#> TCGA.HC.8264.01 2 0.000
#> TCGA.EJ.A8FU.01 1 0.000
#> TCGA.EJ.A65M.01 2 0.000
#> TCGA.EJ.A8FN.01 2 0.000
#> TCGA.HI.7171.01 2 0.000
#> TCGA.XK.AAJP.01 2 0.000
#> TCGA.HC.7212.01 2 0.000
#> TCGA.ZG.A9MC.01 3 0.000
#> TCGA.2A.A8VO.01 2 0.000
#> TCGA.HC.8259.01 2 0.000
#> TCGA.G9.6378.01 3 0.000
#> TCGA.J4.A83L.01 2 1.000
#> TCGA.VN.A88P.01 2 0.000
#> TCGA.EJ.5507.01 2 0.000
#> TCGA.J9.A8CK.01 2 1.000
#> TCGA.CH.5744.01 2 0.000
#> TCGA.ZG.A9N3.01 3 1.000
#> TCGA.G9.6354.01 2 0.000
#> TCGA.VN.A88O.01 2 0.000
#> TCGA.EJ.5502.01 3 0.000
#> TCGA.HC.7079.01 1 1.000
#> TCGA.G9.6369.01 2 0.000
#> TCGA.KK.A6E1.01 2 0.000
#> TCGA.HC.7211.01 2 0.000
#> TCGA.KK.A8I6.01 2 0.000
#> TCGA.XJ.A83F.01 2 0.000
#> TCGA.EJ.7785.01 3 0.000
#> TCGA.G9.A9S4.01 2 0.000
#> TCGA.VP.A87B.01 2 0.000
#> TCGA.YL.A8SR.01 2 0.000
#> TCGA.EJ.7327.01 2 0.000
#> TCGA.4L.AA1F.01 3 0.000
#> TCGA.KK.A7AY.01 2 0.000
#> TCGA.EJ.A65G.01 2 0.000
#> TCGA.2A.AAYU.01 2 0.000
#> TCGA.HC.A76W.01 2 0.000
#> TCGA.EJ.5516.01 3 0.000
#> TCGA.G9.A9S7.01 2 0.000
#> TCGA.HC.8216.01 2 0.000
#> TCGA.CH.5794.01 2 0.000
#> TCGA.V1.A9OA.01 3 1.000
#> TCGA.J9.A52E.01 2 0.000
#> TCGA.HC.7818.01 2 0.000
#> TCGA.G9.7525.01 2 0.000
#> TCGA.FC.7961.01 2 0.249
#> TCGA.CH.5767.11 1 0.000
#> TCGA.EJ.5504.01 2 0.000
#> TCGA.VP.A87J.01 2 0.000
#> TCGA.J4.A67S.01 3 1.000
#> TCGA.KK.A8IK.01 2 0.000
#> TCGA.HC.A6AQ.01 3 1.000
#> TCGA.CH.5763.01 1 0.000
#> TCGA.HC.A8D1.01 3 0.000
#> TCGA.KK.A7AU.01 2 0.000
#> TCGA.CH.5766.01 3 1.000
#> TCGA.EJ.7781.11 1 0.000
#> TCGA.KK.A7B0.01 3 0.000
#> TCGA.EJ.7321.01 2 0.000
#> TCGA.G9.6385.11 1 0.000
#> TCGA.VN.A943.01 2 0.000
#> TCGA.KK.A59X.01 2 0.000
#> TCGA.KK.A8I4.01 3 0.000
#> TCGA.G9.6496.11 1 0.000
#> TCGA.G9.7523.01 3 1.000
#> TCGA.EJ.5494.01 2 0.000
#> TCGA.2A.A8VT.01 2 0.000
#> TCGA.HC.7213.01 2 0.000
#> TCGA.G9.7519.01 2 0.000
#> TCGA.CH.5764.11 1 0.000
#> TCGA.CH.5772.01 2 0.000
#> TCGA.EJ.7325.01 2 0.000
#> TCGA.G9.6356.11 1 0.000
#> TCGA.ZG.A9LM.01 2 0.000
#> TCGA.XJ.A9DK.01 1 0.000
#> TCGA.EJ.7789.01 2 0.000
#> TCGA.HC.8257.01 2 0.000
#> TCGA.EJ.A7NG.01 1 0.249
#> TCGA.EJ.7318.01 2 0.000
#> TCGA.EJ.5512.01 3 0.000
#> TCGA.EJ.A46E.01 1 0.000
#> TCGA.FC.A4JI.01 2 0.000
#> TCGA.J9.A8CM.01 2 0.000
#> TCGA.CH.5771.11 1 0.000
#> TCGA.KC.A4BR.01 1 1.000
#> TCGA.2A.AAYO.01 2 0.000
#> TCGA.2A.A8W3.01 3 0.000
#> TCGA.CH.5768.11 1 0.498
#> TCGA.G9.6364.01 2 0.000
#> TCGA.YL.A8SL.01 2 0.000
#> TCGA.KK.A5A1.01 2 0.000
#> TCGA.YL.A9WL.01 2 0.000
#> TCGA.HC.A6HX.01 3 0.000
#> TCGA.M7.A720.01 1 0.000
#> TCGA.HC.7080.01 2 0.000
#> TCGA.V1.A9O5.06 2 0.000
#> TCGA.KC.A7F5.01 2 0.000
#> TCGA.EJ.7331.01 3 1.000
#> TCGA.ZG.A9LY.01 3 0.000
#> TCGA.G9.6494.01 2 0.000
#> TCGA.M7.A71Y.01 1 0.000
#> TCGA.FC.A66V.01 1 0.000
#> TCGA.EJ.7793.01 3 0.000
#> TCGA.EJ.A8FS.01 2 0.000
#> TCGA.XK.AAJU.01 1 0.000
#> TCGA.HC.8266.01 3 0.000
#> TCGA.YL.A8HL.01 2 0.000
#> TCGA.VN.A88I.01 1 0.249
#> TCGA.HI.7169.01 2 0.000
#> TCGA.CH.5753.01 2 0.000
#> TCGA.J4.A67K.01 2 0.000
#> TCGA.QU.A6IM.01 2 0.000
#> TCGA.HC.A9TE.01 2 0.000
#> TCGA.EJ.7115.01 2 0.000
#> TCGA.HC.7745.11 1 0.000
#> TCGA.EJ.5531.01 3 0.000
#> TCGA.YL.A8SH.01 2 0.000
#> TCGA.G9.6362.01 2 0.000
#> TCGA.HC.8258.01 3 0.000
#> TCGA.EJ.5530.01 2 0.000
#> TCGA.VN.A88M.01 2 0.000
#> TCGA.EJ.7782.01 2 0.000
#> TCGA.YL.A8SF.01 2 0.000
#> TCGA.KK.A6E2.01 2 0.000
#> TCGA.CH.5792.01 3 0.000
#> TCGA.J4.A6G1.01 3 0.000
#> TCGA.J4.A6M7.01 2 0.000
#> TCGA.VP.A872.01 2 0.000
#> TCGA.V1.A8ML.01 2 0.000
#> TCGA.HC.7744.01 2 0.000
#> TCGA.G9.6347.01 3 0.000
#> TCGA.EJ.A46I.01 3 0.000
#> TCGA.XK.AAJ3.01 2 0.000
#> TCGA.HC.A8CY.01 2 0.000
#> TCGA.KK.A6E0.01 2 0.000
#> TCGA.XK.AAK1.01 2 0.000
#> TCGA.XK.AAIW.01 2 0.000
#> TCGA.HC.8260.01 3 1.000
#> TCGA.HC.7737.11 1 0.000
#> TCGA.EJ.7786.11 1 0.000
#> TCGA.HC.7740.01 3 0.000
#> TCGA.TP.A8TV.01 2 0.000
#> TCGA.FC.A6HD.01 2 0.000
#> TCGA.EJ.8472.01 2 0.000
#> TCGA.CH.5745.01 2 0.000
#> TCGA.EJ.5508.01 3 0.000
#> TCGA.EJ.A7NH.01 3 0.000
#> TCGA.KK.A7B2.01 3 1.000
#> TCGA.CH.5740.01 2 0.000
#> TCGA.YL.A9WH.01 2 0.000
#> TCGA.FC.A8O0.01 1 0.000
#> TCGA.J9.A52C.01 3 0.000
#> TCGA.FC.7708.01 3 0.000
#> TCGA.HC.7742.11 3 1.000
#> TCGA.G9.6351.11 3 1.000
#> TCGA.KK.A7AW.01 2 0.000
#> TCGA.G9.7509.01 2 0.000
#> TCGA.J4.A67R.01 3 0.000
#> TCGA.WW.A8ZI.01 2 0.000
#> TCGA.KK.A8IJ.01 2 0.000
#> TCGA.J4.A83N.01 2 0.000
#> TCGA.HC.A6AN.01 2 0.000
#> TCGA.G9.6348.11 1 0.000
#> TCGA.EJ.5499.01 3 0.000
#> TCGA.G9.6367.11 1 0.000
#> TCGA.QU.A6IL.01 2 0.000
#> TCGA.CH.5738.01 3 0.000
#> TCGA.V1.A9ZI.01 2 0.000
#> TCGA.CH.5748.01 2 0.000
#> TCGA.YL.A8SQ.01 2 0.000
#> TCGA.G9.7522.01 3 0.000
#> TCGA.HC.A6AP.01 3 0.000
#> TCGA.EJ.7785.11 1 0.000
#> TCGA.KK.A7B4.01 2 0.000
#> TCGA.J4.A83J.01 2 0.000
#> TCGA.V1.A8MU.01 3 1.000
#> TCGA.EJ.5510.01 3 0.000
#> TCGA.EJ.7327.11 1 0.000
#> TCGA.CH.5746.01 3 0.000
#> TCGA.V1.A9Z7.01 2 0.000
#> TCGA.M7.A725.01 2 0.000
#> TCGA.G9.6384.11 1 0.000
#> TCGA.XJ.A9DI.01 1 0.000
#> TCGA.J4.A67N.01 2 0.000
#> TCGA.XJ.A83G.01 2 0.000
#> TCGA.ZG.A8QZ.01 3 0.000
#> TCGA.TK.A8OK.01 3 0.000
#> TCGA.VP.A876.01 2 0.000
#> TCGA.KK.A6E5.01 2 0.000
#> TCGA.X4.A8KQ.01 3 0.000
#> TCGA.KK.A8IL.01 2 0.000
#> TCGA.HC.7820.01 3 0.498
#> TCGA.CH.5739.01 2 0.000
#> TCGA.HC.7750.01 3 0.000
#> TCGA.YL.A9WX.01 3 1.000
#> TCGA.EJ.5518.01 2 0.000
#> TCGA.ZG.A9NI.01 2 0.000
#> TCGA.YL.A9WY.01 3 0.000
#> TCGA.CH.5763.11 1 0.000
#> TCGA.EJ.5515.01 1 0.000
#> TCGA.KK.A8IH.01 2 0.000
#> TCGA.VP.A87K.01 2 0.000
#> TCGA.HC.A6HY.01 2 0.000
#> TCGA.HC.7211.11 1 0.000
#> TCGA.HC.A632.01 2 0.000
#> TCGA.G9.6496.01 2 0.000
#> TCGA.EJ.A7NM.01 2 0.000
#> TCGA.ZG.A9L6.01 3 0.000
#> TCGA.2A.A8VV.01 2 0.000
#> TCGA.VP.A87E.01 3 0.000
#> TCGA.CH.5764.01 2 0.000
#> TCGA.EJ.5525.01 2 0.000
#> TCGA.CH.5772.11 1 0.000
#> TCGA.KK.A59Z.01 2 0.000
#> TCGA.V1.A9ZR.01 3 0.000
#> TCGA.EJ.A6RC.01 3 0.249
#> TCGA.EJ.7792.01 3 0.000
#> TCGA.HC.A9TH.01 2 0.000
#> TCGA.M7.A723.01 1 0.000
#> TCGA.EJ.7789.11 1 0.000
#> TCGA.HC.7752.01 2 0.000
#> TCGA.EJ.A65J.01 2 0.000
#> TCGA.V1.A8WV.01 3 1.000
#> TCGA.2A.A8VX.01 2 0.000
#> TCGA.V1.A9OT.01 2 0.000
#> TCGA.KC.A7FA.01 2 0.000
#> TCGA.G9.6373.11 1 0.000
#> TCGA.G9.6370.01 1 0.000
#> TCGA.CH.5771.01 3 0.000
#> TCGA.YL.A8SJ.01 2 1.000
#> TCGA.HC.7738.01 2 0.000
#> TCGA.EJ.A6RA.01 3 0.000
#> TCGA.J4.8198.01 2 0.000
#> TCGA.EJ.7123.01 2 0.000
#> TCGA.2A.A8W1.01 2 0.000
#> TCGA.G9.6363.01 2 0.000
#> TCGA.ZG.A9L2.01 3 0.000
#> TCGA.HC.7749.01 2 0.000
#> TCGA.CH.5768.01 2 0.000
#> TCGA.KK.A6E7.01 2 0.000
#> TCGA.G9.6332.01 2 0.000
#> TCGA.EJ.A46G.01 2 0.000
#> TCGA.V1.A9OX.01 2 0.498
#> TCGA.J4.A6G3.01 3 0.000
#> TCGA.VN.A88L.01 2 0.000
#> TCGA.EJ.7312.01 2 0.000
#> TCGA.V1.A8MM.01 2 0.000
#> TCGA.EJ.A65F.01 2 0.000
#> TCGA.G9.6498.01 2 0.000
#> TCGA.EJ.5505.01 3 0.000
#> TCGA.CH.5761.11 1 0.000
#> TCGA.HC.8261.01 3 1.000
#> TCGA.XQ.A8TB.01 2 0.000
#> TCGA.G9.6329.01 3 0.000
#> TCGA.EJ.5496.01 3 1.000
get_classes(res, k = 4)
#> class p
#> TCGA.G9.6343.01 4 1.000
#> TCGA.KK.A8IA.01 2 0.000
#> TCGA.KK.A6E4.01 2 0.000
#> TCGA.EJ.AB20.01 1 0.000
#> TCGA.H9.7775.01 2 0.000
#> TCGA.XJ.A9DX.01 2 0.000
#> TCGA.KK.A6E6.01 2 1.000
#> TCGA.G9.6339.01 4 0.000
#> TCGA.EJ.5509.01 4 0.000
#> TCGA.EJ.5521.01 4 0.000
#> TCGA.YL.A8SB.01 4 0.000
#> TCGA.V1.A9OF.01 2 0.000
#> TCGA.CH.5754.01 2 1.000
#> TCGA.EJ.7125.01 2 0.000
#> TCGA.EJ.7797.01 3 0.000
#> TCGA.YL.A9WI.01 2 0.000
#> TCGA.EJ.7314.01 4 0.000
#> TCGA.XA.A8JR.01 4 0.000
#> TCGA.EJ.7781.01 4 0.000
#> TCGA.QU.A6IN.01 2 0.000
#> TCGA.CH.5751.01 2 1.000
#> TCGA.V1.A8WL.01 2 0.000
#> TCGA.HC.A6AO.01 2 0.000
#> TCGA.KK.A7B3.01 2 0.000
#> TCGA.XK.AAJT.01 4 1.000
#> TCGA.EJ.AB27.01 3 0.000
#> TCGA.CH.5788.01 2 0.000
#> TCGA.KK.A8I5.01 2 0.000
#> TCGA.YL.A8S9.01 2 0.000
#> TCGA.CH.5761.01 2 0.000
#> TCGA.KK.A7AZ.01 2 0.000
#> TCGA.G9.6366.01 4 0.000
#> TCGA.HC.7819.01 2 0.000
#> TCGA.KC.A4BN.01 4 0.000
#> TCGA.KK.A8IG.01 2 1.000
#> TCGA.ZG.A8QW.01 3 0.000
#> TCGA.EJ.7786.01 4 0.000
#> TCGA.J4.A83K.01 4 0.000
#> TCGA.YL.A8HK.01 3 1.000
#> TCGA.EJ.5501.01 3 0.000
#> TCGA.EJ.8470.01 4 0.000
#> TCGA.J9.A8CL.01 2 0.000
#> TCGA.EJ.A7NF.01 2 0.000
#> TCGA.CH.5762.11 1 0.000
#> TCGA.XK.AAJA.01 2 0.000
#> TCGA.EJ.7330.01 3 0.000
#> TCGA.VP.AA1N.01 4 1.000
#> TCGA.EJ.5524.01 4 0.000
#> TCGA.KK.A6E8.01 2 0.000
#> TCGA.HC.7821.01 2 0.000
#> TCGA.HC.7209.01 4 0.000
#> TCGA.HC.7742.01 4 0.000
#> TCGA.G9.6351.01 3 0.000
#> TCGA.EJ.8474.01 2 0.000
#> TCGA.HC.7075.01 2 0.000
#> TCGA.J9.A8CP.01 2 1.000
#> TCGA.KK.A8IM.01 3 0.000
#> TCGA.G9.6348.01 3 0.000
#> TCGA.CH.5789.01 1 0.000
#> TCGA.KC.A7F6.01 2 0.000
#> TCGA.G9.6333.11 1 0.000
#> TCGA.KC.A4BL.01 3 0.000
#> TCGA.J4.A67Q.01 4 0.000
#> TCGA.2A.A8VL.01 4 0.000
#> TCGA.V1.A9ZK.01 3 0.000
#> TCGA.V1.A9O5.01 4 0.000
#> TCGA.VP.A879.01 4 0.000
#> TCGA.HC.7819.11 1 0.000
#> TCGA.VN.A88Q.01 2 1.000
#> TCGA.HC.7737.01 4 0.000
#> TCGA.V1.A8WS.01 2 0.000
#> TCGA.HC.8213.01 2 0.000
#> TCGA.M7.A721.01 4 0.000
#> TCGA.ZG.A9LZ.01 2 0.000
#> TCGA.CH.5765.01 2 0.000
#> TCGA.V1.A8WW.01 2 0.000
#> TCGA.HC.A48F.01 2 0.000
#> TCGA.V1.A9OQ.01 2 0.000
#> TCGA.EJ.5514.01 4 1.000
#> TCGA.G9.6384.01 4 0.000
#> TCGA.V1.A9ZG.01 3 0.000
#> TCGA.YL.A8HM.01 2 0.000
#> TCGA.G9.6377.01 2 0.000
#> TCGA.M7.A722.01 2 0.000
#> TCGA.G9.6361.01 2 0.000
#> TCGA.EJ.5511.01 2 0.000
#> TCGA.ZG.A9KY.01 2 0.000
#> TCGA.EJ.7784.11 1 0.000
#> TCGA.ZG.A9LN.01 4 0.000
#> TCGA.EJ.5526.01 4 0.000
#> TCGA.HC.7820.11 1 0.000
#> TCGA.YJ.A8SW.01 2 0.000
#> TCGA.EJ.7794.01 3 0.000
#> TCGA.EJ.A46B.01 3 0.000
#> TCGA.EJ.5542.01 4 0.000
#> TCGA.YL.A9WJ.01 4 1.000
#> TCGA.EJ.7328.11 1 0.000
#> TCGA.V1.A9Z8.01 4 0.000
#> TCGA.EJ.A46F.01 2 0.000
#> TCGA.YL.A8SK.01 4 1.000
#> TCGA.MG.AAMC.01 2 0.000
#> TCGA.X4.A8KS.01 3 0.000
#> TCGA.J4.A67M.01 4 0.000
#> TCGA.ZG.A9L0.01 2 0.000
#> TCGA.HC.7077.01 2 0.000
#> TCGA.CH.5769.01 4 1.000
#> TCGA.G9.6353.11 1 0.000
#> TCGA.G9.6499.01 4 0.000
#> TCGA.EJ.5519.01 2 0.000
#> TCGA.J4.A67T.01 4 0.000
#> TCGA.HC.7748.01 4 0.000
#> TCGA.VN.A88R.01 2 0.000
#> TCGA.H9.A6BY.01 2 0.000
#> TCGA.G9.6365.01 4 0.000
#> TCGA.EJ.7317.11 1 0.000
#> TCGA.G9.7510.01 4 0.000
#> TCGA.KK.A6E3.01 4 0.000
#> TCGA.G9.6336.01 3 0.000
#> TCGA.EJ.5517.01 2 0.000
#> TCGA.V1.A8MG.01 4 1.000
#> TCGA.KC.A7FE.01 3 0.000
#> TCGA.HC.7817.01 3 0.000
#> TCGA.J4.AAU2.01 2 0.000
#> TCGA.V1.A8MJ.01 3 0.000
#> TCGA.VP.A87C.01 4 0.000
#> TCGA.EJ.A7NN.01 2 0.751
#> TCGA.HC.A8D0.01 3 0.000
#> TCGA.EJ.7792.11 1 0.000
#> TCGA.EJ.5497.01 4 0.000
#> TCGA.Y6.A9XI.01 2 0.000
#> TCGA.HC.7752.11 1 0.000
#> TCGA.SU.A7E7.01 3 0.000
#> TCGA.G9.6342.11 1 0.000
#> TCGA.HC.8265.01 4 1.000
#> TCGA.CH.5737.01 2 0.000
#> TCGA.G9.6338.01 2 0.000
#> TCGA.KK.A7AV.01 4 0.000
#> TCGA.EJ.7218.01 2 0.000
#> TCGA.YL.A8SC.01 2 1.000
#> TCGA.XK.AAJR.01 4 0.000
#> TCGA.2A.AAYF.01 2 0.000
#> TCGA.V1.A8X3.01 2 1.000
#> TCGA.KK.A6DY.01 4 0.000
#> TCGA.M7.A71Z.01 2 0.000
#> TCGA.EJ.7123.11 1 0.000
#> TCGA.G9.6363.11 4 0.000
#> TCGA.KK.A8I8.01 2 1.000
#> TCGA.KC.A4BV.01 2 0.000
#> TCGA.G9.6332.11 1 0.000
#> TCGA.CH.5750.01 2 0.000
#> TCGA.ZG.A9ND.01 2 0.000
#> TCGA.EJ.A65B.01 3 0.000
#> TCGA.QU.A6IO.01 2 0.253
#> TCGA.EJ.5503.01 1 0.000
#> TCGA.ZG.A9LU.01 3 1.000
#> TCGA.EJ.8469.01 2 0.000
#> TCGA.XJ.A83H.01 4 0.000
#> TCGA.EJ.7315.01 2 0.000
#> TCGA.ZG.A8QY.01 4 0.000
#> TCGA.YL.A8SP.01 2 0.000
#> TCGA.CH.5791.01 2 0.000
#> TCGA.V1.A9OY.01 4 0.000
#> TCGA.KC.A4BO.01 1 0.000
#> TCGA.HC.A76X.01 2 0.000
#> TCGA.YL.A8SO.01 4 0.000
#> TCGA.KK.A8IF.01 2 0.000
#> TCGA.EJ.A7NK.01 1 0.000
#> TCGA.ZG.A9L4.01 4 0.502
#> TCGA.EJ.5522.01 4 0.000
#> TCGA.HC.7747.01 3 0.000
#> TCGA.EJ.7125.11 1 0.000
#> TCGA.ZG.A9M4.01 4 1.000
#> TCGA.EJ.A65D.01 2 0.000
#> TCGA.HC.A4ZV.01 2 0.000
#> TCGA.G9.A9S0.01 4 0.000
#> TCGA.EJ.5506.01 1 0.000
#> TCGA.KK.A7AP.01 2 0.000
#> TCGA.VP.A87D.01 2 0.000
#> TCGA.TP.A8TT.01 4 0.000
#> TCGA.KK.A8II.01 2 0.000
#> TCGA.V1.A9Z9.01 4 1.000
#> TCGA.ZG.A9LS.01 4 0.000
#> TCGA.HC.7232.01 4 1.000
#> TCGA.EJ.A8FO.01 3 0.000
#> TCGA.J9.A52B.01 2 0.000
#> TCGA.CH.5767.01 2 0.000
#> TCGA.J4.AATV.01 3 0.000
#> TCGA.HC.7081.01 2 1.000
#> TCGA.CH.5743.01 1 0.000
#> TCGA.V1.A9OH.01 4 0.000
#> TCGA.CH.5752.01 2 0.000
#> TCGA.VP.A87H.01 4 0.000
#> TCGA.G9.7521.01 2 1.000
#> TCGA.YL.A8HO.01 4 0.000
#> TCGA.YL.A9WK.01 2 0.000
#> TCGA.J4.A83M.01 2 0.000
#> TCGA.VP.A878.01 3 0.000
#> TCGA.CH.5766.11 1 0.000
#> TCGA.HC.7736.01 4 0.000
#> TCGA.G9.6385.01 1 0.000
#> TCGA.VN.A88N.01 4 0.000
#> TCGA.HC.7745.01 3 0.000
#> TCGA.HC.7078.01 2 0.000
#> TCGA.FC.A5OB.01 2 0.000
#> TCGA.G9.6379.01 4 0.000
#> TCGA.QU.A6IP.01 4 0.000
#> TCGA.J4.AATZ.01 2 0.000
#> TCGA.V1.A9O9.01 4 0.000
#> TCGA.V1.A9OL.01 2 0.000
#> TCGA.HC.7210.01 4 0.000
#> TCGA.KK.A8I7.01 3 0.000
#> TCGA.EJ.7791.01 3 0.000
#> TCGA.CH.5762.01 3 0.000
#> TCGA.EJ.5527.01 4 0.000
#> TCGA.KK.A8IC.01 3 0.000
#> TCGA.G9.6356.01 3 0.000
#> TCGA.J9.A52D.01 2 0.000
#> TCGA.EJ.7788.01 2 0.000
#> TCGA.ZG.A9LB.01 4 1.000
#> TCGA.J9.A8CN.01 2 0.000
#> TCGA.ZG.A9L1.01 2 0.000
#> TCGA.G9.6333.01 4 0.000
#> TCGA.VP.A875.01 2 0.000
#> TCGA.EJ.8468.01 2 1.000
#> TCGA.EJ.5495.01 4 0.000
#> TCGA.H9.A6BX.01 1 0.000
#> TCGA.KK.A59Y.01 2 0.000
#> TCGA.V1.A8WN.01 3 0.000
#> TCGA.KK.A7B1.01 4 0.000
#> TCGA.G9.6362.11 2 0.000
#> TCGA.G9.6364.11 1 0.000
#> TCGA.HC.A631.01 2 0.000
#> TCGA.YL.A8SA.01 2 0.000
#> TCGA.HC.8262.01 4 1.000
#> TCGA.CH.5765.11 1 1.000
#> TCGA.KC.A7FD.01 2 0.000
#> TCGA.HI.7170.01 4 0.000
#> TCGA.J4.A67L.01 4 0.000
#> TCGA.V1.A9O7.01 3 0.000
#> TCGA.HC.A6AS.01 4 0.000
#> TCGA.EJ.7784.01 2 0.000
#> TCGA.EJ.7331.11 1 0.000
#> TCGA.KC.A7F3.01 4 0.000
#> TCGA.G9.6494.11 1 0.000
#> TCGA.HC.8256.01 4 1.000
#> TCGA.J4.A83I.01 2 0.000
#> TCGA.G9.6373.01 2 0.000
#> TCGA.EJ.7794.11 1 0.000
#> TCGA.G9.6371.01 2 0.000
#> TCGA.XQ.A8TA.01 2 0.000
#> TCGA.EJ.5498.01 3 0.000
#> TCGA.EJ.7328.01 3 0.000
#> TCGA.EJ.A46D.01 3 0.000
#> TCGA.ZG.A9L9.01 2 0.000
#> TCGA.YL.A8SI.01 4 0.000
#> TCGA.M7.A724.01 2 0.000
#> TCGA.VN.A88K.01 2 0.000
#> TCGA.EJ.A8FP.01 1 0.000
#> TCGA.V1.A8MK.01 3 0.000
#> TCGA.YL.A8HJ.01 3 0.000
#> TCGA.KK.A8ID.01 2 0.000
#> TCGA.CH.5769.11 4 0.000
#> TCGA.G9.6353.01 3 0.000
#> TCGA.G9.6499.11 4 0.502
#> TCGA.KK.A8I9.01 4 0.000
#> TCGA.G9.6365.11 1 0.000
#> TCGA.EJ.A46H.01 1 0.000
#> TCGA.EJ.7317.01 4 1.000
#> TCGA.YL.A8S8.01 2 1.000
#> TCGA.XJ.A9DQ.01 1 0.498
#> TCGA.EJ.7782.11 1 0.000
#> TCGA.J4.A67O.01 3 0.000
#> TCGA.Y6.A8TL.01 4 0.000
#> TCGA.XK.AAIV.01 4 0.000
#> TCGA.CH.5790.01 2 0.000
#> TCGA.HC.7231.01 2 0.000
#> TCGA.ZG.A9L5.01 2 0.000
#> TCGA.V1.A8MF.01 4 0.000
#> TCGA.EJ.A7NJ.01 1 0.000
#> TCGA.EJ.A65E.01 4 0.249
#> TCGA.ZG.A8QX.01 4 0.000
#> TCGA.G9.6367.01 1 0.000
#> TCGA.G9.6342.01 4 0.000
#> TCGA.KK.A8IB.01 4 0.000
#> TCGA.HC.7230.01 2 0.000
#> TCGA.XK.AAIR.01 3 0.000
#> TCGA.CH.5741.01 2 0.000
#> TCGA.KK.A59V.01 2 0.000
#> TCGA.J4.8200.01 4 0.000
#> TCGA.KK.A7AQ.01 2 0.000
#> TCGA.EJ.5532.01 4 1.000
#> TCGA.HI.7168.01 2 1.000
#> TCGA.HC.7233.01 4 1.000
#> TCGA.HC.A6AL.01 2 0.000
#> TCGA.EJ.7783.01 4 0.000
#> TCGA.HC.8264.01 2 0.000
#> TCGA.EJ.A8FU.01 1 0.000
#> TCGA.EJ.A65M.01 4 1.000
#> TCGA.EJ.A8FN.01 2 0.000
#> TCGA.HI.7171.01 2 0.000
#> TCGA.XK.AAJP.01 2 0.000
#> TCGA.HC.7212.01 2 0.000
#> TCGA.ZG.A9MC.01 3 0.000
#> TCGA.2A.A8VO.01 2 0.000
#> TCGA.HC.8259.01 2 0.000
#> TCGA.G9.6378.01 3 0.000
#> TCGA.J4.A83L.01 4 0.000
#> TCGA.VN.A88P.01 2 0.000
#> TCGA.EJ.5507.01 4 1.000
#> TCGA.J9.A8CK.01 4 0.000
#> TCGA.CH.5744.01 4 0.000
#> TCGA.ZG.A9N3.01 4 0.000
#> TCGA.G9.6354.01 4 1.000
#> TCGA.VN.A88O.01 2 0.000
#> TCGA.EJ.5502.01 4 0.000
#> TCGA.HC.7079.01 3 1.000
#> TCGA.G9.6369.01 2 0.000
#> TCGA.KK.A6E1.01 2 0.000
#> TCGA.HC.7211.01 2 1.000
#> TCGA.KK.A8I6.01 4 0.000
#> TCGA.XJ.A83F.01 2 0.000
#> TCGA.EJ.7785.01 4 0.000
#> TCGA.G9.A9S4.01 2 0.000
#> TCGA.VP.A87B.01 2 0.000
#> TCGA.YL.A8SR.01 2 0.000
#> TCGA.EJ.7327.01 4 0.000
#> TCGA.4L.AA1F.01 4 0.000
#> TCGA.KK.A7AY.01 2 0.000
#> TCGA.EJ.A65G.01 2 1.000
#> TCGA.2A.AAYU.01 2 0.000
#> TCGA.HC.A76W.01 4 1.000
#> TCGA.EJ.5516.01 3 0.000
#> TCGA.G9.A9S7.01 4 0.000
#> TCGA.HC.8216.01 4 0.000
#> TCGA.CH.5794.01 4 0.000
#> TCGA.V1.A9OA.01 4 0.000
#> TCGA.J9.A52E.01 4 0.000
#> TCGA.HC.7818.01 4 0.000
#> TCGA.G9.7525.01 2 0.000
#> TCGA.FC.7961.01 4 0.000
#> TCGA.CH.5767.11 1 0.000
#> TCGA.EJ.5504.01 2 0.000
#> TCGA.VP.A87J.01 2 0.000
#> TCGA.J4.A67S.01 4 0.000
#> TCGA.KK.A8IK.01 2 0.000
#> TCGA.HC.A6AQ.01 4 0.000
#> TCGA.CH.5763.01 1 0.000
#> TCGA.HC.A8D1.01 3 0.000
#> TCGA.KK.A7AU.01 2 0.000
#> TCGA.CH.5766.01 4 0.000
#> TCGA.EJ.7781.11 1 0.000
#> TCGA.KK.A7B0.01 3 0.000
#> TCGA.EJ.7321.01 2 0.000
#> TCGA.G9.6385.11 1 0.000
#> TCGA.VN.A943.01 2 0.000
#> TCGA.KK.A59X.01 2 0.000
#> TCGA.KK.A8I4.01 4 0.000
#> TCGA.G9.6496.11 1 0.000
#> TCGA.G9.7523.01 4 0.000
#> TCGA.EJ.5494.01 2 0.000
#> TCGA.2A.A8VT.01 4 1.000
#> TCGA.HC.7213.01 2 0.000
#> TCGA.G9.7519.01 4 0.000
#> TCGA.CH.5764.11 1 0.000
#> TCGA.CH.5772.01 2 0.000
#> TCGA.EJ.7325.01 2 0.000
#> TCGA.G9.6356.11 1 0.000
#> TCGA.ZG.A9LM.01 4 1.000
#> TCGA.XJ.A9DK.01 1 0.000
#> TCGA.EJ.7789.01 2 0.000
#> TCGA.HC.8257.01 2 0.000
#> TCGA.EJ.A7NG.01 3 1.000
#> TCGA.EJ.7318.01 4 1.000
#> TCGA.EJ.5512.01 3 0.000
#> TCGA.EJ.A46E.01 1 0.000
#> TCGA.FC.A4JI.01 2 0.000
#> TCGA.J9.A8CM.01 4 1.000
#> TCGA.CH.5771.11 1 0.000
#> TCGA.KC.A4BR.01 3 1.000
#> TCGA.2A.AAYO.01 2 0.000
#> TCGA.2A.A8W3.01 4 0.000
#> TCGA.CH.5768.11 3 1.000
#> TCGA.G9.6364.01 4 0.000
#> TCGA.YL.A8SL.01 2 0.000
#> TCGA.KK.A5A1.01 2 0.000
#> TCGA.YL.A9WL.01 2 0.000
#> TCGA.HC.A6HX.01 3 0.000
#> TCGA.M7.A720.01 1 0.000
#> TCGA.HC.7080.01 2 0.000
#> TCGA.V1.A9O5.06 2 0.000
#> TCGA.KC.A7F5.01 2 0.000
#> TCGA.EJ.7331.01 4 0.000
#> TCGA.ZG.A9LY.01 3 0.000
#> TCGA.G9.6494.01 4 0.000
#> TCGA.M7.A71Y.01 1 1.000
#> TCGA.FC.A66V.01 1 0.000
#> TCGA.EJ.7793.01 3 0.000
#> TCGA.EJ.A8FS.01 2 0.000
#> TCGA.XK.AAJU.01 1 0.000
#> TCGA.HC.8266.01 3 0.000
#> TCGA.YL.A8HL.01 2 0.000
#> TCGA.VN.A88I.01 3 1.000
#> TCGA.HI.7169.01 4 0.000
#> TCGA.CH.5753.01 2 0.000
#> TCGA.J4.A67K.01 4 0.000
#> TCGA.QU.A6IM.01 4 0.000
#> TCGA.HC.A9TE.01 2 0.000
#> TCGA.EJ.7115.01 4 1.000
#> TCGA.HC.7745.11 1 0.000
#> TCGA.EJ.5531.01 3 0.000
#> TCGA.YL.A8SH.01 2 0.000
#> TCGA.G9.6362.01 2 0.000
#> TCGA.HC.8258.01 3 0.000
#> TCGA.EJ.5530.01 2 0.000
#> TCGA.VN.A88M.01 2 0.000
#> TCGA.EJ.7782.01 2 0.000
#> TCGA.YL.A8SF.01 2 1.000
#> TCGA.KK.A6E2.01 2 0.000
#> TCGA.CH.5792.01 4 0.000
#> TCGA.J4.A6G1.01 3 0.000
#> TCGA.J4.A6M7.01 2 0.000
#> TCGA.VP.A872.01 2 1.000
#> TCGA.V1.A8ML.01 4 1.000
#> TCGA.HC.7744.01 2 0.000
#> TCGA.G9.6347.01 3 0.000
#> TCGA.EJ.A46I.01 3 0.000
#> TCGA.XK.AAJ3.01 2 0.000
#> TCGA.HC.A8CY.01 2 0.000
#> TCGA.KK.A6E0.01 2 0.000
#> TCGA.XK.AAK1.01 2 0.000
#> TCGA.XK.AAIW.01 2 0.000
#> TCGA.HC.8260.01 3 0.000
#> TCGA.HC.7737.11 1 0.000
#> TCGA.EJ.7786.11 1 0.000
#> TCGA.HC.7740.01 3 0.000
#> TCGA.TP.A8TV.01 2 0.000
#> TCGA.FC.A6HD.01 2 0.000
#> TCGA.EJ.8472.01 2 0.000
#> TCGA.CH.5745.01 4 0.000
#> TCGA.EJ.5508.01 4 0.000
#> TCGA.EJ.A7NH.01 3 0.000
#> TCGA.KK.A7B2.01 3 1.000
#> TCGA.CH.5740.01 2 1.000
#> TCGA.YL.A9WH.01 2 0.000
#> TCGA.FC.A8O0.01 1 0.000
#> TCGA.J9.A52C.01 3 0.000
#> TCGA.FC.7708.01 3 0.000
#> TCGA.HC.7742.11 3 0.000
#> TCGA.G9.6351.11 3 0.000
#> TCGA.KK.A7AW.01 2 0.000
#> TCGA.G9.7509.01 4 1.000
#> TCGA.J4.A67R.01 3 0.000
#> TCGA.WW.A8ZI.01 2 0.000
#> TCGA.KK.A8IJ.01 4 0.000
#> TCGA.J4.A83N.01 2 0.000
#> TCGA.HC.A6AN.01 2 0.000
#> TCGA.G9.6348.11 1 0.000
#> TCGA.EJ.5499.01 4 0.000
#> TCGA.G9.6367.11 1 0.000
#> TCGA.QU.A6IL.01 2 0.000
#> TCGA.CH.5738.01 4 0.000
#> TCGA.V1.A9ZI.01 2 0.000
#> TCGA.CH.5748.01 4 1.000
#> TCGA.YL.A8SQ.01 2 0.000
#> TCGA.G9.7522.01 3 0.000
#> TCGA.HC.A6AP.01 4 0.000
#> TCGA.EJ.7785.11 1 0.000
#> TCGA.KK.A7B4.01 2 0.000
#> TCGA.J4.A83J.01 2 0.000
#> TCGA.V1.A8MU.01 4 0.000
#> TCGA.EJ.5510.01 3 0.000
#> TCGA.EJ.7327.11 1 0.000
#> TCGA.CH.5746.01 3 0.000
#> TCGA.V1.A9Z7.01 4 0.000
#> TCGA.M7.A725.01 2 0.000
#> TCGA.G9.6384.11 1 0.000
#> TCGA.XJ.A9DI.01 1 0.000
#> TCGA.J4.A67N.01 2 0.000
#> TCGA.XJ.A83G.01 2 0.000
#> TCGA.ZG.A8QZ.01 3 0.000
#> TCGA.TK.A8OK.01 4 0.000
#> TCGA.VP.A876.01 2 0.000
#> TCGA.KK.A6E5.01 2 1.000
#> TCGA.X4.A8KQ.01 4 0.000
#> TCGA.KK.A8IL.01 4 1.000
#> TCGA.HC.7820.01 4 0.000
#> TCGA.CH.5739.01 2 0.000
#> TCGA.HC.7750.01 4 0.000
#> TCGA.YL.A9WX.01 3 1.000
#> TCGA.EJ.5518.01 4 0.000
#> TCGA.ZG.A9NI.01 2 1.000
#> TCGA.YL.A9WY.01 4 0.000
#> TCGA.CH.5763.11 1 0.000
#> TCGA.EJ.5515.01 1 0.000
#> TCGA.KK.A8IH.01 2 0.000
#> TCGA.VP.A87K.01 2 0.000
#> TCGA.HC.A6HY.01 2 1.000
#> TCGA.HC.7211.11 1 0.000
#> TCGA.HC.A632.01 2 0.000
#> TCGA.G9.6496.01 2 0.000
#> TCGA.EJ.A7NM.01 2 0.000
#> TCGA.ZG.A9L6.01 3 0.000
#> TCGA.2A.A8VV.01 2 0.000
#> TCGA.VP.A87E.01 4 0.747
#> TCGA.CH.5764.01 4 0.000
#> TCGA.EJ.5525.01 2 0.000
#> TCGA.CH.5772.11 1 0.000
#> TCGA.KK.A59Z.01 2 0.000
#> TCGA.V1.A9ZR.01 4 0.000
#> TCGA.EJ.A6RC.01 4 0.000
#> TCGA.EJ.7792.01 4 0.000
#> TCGA.HC.A9TH.01 2 1.000
#> TCGA.M7.A723.01 3 1.000
#> TCGA.EJ.7789.11 1 0.000
#> TCGA.HC.7752.01 2 0.000
#> TCGA.EJ.A65J.01 2 0.000
#> TCGA.V1.A8WV.01 4 0.000
#> TCGA.2A.A8VX.01 2 0.000
#> TCGA.V1.A9OT.01 2 0.000
#> TCGA.KC.A7FA.01 2 0.000
#> TCGA.G9.6373.11 1 0.000
#> TCGA.G9.6370.01 1 0.000
#> TCGA.CH.5771.01 3 0.000
#> TCGA.YL.A8SJ.01 4 0.000
#> TCGA.HC.7738.01 2 0.000
#> TCGA.EJ.A6RA.01 3 0.000
#> TCGA.J4.8198.01 2 0.000
#> TCGA.EJ.7123.01 2 0.000
#> TCGA.2A.A8W1.01 2 0.000
#> TCGA.G9.6363.01 4 0.000
#> TCGA.ZG.A9L2.01 4 0.000
#> TCGA.HC.7749.01 2 1.000
#> TCGA.CH.5768.01 2 0.000
#> TCGA.KK.A6E7.01 4 1.000
#> TCGA.G9.6332.01 2 0.000
#> TCGA.EJ.A46G.01 2 0.000
#> TCGA.V1.A9OX.01 4 0.000
#> TCGA.J4.A6G3.01 3 0.000
#> TCGA.VN.A88L.01 4 1.000
#> TCGA.EJ.7312.01 2 0.000
#> TCGA.V1.A8MM.01 2 0.000
#> TCGA.EJ.A65F.01 2 0.000
#> TCGA.G9.6498.01 2 0.000
#> TCGA.EJ.5505.01 4 0.000
#> TCGA.CH.5761.11 1 0.000
#> TCGA.HC.8261.01 4 0.000
#> TCGA.XQ.A8TB.01 2 0.000
#> TCGA.G9.6329.01 3 0.000
#> TCGA.EJ.5496.01 4 0.000
get_classes(res, k = 5)
#> class p
#> TCGA.G9.6343.01 4 0.000
#> TCGA.KK.A8IA.01 2 0.000
#> TCGA.KK.A6E4.01 2 0.000
#> TCGA.EJ.AB20.01 1 0.000
#> TCGA.H9.7775.01 2 0.000
#> TCGA.XJ.A9DX.01 2 0.000
#> TCGA.KK.A6E6.01 4 0.000
#> TCGA.G9.6339.01 4 0.000
#> TCGA.EJ.5509.01 4 0.000
#> TCGA.EJ.5521.01 4 0.000
#> TCGA.YL.A8SB.01 5 0.000
#> TCGA.V1.A9OF.01 2 0.000
#> TCGA.CH.5754.01 4 0.000
#> TCGA.EJ.7125.01 2 1.000
#> TCGA.EJ.7797.01 5 0.000
#> TCGA.YL.A9WI.01 2 0.000
#> TCGA.EJ.7314.01 4 0.000
#> TCGA.XA.A8JR.01 4 0.000
#> TCGA.EJ.7781.01 4 0.000
#> TCGA.QU.A6IN.01 2 0.000
#> TCGA.CH.5751.01 4 0.000
#> TCGA.V1.A8WL.01 4 1.000
#> TCGA.HC.A6AO.01 2 0.000
#> TCGA.KK.A7B3.01 2 1.000
#> TCGA.XK.AAJT.01 4 0.000
#> TCGA.EJ.AB27.01 3 0.000
#> TCGA.CH.5788.01 2 0.000
#> TCGA.KK.A8I5.01 2 0.000
#> TCGA.YL.A8S9.01 2 0.000
#> TCGA.CH.5761.01 2 1.000
#> TCGA.KK.A7AZ.01 2 0.000
#> TCGA.G9.6366.01 4 0.000
#> TCGA.HC.7819.01 2 0.000
#> TCGA.KC.A4BN.01 4 0.000
#> TCGA.KK.A8IG.01 4 0.000
#> TCGA.ZG.A8QW.01 5 0.000
#> TCGA.EJ.7786.01 4 0.000
#> TCGA.J4.A83K.01 4 0.000
#> TCGA.YL.A8HK.01 5 0.000
#> TCGA.EJ.5501.01 5 0.000
#> TCGA.EJ.8470.01 4 0.000
#> TCGA.J9.A8CL.01 2 0.000
#> TCGA.EJ.A7NF.01 2 0.000
#> TCGA.CH.5762.11 1 0.000
#> TCGA.XK.AAJA.01 2 0.000
#> TCGA.EJ.7330.01 5 0.000
#> TCGA.VP.AA1N.01 4 0.000
#> TCGA.EJ.5524.01 4 0.000
#> TCGA.KK.A6E8.01 2 0.000
#> TCGA.HC.7821.01 2 0.000
#> TCGA.HC.7209.01 4 0.000
#> TCGA.HC.7742.01 4 0.000
#> TCGA.G9.6351.01 5 0.000
#> TCGA.EJ.8474.01 2 0.000
#> TCGA.HC.7075.01 2 0.000
#> TCGA.J9.A8CP.01 4 0.000
#> TCGA.KK.A8IM.01 5 0.000
#> TCGA.G9.6348.01 5 0.000
#> TCGA.CH.5789.01 1 0.000
#> TCGA.KC.A7F6.01 2 1.000
#> TCGA.G9.6333.11 1 0.000
#> TCGA.KC.A4BL.01 3 0.000
#> TCGA.J4.A67Q.01 5 0.751
#> TCGA.2A.A8VL.01 5 0.000
#> TCGA.V1.A9ZK.01 5 0.000
#> TCGA.V1.A9O5.01 4 0.000
#> TCGA.VP.A879.01 4 0.253
#> TCGA.HC.7819.11 1 0.000
#> TCGA.VN.A88Q.01 4 0.000
#> TCGA.HC.7737.01 5 0.000
#> TCGA.V1.A8WS.01 2 0.000
#> TCGA.HC.8213.01 2 0.000
#> TCGA.M7.A721.01 4 0.000
#> TCGA.ZG.A9LZ.01 2 0.000
#> TCGA.CH.5765.01 2 0.000
#> TCGA.V1.A8WW.01 2 0.000
#> TCGA.HC.A48F.01 2 0.000
#> TCGA.V1.A9OQ.01 2 0.000
#> TCGA.EJ.5514.01 4 0.000
#> TCGA.G9.6384.01 5 0.000
#> TCGA.V1.A9ZG.01 5 0.000
#> TCGA.YL.A8HM.01 2 0.000
#> TCGA.G9.6377.01 2 1.000
#> TCGA.M7.A722.01 2 0.000
#> TCGA.G9.6361.01 2 0.000
#> TCGA.EJ.5511.01 2 0.000
#> TCGA.ZG.A9KY.01 2 0.000
#> TCGA.EJ.7784.11 1 0.000
#> TCGA.ZG.A9LN.01 5 0.000
#> TCGA.EJ.5526.01 4 0.000
#> TCGA.HC.7820.11 1 0.000
#> TCGA.YJ.A8SW.01 2 0.000
#> TCGA.EJ.7794.01 5 0.000
#> TCGA.EJ.A46B.01 3 0.000
#> TCGA.EJ.5542.01 4 0.000
#> TCGA.YL.A9WJ.01 5 0.000
#> TCGA.EJ.7328.11 1 0.000
#> TCGA.V1.A9Z8.01 5 0.000
#> TCGA.EJ.A46F.01 2 0.000
#> TCGA.YL.A8SK.01 5 0.000
#> TCGA.MG.AAMC.01 2 0.000
#> TCGA.X4.A8KS.01 3 0.000
#> TCGA.J4.A67M.01 5 0.000
#> TCGA.ZG.A9L0.01 2 0.000
#> TCGA.HC.7077.01 2 0.000
#> TCGA.CH.5769.01 4 0.000
#> TCGA.G9.6353.11 1 0.000
#> TCGA.G9.6499.01 5 1.000
#> TCGA.EJ.5519.01 2 1.000
#> TCGA.J4.A67T.01 5 1.000
#> TCGA.HC.7748.01 4 0.000
#> TCGA.VN.A88R.01 2 0.000
#> TCGA.H9.A6BY.01 2 0.000
#> TCGA.G9.6365.01 4 0.000
#> TCGA.EJ.7317.11 1 0.000
#> TCGA.G9.7510.01 4 0.000
#> TCGA.KK.A6E3.01 5 0.000
#> TCGA.G9.6336.01 5 1.000
#> TCGA.EJ.5517.01 2 1.000
#> TCGA.V1.A8MG.01 4 0.000
#> TCGA.KC.A7FE.01 3 0.000
#> TCGA.HC.7817.01 3 0.000
#> TCGA.J4.AAU2.01 2 0.000
#> TCGA.V1.A8MJ.01 5 0.000
#> TCGA.VP.A87C.01 5 0.000
#> TCGA.EJ.A7NN.01 4 0.000
#> TCGA.HC.A8D0.01 3 0.000
#> TCGA.EJ.7792.11 1 0.000
#> TCGA.EJ.5497.01 5 0.000
#> TCGA.Y6.A9XI.01 2 0.000
#> TCGA.HC.7752.11 1 0.000
#> TCGA.SU.A7E7.01 3 0.000
#> TCGA.G9.6342.11 3 1.000
#> TCGA.HC.8265.01 4 0.000
#> TCGA.CH.5737.01 2 0.000
#> TCGA.G9.6338.01 2 0.000
#> TCGA.KK.A7AV.01 4 0.000
#> TCGA.EJ.7218.01 4 1.000
#> TCGA.YL.A8SC.01 4 0.000
#> TCGA.XK.AAJR.01 5 0.000
#> TCGA.2A.AAYF.01 2 0.000
#> TCGA.V1.A8X3.01 4 0.000
#> TCGA.KK.A6DY.01 4 0.000
#> TCGA.M7.A71Z.01 2 0.000
#> TCGA.EJ.7123.11 1 0.000
#> TCGA.G9.6363.11 5 0.000
#> TCGA.KK.A8I8.01 4 1.000
#> TCGA.KC.A4BV.01 2 1.000
#> TCGA.G9.6332.11 1 0.000
#> TCGA.CH.5750.01 2 0.000
#> TCGA.ZG.A9ND.01 2 0.000
#> TCGA.EJ.A65B.01 3 0.000
#> TCGA.QU.A6IO.01 4 1.000
#> TCGA.EJ.5503.01 1 0.000
#> TCGA.ZG.A9LU.01 3 0.000
#> TCGA.EJ.8469.01 2 0.000
#> TCGA.XJ.A83H.01 4 1.000
#> TCGA.EJ.7315.01 2 0.000
#> TCGA.ZG.A8QY.01 4 0.000
#> TCGA.YL.A8SP.01 2 0.000
#> TCGA.CH.5791.01 2 0.751
#> TCGA.V1.A9OY.01 5 1.000
#> TCGA.KC.A4BO.01 1 0.000
#> TCGA.HC.A76X.01 2 0.000
#> TCGA.YL.A8SO.01 4 0.000
#> TCGA.KK.A8IF.01 2 0.000
#> TCGA.EJ.A7NK.01 1 1.000
#> TCGA.ZG.A9L4.01 5 0.000
#> TCGA.EJ.5522.01 4 1.000
#> TCGA.HC.7747.01 5 0.000
#> TCGA.EJ.7125.11 1 0.000
#> TCGA.ZG.A9M4.01 4 0.000
#> TCGA.EJ.A65D.01 2 0.000
#> TCGA.HC.A4ZV.01 2 0.000
#> TCGA.G9.A9S0.01 4 0.000
#> TCGA.EJ.5506.01 3 1.000
#> TCGA.KK.A7AP.01 2 0.000
#> TCGA.VP.A87D.01 2 0.000
#> TCGA.TP.A8TT.01 4 0.000
#> TCGA.KK.A8II.01 2 0.000
#> TCGA.V1.A9Z9.01 4 0.000
#> TCGA.ZG.A9LS.01 5 0.000
#> TCGA.HC.7232.01 4 0.000
#> TCGA.EJ.A8FO.01 3 0.000
#> TCGA.J9.A52B.01 2 1.000
#> TCGA.CH.5767.01 2 0.000
#> TCGA.J4.AATV.01 3 0.000
#> TCGA.HC.7081.01 4 0.000
#> TCGA.CH.5743.01 1 0.000
#> TCGA.V1.A9OH.01 5 0.000
#> TCGA.CH.5752.01 2 0.000
#> TCGA.VP.A87H.01 4 0.000
#> TCGA.G9.7521.01 4 0.000
#> TCGA.YL.A8HO.01 4 0.000
#> TCGA.YL.A9WK.01 2 0.747
#> TCGA.J4.A83M.01 4 1.000
#> TCGA.VP.A878.01 5 0.000
#> TCGA.CH.5766.11 1 0.000
#> TCGA.HC.7736.01 4 0.000
#> TCGA.G9.6385.01 1 1.000
#> TCGA.VN.A88N.01 4 0.000
#> TCGA.HC.7745.01 5 0.000
#> TCGA.HC.7078.01 2 0.000
#> TCGA.FC.A5OB.01 2 0.000
#> TCGA.G9.6379.01 5 0.000
#> TCGA.QU.A6IP.01 4 0.000
#> TCGA.J4.AATZ.01 2 0.000
#> TCGA.V1.A9O9.01 4 0.000
#> TCGA.V1.A9OL.01 2 1.000
#> TCGA.HC.7210.01 4 0.000
#> TCGA.KK.A8I7.01 3 0.000
#> TCGA.EJ.7791.01 3 0.000
#> TCGA.CH.5762.01 5 0.000
#> TCGA.EJ.5527.01 5 0.000
#> TCGA.KK.A8IC.01 3 0.000
#> TCGA.G9.6356.01 5 0.000
#> TCGA.J9.A52D.01 2 0.000
#> TCGA.EJ.7788.01 2 0.000
#> TCGA.ZG.A9LB.01 4 0.000
#> TCGA.J9.A8CN.01 2 0.000
#> TCGA.ZG.A9L1.01 2 0.000
#> TCGA.G9.6333.01 5 0.000
#> TCGA.VP.A875.01 2 0.000
#> TCGA.EJ.8468.01 4 0.000
#> TCGA.EJ.5495.01 5 0.000
#> TCGA.H9.A6BX.01 1 0.000
#> TCGA.KK.A59Y.01 2 0.000
#> TCGA.V1.A8WN.01 5 0.000
#> TCGA.KK.A7B1.01 4 0.000
#> TCGA.G9.6362.11 2 0.000
#> TCGA.G9.6364.11 1 0.000
#> TCGA.HC.A631.01 2 0.000
#> TCGA.YL.A8SA.01 2 0.000
#> TCGA.HC.8262.01 4 0.000
#> TCGA.CH.5765.11 3 0.000
#> TCGA.KC.A7FD.01 2 0.000
#> TCGA.HI.7170.01 4 0.000
#> TCGA.J4.A67L.01 4 0.000
#> TCGA.V1.A9O7.01 3 0.000
#> TCGA.HC.A6AS.01 5 0.000
#> TCGA.EJ.7784.01 2 0.000
#> TCGA.EJ.7331.11 1 0.000
#> TCGA.KC.A7F3.01 4 1.000
#> TCGA.G9.6494.11 1 0.000
#> TCGA.HC.8256.01 4 0.000
#> TCGA.J4.A83I.01 2 0.000
#> TCGA.G9.6373.01 2 0.000
#> TCGA.EJ.7794.11 1 0.000
#> TCGA.G9.6371.01 2 0.000
#> TCGA.XQ.A8TA.01 2 0.000
#> TCGA.EJ.5498.01 3 0.000
#> TCGA.EJ.7328.01 5 0.000
#> TCGA.EJ.A46D.01 3 0.000
#> TCGA.ZG.A9L9.01 2 0.000
#> TCGA.YL.A8SI.01 5 0.000
#> TCGA.M7.A724.01 2 0.000
#> TCGA.VN.A88K.01 2 0.000
#> TCGA.EJ.A8FP.01 1 0.000
#> TCGA.V1.A8MK.01 3 0.000
#> TCGA.YL.A8HJ.01 3 0.747
#> TCGA.KK.A8ID.01 2 0.000
#> TCGA.CH.5769.11 4 0.000
#> TCGA.G9.6353.01 3 0.000
#> TCGA.G9.6499.11 4 0.000
#> TCGA.KK.A8I9.01 4 0.000
#> TCGA.G9.6365.11 1 0.000
#> TCGA.EJ.A46H.01 1 0.000
#> TCGA.EJ.7317.01 4 0.000
#> TCGA.YL.A8S8.01 4 0.000
#> TCGA.XJ.A9DQ.01 3 1.000
#> TCGA.EJ.7782.11 1 0.000
#> TCGA.J4.A67O.01 5 0.000
#> TCGA.Y6.A8TL.01 4 0.000
#> TCGA.XK.AAIV.01 5 0.000
#> TCGA.CH.5790.01 2 0.000
#> TCGA.HC.7231.01 2 0.000
#> TCGA.ZG.A9L5.01 2 0.000
#> TCGA.V1.A8MF.01 4 0.000
#> TCGA.EJ.A7NJ.01 1 0.000
#> TCGA.EJ.A65E.01 4 0.000
#> TCGA.ZG.A8QX.01 4 0.000
#> TCGA.G9.6367.01 1 0.000
#> TCGA.G9.6342.01 4 0.000
#> TCGA.KK.A8IB.01 5 0.000
#> TCGA.HC.7230.01 2 0.000
#> TCGA.XK.AAIR.01 5 1.000
#> TCGA.CH.5741.01 2 0.000
#> TCGA.KK.A59V.01 2 1.000
#> TCGA.J4.8200.01 4 0.000
#> TCGA.KK.A7AQ.01 2 0.000
#> TCGA.EJ.5532.01 4 0.000
#> TCGA.HI.7168.01 4 0.000
#> TCGA.HC.7233.01 4 0.000
#> TCGA.HC.A6AL.01 2 0.000
#> TCGA.EJ.7783.01 5 0.000
#> TCGA.HC.8264.01 2 0.000
#> TCGA.EJ.A8FU.01 1 0.000
#> TCGA.EJ.A65M.01 4 0.000
#> TCGA.EJ.A8FN.01 4 0.747
#> TCGA.HI.7171.01 2 0.000
#> TCGA.XK.AAJP.01 2 0.000
#> TCGA.HC.7212.01 2 0.000
#> TCGA.ZG.A9MC.01 3 0.000
#> TCGA.2A.A8VO.01 2 0.000
#> TCGA.HC.8259.01 2 0.000
#> TCGA.G9.6378.01 3 0.000
#> TCGA.J4.A83L.01 4 0.000
#> TCGA.VN.A88P.01 2 0.000
#> TCGA.EJ.5507.01 4 0.000
#> TCGA.J9.A8CK.01 4 0.000
#> TCGA.CH.5744.01 4 0.000
#> TCGA.ZG.A9N3.01 4 1.000
#> TCGA.G9.6354.01 4 0.000
#> TCGA.VN.A88O.01 4 1.000
#> TCGA.EJ.5502.01 5 0.000
#> TCGA.HC.7079.01 3 0.000
#> TCGA.G9.6369.01 2 0.000
#> TCGA.KK.A6E1.01 2 0.000
#> TCGA.HC.7211.01 4 0.000
#> TCGA.KK.A8I6.01 4 0.000
#> TCGA.XJ.A83F.01 2 0.000
#> TCGA.EJ.7785.01 5 0.000
#> TCGA.G9.A9S4.01 2 0.000
#> TCGA.VP.A87B.01 2 0.000
#> TCGA.YL.A8SR.01 2 1.000
#> TCGA.EJ.7327.01 4 0.000
#> TCGA.4L.AA1F.01 5 1.000
#> TCGA.KK.A7AY.01 2 0.000
#> TCGA.EJ.A65G.01 4 0.000
#> TCGA.2A.AAYU.01 2 0.000
#> TCGA.HC.A76W.01 4 0.000
#> TCGA.EJ.5516.01 5 0.000
#> TCGA.G9.A9S7.01 4 0.000
#> TCGA.HC.8216.01 4 0.000
#> TCGA.CH.5794.01 4 0.000
#> TCGA.V1.A9OA.01 4 0.000
#> TCGA.J9.A52E.01 4 0.000
#> TCGA.HC.7818.01 4 0.000
#> TCGA.G9.7525.01 2 0.000
#> TCGA.FC.7961.01 4 0.000
#> TCGA.CH.5767.11 1 0.000
#> TCGA.EJ.5504.01 4 1.000
#> TCGA.VP.A87J.01 2 0.000
#> TCGA.J4.A67S.01 4 0.000
#> TCGA.KK.A8IK.01 2 0.000
#> TCGA.HC.A6AQ.01 4 0.000
#> TCGA.CH.5763.01 1 1.000
#> TCGA.HC.A8D1.01 3 0.000
#> TCGA.KK.A7AU.01 2 0.000
#> TCGA.CH.5766.01 4 0.502
#> TCGA.EJ.7781.11 1 0.000
#> TCGA.KK.A7B0.01 5 1.000
#> TCGA.EJ.7321.01 4 1.000
#> TCGA.G9.6385.11 1 0.000
#> TCGA.VN.A943.01 2 0.000
#> TCGA.KK.A59X.01 2 0.000
#> TCGA.KK.A8I4.01 5 0.000
#> TCGA.G9.6496.11 1 0.000
#> TCGA.G9.7523.01 4 0.000
#> TCGA.EJ.5494.01 2 0.000
#> TCGA.2A.A8VT.01 4 0.000
#> TCGA.HC.7213.01 2 0.000
#> TCGA.G9.7519.01 4 0.000
#> TCGA.CH.5764.11 1 0.000
#> TCGA.CH.5772.01 2 0.000
#> TCGA.EJ.7325.01 2 0.000
#> TCGA.G9.6356.11 1 0.000
#> TCGA.ZG.A9LM.01 4 0.000
#> TCGA.XJ.A9DK.01 1 0.000
#> TCGA.EJ.7789.01 2 0.000
#> TCGA.HC.8257.01 2 0.000
#> TCGA.EJ.A7NG.01 3 0.000
#> TCGA.EJ.7318.01 4 0.000
#> TCGA.EJ.5512.01 5 0.000
#> TCGA.EJ.A46E.01 1 0.000
#> TCGA.FC.A4JI.01 2 0.000
#> TCGA.J9.A8CM.01 4 0.000
#> TCGA.CH.5771.11 1 0.000
#> TCGA.KC.A4BR.01 3 0.000
#> TCGA.2A.AAYO.01 2 0.000
#> TCGA.2A.A8W3.01 5 0.000
#> TCGA.CH.5768.11 3 0.000
#> TCGA.G9.6364.01 4 0.000
#> TCGA.YL.A8SL.01 2 0.000
#> TCGA.KK.A5A1.01 2 0.000
#> TCGA.YL.A9WL.01 2 0.000
#> TCGA.HC.A6HX.01 3 0.000
#> TCGA.M7.A720.01 1 0.000
#> TCGA.HC.7080.01 2 0.000
#> TCGA.V1.A9O5.06 2 0.000
#> TCGA.KC.A7F5.01 2 0.000
#> TCGA.EJ.7331.01 4 0.253
#> TCGA.ZG.A9LY.01 5 0.000
#> TCGA.G9.6494.01 4 0.000
#> TCGA.M7.A71Y.01 3 0.000
#> TCGA.FC.A66V.01 1 0.000
#> TCGA.EJ.7793.01 5 1.000
#> TCGA.EJ.A8FS.01 2 0.000
#> TCGA.XK.AAJU.01 1 0.000
#> TCGA.HC.8266.01 5 0.000
#> TCGA.YL.A8HL.01 2 0.000
#> TCGA.VN.A88I.01 3 0.000
#> TCGA.HI.7169.01 4 0.000
#> TCGA.CH.5753.01 2 0.000
#> TCGA.J4.A67K.01 4 0.000
#> TCGA.QU.A6IM.01 4 0.000
#> TCGA.HC.A9TE.01 4 1.000
#> TCGA.EJ.7115.01 4 0.000
#> TCGA.HC.7745.11 1 0.000
#> TCGA.EJ.5531.01 3 0.000
#> TCGA.YL.A8SH.01 2 1.000
#> TCGA.G9.6362.01 2 0.000
#> TCGA.HC.8258.01 3 0.000
#> TCGA.EJ.5530.01 2 0.000
#> TCGA.VN.A88M.01 2 0.000
#> TCGA.EJ.7782.01 2 0.000
#> TCGA.YL.A8SF.01 4 0.000
#> TCGA.KK.A6E2.01 2 0.000
#> TCGA.CH.5792.01 5 0.000
#> TCGA.J4.A6G1.01 3 0.000
#> TCGA.J4.A6M7.01 2 0.000
#> TCGA.VP.A872.01 4 0.000
#> TCGA.V1.A8ML.01 4 0.000
#> TCGA.HC.7744.01 2 0.000
#> TCGA.G9.6347.01 5 0.000
#> TCGA.EJ.A46I.01 5 0.498
#> TCGA.XK.AAJ3.01 2 0.000
#> TCGA.HC.A8CY.01 2 0.000
#> TCGA.KK.A6E0.01 2 1.000
#> TCGA.XK.AAK1.01 2 0.000
#> TCGA.XK.AAIW.01 2 0.000
#> TCGA.HC.8260.01 3 0.000
#> TCGA.HC.7737.11 1 0.000
#> TCGA.EJ.7786.11 1 0.000
#> TCGA.HC.7740.01 3 0.000
#> TCGA.TP.A8TV.01 2 0.000
#> TCGA.FC.A6HD.01 2 0.000
#> TCGA.EJ.8472.01 2 0.000
#> TCGA.CH.5745.01 4 0.000
#> TCGA.EJ.5508.01 5 0.000
#> TCGA.EJ.A7NH.01 5 0.000
#> TCGA.KK.A7B2.01 3 0.000
#> TCGA.CH.5740.01 4 0.249
#> TCGA.YL.A9WH.01 2 0.000
#> TCGA.FC.A8O0.01 1 0.000
#> TCGA.J9.A52C.01 5 0.000
#> TCGA.FC.7708.01 5 0.000
#> TCGA.HC.7742.11 3 0.000
#> TCGA.G9.6351.11 3 0.000
#> TCGA.KK.A7AW.01 2 0.000
#> TCGA.G9.7509.01 4 0.000
#> TCGA.J4.A67R.01 5 1.000
#> TCGA.WW.A8ZI.01 2 0.000
#> TCGA.KK.A8IJ.01 4 0.000
#> TCGA.J4.A83N.01 2 1.000
#> TCGA.HC.A6AN.01 2 0.751
#> TCGA.G9.6348.11 1 0.000
#> TCGA.EJ.5499.01 5 0.000
#> TCGA.G9.6367.11 1 0.000
#> TCGA.QU.A6IL.01 2 0.000
#> TCGA.CH.5738.01 5 1.000
#> TCGA.V1.A9ZI.01 2 0.000
#> TCGA.CH.5748.01 4 0.000
#> TCGA.YL.A8SQ.01 2 0.000
#> TCGA.G9.7522.01 5 0.000
#> TCGA.HC.A6AP.01 5 0.000
#> TCGA.EJ.7785.11 1 0.000
#> TCGA.KK.A7B4.01 2 0.000
#> TCGA.J4.A83J.01 2 1.000
#> TCGA.V1.A8MU.01 4 1.000
#> TCGA.EJ.5510.01 5 0.000
#> TCGA.EJ.7327.11 1 0.000
#> TCGA.CH.5746.01 5 0.000
#> TCGA.V1.A9Z7.01 4 0.000
#> TCGA.M7.A725.01 2 0.000
#> TCGA.G9.6384.11 1 0.000
#> TCGA.XJ.A9DI.01 1 1.000
#> TCGA.J4.A67N.01 2 0.000
#> TCGA.XJ.A83G.01 2 0.000
#> TCGA.ZG.A8QZ.01 5 0.000
#> TCGA.TK.A8OK.01 5 0.502
#> TCGA.VP.A876.01 2 0.000
#> TCGA.KK.A6E5.01 4 1.000
#> TCGA.X4.A8KQ.01 5 0.502
#> TCGA.KK.A8IL.01 4 0.000
#> TCGA.HC.7820.01 4 1.000
#> TCGA.CH.5739.01 2 0.000
#> TCGA.HC.7750.01 5 0.000
#> TCGA.YL.A9WX.01 3 0.000
#> TCGA.EJ.5518.01 4 0.000
#> TCGA.ZG.A9NI.01 4 0.000
#> TCGA.YL.A9WY.01 5 0.000
#> TCGA.CH.5763.11 1 0.000
#> TCGA.EJ.5515.01 1 0.000
#> TCGA.KK.A8IH.01 2 0.000
#> TCGA.VP.A87K.01 2 0.000
#> TCGA.HC.A6HY.01 4 1.000
#> TCGA.HC.7211.11 1 0.000
#> TCGA.HC.A632.01 2 0.000
#> TCGA.G9.6496.01 2 0.000
#> TCGA.EJ.A7NM.01 4 1.000
#> TCGA.ZG.A9L6.01 3 0.000
#> TCGA.2A.A8VV.01 2 0.000
#> TCGA.VP.A87E.01 5 0.000
#> TCGA.CH.5764.01 4 0.000
#> TCGA.EJ.5525.01 2 0.000
#> TCGA.CH.5772.11 1 0.000
#> TCGA.KK.A59Z.01 2 0.000
#> TCGA.V1.A9ZR.01 5 1.000
#> TCGA.EJ.A6RC.01 4 0.000
#> TCGA.EJ.7792.01 5 0.000
#> TCGA.HC.A9TH.01 4 0.000
#> TCGA.M7.A723.01 3 0.000
#> TCGA.EJ.7789.11 1 0.000
#> TCGA.HC.7752.01 2 0.000
#> TCGA.EJ.A65J.01 2 0.000
#> TCGA.V1.A8WV.01 4 1.000
#> TCGA.2A.A8VX.01 2 0.000
#> TCGA.V1.A9OT.01 2 0.000
#> TCGA.KC.A7FA.01 2 0.000
#> TCGA.G9.6373.11 1 0.000
#> TCGA.G9.6370.01 1 0.000
#> TCGA.CH.5771.01 3 0.249
#> TCGA.YL.A8SJ.01 4 0.000
#> TCGA.HC.7738.01 2 0.000
#> TCGA.EJ.A6RA.01 3 0.000
#> TCGA.J4.8198.01 2 1.000
#> TCGA.EJ.7123.01 2 0.000
#> TCGA.2A.A8W1.01 2 0.000
#> TCGA.G9.6363.01 4 0.000
#> TCGA.ZG.A9L2.01 5 0.000
#> TCGA.HC.7749.01 4 1.000
#> TCGA.CH.5768.01 2 0.000
#> TCGA.KK.A6E7.01 4 0.000
#> TCGA.G9.6332.01 2 0.000
#> TCGA.EJ.A46G.01 2 0.000
#> TCGA.V1.A9OX.01 4 0.000
#> TCGA.J4.A6G3.01 3 0.751
#> TCGA.VN.A88L.01 4 0.000
#> TCGA.EJ.7312.01 2 0.000
#> TCGA.V1.A8MM.01 2 0.000
#> TCGA.EJ.A65F.01 2 0.000
#> TCGA.G9.6498.01 2 1.000
#> TCGA.EJ.5505.01 5 0.000
#> TCGA.CH.5761.11 1 0.000
#> TCGA.HC.8261.01 4 0.000
#> TCGA.XQ.A8TB.01 4 1.000
#> TCGA.G9.6329.01 3 1.000
#> TCGA.EJ.5496.01 4 0.000
get_classes(res, k = 6)
#> class p
#> TCGA.G9.6343.01 4 1.000
#> TCGA.KK.A8IA.01 2 0.000
#> TCGA.KK.A6E4.01 2 0.000
#> TCGA.EJ.AB20.01 1 0.000
#> TCGA.H9.7775.01 2 0.000
#> TCGA.XJ.A9DX.01 4 0.000
#> TCGA.KK.A6E6.01 4 0.000
#> TCGA.G9.6339.01 6 0.000
#> TCGA.EJ.5509.01 6 1.000
#> TCGA.EJ.5521.01 6 0.000
#> TCGA.YL.A8SB.01 6 0.000
#> TCGA.V1.A9OF.01 2 0.000
#> TCGA.CH.5754.01 4 0.000
#> TCGA.EJ.7125.01 4 0.000
#> TCGA.EJ.7797.01 5 0.000
#> TCGA.YL.A9WI.01 2 0.000
#> TCGA.EJ.7314.01 4 1.000
#> TCGA.XA.A8JR.01 6 0.000
#> TCGA.EJ.7781.01 6 1.000
#> TCGA.QU.A6IN.01 2 0.000
#> TCGA.CH.5751.01 4 0.000
#> TCGA.V1.A8WL.01 4 0.000
#> TCGA.HC.A6AO.01 2 0.000
#> TCGA.KK.A7B3.01 4 0.000
#> TCGA.XK.AAJT.01 4 0.000
#> TCGA.EJ.AB27.01 5 1.000
#> TCGA.CH.5788.01 2 0.000
#> TCGA.KK.A8I5.01 2 0.000
#> TCGA.YL.A8S9.01 2 0.000
#> TCGA.CH.5761.01 4 0.000
#> TCGA.KK.A7AZ.01 2 0.000
#> TCGA.G9.6366.01 4 1.000
#> TCGA.HC.7819.01 2 0.000
#> TCGA.KC.A4BN.01 6 1.000
#> TCGA.KK.A8IG.01 4 0.000
#> TCGA.ZG.A8QW.01 5 0.000
#> TCGA.EJ.7786.01 6 1.000
#> TCGA.J4.A83K.01 6 1.000
#> TCGA.YL.A8HK.01 5 0.000
#> TCGA.EJ.5501.01 5 0.000
#> TCGA.EJ.8470.01 6 0.000
#> TCGA.J9.A8CL.01 2 0.000
#> TCGA.EJ.A7NF.01 2 1.000
#> TCGA.CH.5762.11 1 0.000
#> TCGA.XK.AAJA.01 4 0.000
#> TCGA.EJ.7330.01 5 0.000
#> TCGA.VP.AA1N.01 4 0.000
#> TCGA.EJ.5524.01 4 1.000
#> TCGA.KK.A6E8.01 2 0.000
#> TCGA.HC.7821.01 2 0.000
#> TCGA.HC.7209.01 6 0.000
#> TCGA.HC.7742.01 4 0.000
#> TCGA.G9.6351.01 5 0.000
#> TCGA.EJ.8474.01 2 1.000
#> TCGA.HC.7075.01 2 0.000
#> TCGA.J9.A8CP.01 4 0.000
#> TCGA.KK.A8IM.01 5 0.000
#> TCGA.G9.6348.01 5 0.000
#> TCGA.CH.5789.01 1 0.000
#> TCGA.KC.A7F6.01 4 0.000
#> TCGA.G9.6333.11 1 0.000
#> TCGA.KC.A4BL.01 3 0.000
#> TCGA.J4.A67Q.01 6 0.000
#> TCGA.2A.A8VL.01 6 0.000
#> TCGA.V1.A9ZK.01 5 0.000
#> TCGA.V1.A9O5.01 4 1.000
#> TCGA.VP.A879.01 6 0.000
#> TCGA.HC.7819.11 1 0.000
#> TCGA.VN.A88Q.01 4 0.000
#> TCGA.HC.7737.01 6 1.000
#> TCGA.V1.A8WS.01 4 0.000
#> TCGA.HC.8213.01 2 0.000
#> TCGA.M7.A721.01 6 0.000
#> TCGA.ZG.A9LZ.01 2 0.000
#> TCGA.CH.5765.01 2 0.000
#> TCGA.V1.A8WW.01 2 0.000
#> TCGA.HC.A48F.01 2 0.000
#> TCGA.V1.A9OQ.01 2 0.000
#> TCGA.EJ.5514.01 4 0.000
#> TCGA.G9.6384.01 6 0.000
#> TCGA.V1.A9ZG.01 5 0.000
#> TCGA.YL.A8HM.01 2 0.000
#> TCGA.G9.6377.01 4 0.000
#> TCGA.M7.A722.01 2 0.000
#> TCGA.G9.6361.01 2 0.000
#> TCGA.EJ.5511.01 2 0.000
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#> TCGA.G9.6332.01 2 0.000
#> TCGA.EJ.A46G.01 2 0.000
#> TCGA.V1.A9OX.01 6 0.000
#> TCGA.J4.A6G3.01 5 0.000
#> TCGA.VN.A88L.01 4 0.000
#> TCGA.EJ.7312.01 2 0.000
#> TCGA.V1.A8MM.01 2 0.000
#> TCGA.EJ.A65F.01 2 1.000
#> TCGA.G9.6498.01 4 0.000
#> TCGA.EJ.5505.01 6 0.000
#> TCGA.CH.5761.11 1 0.000
#> TCGA.HC.8261.01 6 0.000
#> TCGA.XQ.A8TB.01 4 0.000
#> TCGA.G9.6329.01 5 0.000
#> TCGA.EJ.5496.01 6 0.000
get_classes(res, k = 7)
#> class p
#> TCGA.G9.6343.01 7 0.000
#> TCGA.KK.A8IA.01 2 0.000
#> TCGA.KK.A6E4.01 2 0.000
#> TCGA.EJ.AB20.01 1 1.000
#> TCGA.H9.7775.01 2 0.000
#> TCGA.XJ.A9DX.01 4 0.000
#> TCGA.KK.A6E6.01 4 0.000
#> TCGA.G9.6339.01 6 0.000
#> TCGA.EJ.5509.01 6 1.000
#> TCGA.EJ.5521.01 6 1.000
#> TCGA.YL.A8SB.01 6 0.000
#> TCGA.V1.A9OF.01 2 0.000
#> TCGA.CH.5754.01 4 0.000
#> TCGA.EJ.7125.01 4 0.000
#> TCGA.EJ.7797.01 5 0.000
#> TCGA.YL.A9WI.01 2 0.000
#> TCGA.EJ.7314.01 4 1.000
#> TCGA.XA.A8JR.01 6 0.000
#> TCGA.EJ.7781.01 7 1.000
#> TCGA.QU.A6IN.01 2 0.000
#> TCGA.CH.5751.01 4 0.249
#> TCGA.V1.A8WL.01 4 0.000
#> TCGA.HC.A6AO.01 2 0.000
#> TCGA.KK.A7B3.01 4 0.000
#> TCGA.XK.AAJT.01 4 0.000
#> TCGA.EJ.AB27.01 5 1.000
#> TCGA.CH.5788.01 2 0.000
#> TCGA.KK.A8I5.01 2 0.000
#> TCGA.YL.A8S9.01 2 0.000
#> TCGA.CH.5761.01 4 0.000
#> TCGA.KK.A7AZ.01 2 0.000
#> TCGA.G9.6366.01 7 1.000
#> TCGA.HC.7819.01 2 0.000
#> TCGA.KC.A4BN.01 7 1.000
#> TCGA.KK.A8IG.01 4 0.000
#> TCGA.ZG.A8QW.01 5 0.000
#> TCGA.EJ.7786.01 7 0.249
#> TCGA.J4.A83K.01 6 1.000
#> TCGA.YL.A8HK.01 5 0.000
#> TCGA.EJ.5501.01 5 0.000
#> TCGA.EJ.8470.01 6 0.000
#> TCGA.J9.A8CL.01 2 0.000
#> TCGA.EJ.A7NF.01 4 1.000
#> TCGA.CH.5762.11 1 0.000
#> TCGA.XK.AAJA.01 4 0.000
#> TCGA.EJ.7330.01 5 0.000
#> TCGA.VP.AA1N.01 4 0.000
#> TCGA.EJ.5524.01 6 1.000
#> TCGA.KK.A6E8.01 2 0.000
#> TCGA.HC.7821.01 2 0.000
#> TCGA.HC.7209.01 6 0.000
#> TCGA.HC.7742.01 7 0.000
#> TCGA.G9.6351.01 5 0.000
#> TCGA.EJ.8474.01 2 1.000
#> TCGA.HC.7075.01 2 1.000
#> TCGA.J9.A8CP.01 4 0.000
#> TCGA.KK.A8IM.01 5 0.000
#> TCGA.G9.6348.01 5 0.000
#> TCGA.CH.5789.01 1 1.000
#> TCGA.KC.A7F6.01 4 0.000
#> TCGA.G9.6333.11 1 0.000
#> TCGA.KC.A4BL.01 3 0.000
#> TCGA.J4.A67Q.01 6 0.000
#> TCGA.2A.A8VL.01 6 0.000
#> TCGA.V1.A9ZK.01 5 0.000
#> TCGA.V1.A9O5.01 6 1.000
#> TCGA.VP.A879.01 6 0.000
#> TCGA.HC.7819.11 1 0.000
#> TCGA.VN.A88Q.01 4 0.000
#> TCGA.HC.7737.01 5 0.249
#> TCGA.V1.A8WS.01 4 0.000
#> TCGA.HC.8213.01 2 0.000
#> TCGA.M7.A721.01 6 0.000
#> TCGA.ZG.A9LZ.01 2 0.000
#> TCGA.CH.5765.01 2 1.000
#> TCGA.V1.A8WW.01 2 0.000
#> TCGA.HC.A48F.01 2 0.000
#> TCGA.V1.A9OQ.01 2 0.253
#> TCGA.EJ.5514.01 4 0.000
#> TCGA.G9.6384.01 6 0.000
#> TCGA.V1.A9ZG.01 5 0.000
#> TCGA.YL.A8HM.01 2 0.000
#> TCGA.G9.6377.01 4 0.000
#> TCGA.M7.A722.01 2 0.000
#> TCGA.G9.6361.01 2 1.000
#> TCGA.EJ.5511.01 2 0.000
#> TCGA.ZG.A9KY.01 4 0.000
#> TCGA.EJ.7784.11 1 0.000
#> TCGA.ZG.A9LN.01 5 0.000
#> TCGA.EJ.5526.01 6 0.249
#> TCGA.HC.7820.11 1 0.000
#> TCGA.YJ.A8SW.01 2 0.000
#> TCGA.EJ.7794.01 5 0.000
#> TCGA.EJ.A46B.01 3 0.000
#> TCGA.EJ.5542.01 6 1.000
#> TCGA.YL.A9WJ.01 5 0.000
#> TCGA.EJ.7328.11 1 0.000
#> TCGA.V1.A9Z8.01 6 0.000
#> TCGA.EJ.A46F.01 2 0.000
#> TCGA.YL.A8SK.01 5 0.249
#> TCGA.MG.AAMC.01 2 0.000
#> TCGA.X4.A8KS.01 3 0.000
#> TCGA.J4.A67M.01 6 0.000
#> TCGA.ZG.A9L0.01 4 0.000
#> TCGA.HC.7077.01 2 0.000
#> TCGA.CH.5769.01 4 0.000
#> TCGA.G9.6353.11 1 0.000
#> TCGA.G9.6499.01 6 0.000
#> TCGA.EJ.5519.01 4 0.000
#> TCGA.J4.A67T.01 6 0.000
#> TCGA.HC.7748.01 6 0.000
#> TCGA.VN.A88R.01 4 0.253
#> TCGA.H9.A6BY.01 2 1.000
#> TCGA.G9.6365.01 6 0.000
#> TCGA.EJ.7317.11 1 0.000
#> TCGA.G9.7510.01 6 0.000
#> TCGA.KK.A6E3.01 6 0.000
#> TCGA.G9.6336.01 5 0.000
#> TCGA.EJ.5517.01 4 0.000
#> TCGA.V1.A8MG.01 4 0.249
#> TCGA.KC.A7FE.01 3 0.000
#> TCGA.HC.7817.01 5 1.000
#> TCGA.J4.AAU2.01 4 1.000
#> TCGA.V1.A8MJ.01 5 0.000
#> TCGA.VP.A87C.01 6 0.000
#> TCGA.EJ.A7NN.01 7 1.000
#> TCGA.HC.A8D0.01 3 0.000
#> TCGA.EJ.7792.11 1 0.000
#> TCGA.EJ.5497.01 6 0.000
#> TCGA.Y6.A9XI.01 2 0.000
#> TCGA.HC.7752.11 1 1.000
#> TCGA.SU.A7E7.01 5 0.000
#> TCGA.G9.6342.11 3 0.000
#> TCGA.HC.8265.01 4 0.249
#> TCGA.CH.5737.01 2 0.000
#> TCGA.G9.6338.01 2 0.000
#> TCGA.KK.A7AV.01 6 0.000
#> TCGA.EJ.7218.01 4 1.000
#> TCGA.YL.A8SC.01 4 0.000
#> TCGA.XK.AAJR.01 6 0.000
#> TCGA.2A.AAYF.01 2 0.000
#> TCGA.V1.A8X3.01 4 0.000
#> TCGA.KK.A6DY.01 4 1.000
#> TCGA.M7.A71Z.01 2 0.000
#> TCGA.EJ.7123.11 1 0.000
#> TCGA.G9.6363.11 6 0.000
#> TCGA.KK.A8I8.01 4 0.000
#> TCGA.KC.A4BV.01 4 0.000
#> TCGA.G9.6332.11 1 0.000
#> TCGA.CH.5750.01 4 0.000
#> TCGA.ZG.A9ND.01 2 0.000
#> TCGA.EJ.A65B.01 5 1.000
#> TCGA.QU.A6IO.01 4 0.000
#> TCGA.EJ.5503.01 1 0.000
#> TCGA.ZG.A9LU.01 3 0.000
#> TCGA.EJ.8469.01 2 0.000
#> TCGA.XJ.A83H.01 6 0.000
#> TCGA.EJ.7315.01 4 0.000
#> TCGA.ZG.A8QY.01 7 1.000
#> TCGA.YL.A8SP.01 2 0.000
#> TCGA.CH.5791.01 4 0.000
#> TCGA.V1.A9OY.01 6 0.000
#> TCGA.KC.A4BO.01 1 0.000
#> TCGA.HC.A76X.01 2 0.000
#> TCGA.YL.A8SO.01 6 0.000
#> TCGA.KK.A8IF.01 2 0.000
#> TCGA.EJ.A7NK.01 1 1.000
#> TCGA.ZG.A9L4.01 5 0.000
#> TCGA.EJ.5522.01 6 0.000
#> TCGA.HC.7747.01 5 0.000
#> TCGA.EJ.7125.11 1 0.000
#> TCGA.ZG.A9M4.01 4 1.000
#> TCGA.EJ.A65D.01 2 0.000
#> TCGA.HC.A4ZV.01 4 0.000
#> TCGA.G9.A9S0.01 6 0.000
#> TCGA.EJ.5506.01 3 0.000
#> TCGA.KK.A7AP.01 2 0.000
#> TCGA.VP.A87D.01 2 1.000
#> TCGA.TP.A8TT.01 6 1.000
#> TCGA.KK.A8II.01 2 0.000
#> TCGA.V1.A9Z9.01 4 0.000
#> TCGA.ZG.A9LS.01 6 0.000
#> TCGA.HC.7232.01 4 0.000
#> TCGA.EJ.A8FO.01 3 1.000
#> TCGA.J9.A52B.01 4 0.000
#> TCGA.CH.5767.01 2 0.000
#> TCGA.J4.AATV.01 3 1.000
#> TCGA.HC.7081.01 4 0.000
#> TCGA.CH.5743.01 1 0.000
#> TCGA.V1.A9OH.01 6 0.000
#> TCGA.CH.5752.01 2 0.000
#> TCGA.VP.A87H.01 6 1.000
#> TCGA.G9.7521.01 4 1.000
#> TCGA.YL.A8HO.01 6 0.000
#> TCGA.YL.A9WK.01 4 0.000
#> TCGA.J4.A83M.01 4 0.000
#> TCGA.VP.A878.01 5 0.000
#> TCGA.CH.5766.11 1 0.000
#> TCGA.HC.7736.01 4 0.498
#> TCGA.G9.6385.01 3 0.000
#> TCGA.VN.A88N.01 7 1.000
#> TCGA.HC.7745.01 5 0.000
#> TCGA.HC.7078.01 2 1.000
#> TCGA.FC.A5OB.01 2 0.000
#> TCGA.G9.6379.01 6 0.000
#> TCGA.QU.A6IP.01 6 0.000
#> TCGA.J4.AATZ.01 4 1.000
#> TCGA.V1.A9O9.01 6 0.000
#> TCGA.V1.A9OL.01 4 0.000
#> TCGA.HC.7210.01 6 0.000
#> TCGA.KK.A8I7.01 3 0.000
#> TCGA.EJ.7791.01 3 0.000
#> TCGA.CH.5762.01 5 0.000
#> TCGA.EJ.5527.01 6 0.000
#> TCGA.KK.A8IC.01 5 0.751
#> TCGA.G9.6356.01 5 0.000
#> TCGA.J9.A52D.01 2 0.000
#> TCGA.EJ.7788.01 4 0.000
#> TCGA.ZG.A9LB.01 4 0.000
#> TCGA.J9.A8CN.01 2 0.000
#> TCGA.ZG.A9L1.01 4 0.253
#> TCGA.G9.6333.01 6 0.000
#> TCGA.VP.A875.01 2 0.000
#> TCGA.EJ.8468.01 4 0.000
#> TCGA.EJ.5495.01 6 0.000
#> TCGA.H9.A6BX.01 1 0.000
#> TCGA.KK.A59Y.01 2 0.000
#> TCGA.V1.A8WN.01 5 0.000
#> TCGA.KK.A7B1.01 6 0.000
#> TCGA.G9.6362.11 2 0.000
#> TCGA.G9.6364.11 1 1.000
#> TCGA.HC.A631.01 2 0.000
#> TCGA.YL.A8SA.01 2 0.000
#> TCGA.HC.8262.01 4 0.000
#> TCGA.CH.5765.11 3 0.000
#> TCGA.KC.A7FD.01 2 0.000
#> TCGA.HI.7170.01 6 0.000
#> TCGA.J4.A67L.01 6 0.000
#> TCGA.V1.A9O7.01 5 0.000
#> TCGA.HC.A6AS.01 6 0.000
#> TCGA.EJ.7784.01 2 0.000
#> TCGA.EJ.7331.11 1 0.000
#> TCGA.KC.A7F3.01 6 0.000
#> TCGA.G9.6494.11 1 0.000
#> TCGA.HC.8256.01 4 0.000
#> TCGA.J4.A83I.01 2 0.000
#> TCGA.G9.6373.01 4 0.000
#> TCGA.EJ.7794.11 1 0.000
#> TCGA.G9.6371.01 4 0.000
#> TCGA.XQ.A8TA.01 2 0.000
#> TCGA.EJ.5498.01 5 1.000
#> TCGA.EJ.7328.01 5 0.000
#> TCGA.EJ.A46D.01 5 1.000
#> TCGA.ZG.A9L9.01 4 0.000
#> TCGA.YL.A8SI.01 6 0.000
#> TCGA.M7.A724.01 2 0.000
#> TCGA.VN.A88K.01 2 0.000
#> TCGA.EJ.A8FP.01 1 0.000
#> TCGA.V1.A8MK.01 3 0.000
#> TCGA.YL.A8HJ.01 5 0.000
#> TCGA.KK.A8ID.01 2 0.000
#> TCGA.CH.5769.11 6 0.000
#> TCGA.G9.6353.01 3 0.000
#> TCGA.G9.6499.11 4 0.000
#> TCGA.KK.A8I9.01 6 0.000
#> TCGA.G9.6365.11 1 0.000
#> TCGA.EJ.A46H.01 1 0.000
#> TCGA.EJ.7317.01 4 1.000
#> TCGA.YL.A8S8.01 4 0.000
#> TCGA.XJ.A9DQ.01 3 0.000
#> TCGA.EJ.7782.11 1 0.000
#> TCGA.J4.A67O.01 5 0.000
#> TCGA.Y6.A8TL.01 6 1.000
#> TCGA.XK.AAIV.01 5 1.000
#> TCGA.CH.5790.01 2 0.000
#> TCGA.HC.7231.01 4 0.000
#> TCGA.ZG.A9L5.01 2 0.000
#> TCGA.V1.A8MF.01 7 1.000
#> TCGA.EJ.A7NJ.01 1 1.000
#> TCGA.EJ.A65E.01 4 0.000
#> TCGA.ZG.A8QX.01 6 0.000
#> TCGA.G9.6367.01 1 0.000
#> TCGA.G9.6342.01 6 0.000
#> TCGA.KK.A8IB.01 6 0.000
#> TCGA.HC.7230.01 2 0.000
#> TCGA.XK.AAIR.01 5 0.000
#> TCGA.CH.5741.01 2 0.000
#> TCGA.KK.A59V.01 4 0.000
#> TCGA.J4.8200.01 6 1.000
#> TCGA.KK.A7AQ.01 2 0.000
#> TCGA.EJ.5532.01 4 0.000
#> TCGA.HI.7168.01 4 0.000
#> TCGA.HC.7233.01 7 1.000
#> TCGA.HC.A6AL.01 4 0.000
#> TCGA.EJ.7783.01 6 0.000
#> TCGA.HC.8264.01 4 0.000
#> TCGA.EJ.A8FU.01 1 0.000
#> TCGA.EJ.A65M.01 4 0.000
#> TCGA.EJ.A8FN.01 4 0.751
#> TCGA.HI.7171.01 2 0.000
#> TCGA.XK.AAJP.01 2 0.000
#> TCGA.HC.7212.01 2 0.000
#> TCGA.ZG.A9MC.01 3 0.000
#> TCGA.2A.A8VO.01 2 0.000
#> TCGA.HC.8259.01 2 0.000
#> TCGA.G9.6378.01 5 0.751
#> TCGA.J4.A83L.01 6 0.502
#> TCGA.VN.A88P.01 2 0.000
#> TCGA.EJ.5507.01 4 0.498
#> TCGA.J9.A8CK.01 6 0.000
#> TCGA.CH.5744.01 6 1.000
#> TCGA.ZG.A9N3.01 6 0.000
#> TCGA.G9.6354.01 4 0.000
#> TCGA.VN.A88O.01 4 0.000
#> TCGA.EJ.5502.01 5 0.000
#> TCGA.HC.7079.01 3 0.000
#> TCGA.G9.6369.01 2 0.000
#> TCGA.KK.A6E1.01 2 0.000
#> TCGA.HC.7211.01 7 0.000
#> TCGA.KK.A8I6.01 4 1.000
#> TCGA.XJ.A83F.01 2 0.000
#> TCGA.EJ.7785.01 6 0.000
#> TCGA.G9.A9S4.01 2 0.000
#> TCGA.VP.A87B.01 2 0.000
#> TCGA.YL.A8SR.01 4 0.000
#> TCGA.EJ.7327.01 4 0.000
#> TCGA.4L.AA1F.01 6 0.000
#> TCGA.KK.A7AY.01 4 0.000
#> TCGA.EJ.A65G.01 7 0.000
#> TCGA.2A.AAYU.01 2 0.000
#> TCGA.HC.A76W.01 4 0.000
#> TCGA.EJ.5516.01 5 0.000
#> TCGA.G9.A9S7.01 4 1.000
#> TCGA.HC.8216.01 6 1.000
#> TCGA.CH.5794.01 6 1.000
#> TCGA.V1.A9OA.01 6 0.000
#> TCGA.J9.A52E.01 4 1.000
#> TCGA.HC.7818.01 4 1.000
#> TCGA.G9.7525.01 4 1.000
#> TCGA.FC.7961.01 6 0.000
#> TCGA.CH.5767.11 1 0.000
#> TCGA.EJ.5504.01 4 0.000
#> TCGA.VP.A87J.01 2 0.000
#> TCGA.J4.A67S.01 6 0.000
#> TCGA.KK.A8IK.01 2 0.000
#> TCGA.HC.A6AQ.01 6 0.000
#> TCGA.CH.5763.01 3 1.000
#> TCGA.HC.A8D1.01 3 0.000
#> TCGA.KK.A7AU.01 2 0.000
#> TCGA.CH.5766.01 6 0.000
#> TCGA.EJ.7781.11 1 0.000
#> TCGA.KK.A7B0.01 5 0.000
#> TCGA.EJ.7321.01 4 0.000
#> TCGA.G9.6385.11 1 0.000
#> TCGA.VN.A943.01 2 0.000
#> TCGA.KK.A59X.01 2 0.000
#> TCGA.KK.A8I4.01 6 1.000
#> TCGA.G9.6496.11 1 0.000
#> TCGA.G9.7523.01 6 0.000
#> TCGA.EJ.5494.01 4 1.000
#> TCGA.2A.A8VT.01 4 0.000
#> TCGA.HC.7213.01 2 1.000
#> TCGA.G9.7519.01 7 1.000
#> TCGA.CH.5764.11 1 0.000
#> TCGA.CH.5772.01 2 0.000
#> TCGA.EJ.7325.01 2 0.000
#> TCGA.G9.6356.11 1 0.000
#> TCGA.ZG.A9LM.01 4 0.000
#> TCGA.XJ.A9DK.01 1 0.000
#> TCGA.EJ.7789.01 2 0.000
#> TCGA.HC.8257.01 4 1.000
#> TCGA.EJ.A7NG.01 3 0.000
#> TCGA.EJ.7318.01 4 0.000
#> TCGA.EJ.5512.01 5 0.000
#> TCGA.EJ.A46E.01 1 0.000
#> TCGA.FC.A4JI.01 2 0.000
#> TCGA.J9.A8CM.01 4 0.000
#> TCGA.CH.5771.11 1 0.000
#> TCGA.KC.A4BR.01 3 0.000
#> TCGA.2A.AAYO.01 4 0.000
#> TCGA.2A.A8W3.01 6 0.000
#> TCGA.CH.5768.11 3 0.000
#> TCGA.G9.6364.01 4 1.000
#> TCGA.YL.A8SL.01 2 0.000
#> TCGA.KK.A5A1.01 2 0.000
#> TCGA.YL.A9WL.01 2 0.000
#> TCGA.HC.A6HX.01 3 0.000
#> TCGA.M7.A720.01 1 1.000
#> TCGA.HC.7080.01 2 0.000
#> TCGA.V1.A9O5.06 2 0.000
#> TCGA.KC.A7F5.01 2 0.000
#> TCGA.EJ.7331.01 6 0.000
#> TCGA.ZG.A9LY.01 5 0.000
#> TCGA.G9.6494.01 6 0.249
#> TCGA.M7.A71Y.01 3 0.000
#> TCGA.FC.A66V.01 1 0.000
#> TCGA.EJ.7793.01 5 0.000
#> TCGA.EJ.A8FS.01 2 0.000
#> TCGA.XK.AAJU.01 1 0.000
#> TCGA.HC.8266.01 5 0.000
#> TCGA.YL.A8HL.01 2 1.000
#> TCGA.VN.A88I.01 3 0.000
#> TCGA.HI.7169.01 4 1.000
#> TCGA.CH.5753.01 2 0.000
#> TCGA.J4.A67K.01 6 1.000
#> TCGA.QU.A6IM.01 7 1.000
#> TCGA.HC.A9TE.01 4 0.000
#> TCGA.EJ.7115.01 4 0.000
#> TCGA.HC.7745.11 1 0.000
#> TCGA.EJ.5531.01 5 0.000
#> TCGA.YL.A8SH.01 4 0.000
#> TCGA.G9.6362.01 2 0.000
#> TCGA.HC.8258.01 3 0.000
#> TCGA.EJ.5530.01 2 1.000
#> TCGA.VN.A88M.01 2 0.000
#> TCGA.EJ.7782.01 4 0.751
#> TCGA.YL.A8SF.01 4 0.000
#> TCGA.KK.A6E2.01 2 0.000
#> TCGA.CH.5792.01 6 0.000
#> TCGA.J4.A6G1.01 3 0.000
#> TCGA.J4.A6M7.01 2 0.000
#> TCGA.VP.A872.01 4 0.000
#> TCGA.V1.A8ML.01 4 0.000
#> TCGA.HC.7744.01 2 0.000
#> TCGA.G9.6347.01 5 0.000
#> TCGA.EJ.A46I.01 5 0.000
#> TCGA.XK.AAJ3.01 2 0.000
#> TCGA.HC.A8CY.01 2 1.000
#> TCGA.KK.A6E0.01 4 0.000
#> TCGA.XK.AAK1.01 2 0.000
#> TCGA.XK.AAIW.01 2 0.000
#> TCGA.HC.8260.01 3 0.000
#> TCGA.HC.7737.11 1 0.000
#> TCGA.EJ.7786.11 1 0.000
#> TCGA.HC.7740.01 3 0.000
#> TCGA.TP.A8TV.01 2 0.000
#> TCGA.FC.A6HD.01 2 0.000
#> TCGA.EJ.8472.01 2 0.000
#> TCGA.CH.5745.01 6 1.000
#> TCGA.EJ.5508.01 6 0.000
#> TCGA.EJ.A7NH.01 5 0.000
#> TCGA.KK.A7B2.01 3 0.000
#> TCGA.CH.5740.01 4 0.000
#> TCGA.YL.A9WH.01 2 0.000
#> TCGA.FC.A8O0.01 1 0.249
#> TCGA.J9.A52C.01 5 0.000
#> TCGA.FC.7708.01 5 0.000
#> TCGA.HC.7742.11 3 0.000
#> TCGA.G9.6351.11 3 0.000
#> TCGA.KK.A7AW.01 2 1.000
#> TCGA.G9.7509.01 4 0.000
#> TCGA.J4.A67R.01 5 0.000
#> TCGA.WW.A8ZI.01 2 0.000
#> TCGA.KK.A8IJ.01 7 1.000
#> TCGA.J4.A83N.01 4 0.000
#> TCGA.HC.A6AN.01 4 0.000
#> TCGA.G9.6348.11 1 0.000
#> TCGA.EJ.5499.01 6 0.000
#> TCGA.G9.6367.11 1 0.000
#> TCGA.QU.A6IL.01 2 0.000
#> TCGA.CH.5738.01 6 0.000
#> TCGA.V1.A9ZI.01 2 1.000
#> TCGA.CH.5748.01 7 0.000
#> TCGA.YL.A8SQ.01 2 0.000
#> TCGA.G9.7522.01 5 0.000
#> TCGA.HC.A6AP.01 6 0.000
#> TCGA.EJ.7785.11 1 0.000
#> TCGA.KK.A7B4.01 2 1.000
#> TCGA.J4.A83J.01 4 0.000
#> TCGA.V1.A8MU.01 6 0.000
#> TCGA.EJ.5510.01 5 0.000
#> TCGA.EJ.7327.11 1 0.000
#> TCGA.CH.5746.01 5 0.000
#> TCGA.V1.A9Z7.01 6 1.000
#> TCGA.M7.A725.01 2 0.000
#> TCGA.G9.6384.11 1 0.000
#> TCGA.XJ.A9DI.01 3 1.000
#> TCGA.J4.A67N.01 2 1.000
#> TCGA.XJ.A83G.01 4 1.000
#> TCGA.ZG.A8QZ.01 5 0.000
#> TCGA.TK.A8OK.01 6 0.000
#> TCGA.VP.A876.01 2 0.000
#> TCGA.KK.A6E5.01 4 0.000
#> TCGA.X4.A8KQ.01 6 0.000
#> TCGA.KK.A8IL.01 4 1.000
#> TCGA.HC.7820.01 6 0.000
#> TCGA.CH.5739.01 4 0.000
#> TCGA.HC.7750.01 5 0.502
#> TCGA.YL.A9WX.01 3 0.000
#> TCGA.EJ.5518.01 6 0.000
#> TCGA.ZG.A9NI.01 4 0.000
#> TCGA.YL.A9WY.01 6 0.000
#> TCGA.CH.5763.11 1 0.000
#> TCGA.EJ.5515.01 1 0.000
#> TCGA.KK.A8IH.01 4 1.000
#> TCGA.VP.A87K.01 2 0.000
#> TCGA.HC.A6HY.01 4 0.000
#> TCGA.HC.7211.11 1 0.000
#> TCGA.HC.A632.01 4 0.253
#> TCGA.G9.6496.01 2 0.000
#> TCGA.EJ.A7NM.01 4 0.000
#> TCGA.ZG.A9L6.01 5 0.000
#> TCGA.2A.A8VV.01 2 0.000
#> TCGA.VP.A87E.01 5 1.000
#> TCGA.CH.5764.01 6 1.000
#> TCGA.EJ.5525.01 2 0.000
#> TCGA.CH.5772.11 1 0.000
#> TCGA.KK.A59Z.01 2 0.000
#> TCGA.V1.A9ZR.01 6 0.000
#> TCGA.EJ.A6RC.01 6 0.000
#> TCGA.EJ.7792.01 6 0.000
#> TCGA.HC.A9TH.01 4 0.000
#> TCGA.M7.A723.01 3 0.000
#> TCGA.EJ.7789.11 1 0.000
#> TCGA.HC.7752.01 2 0.000
#> TCGA.EJ.A65J.01 2 0.000
#> TCGA.V1.A8WV.01 6 0.000
#> TCGA.2A.A8VX.01 2 0.000
#> TCGA.V1.A9OT.01 2 0.253
#> TCGA.KC.A7FA.01 2 1.000
#> TCGA.G9.6373.11 1 0.000
#> TCGA.G9.6370.01 1 0.498
#> TCGA.CH.5771.01 5 0.000
#> TCGA.YL.A8SJ.01 6 0.502
#> TCGA.HC.7738.01 4 0.000
#> TCGA.EJ.A6RA.01 3 0.000
#> TCGA.J4.8198.01 4 0.000
#> TCGA.EJ.7123.01 4 0.000
#> TCGA.2A.A8W1.01 2 0.000
#> TCGA.G9.6363.01 6 0.000
#> TCGA.ZG.A9L2.01 5 0.000
#> TCGA.HC.7749.01 4 0.000
#> TCGA.CH.5768.01 4 0.000
#> TCGA.KK.A6E7.01 4 0.000
#> TCGA.G9.6332.01 2 0.000
#> TCGA.EJ.A46G.01 2 0.000
#> TCGA.V1.A9OX.01 6 0.253
#> TCGA.J4.A6G3.01 5 0.000
#> TCGA.VN.A88L.01 4 0.000
#> TCGA.EJ.7312.01 2 0.000
#> TCGA.V1.A8MM.01 2 0.000
#> TCGA.EJ.A65F.01 4 1.000
#> TCGA.G9.6498.01 4 0.000
#> TCGA.EJ.5505.01 6 0.000
#> TCGA.CH.5761.11 1 0.000
#> TCGA.HC.8261.01 6 0.000
#> TCGA.XQ.A8TB.01 4 0.000
#> TCGA.G9.6329.01 5 0.000
#> TCGA.EJ.5496.01 6 0.000
get_classes(res, k = 8)
#> class p
#> TCGA.G9.6343.01 7 1.000
#> TCGA.KK.A8IA.01 2 0.000
#> TCGA.KK.A6E4.01 2 0.000
#> TCGA.EJ.AB20.01 8 0.000
#> TCGA.H9.7775.01 2 0.000
#> TCGA.XJ.A9DX.01 4 0.000
#> TCGA.KK.A6E6.01 4 0.000
#> TCGA.G9.6339.01 6 0.000
#> TCGA.EJ.5509.01 6 0.000
#> TCGA.EJ.5521.01 6 0.000
#> TCGA.YL.A8SB.01 6 0.000
#> TCGA.V1.A9OF.01 2 0.000
#> TCGA.CH.5754.01 4 1.000
#> TCGA.EJ.7125.01 4 0.000
#> TCGA.EJ.7797.01 5 0.000
#> TCGA.YL.A9WI.01 2 0.000
#> TCGA.EJ.7314.01 6 1.000
#> TCGA.XA.A8JR.01 6 0.000
#> TCGA.EJ.7781.01 6 1.000
#> TCGA.QU.A6IN.01 2 0.000
#> TCGA.CH.5751.01 7 1.000
#> TCGA.V1.A8WL.01 4 0.000
#> TCGA.HC.A6AO.01 2 0.000
#> TCGA.KK.A7B3.01 4 0.000
#> TCGA.XK.AAJT.01 4 1.000
#> TCGA.EJ.AB27.01 5 1.000
#> TCGA.CH.5788.01 2 0.000
#> TCGA.KK.A8I5.01 2 0.000
#> TCGA.YL.A8S9.01 2 0.000
#> TCGA.CH.5761.01 4 0.000
#> TCGA.KK.A7AZ.01 2 0.000
#> TCGA.G9.6366.01 6 1.000
#> TCGA.HC.7819.01 2 0.000
#> TCGA.KC.A4BN.01 6 1.000
#> TCGA.KK.A8IG.01 4 1.000
#> TCGA.ZG.A8QW.01 5 0.000
#> TCGA.EJ.7786.01 7 1.000
#> TCGA.J4.A83K.01 6 1.000
#> TCGA.YL.A8HK.01 5 0.000
#> TCGA.EJ.5501.01 5 0.000
#> TCGA.EJ.8470.01 6 0.000
#> TCGA.J9.A8CL.01 2 0.000
#> TCGA.EJ.A7NF.01 4 0.000
#> TCGA.CH.5762.11 1 0.000
#> TCGA.XK.AAJA.01 4 0.000
#> TCGA.EJ.7330.01 5 0.000
#> TCGA.VP.AA1N.01 4 1.000
#> TCGA.EJ.5524.01 6 1.000
#> TCGA.KK.A6E8.01 2 0.000
#> TCGA.HC.7821.01 2 0.000
#> TCGA.HC.7209.01 6 0.000
#> TCGA.HC.7742.01 7 1.000
#> TCGA.G9.6351.01 5 0.000
#> TCGA.EJ.8474.01 4 1.000
#> TCGA.HC.7075.01 7 1.000
#> TCGA.J9.A8CP.01 4 1.000
#> TCGA.KK.A8IM.01 5 0.000
#> TCGA.G9.6348.01 5 0.000
#> TCGA.CH.5789.01 1 0.000
#> TCGA.KC.A7F6.01 4 0.000
#> TCGA.G9.6333.11 1 0.000
#> TCGA.KC.A4BL.01 3 0.000
#> TCGA.J4.A67Q.01 6 0.000
#> TCGA.2A.A8VL.01 6 0.000
#> TCGA.V1.A9ZK.01 5 0.000
#> TCGA.V1.A9O5.01 6 1.000
#> TCGA.VP.A879.01 6 0.000
#> TCGA.HC.7819.11 1 0.000
#> TCGA.VN.A88Q.01 4 1.000
#> TCGA.HC.7737.01 6 0.000
#> TCGA.V1.A8WS.01 4 0.000
#> TCGA.HC.8213.01 2 0.000
#> TCGA.M7.A721.01 6 0.000
#> TCGA.ZG.A9LZ.01 2 0.000
#> TCGA.CH.5765.01 4 1.000
#> TCGA.V1.A8WW.01 2 0.000
#> TCGA.HC.A48F.01 2 0.000
#> TCGA.V1.A9OQ.01 2 0.000
#> TCGA.EJ.5514.01 4 1.000
#> TCGA.G9.6384.01 6 0.000
#> TCGA.V1.A9ZG.01 5 0.000
#> TCGA.YL.A8HM.01 2 0.000
#> TCGA.G9.6377.01 4 0.000
#> TCGA.M7.A722.01 2 0.000
#> TCGA.G9.6361.01 2 1.000
#> TCGA.EJ.5511.01 2 0.747
#> TCGA.ZG.A9KY.01 4 0.000
#> TCGA.EJ.7784.11 1 0.000
#> TCGA.ZG.A9LN.01 5 1.000
#> TCGA.EJ.5526.01 6 0.000
#> TCGA.HC.7820.11 1 0.000
#> TCGA.YJ.A8SW.01 2 0.000
#> TCGA.EJ.7794.01 5 0.000
#> TCGA.EJ.A46B.01 3 0.000
#> TCGA.EJ.5542.01 6 0.000
#> TCGA.YL.A9WJ.01 5 0.000
#> TCGA.EJ.7328.11 1 0.000
#> TCGA.V1.A9Z8.01 6 0.000
#> TCGA.EJ.A46F.01 2 0.000
#> TCGA.YL.A8SK.01 5 1.000
#> TCGA.MG.AAMC.01 2 0.000
#> TCGA.X4.A8KS.01 3 0.000
#> TCGA.J4.A67M.01 6 0.000
#> TCGA.ZG.A9L0.01 4 0.000
#> TCGA.HC.7077.01 2 0.000
#> TCGA.CH.5769.01 4 1.000
#> TCGA.G9.6353.11 1 0.000
#> TCGA.G9.6499.01 6 0.000
#> TCGA.EJ.5519.01 4 0.000
#> TCGA.J4.A67T.01 6 0.000
#> TCGA.HC.7748.01 6 0.000
#> TCGA.VN.A88R.01 4 0.000
#> TCGA.H9.A6BY.01 4 0.000
#> TCGA.G9.6365.01 6 0.000
#> TCGA.EJ.7317.11 1 0.000
#> TCGA.G9.7510.01 6 0.000
#> TCGA.KK.A6E3.01 6 0.000
#> TCGA.G9.6336.01 5 0.000
#> TCGA.EJ.5517.01 7 1.000
#> TCGA.V1.A8MG.01 4 1.000
#> TCGA.KC.A7FE.01 3 0.000
#> TCGA.HC.7817.01 5 1.000
#> TCGA.J4.AAU2.01 7 0.000
#> TCGA.V1.A8MJ.01 5 0.000
#> TCGA.VP.A87C.01 6 0.000
#> TCGA.EJ.A7NN.01 7 0.747
#> TCGA.HC.A8D0.01 3 0.000
#> TCGA.EJ.7792.11 1 0.000
#> TCGA.EJ.5497.01 6 0.000
#> TCGA.Y6.A9XI.01 2 0.000
#> TCGA.HC.7752.11 8 0.000
#> TCGA.SU.A7E7.01 5 0.000
#> TCGA.G9.6342.11 3 0.000
#> TCGA.HC.8265.01 4 1.000
#> TCGA.CH.5737.01 2 0.000
#> TCGA.G9.6338.01 2 0.000
#> TCGA.KK.A7AV.01 6 0.000
#> TCGA.EJ.7218.01 7 1.000
#> TCGA.YL.A8SC.01 4 1.000
#> TCGA.XK.AAJR.01 6 0.000
#> TCGA.2A.AAYF.01 2 0.000
#> TCGA.V1.A8X3.01 4 0.000
#> TCGA.KK.A6DY.01 6 1.000
#> TCGA.M7.A71Z.01 2 0.000
#> TCGA.EJ.7123.11 1 0.000
#> TCGA.G9.6363.11 6 0.000
#> TCGA.KK.A8I8.01 4 0.000
#> TCGA.KC.A4BV.01 4 0.000
#> TCGA.G9.6332.11 1 0.000
#> TCGA.CH.5750.01 4 0.000
#> TCGA.ZG.A9ND.01 2 0.000
#> TCGA.EJ.A65B.01 5 1.000
#> TCGA.QU.A6IO.01 4 0.000
#> TCGA.EJ.5503.01 1 0.000
#> TCGA.ZG.A9LU.01 3 0.000
#> TCGA.EJ.8469.01 2 0.000
#> TCGA.XJ.A83H.01 6 0.000
#> TCGA.EJ.7315.01 4 0.000
#> TCGA.ZG.A8QY.01 6 1.000
#> TCGA.YL.A8SP.01 2 0.000
#> TCGA.CH.5791.01 4 0.000
#> TCGA.V1.A9OY.01 6 0.000
#> TCGA.KC.A4BO.01 1 0.000
#> TCGA.HC.A76X.01 2 0.000
#> TCGA.YL.A8SO.01 6 0.000
#> TCGA.KK.A8IF.01 2 0.000
#> TCGA.EJ.A7NK.01 1 0.249
#> TCGA.ZG.A9L4.01 5 0.000
#> TCGA.EJ.5522.01 6 0.000
#> TCGA.HC.7747.01 5 0.000
#> TCGA.EJ.7125.11 1 0.000
#> TCGA.ZG.A9M4.01 7 1.000
#> TCGA.EJ.A65D.01 2 0.000
#> TCGA.HC.A4ZV.01 4 0.000
#> TCGA.G9.A9S0.01 6 0.000
#> TCGA.EJ.5506.01 3 0.000
#> TCGA.KK.A7AP.01 2 0.000
#> TCGA.VP.A87D.01 2 0.000
#> TCGA.TP.A8TT.01 6 1.000
#> TCGA.KK.A8II.01 2 0.000
#> TCGA.V1.A9Z9.01 4 1.000
#> TCGA.ZG.A9LS.01 6 0.000
#> TCGA.HC.7232.01 4 1.000
#> TCGA.EJ.A8FO.01 3 1.000
#> TCGA.J9.A52B.01 4 0.000
#> TCGA.CH.5767.01 2 0.000
#> TCGA.J4.AATV.01 3 1.000
#> TCGA.HC.7081.01 4 0.000
#> TCGA.CH.5743.01 1 0.000
#> TCGA.V1.A9OH.01 6 0.000
#> TCGA.CH.5752.01 2 0.000
#> TCGA.VP.A87H.01 6 1.000
#> TCGA.G9.7521.01 7 1.000
#> TCGA.YL.A8HO.01 6 0.000
#> TCGA.YL.A9WK.01 4 0.000
#> TCGA.J4.A83M.01 4 0.000
#> TCGA.VP.A878.01 5 0.000
#> TCGA.CH.5766.11 1 0.000
#> TCGA.HC.7736.01 4 1.000
#> TCGA.G9.6385.01 8 0.000
#> TCGA.VN.A88N.01 6 0.000
#> TCGA.HC.7745.01 5 0.000
#> TCGA.HC.7078.01 2 1.000
#> TCGA.FC.A5OB.01 2 0.000
#> TCGA.G9.6379.01 6 0.000
#> TCGA.QU.A6IP.01 6 0.000
#> TCGA.J4.AATZ.01 4 0.000
#> TCGA.V1.A9O9.01 6 0.000
#> TCGA.V1.A9OL.01 4 0.000
#> TCGA.HC.7210.01 6 0.000
#> TCGA.KK.A8I7.01 3 0.000
#> TCGA.EJ.7791.01 3 0.000
#> TCGA.CH.5762.01 5 0.000
#> TCGA.EJ.5527.01 6 0.000
#> TCGA.KK.A8IC.01 5 0.751
#> TCGA.G9.6356.01 5 0.000
#> TCGA.J9.A52D.01 2 0.000
#> TCGA.EJ.7788.01 4 0.000
#> TCGA.ZG.A9LB.01 4 1.000
#> TCGA.J9.A8CN.01 2 0.000
#> TCGA.ZG.A9L1.01 4 0.000
#> TCGA.G9.6333.01 6 0.000
#> TCGA.VP.A875.01 2 0.000
#> TCGA.EJ.8468.01 4 0.000
#> TCGA.EJ.5495.01 6 0.000
#> TCGA.H9.A6BX.01 1 0.000
#> TCGA.KK.A59Y.01 2 0.000
#> TCGA.V1.A8WN.01 5 0.000
#> TCGA.KK.A7B1.01 6 0.000
#> TCGA.G9.6362.11 2 0.000
#> TCGA.G9.6364.11 8 0.000
#> TCGA.HC.A631.01 2 0.000
#> TCGA.YL.A8SA.01 2 0.000
#> TCGA.HC.8262.01 4 0.000
#> TCGA.CH.5765.11 3 0.000
#> TCGA.KC.A7FD.01 2 0.000
#> TCGA.HI.7170.01 6 0.000
#> TCGA.J4.A67L.01 6 0.000
#> TCGA.V1.A9O7.01 5 0.000
#> TCGA.HC.A6AS.01 6 0.000
#> TCGA.EJ.7784.01 2 0.000
#> TCGA.EJ.7331.11 8 1.000
#> TCGA.KC.A7F3.01 6 0.000
#> TCGA.G9.6494.11 1 0.000
#> TCGA.HC.8256.01 4 1.000
#> TCGA.J4.A83I.01 2 0.000
#> TCGA.G9.6373.01 4 0.000
#> TCGA.EJ.7794.11 1 0.000
#> TCGA.G9.6371.01 4 0.000
#> TCGA.XQ.A8TA.01 2 0.000
#> TCGA.EJ.5498.01 5 1.000
#> TCGA.EJ.7328.01 5 0.000
#> TCGA.EJ.A46D.01 5 1.000
#> TCGA.ZG.A9L9.01 4 0.000
#> TCGA.YL.A8SI.01 6 0.000
#> TCGA.M7.A724.01 2 0.000
#> TCGA.VN.A88K.01 2 0.000
#> TCGA.EJ.A8FP.01 1 0.000
#> TCGA.V1.A8MK.01 3 1.000
#> TCGA.YL.A8HJ.01 5 0.000
#> TCGA.KK.A8ID.01 2 0.000
#> TCGA.CH.5769.11 6 0.000
#> TCGA.G9.6353.01 3 0.000
#> TCGA.G9.6499.11 4 1.000
#> TCGA.KK.A8I9.01 6 0.000
#> TCGA.G9.6365.11 1 0.000
#> TCGA.EJ.A46H.01 1 0.000
#> TCGA.EJ.7317.01 7 1.000
#> TCGA.YL.A8S8.01 4 0.000
#> TCGA.XJ.A9DQ.01 3 0.000
#> TCGA.EJ.7782.11 1 0.000
#> TCGA.J4.A67O.01 5 0.000
#> TCGA.Y6.A8TL.01 6 1.000
#> TCGA.XK.AAIV.01 6 0.000
#> TCGA.CH.5790.01 2 0.000
#> TCGA.HC.7231.01 4 0.000
#> TCGA.ZG.A9L5.01 2 0.000
#> TCGA.V1.A8MF.01 6 1.000
#> TCGA.EJ.A7NJ.01 1 0.000
#> TCGA.EJ.A65E.01 4 1.000
#> TCGA.ZG.A8QX.01 6 0.000
#> TCGA.G9.6367.01 1 0.000
#> TCGA.G9.6342.01 6 0.000
#> TCGA.KK.A8IB.01 6 0.000
#> TCGA.HC.7230.01 2 0.000
#> TCGA.XK.AAIR.01 5 0.000
#> TCGA.CH.5741.01 2 0.000
#> TCGA.KK.A59V.01 4 1.000
#> TCGA.J4.8200.01 6 0.000
#> TCGA.KK.A7AQ.01 2 0.000
#> TCGA.EJ.5532.01 4 1.000
#> TCGA.HI.7168.01 4 0.000
#> TCGA.HC.7233.01 7 1.000
#> TCGA.HC.A6AL.01 4 0.000
#> TCGA.EJ.7783.01 6 0.000
#> TCGA.HC.8264.01 4 0.000
#> TCGA.EJ.A8FU.01 1 0.000
#> TCGA.EJ.A65M.01 4 0.000
#> TCGA.EJ.A8FN.01 7 1.000
#> TCGA.HI.7171.01 2 0.000
#> TCGA.XK.AAJP.01 2 0.000
#> TCGA.HC.7212.01 2 0.000
#> TCGA.ZG.A9MC.01 3 0.000
#> TCGA.2A.A8VO.01 2 0.000
#> TCGA.HC.8259.01 2 0.000
#> TCGA.G9.6378.01 5 1.000
#> TCGA.J4.A83L.01 6 0.000
#> TCGA.VN.A88P.01 2 0.000
#> TCGA.EJ.5507.01 4 1.000
#> TCGA.J9.A8CK.01 6 0.000
#> TCGA.CH.5744.01 6 1.000
#> TCGA.ZG.A9N3.01 7 1.000
#> TCGA.G9.6354.01 4 0.000
#> TCGA.VN.A88O.01 4 0.000
#> TCGA.EJ.5502.01 6 0.249
#> TCGA.HC.7079.01 3 0.000
#> TCGA.G9.6369.01 2 0.000
#> TCGA.KK.A6E1.01 2 0.000
#> TCGA.HC.7211.01 7 1.000
#> TCGA.KK.A8I6.01 4 1.000
#> TCGA.XJ.A83F.01 2 0.000
#> TCGA.EJ.7785.01 6 0.000
#> TCGA.G9.A9S4.01 2 0.000
#> TCGA.VP.A87B.01 2 0.000
#> TCGA.YL.A8SR.01 4 0.000
#> TCGA.EJ.7327.01 4 1.000
#> TCGA.4L.AA1F.01 6 0.000
#> TCGA.KK.A7AY.01 4 0.000
#> TCGA.EJ.A65G.01 7 0.000
#> TCGA.2A.AAYU.01 2 0.000
#> TCGA.HC.A76W.01 4 1.000
#> TCGA.EJ.5516.01 5 0.000
#> TCGA.G9.A9S7.01 4 1.000
#> TCGA.HC.8216.01 6 0.000
#> TCGA.CH.5794.01 6 0.000
#> TCGA.V1.A9OA.01 6 0.000
#> TCGA.J9.A52E.01 6 1.000
#> TCGA.HC.7818.01 6 1.000
#> TCGA.G9.7525.01 4 0.000
#> TCGA.FC.7961.01 6 0.000
#> TCGA.CH.5767.11 1 0.000
#> TCGA.EJ.5504.01 4 0.000
#> TCGA.VP.A87J.01 2 0.000
#> TCGA.J4.A67S.01 6 0.000
#> TCGA.KK.A8IK.01 2 0.000
#> TCGA.HC.A6AQ.01 6 0.000
#> TCGA.CH.5763.01 1 1.000
#> TCGA.HC.A8D1.01 3 0.000
#> TCGA.KK.A7AU.01 2 0.000
#> TCGA.CH.5766.01 6 0.000
#> TCGA.EJ.7781.11 1 0.000
#> TCGA.KK.A7B0.01 5 0.000
#> TCGA.EJ.7321.01 4 0.000
#> TCGA.G9.6385.11 8 1.000
#> TCGA.VN.A943.01 2 0.000
#> TCGA.KK.A59X.01 2 0.000
#> TCGA.KK.A8I4.01 6 0.000
#> TCGA.G9.6496.11 1 0.000
#> TCGA.G9.7523.01 6 0.000
#> TCGA.EJ.5494.01 4 0.498
#> TCGA.2A.A8VT.01 4 0.249
#> TCGA.HC.7213.01 2 0.000
#> TCGA.G9.7519.01 6 1.000
#> TCGA.CH.5764.11 1 0.000
#> TCGA.CH.5772.01 2 0.000
#> TCGA.EJ.7325.01 2 0.000
#> TCGA.G9.6356.11 1 0.000
#> TCGA.ZG.A9LM.01 4 1.000
#> TCGA.XJ.A9DK.01 1 0.000
#> TCGA.EJ.7789.01 2 0.000
#> TCGA.HC.8257.01 4 0.000
#> TCGA.EJ.A7NG.01 3 0.000
#> TCGA.EJ.7318.01 4 1.000
#> TCGA.EJ.5512.01 5 0.000
#> TCGA.EJ.A46E.01 1 0.000
#> TCGA.FC.A4JI.01 2 0.000
#> TCGA.J9.A8CM.01 4 1.000
#> TCGA.CH.5771.11 1 0.000
#> TCGA.KC.A4BR.01 3 0.000
#> TCGA.2A.AAYO.01 4 0.000
#> TCGA.2A.A8W3.01 6 0.000
#> TCGA.CH.5768.11 3 0.000
#> TCGA.G9.6364.01 6 1.000
#> TCGA.YL.A8SL.01 2 0.000
#> TCGA.KK.A5A1.01 2 0.000
#> TCGA.YL.A9WL.01 2 0.000
#> TCGA.HC.A6HX.01 3 0.000
#> TCGA.M7.A720.01 1 0.000
#> TCGA.HC.7080.01 2 0.000
#> TCGA.V1.A9O5.06 2 0.000
#> TCGA.KC.A7F5.01 2 0.000
#> TCGA.EJ.7331.01 6 0.000
#> TCGA.ZG.A9LY.01 5 0.000
#> TCGA.G9.6494.01 6 0.000
#> TCGA.M7.A71Y.01 3 0.000
#> TCGA.FC.A66V.01 1 0.000
#> TCGA.EJ.7793.01 5 0.000
#> TCGA.EJ.A8FS.01 2 0.000
#> TCGA.XK.AAJU.01 1 0.000
#> TCGA.HC.8266.01 5 0.000
#> TCGA.YL.A8HL.01 4 0.000
#> TCGA.VN.A88I.01 3 0.000
#> TCGA.HI.7169.01 4 1.000
#> TCGA.CH.5753.01 2 0.000
#> TCGA.J4.A67K.01 6 1.000
#> TCGA.QU.A6IM.01 4 1.000
#> TCGA.HC.A9TE.01 4 0.000
#> TCGA.EJ.7115.01 4 1.000
#> TCGA.HC.7745.11 1 0.000
#> TCGA.EJ.5531.01 5 0.000
#> TCGA.YL.A8SH.01 4 0.000
#> TCGA.G9.6362.01 2 0.000
#> TCGA.HC.8258.01 3 1.000
#> TCGA.EJ.5530.01 2 0.000
#> TCGA.VN.A88M.01 2 0.000
#> TCGA.EJ.7782.01 4 0.000
#> TCGA.YL.A8SF.01 4 0.000
#> TCGA.KK.A6E2.01 2 0.000
#> TCGA.CH.5792.01 6 0.000
#> TCGA.J4.A6G1.01 3 0.000
#> TCGA.J4.A6M7.01 2 0.000
#> TCGA.VP.A872.01 4 1.000
#> TCGA.V1.A8ML.01 4 1.000
#> TCGA.HC.7744.01 2 0.000
#> TCGA.G9.6347.01 5 0.000
#> TCGA.EJ.A46I.01 5 0.000
#> TCGA.XK.AAJ3.01 2 0.000
#> TCGA.HC.A8CY.01 2 0.498
#> TCGA.KK.A6E0.01 4 0.000
#> TCGA.XK.AAK1.01 2 0.000
#> TCGA.XK.AAIW.01 2 0.000
#> TCGA.HC.8260.01 3 0.000
#> TCGA.HC.7737.11 1 0.000
#> TCGA.EJ.7786.11 8 0.000
#> TCGA.HC.7740.01 3 1.000
#> TCGA.TP.A8TV.01 2 0.000
#> TCGA.FC.A6HD.01 2 0.000
#> TCGA.EJ.8472.01 2 0.000
#> TCGA.CH.5745.01 6 1.000
#> TCGA.EJ.5508.01 6 0.000
#> TCGA.EJ.A7NH.01 5 0.000
#> TCGA.KK.A7B2.01 3 0.000
#> TCGA.CH.5740.01 4 0.000
#> TCGA.YL.A9WH.01 2 0.000
#> TCGA.FC.A8O0.01 8 0.000
#> TCGA.J9.A52C.01 5 0.000
#> TCGA.FC.7708.01 5 0.000
#> TCGA.HC.7742.11 3 0.000
#> TCGA.G9.6351.11 3 0.000
#> TCGA.KK.A7AW.01 2 1.000
#> TCGA.G9.7509.01 4 1.000
#> TCGA.J4.A67R.01 5 0.000
#> TCGA.WW.A8ZI.01 2 0.000
#> TCGA.KK.A8IJ.01 6 1.000
#> TCGA.J4.A83N.01 4 0.000
#> TCGA.HC.A6AN.01 4 0.000
#> TCGA.G9.6348.11 1 0.000
#> TCGA.EJ.5499.01 6 0.000
#> TCGA.G9.6367.11 1 0.000
#> TCGA.QU.A6IL.01 2 0.000
#> TCGA.CH.5738.01 6 0.000
#> TCGA.V1.A9ZI.01 2 0.249
#> TCGA.CH.5748.01 7 1.000
#> TCGA.YL.A8SQ.01 2 0.000
#> TCGA.G9.7522.01 5 0.000
#> TCGA.HC.A6AP.01 6 0.000
#> TCGA.EJ.7785.11 1 0.000
#> TCGA.KK.A7B4.01 2 0.498
#> TCGA.J4.A83J.01 4 1.000
#> TCGA.V1.A8MU.01 6 0.000
#> TCGA.EJ.5510.01 5 0.000
#> TCGA.EJ.7327.11 8 0.000
#> TCGA.CH.5746.01 5 0.000
#> TCGA.V1.A9Z7.01 6 1.000
#> TCGA.M7.A725.01 2 0.000
#> TCGA.G9.6384.11 1 0.000
#> TCGA.XJ.A9DI.01 3 1.000
#> TCGA.J4.A67N.01 4 0.000
#> TCGA.XJ.A83G.01 4 0.000
#> TCGA.ZG.A8QZ.01 5 0.000
#> TCGA.TK.A8OK.01 6 0.000
#> TCGA.VP.A876.01 2 0.000
#> TCGA.KK.A6E5.01 4 0.000
#> TCGA.X4.A8KQ.01 6 0.000
#> TCGA.KK.A8IL.01 4 1.000
#> TCGA.HC.7820.01 6 0.000
#> TCGA.CH.5739.01 4 0.000
#> TCGA.HC.7750.01 6 0.000
#> TCGA.YL.A9WX.01 3 0.000
#> TCGA.EJ.5518.01 6 0.000
#> TCGA.ZG.A9NI.01 4 1.000
#> TCGA.YL.A9WY.01 6 0.000
#> TCGA.CH.5763.11 1 0.000
#> TCGA.EJ.5515.01 1 0.000
#> TCGA.KK.A8IH.01 4 0.000
#> TCGA.VP.A87K.01 2 0.000
#> TCGA.HC.A6HY.01 4 0.000
#> TCGA.HC.7211.11 1 0.000
#> TCGA.HC.A632.01 4 0.000
#> TCGA.G9.6496.01 2 0.000
#> TCGA.EJ.A7NM.01 4 1.000
#> TCGA.ZG.A9L6.01 5 0.000
#> TCGA.2A.A8VV.01 2 0.000
#> TCGA.VP.A87E.01 5 0.000
#> TCGA.CH.5764.01 6 1.000
#> TCGA.EJ.5525.01 2 0.000
#> TCGA.CH.5772.11 1 0.000
#> TCGA.KK.A59Z.01 2 0.000
#> TCGA.V1.A9ZR.01 6 0.000
#> TCGA.EJ.A6RC.01 6 0.000
#> TCGA.EJ.7792.01 6 0.000
#> TCGA.HC.A9TH.01 4 1.000
#> TCGA.M7.A723.01 3 0.000
#> TCGA.EJ.7789.11 1 0.000
#> TCGA.HC.7752.01 2 0.000
#> TCGA.EJ.A65J.01 2 0.000
#> TCGA.V1.A8WV.01 6 0.000
#> TCGA.2A.A8VX.01 2 0.000
#> TCGA.V1.A9OT.01 2 0.000
#> TCGA.KC.A7FA.01 2 0.751
#> TCGA.G9.6373.11 1 0.000
#> TCGA.G9.6370.01 1 0.000
#> TCGA.CH.5771.01 5 0.000
#> TCGA.YL.A8SJ.01 6 0.000
#> TCGA.HC.7738.01 4 0.000
#> TCGA.EJ.A6RA.01 3 1.000
#> TCGA.J4.8198.01 4 0.000
#> TCGA.EJ.7123.01 4 0.000
#> TCGA.2A.A8W1.01 2 0.000
#> TCGA.G9.6363.01 6 0.000
#> TCGA.ZG.A9L2.01 5 1.000
#> TCGA.HC.7749.01 4 0.000
#> TCGA.CH.5768.01 4 0.000
#> TCGA.KK.A6E7.01 4 1.000
#> TCGA.G9.6332.01 2 0.000
#> TCGA.EJ.A46G.01 2 0.000
#> TCGA.V1.A9OX.01 6 0.000
#> TCGA.J4.A6G3.01 5 0.000
#> TCGA.VN.A88L.01 4 1.000
#> TCGA.EJ.7312.01 2 0.000
#> TCGA.V1.A8MM.01 2 0.000
#> TCGA.EJ.A65F.01 4 0.000
#> TCGA.G9.6498.01 7 0.000
#> TCGA.EJ.5505.01 6 0.000
#> TCGA.CH.5761.11 1 0.000
#> TCGA.HC.8261.01 6 0.000
#> TCGA.XQ.A8TB.01 4 0.000
#> TCGA.G9.6329.01 5 0.000
#> TCGA.EJ.5496.01 6 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011-leaf , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 , Node053-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 64 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.535 0.883 0.910 0.3088 0.671 0.671
#> 3 3 0.736 0.958 0.967 0.4508 0.886 0.830
#> 4 4 0.708 0.851 0.912 0.3405 0.815 0.678
#> 5 5 0.807 0.928 0.932 0.1763 0.851 0.641
#> 6 6 0.780 0.673 0.869 0.0949 0.986 0.950
#> 7 7 0.738 0.667 0.790 0.0609 0.911 0.664
#> 8 8 0.690 0.553 0.746 0.0275 0.939 0.716
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.EJ.AB20.01 2 0.795 1.000 0.24 0.76
#> TCGA.CH.5762.11 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5789.01 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6333.11 1 0.000 0.935 1.00 0.00
#> TCGA.HC.7819.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7784.11 1 0.000 0.935 1.00 0.00
#> TCGA.HC.7820.11 1 0.999 0.173 0.52 0.48
#> TCGA.EJ.7328.11 2 0.795 1.000 0.24 0.76
#> TCGA.G9.6353.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7317.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7792.11 1 0.000 0.935 1.00 0.00
#> TCGA.HC.7752.11 2 0.795 1.000 0.24 0.76
#> TCGA.EJ.7123.11 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6332.11 1 0.999 0.173 0.52 0.48
#> TCGA.EJ.5503.01 1 0.000 0.935 1.00 0.00
#> TCGA.KC.A4BO.01 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.A7NK.01 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7125.11 2 0.795 1.000 0.24 0.76
#> TCGA.CH.5743.01 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5766.11 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6385.01 2 0.795 1.000 0.24 0.76
#> TCGA.H9.A6BX.01 2 0.795 1.000 0.24 0.76
#> TCGA.G9.6364.11 2 0.795 1.000 0.24 0.76
#> TCGA.EJ.7331.11 2 0.795 1.000 0.24 0.76
#> TCGA.G9.6494.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7794.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.A8FP.01 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6365.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.A46H.01 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7782.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.A7NJ.01 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6367.01 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.A8FU.01 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5767.11 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5763.01 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7781.11 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6385.11 2 0.795 1.000 0.24 0.76
#> TCGA.G9.6496.11 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5764.11 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6356.11 1 0.000 0.935 1.00 0.00
#> TCGA.XJ.A9DK.01 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.A46E.01 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5771.11 1 0.000 0.935 1.00 0.00
#> TCGA.M7.A720.01 1 0.000 0.935 1.00 0.00
#> TCGA.FC.A66V.01 1 0.000 0.935 1.00 0.00
#> TCGA.XK.AAJU.01 1 0.000 0.935 1.00 0.00
#> TCGA.HC.7745.11 1 0.999 0.173 0.52 0.48
#> TCGA.HC.7737.11 1 0.999 0.173 0.52 0.48
#> TCGA.EJ.7786.11 2 0.795 1.000 0.24 0.76
#> TCGA.FC.A8O0.01 2 0.795 1.000 0.24 0.76
#> TCGA.G9.6348.11 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6367.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7785.11 1 0.795 0.538 0.76 0.24
#> TCGA.EJ.7327.11 2 0.795 1.000 0.24 0.76
#> TCGA.G9.6384.11 1 0.000 0.935 1.00 0.00
#> TCGA.XJ.A9DI.01 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5763.11 2 0.795 1.000 0.24 0.76
#> TCGA.EJ.5515.01 1 0.000 0.935 1.00 0.00
#> TCGA.HC.7211.11 1 0.999 0.173 0.52 0.48
#> TCGA.CH.5772.11 1 0.000 0.935 1.00 0.00
#> TCGA.EJ.7789.11 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6373.11 1 0.000 0.935 1.00 0.00
#> TCGA.G9.6370.01 1 0.000 0.935 1.00 0.00
#> TCGA.CH.5761.11 1 0.000 0.935 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EJ.AB20.01 2 0.254 0.934 0.00 0.92 0.08
#> TCGA.CH.5762.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5789.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6333.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.HC.7819.11 1 0.404 0.867 0.88 0.08 0.04
#> TCGA.EJ.7784.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.HC.7820.11 3 0.334 1.000 0.12 0.00 0.88
#> TCGA.EJ.7328.11 2 0.153 0.931 0.00 0.96 0.04
#> TCGA.G9.6353.11 1 0.404 0.867 0.88 0.08 0.04
#> TCGA.EJ.7317.11 1 0.404 0.867 0.88 0.08 0.04
#> TCGA.EJ.7792.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.HC.7752.11 2 0.254 0.934 0.00 0.92 0.08
#> TCGA.EJ.7123.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6332.11 3 0.334 1.000 0.12 0.00 0.88
#> TCGA.EJ.5503.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.KC.A4BO.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.A7NK.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.7125.11 2 0.153 0.931 0.00 0.96 0.04
#> TCGA.CH.5743.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5766.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6385.01 2 0.254 0.934 0.00 0.92 0.08
#> TCGA.H9.A6BX.01 2 0.153 0.931 0.00 0.96 0.04
#> TCGA.G9.6364.11 2 0.254 0.934 0.00 0.92 0.08
#> TCGA.EJ.7331.11 2 0.000 0.939 0.00 1.00 0.00
#> TCGA.G9.6494.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.7794.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.A8FP.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6365.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.A46H.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.7782.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.A7NJ.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6367.01 1 0.404 0.867 0.88 0.08 0.04
#> TCGA.EJ.A8FU.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5767.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5763.01 1 0.404 0.867 0.88 0.08 0.04
#> TCGA.EJ.7781.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6385.11 2 0.153 0.931 0.00 0.96 0.04
#> TCGA.G9.6496.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5764.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6356.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.XJ.A9DK.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.A46E.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5771.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.M7.A720.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.FC.A66V.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.XK.AAJU.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.HC.7745.11 3 0.334 1.000 0.12 0.00 0.88
#> TCGA.HC.7737.11 3 0.334 1.000 0.12 0.00 0.88
#> TCGA.EJ.7786.11 2 0.000 0.939 0.00 1.00 0.00
#> TCGA.FC.A8O0.01 2 0.254 0.934 0.00 0.92 0.08
#> TCGA.G9.6348.11 1 0.404 0.867 0.88 0.08 0.04
#> TCGA.G9.6367.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.7785.11 1 0.404 0.867 0.88 0.08 0.04
#> TCGA.EJ.7327.11 2 0.254 0.934 0.00 0.92 0.08
#> TCGA.G9.6384.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.XJ.A9DI.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5763.11 2 0.153 0.931 0.00 0.96 0.04
#> TCGA.EJ.5515.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.HC.7211.11 3 0.334 1.000 0.12 0.00 0.88
#> TCGA.CH.5772.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EJ.7789.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6373.11 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.G9.6370.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.CH.5761.11 1 0.000 0.978 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.EJ.AB20.01 2 0.0000 0.875 0.00 1.00 0 0.00
#> TCGA.CH.5762.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.CH.5789.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.G9.6333.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.HC.7819.11 4 0.3975 0.783 0.24 0.00 0 0.76
#> TCGA.EJ.7784.11 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.HC.7820.11 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EJ.7328.11 4 0.3975 0.598 0.00 0.24 0 0.76
#> TCGA.G9.6353.11 4 0.3975 0.783 0.24 0.00 0 0.76
#> TCGA.EJ.7317.11 4 0.3975 0.783 0.24 0.00 0 0.76
#> TCGA.EJ.7792.11 1 0.3801 0.784 0.78 0.00 0 0.22
#> TCGA.HC.7752.11 2 0.0000 0.875 0.00 1.00 0 0.00
#> TCGA.EJ.7123.11 4 0.0000 0.580 0.00 0.00 0 1.00
#> TCGA.G9.6332.11 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EJ.5503.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.KC.A4BO.01 1 0.1211 0.908 0.96 0.00 0 0.04
#> TCGA.EJ.A7NK.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.EJ.7125.11 4 0.3975 0.598 0.00 0.24 0 0.76
#> TCGA.CH.5743.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.CH.5766.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.G9.6385.01 2 0.0000 0.875 0.00 1.00 0 0.00
#> TCGA.H9.A6BX.01 4 0.3975 0.598 0.00 0.24 0 0.76
#> TCGA.G9.6364.11 2 0.0000 0.875 0.00 1.00 0 0.00
#> TCGA.EJ.7331.11 2 0.3975 0.710 0.00 0.76 0 0.24
#> TCGA.G9.6494.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.EJ.7794.11 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.EJ.A8FP.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.G9.6365.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.EJ.A46H.01 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.EJ.7782.11 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.EJ.A7NJ.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.G9.6367.01 4 0.4406 0.705 0.30 0.00 0 0.70
#> TCGA.EJ.A8FU.01 1 0.0707 0.914 0.98 0.00 0 0.02
#> TCGA.CH.5767.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.CH.5763.01 4 0.3975 0.783 0.24 0.00 0 0.76
#> TCGA.EJ.7781.11 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.G9.6385.11 2 0.4522 0.572 0.00 0.68 0 0.32
#> TCGA.G9.6496.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.CH.5764.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.G9.6356.11 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.XJ.A9DK.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.EJ.A46E.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.CH.5771.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.M7.A720.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.FC.A66V.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.XK.AAJU.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.HC.7745.11 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.HC.7737.11 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EJ.7786.11 2 0.3975 0.710 0.00 0.76 0 0.24
#> TCGA.FC.A8O0.01 2 0.0000 0.875 0.00 1.00 0 0.00
#> TCGA.G9.6348.11 4 0.3975 0.783 0.24 0.00 0 0.76
#> TCGA.G9.6367.11 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.EJ.7785.11 4 0.3400 0.763 0.18 0.00 0 0.82
#> TCGA.EJ.7327.11 2 0.0000 0.875 0.00 1.00 0 0.00
#> TCGA.G9.6384.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.XJ.A9DI.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.CH.5763.11 4 0.3975 0.598 0.00 0.24 0 0.76
#> TCGA.EJ.5515.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.HC.7211.11 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.CH.5772.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.EJ.7789.11 1 0.3975 0.767 0.76 0.00 0 0.24
#> TCGA.G9.6373.11 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.G9.6370.01 1 0.0000 0.932 1.00 0.00 0 0.00
#> TCGA.CH.5761.11 1 0.0000 0.932 1.00 0.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EJ.AB20.01 2 0.1043 0.937 0.00 0.96 0.00 0.00 0.04
#> TCGA.CH.5762.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5789.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6333.11 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.HC.7819.11 4 0.2438 0.890 0.06 0.00 0.00 0.90 0.04
#> TCGA.EJ.7784.11 5 0.2516 0.938 0.14 0.00 0.00 0.00 0.86
#> TCGA.HC.7820.11 3 0.0000 0.994 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.7328.11 4 0.2754 0.856 0.00 0.08 0.00 0.88 0.04
#> TCGA.G9.6353.11 4 0.2438 0.890 0.06 0.00 0.00 0.90 0.04
#> TCGA.EJ.7317.11 4 0.2438 0.890 0.06 0.00 0.00 0.90 0.04
#> TCGA.EJ.7792.11 5 0.3106 0.896 0.14 0.00 0.00 0.02 0.84
#> TCGA.HC.7752.11 2 0.0000 0.939 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7123.11 5 0.3037 0.740 0.04 0.00 0.00 0.10 0.86
#> TCGA.G9.6332.11 3 0.0609 0.986 0.00 0.00 0.98 0.02 0.00
#> TCGA.EJ.5503.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BO.01 1 0.2438 0.905 0.90 0.00 0.00 0.04 0.06
#> TCGA.EJ.A7NK.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7125.11 4 0.2331 0.863 0.00 0.08 0.00 0.90 0.02
#> TCGA.CH.5743.01 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.CH.5766.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6385.01 2 0.0609 0.937 0.00 0.98 0.00 0.00 0.02
#> TCGA.H9.A6BX.01 4 0.2331 0.863 0.00 0.08 0.00 0.90 0.02
#> TCGA.G9.6364.11 2 0.1043 0.937 0.00 0.96 0.00 0.00 0.04
#> TCGA.EJ.7331.11 2 0.3697 0.860 0.00 0.82 0.00 0.10 0.08
#> TCGA.G9.6494.11 1 0.0609 0.962 0.98 0.00 0.00 0.00 0.02
#> TCGA.EJ.7794.11 5 0.2516 0.938 0.14 0.00 0.00 0.00 0.86
#> TCGA.EJ.A8FP.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6365.11 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.EJ.A46H.01 5 0.3521 0.929 0.14 0.00 0.00 0.04 0.82
#> TCGA.EJ.7782.11 5 0.3319 0.930 0.16 0.00 0.00 0.02 0.82
#> TCGA.EJ.A7NJ.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6367.01 4 0.3291 0.833 0.12 0.00 0.00 0.84 0.04
#> TCGA.EJ.A8FU.01 1 0.1648 0.926 0.94 0.00 0.00 0.02 0.04
#> TCGA.CH.5767.11 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.CH.5763.01 4 0.3037 0.852 0.10 0.00 0.00 0.86 0.04
#> TCGA.EJ.7781.11 5 0.2732 0.910 0.16 0.00 0.00 0.00 0.84
#> TCGA.G9.6385.11 4 0.4748 0.545 0.00 0.30 0.00 0.66 0.04
#> TCGA.G9.6496.11 1 0.0609 0.962 0.98 0.00 0.00 0.00 0.02
#> TCGA.CH.5764.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6356.11 5 0.2732 0.920 0.16 0.00 0.00 0.00 0.84
#> TCGA.XJ.A9DK.01 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.EJ.A46E.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5771.11 1 0.1043 0.949 0.96 0.00 0.00 0.00 0.04
#> TCGA.M7.A720.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.FC.A66V.01 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.XK.AAJU.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7745.11 3 0.0000 0.994 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.7737.11 3 0.0609 0.986 0.00 0.00 0.98 0.02 0.00
#> TCGA.EJ.7786.11 2 0.3697 0.860 0.00 0.82 0.00 0.10 0.08
#> TCGA.FC.A8O0.01 2 0.0609 0.933 0.00 0.98 0.00 0.00 0.02
#> TCGA.G9.6348.11 4 0.2438 0.890 0.06 0.00 0.00 0.90 0.04
#> TCGA.G9.6367.11 5 0.2516 0.938 0.14 0.00 0.00 0.00 0.86
#> TCGA.EJ.7785.11 4 0.2616 0.870 0.02 0.00 0.00 0.88 0.10
#> TCGA.EJ.7327.11 2 0.0000 0.939 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6384.11 1 0.0609 0.960 0.98 0.00 0.00 0.02 0.00
#> TCGA.XJ.A9DI.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5763.11 4 0.1732 0.867 0.00 0.08 0.00 0.92 0.00
#> TCGA.EJ.5515.01 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7211.11 3 0.0000 0.994 0.00 0.00 1.00 0.00 0.00
#> TCGA.CH.5772.11 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.EJ.7789.11 5 0.3521 0.929 0.14 0.00 0.00 0.04 0.82
#> TCGA.G9.6373.11 1 0.0609 0.962 0.98 0.00 0.00 0.00 0.02
#> TCGA.G9.6370.01 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
#> TCGA.CH.5761.11 1 0.1043 0.963 0.96 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EJ.AB20.01 2 0.0937 0.8866 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CH.5762.11 1 0.0547 0.6883 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CH.5789.01 1 0.1807 0.6891 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.G9.6333.11 1 0.3163 0.5163 0.82 0.00 0.00 0.00 0.04 0.14
#> TCGA.HC.7819.11 4 0.1092 0.8778 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.EJ.7784.11 5 0.1807 0.9042 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.HC.7820.11 3 0.0000 0.9811 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7328.11 4 0.3409 0.7507 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.G9.6353.11 4 0.0547 0.8758 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.EJ.7317.11 4 0.1092 0.8748 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.EJ.7792.11 5 0.2794 0.8513 0.06 0.00 0.00 0.00 0.86 0.08
#> TCGA.HC.7752.11 2 0.0000 0.8890 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7123.11 5 0.2048 0.8579 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.G9.6332.11 3 0.0937 0.9727 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EJ.5503.01 1 0.1267 0.6925 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.KC.A4BO.01 6 0.5265 0.0000 0.40 0.00 0.00 0.00 0.10 0.50
#> TCGA.EJ.A7NK.01 1 0.1814 0.6689 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.EJ.7125.11 4 0.1814 0.8595 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.CH.5743.01 1 0.4282 -0.3327 0.56 0.00 0.00 0.00 0.02 0.42
#> TCGA.CH.5766.11 1 0.1092 0.6901 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.G9.6385.01 2 0.0547 0.8865 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.H9.A6BX.01 4 0.1814 0.8595 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.G9.6364.11 2 0.0937 0.8866 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EJ.7331.11 2 0.4926 0.6904 0.00 0.64 0.00 0.12 0.00 0.24
#> TCGA.G9.6494.11 1 0.0547 0.6883 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EJ.7794.11 5 0.0547 0.9135 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EJ.A8FP.01 1 0.1092 0.6901 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.G9.6365.11 1 0.4282 -0.3082 0.56 0.00 0.00 0.00 0.02 0.42
#> TCGA.EJ.A46H.01 5 0.1807 0.9106 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.EJ.7782.11 5 0.1807 0.9106 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.EJ.A7NJ.01 1 0.2048 0.6597 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.G9.6367.01 4 0.2882 0.8003 0.10 0.00 0.00 0.86 0.02 0.02
#> TCGA.EJ.A8FU.01 1 0.1480 0.6490 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.CH.5767.11 1 0.4246 -0.3165 0.58 0.00 0.00 0.00 0.02 0.40
#> TCGA.CH.5763.01 4 0.2094 0.8197 0.08 0.00 0.00 0.90 0.02 0.00
#> TCGA.EJ.7781.11 5 0.1556 0.8832 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.G9.6385.11 4 0.4680 0.6412 0.00 0.20 0.00 0.68 0.00 0.12
#> TCGA.G9.6496.11 1 0.1480 0.6732 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.CH.5764.11 1 0.1267 0.6737 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.G9.6356.11 5 0.2190 0.8980 0.04 0.00 0.00 0.00 0.90 0.06
#> TCGA.XJ.A9DK.01 1 0.3756 -0.1665 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.EJ.A46E.01 1 0.3156 0.5913 0.80 0.00 0.00 0.00 0.02 0.18
#> TCGA.CH.5771.11 1 0.0547 0.6853 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.M7.A720.01 1 0.2454 0.6189 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.FC.A66V.01 1 0.4310 -0.4188 0.54 0.00 0.00 0.00 0.02 0.44
#> TCGA.XK.AAJU.01 1 0.1556 0.6808 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.HC.7745.11 3 0.0547 0.9790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HC.7737.11 3 0.0937 0.9727 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EJ.7786.11 2 0.4926 0.6904 0.00 0.64 0.00 0.12 0.00 0.24
#> TCGA.FC.A8O0.01 2 0.0547 0.8825 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.G9.6348.11 4 0.1092 0.8778 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.G9.6367.11 5 0.2190 0.8980 0.04 0.00 0.00 0.00 0.90 0.06
#> TCGA.EJ.7785.11 4 0.3309 0.7529 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.EJ.7327.11 2 0.0000 0.8890 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6384.11 1 0.1807 0.6891 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.XJ.A9DI.01 1 0.2260 0.6337 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.CH.5763.11 4 0.0000 0.8760 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5515.01 1 0.2260 0.6432 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.HC.7211.11 3 0.0547 0.9790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CH.5772.11 1 0.2790 0.5562 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.EJ.7789.11 5 0.1807 0.9106 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.G9.6373.11 1 0.0547 0.6883 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G9.6370.01 1 0.3315 0.4949 0.78 0.00 0.00 0.00 0.02 0.20
#> TCGA.CH.5761.11 1 0.3647 -0.0115 0.64 0.00 0.00 0.00 0.00 0.36
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EJ.AB20.01 2 0.0504 0.8741 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CH.5762.11 7 0.1433 0.7135 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.CH.5789.01 7 0.1363 0.7212 0.04 0.00 0.00 0.00 0.00 0.02 0.94
#> TCGA.G9.6333.11 6 0.4278 0.0283 0.00 0.00 0.00 0.00 0.04 0.50 0.46
#> TCGA.HC.7819.11 4 0.0504 0.8004 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.EJ.7784.11 5 0.2708 0.7634 0.00 0.00 0.00 0.00 0.78 0.22 0.00
#> TCGA.HC.7820.11 3 0.0504 0.9713 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.EJ.7328.11 4 0.3525 0.6250 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.G9.6353.11 4 0.0000 0.8026 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7317.11 4 0.0000 0.8026 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7792.11 5 0.5825 0.6141 0.12 0.00 0.00 0.00 0.58 0.12 0.18
#> TCGA.HC.7752.11 2 0.0000 0.8749 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7123.11 5 0.3307 0.7186 0.24 0.00 0.00 0.00 0.74 0.02 0.00
#> TCGA.G9.6332.11 3 0.1363 0.9644 0.04 0.00 0.94 0.00 0.00 0.02 0.00
#> TCGA.EJ.5503.01 7 0.1928 0.6953 0.02 0.00 0.00 0.00 0.00 0.08 0.90
#> TCGA.KC.A4BO.01 6 0.6578 0.4605 0.26 0.00 0.00 0.00 0.14 0.44 0.16
#> TCGA.EJ.A7NK.01 7 0.1928 0.7049 0.02 0.00 0.00 0.00 0.00 0.08 0.90
#> TCGA.EJ.7125.11 4 0.2572 0.7630 0.20 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.CH.5743.01 6 0.5233 0.6069 0.20 0.00 0.00 0.00 0.00 0.52 0.28
#> TCGA.CH.5766.11 7 0.3519 0.5726 0.04 0.00 0.00 0.00 0.00 0.22 0.74
#> TCGA.G9.6385.01 2 0.1006 0.8630 0.02 0.96 0.00 0.00 0.00 0.02 0.00
#> TCGA.H9.A6BX.01 4 0.2572 0.7630 0.20 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.G9.6364.11 2 0.0504 0.8741 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EJ.7331.11 2 0.4487 0.5980 0.32 0.60 0.00 0.08 0.00 0.00 0.00
#> TCGA.G9.6494.11 7 0.1664 0.7045 0.02 0.00 0.00 0.00 0.00 0.06 0.92
#> TCGA.EJ.7794.11 5 0.0000 0.8011 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.A8FP.01 7 0.0504 0.7227 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.G9.6365.11 6 0.4939 0.5941 0.14 0.00 0.00 0.00 0.00 0.56 0.30
#> TCGA.EJ.A46H.01 5 0.1718 0.7926 0.04 0.00 0.00 0.00 0.92 0.04 0.00
#> TCGA.EJ.7782.11 5 0.1363 0.7970 0.02 0.00 0.00 0.00 0.94 0.04 0.00
#> TCGA.EJ.A7NJ.01 7 0.1928 0.7049 0.02 0.00 0.00 0.00 0.00 0.08 0.90
#> TCGA.G9.6367.01 4 0.4070 0.4870 0.02 0.00 0.00 0.66 0.00 0.02 0.30
#> TCGA.EJ.A8FU.01 7 0.3061 0.6645 0.02 0.00 0.00 0.06 0.00 0.08 0.84
#> TCGA.CH.5767.11 6 0.5007 0.5913 0.16 0.00 0.00 0.00 0.00 0.56 0.28
#> TCGA.CH.5763.01 4 0.2804 0.7446 0.02 0.00 0.00 0.86 0.00 0.06 0.06
#> TCGA.EJ.7781.11 5 0.3307 0.7186 0.24 0.00 0.00 0.00 0.74 0.02 0.00
#> TCGA.G9.6385.11 4 0.5293 0.5614 0.24 0.16 0.00 0.58 0.00 0.02 0.00
#> TCGA.G9.6496.11 7 0.3606 0.4851 0.00 0.00 0.00 0.00 0.02 0.30 0.68
#> TCGA.CH.5764.11 7 0.3867 0.2958 0.02 0.00 0.00 0.00 0.00 0.38 0.60
#> TCGA.G9.6356.11 5 0.2708 0.7634 0.00 0.00 0.00 0.00 0.78 0.22 0.00
#> TCGA.XJ.A9DK.01 6 0.5173 0.5840 0.16 0.00 0.00 0.00 0.00 0.50 0.34
#> TCGA.EJ.A46E.01 7 0.3487 0.5649 0.10 0.00 0.00 0.00 0.00 0.12 0.78
#> TCGA.CH.5771.11 7 0.2569 0.6629 0.00 0.00 0.00 0.00 0.02 0.14 0.84
#> TCGA.M7.A720.01 7 0.3968 0.1592 0.02 0.00 0.00 0.00 0.00 0.44 0.54
#> TCGA.FC.A66V.01 6 0.5325 0.5808 0.22 0.00 0.00 0.00 0.00 0.50 0.28
#> TCGA.XK.AAJU.01 7 0.3755 0.2896 0.02 0.00 0.00 0.00 0.00 0.34 0.64
#> TCGA.HC.7745.11 3 0.1363 0.9644 0.04 0.00 0.94 0.00 0.00 0.02 0.00
#> TCGA.HC.7737.11 3 0.0504 0.9713 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.EJ.7786.11 2 0.4487 0.5980 0.32 0.60 0.00 0.08 0.00 0.00 0.00
#> TCGA.FC.A8O0.01 2 0.0504 0.8723 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6348.11 4 0.0000 0.8026 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6367.11 5 0.2708 0.7634 0.00 0.00 0.00 0.00 0.78 0.22 0.00
#> TCGA.EJ.7785.11 4 0.3459 0.6583 0.40 0.00 0.00 0.60 0.00 0.00 0.00
#> TCGA.EJ.7327.11 2 0.0000 0.8749 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6384.11 7 0.1664 0.7026 0.06 0.00 0.00 0.00 0.00 0.02 0.92
#> TCGA.XJ.A9DI.01 7 0.2722 0.6316 0.04 0.00 0.00 0.00 0.00 0.12 0.84
#> TCGA.CH.5763.11 4 0.1664 0.7818 0.02 0.00 0.00 0.92 0.00 0.06 0.00
#> TCGA.EJ.5515.01 7 0.2572 0.6711 0.08 0.00 0.00 0.00 0.00 0.06 0.86
#> TCGA.HC.7211.11 3 0.0000 0.9727 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5772.11 6 0.3994 -0.0204 0.00 0.00 0.00 0.00 0.02 0.50 0.48
#> TCGA.EJ.7789.11 5 0.1718 0.7926 0.04 0.00 0.00 0.00 0.92 0.04 0.00
#> TCGA.G9.6373.11 7 0.3307 0.5931 0.02 0.00 0.00 0.00 0.00 0.24 0.74
#> TCGA.G9.6370.01 6 0.3558 0.0112 0.00 0.00 0.00 0.00 0.00 0.52 0.48
#> TCGA.CH.5761.11 6 0.5332 0.5700 0.18 0.00 0.00 0.00 0.00 0.44 0.38
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EJ.AB20.01 2 0.4125 -0.59789 0.00 0.52 0.02 0.00 0.00 0.02 0.00 0.44
#> TCGA.CH.5762.11 7 0.0471 0.61816 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CH.5789.01 7 0.1887 0.60850 0.00 0.00 0.06 0.00 0.00 0.04 0.90 0.00
#> TCGA.G9.6333.11 7 0.6321 0.00787 0.00 0.00 0.18 0.00 0.08 0.30 0.42 0.02
#> TCGA.HC.7819.11 4 0.2204 0.74202 0.00 0.00 0.04 0.90 0.00 0.02 0.02 0.02
#> TCGA.EJ.7784.11 5 0.3444 0.71389 0.00 0.00 0.14 0.00 0.78 0.06 0.00 0.02
#> TCGA.HC.7820.11 1 0.0000 0.96823 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7328.11 2 0.4794 -0.01347 0.00 0.48 0.08 0.42 0.00 0.00 0.00 0.02
#> TCGA.G9.6353.11 4 0.0941 0.74601 0.00 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.EJ.7317.11 4 0.2482 0.74071 0.00 0.00 0.06 0.88 0.00 0.02 0.02 0.02
#> TCGA.EJ.7792.11 5 0.5305 0.40445 0.00 0.00 0.28 0.00 0.50 0.02 0.20 0.00
#> TCGA.HC.7752.11 8 0.2938 0.94122 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.EJ.7123.11 5 0.4314 0.61532 0.00 0.00 0.24 0.00 0.66 0.02 0.00 0.08
#> TCGA.G9.6332.11 1 0.0941 0.96018 0.96 0.02 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EJ.5503.01 7 0.2994 0.53226 0.00 0.00 0.06 0.00 0.00 0.14 0.80 0.00
#> TCGA.KC.A4BO.01 6 0.4903 0.65253 0.00 0.00 0.06 0.00 0.06 0.70 0.10 0.08
#> TCGA.EJ.A7NK.01 7 0.2862 0.56050 0.00 0.00 0.08 0.00 0.00 0.10 0.82 0.00
#> TCGA.EJ.7125.11 4 0.1947 0.66043 0.00 0.14 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.CH.5743.01 6 0.2114 0.77419 0.00 0.00 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.CH.5766.11 7 0.3263 0.55069 0.00 0.00 0.12 0.00 0.00 0.10 0.78 0.00
#> TCGA.G9.6385.01 8 0.3374 0.93096 0.00 0.30 0.02 0.00 0.00 0.00 0.00 0.68
#> TCGA.H9.A6BX.01 4 0.1947 0.66043 0.00 0.14 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.G9.6364.11 2 0.4125 -0.59789 0.00 0.52 0.02 0.00 0.00 0.02 0.00 0.44
#> TCGA.EJ.7331.11 2 0.0808 0.30867 0.00 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.G9.6494.11 7 0.3404 0.57083 0.00 0.00 0.24 0.00 0.00 0.04 0.72 0.00
#> TCGA.EJ.7794.11 5 0.0000 0.75147 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A8FP.01 7 0.0941 0.61299 0.00 0.00 0.02 0.00 0.00 0.02 0.96 0.00
#> TCGA.G9.6365.11 6 0.4314 0.69324 0.00 0.00 0.08 0.00 0.00 0.66 0.24 0.02
#> TCGA.EJ.A46H.01 5 0.1804 0.74419 0.00 0.00 0.02 0.00 0.90 0.00 0.00 0.08
#> TCGA.EJ.7782.11 5 0.1557 0.74908 0.00 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.EJ.A7NJ.01 7 0.2725 0.54370 0.00 0.00 0.04 0.00 0.00 0.14 0.82 0.00
#> TCGA.G9.6367.01 4 0.5969 0.04222 0.00 0.00 0.26 0.36 0.00 0.02 0.34 0.02
#> TCGA.EJ.A8FU.01 7 0.2938 0.56853 0.00 0.00 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.CH.5767.11 6 0.2719 0.74065 0.00 0.00 0.02 0.00 0.00 0.80 0.18 0.00
#> TCGA.CH.5763.01 4 0.3637 0.68539 0.00 0.00 0.08 0.80 0.00 0.02 0.06 0.04
#> TCGA.EJ.7781.11 5 0.4314 0.61532 0.00 0.00 0.24 0.00 0.66 0.02 0.00 0.08
#> TCGA.G9.6385.11 4 0.4028 0.44480 0.00 0.28 0.02 0.66 0.00 0.00 0.00 0.04
#> TCGA.G9.6496.11 7 0.4134 0.54592 0.00 0.00 0.30 0.00 0.00 0.08 0.62 0.00
#> TCGA.CH.5764.11 7 0.3934 0.48304 0.00 0.00 0.16 0.00 0.00 0.14 0.70 0.00
#> TCGA.G9.6356.11 5 0.3891 0.70606 0.00 0.00 0.14 0.00 0.76 0.06 0.02 0.02
#> TCGA.XJ.A9DK.01 6 0.3757 0.70506 0.00 0.00 0.06 0.00 0.00 0.68 0.26 0.00
#> TCGA.EJ.A46E.01 7 0.4799 0.27911 0.00 0.00 0.18 0.00 0.00 0.28 0.54 0.00
#> TCGA.CH.5771.11 7 0.3293 0.58409 0.00 0.00 0.22 0.00 0.00 0.04 0.74 0.00
#> TCGA.M7.A720.01 7 0.5101 0.26614 0.00 0.00 0.16 0.00 0.00 0.28 0.54 0.02
#> TCGA.FC.A66V.01 6 0.2888 0.74974 0.00 0.00 0.04 0.00 0.00 0.80 0.16 0.00
#> TCGA.XK.AAJU.01 7 0.4190 0.45490 0.00 0.00 0.14 0.00 0.00 0.20 0.66 0.00
#> TCGA.HC.7745.11 1 0.0471 0.96635 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7737.11 1 0.1741 0.94557 0.92 0.00 0.02 0.00 0.00 0.02 0.00 0.04
#> TCGA.EJ.7786.11 2 0.0808 0.30867 0.00 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.FC.A8O0.01 8 0.4487 0.84237 0.00 0.28 0.08 0.00 0.00 0.02 0.00 0.62
#> TCGA.G9.6348.11 4 0.1874 0.74599 0.00 0.00 0.02 0.92 0.00 0.02 0.02 0.02
#> TCGA.G9.6367.11 5 0.3891 0.70606 0.00 0.00 0.14 0.00 0.76 0.06 0.02 0.02
#> TCGA.EJ.7785.11 2 0.5089 -0.08177 0.00 0.44 0.12 0.42 0.00 0.00 0.00 0.02
#> TCGA.EJ.7327.11 8 0.2938 0.94122 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.G9.6384.11 7 0.3879 0.53925 0.00 0.00 0.14 0.00 0.00 0.10 0.74 0.02
#> TCGA.XJ.A9DI.01 7 0.4531 0.41186 0.00 0.00 0.16 0.00 0.00 0.24 0.60 0.00
#> TCGA.CH.5763.11 4 0.2591 0.70395 0.00 0.00 0.08 0.86 0.00 0.02 0.00 0.04
#> TCGA.EJ.5515.01 7 0.4199 0.27158 0.00 0.00 0.08 0.00 0.00 0.32 0.60 0.00
#> TCGA.HC.7211.11 1 0.0808 0.96206 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CH.5772.11 7 0.5455 0.26375 0.00 0.00 0.28 0.00 0.00 0.24 0.46 0.02
#> TCGA.EJ.7789.11 5 0.2265 0.74532 0.00 0.00 0.02 0.00 0.88 0.02 0.00 0.08
#> TCGA.G9.6373.11 7 0.3845 0.56212 0.00 0.00 0.28 0.00 0.00 0.06 0.66 0.00
#> TCGA.G9.6370.01 7 0.5366 -0.07453 0.00 0.00 0.18 0.00 0.00 0.36 0.44 0.02
#> TCGA.CH.5761.11 6 0.4255 0.58653 0.00 0.00 0.08 0.00 0.00 0.58 0.34 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-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 13 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5389 0.462 0.462
#> 3 3 1.000 1.000 1.000 0.2852 0.795 0.579
#> 4 4 0.769 0.925 0.874 0.1198 0.885 0.625
#> 5 5 0.718 0.798 0.858 0.0555 0.962 0.800
#> 6 6 0.833 0.703 0.860 0.0546 1.000 1.000
#> 7 7 0.795 0.574 0.828 0.0267 0.949 0.667
#> 8 8 0.833 0.514 0.855 0.0306 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.EJ.AB20.01 2 0 1 0 1
#> TCGA.EJ.7328.11 1 0 1 1 0
#> TCGA.HC.7752.11 2 0 1 0 1
#> TCGA.EJ.7125.11 1 0 1 1 0
#> TCGA.G9.6385.01 2 0 1 0 1
#> TCGA.H9.A6BX.01 1 0 1 1 0
#> TCGA.G9.6364.11 2 0 1 0 1
#> TCGA.EJ.7331.11 1 0 1 1 0
#> TCGA.G9.6385.11 1 0 1 1 0
#> TCGA.EJ.7786.11 1 0 1 1 0
#> TCGA.FC.A8O0.01 2 0 1 0 1
#> TCGA.EJ.7327.11 2 0 1 0 1
#> TCGA.CH.5763.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EJ.AB20.01 3 0 1 0 0 1
#> TCGA.EJ.7328.11 1 0 1 1 0 0
#> TCGA.HC.7752.11 2 0 1 0 1 0
#> TCGA.EJ.7125.11 1 0 1 1 0 0
#> TCGA.G9.6385.01 2 0 1 0 1 0
#> TCGA.H9.A6BX.01 1 0 1 1 0 0
#> TCGA.G9.6364.11 3 0 1 0 0 1
#> TCGA.EJ.7331.11 1 0 1 1 0 0
#> TCGA.G9.6385.11 3 0 1 0 0 1
#> TCGA.EJ.7786.11 1 0 1 1 0 0
#> TCGA.FC.A8O0.01 2 0 1 0 1 0
#> TCGA.EJ.7327.11 2 0 1 0 1 0
#> TCGA.CH.5763.11 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EJ.AB20.01 3 0.234 0.826 0.00 0.0 0.90 0.10
#> TCGA.EJ.7328.11 1 0.000 1.000 1.00 0.0 0.00 0.00
#> TCGA.HC.7752.11 2 0.000 0.945 0.00 1.0 0.00 0.00
#> TCGA.EJ.7125.11 4 0.471 1.000 0.36 0.0 0.00 0.64
#> TCGA.G9.6385.01 2 0.000 0.945 0.00 1.0 0.00 0.00
#> TCGA.H9.A6BX.01 1 0.000 1.000 1.00 0.0 0.00 0.00
#> TCGA.G9.6364.11 3 0.000 0.842 0.00 0.0 1.00 0.00
#> TCGA.EJ.7331.11 4 0.471 1.000 0.36 0.0 0.00 0.64
#> TCGA.G9.6385.11 3 0.413 0.695 0.00 0.0 0.74 0.26
#> TCGA.EJ.7786.11 4 0.471 1.000 0.36 0.0 0.00 0.64
#> TCGA.FC.A8O0.01 2 0.361 0.824 0.00 0.8 0.00 0.20
#> TCGA.EJ.7327.11 2 0.000 0.945 0.00 1.0 0.00 0.00
#> TCGA.CH.5763.11 1 0.000 1.000 1.00 0.0 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EJ.AB20.01 3 0.000 0.705 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.7328.11 1 0.327 0.954 0.78 0.00 0.00 0.22 0.00
#> TCGA.HC.7752.11 2 0.000 0.912 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7125.11 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6385.01 2 0.000 0.912 0.00 1.00 0.00 0.00 0.00
#> TCGA.H9.A6BX.01 1 0.327 0.954 0.78 0.00 0.00 0.22 0.00
#> TCGA.G9.6364.11 3 0.275 0.723 0.04 0.00 0.88 0.00 0.08
#> TCGA.EJ.7331.11 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6385.11 3 0.748 0.499 0.06 0.00 0.46 0.20 0.28
#> TCGA.EJ.7786.11 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.FC.A8O0.01 5 0.413 0.000 0.00 0.38 0.00 0.00 0.62
#> TCGA.EJ.7327.11 2 0.228 0.815 0.12 0.88 0.00 0.00 0.00
#> TCGA.CH.5763.11 1 0.513 0.906 0.68 0.00 0.00 0.22 0.10
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EJ.AB20.01 3 0.3819 0.507 0.28 0.00 0.7 0.00 0.00 0.02
#> TCGA.EJ.7328.11 6 0.4609 0.808 0.00 0.00 0.0 0.04 0.42 0.54
#> TCGA.HC.7752.11 2 0.0000 0.872 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EJ.7125.11 4 0.0000 1.000 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.G9.6385.01 2 0.0000 0.872 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.H9.A6BX.01 6 0.4609 0.808 0.00 0.00 0.0 0.04 0.42 0.54
#> TCGA.G9.6364.11 3 0.0000 0.600 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.EJ.7331.11 4 0.0000 1.000 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.G9.6385.11 3 0.5265 0.373 0.40 0.00 0.5 0.10 0.00 0.00
#> TCGA.EJ.7786.11 4 0.0000 1.000 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.FC.A8O0.01 5 0.5289 0.000 0.14 0.28 0.0 0.00 0.58 0.00
#> TCGA.EJ.7327.11 2 0.3156 0.724 0.18 0.80 0.0 0.00 0.00 0.02
#> TCGA.CH.5763.11 6 0.0937 0.574 0.00 0.00 0.0 0.04 0.00 0.96
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EJ.AB20.01 3 0.0000 0.569 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7328.11 6 0.0863 0.820 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.HC.7752.11 2 0.0863 0.751 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7125.11 4 0.1671 0.896 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.G9.6385.01 2 0.0000 0.751 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H9.A6BX.01 6 0.3404 0.820 0.08 0.00 0.00 0.04 0.06 0.82 0.00
#> TCGA.G9.6364.11 3 0.4993 0.471 0.26 0.00 0.64 0.00 0.02 0.04 0.04
#> TCGA.EJ.7331.11 4 0.0000 0.949 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6385.11 1 0.3670 0.000 0.76 0.00 0.10 0.14 0.00 0.00 0.00
#> TCGA.EJ.7786.11 4 0.0000 0.949 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FC.A8O0.01 5 0.2422 0.000 0.00 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.EJ.7327.11 2 0.4714 0.485 0.12 0.60 0.00 0.00 0.00 0.00 0.28
#> TCGA.CH.5763.11 7 0.3841 0.000 0.00 0.00 0.00 0.04 0.00 0.28 0.68
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EJ.AB20.01 8 0.330 0.530 0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.EJ.7328.11 6 0.000 0.683 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.7752.11 2 0.332 0.703 0.00 0.54 0.46 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7125.11 4 0.388 0.741 0.14 0.00 0.02 0.74 0.10 0.00 0.00 0.00
#> TCGA.G9.6385.01 2 0.472 0.703 0.02 0.54 0.36 0.00 0.00 0.00 0.08 0.00
#> TCGA.H9.A6BX.01 6 0.384 0.683 0.02 0.00 0.24 0.00 0.04 0.70 0.00 0.00
#> TCGA.G9.6364.11 8 0.000 0.434 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EJ.7331.11 4 0.000 0.879 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6385.11 1 0.635 0.000 0.38 0.00 0.28 0.02 0.00 0.00 0.06 0.26
#> TCGA.EJ.7786.11 4 0.000 0.879 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A8O0.01 5 0.195 0.000 0.00 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.EJ.7327.11 2 0.000 0.446 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5763.11 7 0.195 0.000 0.00 0.00 0.00 0.00 0.00 0.14 0.86 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011-leaf , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 , Node053-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 193 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 0.4733 0.527 0.527
#> 3 3 1.000 0.979 0.990 0.3789 0.752 0.558
#> 4 4 1.000 0.989 0.995 0.1031 0.888 0.697
#> 5 5 0.850 0.787 0.902 0.0658 0.887 0.636
#> 6 6 0.815 0.756 0.851 0.0420 0.942 0.765
#> 7 7 0.840 0.688 0.830 0.0186 0.971 0.865
#> 8 8 0.842 0.679 0.755 0.0289 0.954 0.773
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.KK.A8IA.01 1 0 1 1 0
#> TCGA.KK.A6E4.01 1 0 1 1 0
#> TCGA.H9.7775.01 1 0 1 1 0
#> TCGA.XJ.A9DX.01 1 0 1 1 0
#> TCGA.V1.A9OF.01 1 0 1 1 0
#> TCGA.EJ.7125.01 2 0 1 0 1
#> TCGA.YL.A9WI.01 2 0 1 0 1
#> TCGA.QU.A6IN.01 1 0 1 1 0
#> TCGA.HC.A6AO.01 2 0 1 0 1
#> TCGA.KK.A7B3.01 1 0 1 1 0
#> TCGA.CH.5788.01 1 0 1 1 0
#> TCGA.KK.A8I5.01 1 0 1 1 0
#> TCGA.YL.A8S9.01 2 0 1 0 1
#> TCGA.CH.5761.01 2 0 1 0 1
#> TCGA.KK.A7AZ.01 1 0 1 1 0
#> TCGA.HC.7819.01 1 0 1 1 0
#> TCGA.J9.A8CL.01 1 0 1 1 0
#> TCGA.EJ.A7NF.01 1 0 1 1 0
#> TCGA.XK.AAJA.01 2 0 1 0 1
#> TCGA.KK.A6E8.01 2 0 1 0 1
#> TCGA.HC.7821.01 1 0 1 1 0
#> TCGA.EJ.8474.01 1 0 1 1 0
#> TCGA.HC.7075.01 1 0 1 1 0
#> TCGA.KC.A7F6.01 1 0 1 1 0
#> TCGA.V1.A8WS.01 1 0 1 1 0
#> TCGA.HC.8213.01 1 0 1 1 0
#> TCGA.ZG.A9LZ.01 1 0 1 1 0
#> TCGA.CH.5765.01 1 0 1 1 0
#> TCGA.V1.A8WW.01 1 0 1 1 0
#> TCGA.HC.A48F.01 1 0 1 1 0
#> TCGA.V1.A9OQ.01 2 0 1 0 1
#> TCGA.YL.A8HM.01 2 0 1 0 1
#> TCGA.G9.6377.01 1 0 1 1 0
#> TCGA.M7.A722.01 2 0 1 0 1
#> TCGA.G9.6361.01 1 0 1 1 0
#> TCGA.EJ.5511.01 1 0 1 1 0
#> TCGA.ZG.A9KY.01 2 0 1 0 1
#> TCGA.YJ.A8SW.01 1 0 1 1 0
#> TCGA.EJ.A46F.01 1 0 1 1 0
#> TCGA.MG.AAMC.01 1 0 1 1 0
#> TCGA.ZG.A9L0.01 2 0 1 0 1
#> TCGA.HC.7077.01 1 0 1 1 0
#> TCGA.EJ.5519.01 2 0 1 0 1
#> TCGA.VN.A88R.01 2 0 1 0 1
#> TCGA.H9.A6BY.01 1 0 1 1 0
#> TCGA.EJ.5517.01 1 0 1 1 0
#> TCGA.J4.AAU2.01 1 0 1 1 0
#> TCGA.Y6.A9XI.01 2 0 1 0 1
#> TCGA.CH.5737.01 2 0 1 0 1
#> TCGA.G9.6338.01 2 0 1 0 1
#> TCGA.2A.AAYF.01 1 0 1 1 0
#> TCGA.M7.A71Z.01 1 0 1 1 0
#> TCGA.KC.A4BV.01 1 0 1 1 0
#> TCGA.CH.5750.01 1 0 1 1 0
#> TCGA.ZG.A9ND.01 2 0 1 0 1
#> TCGA.EJ.8469.01 1 0 1 1 0
#> TCGA.EJ.7315.01 1 0 1 1 0
#> TCGA.YL.A8SP.01 1 0 1 1 0
#> TCGA.CH.5791.01 1 0 1 1 0
#> TCGA.HC.A76X.01 1 0 1 1 0
#> TCGA.KK.A8IF.01 2 0 1 0 1
#> TCGA.EJ.A65D.01 1 0 1 1 0
#> TCGA.HC.A4ZV.01 2 0 1 0 1
#> TCGA.KK.A7AP.01 2 0 1 0 1
#> TCGA.VP.A87D.01 1 0 1 1 0
#> TCGA.KK.A8II.01 1 0 1 1 0
#> TCGA.J9.A52B.01 1 0 1 1 0
#> TCGA.CH.5767.01 2 0 1 0 1
#> TCGA.CH.5752.01 1 0 1 1 0
#> TCGA.YL.A9WK.01 1 0 1 1 0
#> TCGA.HC.7078.01 1 0 1 1 0
#> TCGA.FC.A5OB.01 1 0 1 1 0
#> TCGA.J4.AATZ.01 2 0 1 0 1
#> TCGA.V1.A9OL.01 2 0 1 0 1
#> TCGA.J9.A52D.01 1 0 1 1 0
#> TCGA.EJ.7788.01 1 0 1 1 0
#> TCGA.J9.A8CN.01 2 0 1 0 1
#> TCGA.ZG.A9L1.01 1 0 1 1 0
#> TCGA.VP.A875.01 1 0 1 1 0
#> TCGA.KK.A59Y.01 1 0 1 1 0
#> TCGA.G9.6362.11 1 0 1 1 0
#> TCGA.HC.A631.01 1 0 1 1 0
#> TCGA.YL.A8SA.01 1 0 1 1 0
#> TCGA.KC.A7FD.01 1 0 1 1 0
#> TCGA.EJ.7784.01 1 0 1 1 0
#> TCGA.J4.A83I.01 1 0 1 1 0
#> TCGA.G9.6373.01 1 0 1 1 0
#> TCGA.G9.6371.01 2 0 1 0 1
#> TCGA.XQ.A8TA.01 1 0 1 1 0
#> TCGA.ZG.A9L9.01 1 0 1 1 0
#> TCGA.M7.A724.01 2 0 1 0 1
#> TCGA.VN.A88K.01 1 0 1 1 0
#> TCGA.KK.A8ID.01 2 0 1 0 1
#> TCGA.CH.5790.01 1 0 1 1 0
#> TCGA.HC.7231.01 1 0 1 1 0
#> TCGA.ZG.A9L5.01 2 0 1 0 1
#> TCGA.HC.7230.01 1 0 1 1 0
#> TCGA.CH.5741.01 1 0 1 1 0
#> TCGA.KK.A59V.01 1 0 1 1 0
#> TCGA.KK.A7AQ.01 2 0 1 0 1
#> TCGA.HC.A6AL.01 2 0 1 0 1
#> TCGA.HC.8264.01 2 0 1 0 1
#> TCGA.HI.7171.01 1 0 1 1 0
#> TCGA.XK.AAJP.01 2 0 1 0 1
#> TCGA.HC.7212.01 1 0 1 1 0
#> TCGA.2A.A8VO.01 1 0 1 1 0
#> TCGA.HC.8259.01 1 0 1 1 0
#> TCGA.VN.A88P.01 1 0 1 1 0
#> TCGA.G9.6369.01 2 0 1 0 1
#> TCGA.KK.A6E1.01 2 0 1 0 1
#> TCGA.XJ.A83F.01 1 0 1 1 0
#> TCGA.G9.A9S4.01 1 0 1 1 0
#> TCGA.VP.A87B.01 2 0 1 0 1
#> TCGA.YL.A8SR.01 2 0 1 0 1
#> TCGA.KK.A7AY.01 1 0 1 1 0
#> TCGA.2A.AAYU.01 1 0 1 1 0
#> TCGA.G9.7525.01 1 0 1 1 0
#> TCGA.VP.A87J.01 2 0 1 0 1
#> TCGA.KK.A8IK.01 2 0 1 0 1
#> TCGA.KK.A7AU.01 1 0 1 1 0
#> TCGA.VN.A943.01 2 0 1 0 1
#> TCGA.KK.A59X.01 2 0 1 0 1
#> TCGA.EJ.5494.01 1 0 1 1 0
#> TCGA.HC.7213.01 1 0 1 1 0
#> TCGA.CH.5772.01 1 0 1 1 0
#> TCGA.EJ.7325.01 1 0 1 1 0
#> TCGA.EJ.7789.01 2 0 1 0 1
#> TCGA.HC.8257.01 1 0 1 1 0
#> TCGA.FC.A4JI.01 2 0 1 0 1
#> TCGA.2A.AAYO.01 1 0 1 1 0
#> TCGA.YL.A8SL.01 1 0 1 1 0
#> TCGA.KK.A5A1.01 2 0 1 0 1
#> TCGA.YL.A9WL.01 1 0 1 1 0
#> TCGA.HC.7080.01 2 0 1 0 1
#> TCGA.V1.A9O5.06 2 0 1 0 1
#> TCGA.KC.A7F5.01 2 0 1 0 1
#> TCGA.EJ.A8FS.01 2 0 1 0 1
#> TCGA.YL.A8HL.01 2 0 1 0 1
#> TCGA.CH.5753.01 1 0 1 1 0
#> TCGA.YL.A8SH.01 1 0 1 1 0
#> TCGA.G9.6362.01 1 0 1 1 0
#> TCGA.EJ.5530.01 1 0 1 1 0
#> TCGA.VN.A88M.01 1 0 1 1 0
#> TCGA.EJ.7782.01 2 0 1 0 1
#> TCGA.KK.A6E2.01 1 0 1 1 0
#> TCGA.J4.A6M7.01 1 0 1 1 0
#> TCGA.HC.7744.01 1 0 1 1 0
#> TCGA.XK.AAJ3.01 2 0 1 0 1
#> TCGA.HC.A8CY.01 1 0 1 1 0
#> TCGA.KK.A6E0.01 2 0 1 0 1
#> TCGA.XK.AAK1.01 2 0 1 0 1
#> TCGA.XK.AAIW.01 2 0 1 0 1
#> TCGA.TP.A8TV.01 2 0 1 0 1
#> TCGA.FC.A6HD.01 2 0 1 0 1
#> TCGA.EJ.8472.01 1 0 1 1 0
#> TCGA.YL.A9WH.01 1 0 1 1 0
#> TCGA.KK.A7AW.01 1 0 1 1 0
#> TCGA.WW.A8ZI.01 2 0 1 0 1
#> TCGA.J4.A83N.01 1 0 1 1 0
#> TCGA.HC.A6AN.01 1 0 1 1 0
#> TCGA.QU.A6IL.01 2 0 1 0 1
#> TCGA.V1.A9ZI.01 1 0 1 1 0
#> TCGA.YL.A8SQ.01 1 0 1 1 0
#> TCGA.KK.A7B4.01 1 0 1 1 0
#> TCGA.J4.A83J.01 2 0 1 0 1
#> TCGA.M7.A725.01 2 0 1 0 1
#> TCGA.J4.A67N.01 1 0 1 1 0
#> TCGA.XJ.A83G.01 2 0 1 0 1
#> TCGA.VP.A876.01 1 0 1 1 0
#> TCGA.CH.5739.01 1 0 1 1 0
#> TCGA.KK.A8IH.01 1 0 1 1 0
#> TCGA.VP.A87K.01 1 0 1 1 0
#> TCGA.HC.A632.01 2 0 1 0 1
#> TCGA.G9.6496.01 2 0 1 0 1
#> TCGA.2A.A8VV.01 1 0 1 1 0
#> TCGA.EJ.5525.01 1 0 1 1 0
#> TCGA.KK.A59Z.01 2 0 1 0 1
#> TCGA.HC.7752.01 1 0 1 1 0
#> TCGA.EJ.A65J.01 2 0 1 0 1
#> TCGA.2A.A8VX.01 2 0 1 0 1
#> TCGA.V1.A9OT.01 1 0 1 1 0
#> TCGA.KC.A7FA.01 2 0 1 0 1
#> TCGA.HC.7738.01 2 0 1 0 1
#> TCGA.J4.8198.01 1 0 1 1 0
#> TCGA.EJ.7123.01 2 0 1 0 1
#> TCGA.2A.A8W1.01 2 0 1 0 1
#> TCGA.CH.5768.01 1 0 1 1 0
#> TCGA.G9.6332.01 1 0 1 1 0
#> TCGA.EJ.A46G.01 1 0 1 1 0
#> TCGA.EJ.7312.01 2 0 1 0 1
#> TCGA.V1.A8MM.01 2 0 1 0 1
#> TCGA.EJ.A65F.01 1 0 1 1 0
#> TCGA.G9.6498.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.KK.A8IA.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KK.A6E4.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.H9.7775.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.XJ.A9DX.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A9OF.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.EJ.7125.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.YL.A9WI.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.QU.A6IN.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A6AO.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KK.A7B3.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.CH.5788.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KK.A8I5.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.YL.A8S9.01 2 0.0892 0.976 0.00 0.98 0.02
#> TCGA.CH.5761.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KK.A7AZ.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.HC.7819.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.J9.A8CL.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.EJ.A7NF.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.XK.AAJA.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KK.A6E8.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HC.7821.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.8474.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.7075.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KC.A7F6.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A8WS.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.8213.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A9LZ.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.CH.5765.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A8WW.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A48F.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A9OQ.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.YL.A8HM.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.G9.6377.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.M7.A722.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.G9.6361.01 3 0.2959 0.891 0.10 0.00 0.90
#> TCGA.EJ.5511.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.ZG.A9KY.01 3 0.2066 0.919 0.00 0.06 0.94
#> TCGA.YJ.A8SW.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.A46F.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A9L0.01 2 0.1529 0.960 0.00 0.96 0.04
#> TCGA.HC.7077.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.5519.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.VN.A88R.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.H9.A6BY.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.5517.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.J4.AAU2.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.Y6.A9XI.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.CH.5737.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.G9.6338.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.2A.AAYF.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.M7.A71Z.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KC.A4BV.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.CH.5750.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A9ND.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EJ.8469.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.7315.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.YL.A8SP.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.CH.5791.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A76X.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A8IF.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EJ.A65D.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A4ZV.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KK.A7AP.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.VP.A87D.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A8II.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.J9.A52B.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.CH.5767.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.CH.5752.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.YL.A9WK.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.HC.7078.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.FC.A5OB.01 1 0.1529 0.958 0.96 0.00 0.04
#> TCGA.J4.AATZ.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.V1.A9OL.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.J9.A52D.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.EJ.7788.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.J9.A8CN.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.ZG.A9L1.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.VP.A875.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KK.A59Y.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.6362.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A631.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.YL.A8SA.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KC.A7FD.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.EJ.7784.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.J4.A83I.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.G9.6373.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.6371.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.XQ.A8TA.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.ZG.A9L9.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.M7.A724.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.VN.A88K.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A8ID.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.CH.5790.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.7231.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A9L5.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HC.7230.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.CH.5741.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A59V.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A7AQ.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HC.A6AL.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HC.8264.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.HI.7171.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.XK.AAJP.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.HC.7212.01 1 0.0892 0.978 0.98 0.00 0.02
#> TCGA.2A.A8VO.01 3 0.3340 0.869 0.12 0.00 0.88
#> TCGA.HC.8259.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.VN.A88P.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.G9.6369.01 2 0.1529 0.960 0.00 0.96 0.04
#> TCGA.KK.A6E1.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.XJ.A83F.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.A9S4.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.VP.A87B.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.YL.A8SR.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KK.A7AY.01 3 0.5706 0.560 0.32 0.00 0.68
#> TCGA.2A.AAYU.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.G9.7525.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.VP.A87J.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KK.A8IK.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KK.A7AU.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.VN.A943.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KK.A59X.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EJ.5494.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.HC.7213.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.CH.5772.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.EJ.7325.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.7789.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HC.8257.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.FC.A4JI.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.2A.AAYO.01 1 0.1529 0.958 0.96 0.00 0.04
#> TCGA.YL.A8SL.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A5A1.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.YL.A9WL.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.7080.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.V1.A9O5.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KC.A7F5.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EJ.A8FS.01 2 0.1529 0.960 0.00 0.96 0.04
#> TCGA.YL.A8HL.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.CH.5753.01 1 0.2959 0.887 0.90 0.00 0.10
#> TCGA.YL.A8SH.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.G9.6362.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.5530.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.VN.A88M.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.7782.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.KK.A6E2.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.J4.A6M7.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.7744.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.XK.AAJ3.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HC.A8CY.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KK.A6E0.01 2 0.1529 0.960 0.00 0.96 0.04
#> TCGA.XK.AAK1.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.XK.AAIW.01 2 0.5216 0.664 0.00 0.74 0.26
#> TCGA.TP.A8TV.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.FC.A6HD.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EJ.8472.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A7AW.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.WW.A8ZI.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.J4.A83N.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A6AN.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.QU.A6IL.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.V1.A9ZI.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.YL.A8SQ.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.KK.A7B4.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.J4.A83J.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.M7.A725.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.J4.A67N.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.VP.A876.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A8IH.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.VP.A87K.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A632.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.G9.6496.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.2A.A8VV.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.5525.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A59Z.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HC.7752.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.EJ.A65J.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.2A.A8VX.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.V1.A9OT.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KC.A7FA.01 3 0.0000 0.972 0.00 0.00 1.00
#> TCGA.HC.7738.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.J4.8198.01 3 0.5397 0.639 0.28 0.00 0.72
#> TCGA.EJ.7123.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.2A.A8W1.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.CH.5768.01 3 0.1529 0.949 0.04 0.00 0.96
#> TCGA.G9.6332.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.A46G.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.7312.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.V1.A8MM.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EJ.A65F.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.6498.01 2 0.1529 0.960 0.00 0.96 0.04
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.KK.A8IA.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.KK.A6E4.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.H9.7775.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.XJ.A9DX.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.V1.A9OF.01 3 0.0707 0.978 0.00 0.00 0.98 0.02
#> TCGA.EJ.7125.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.YL.A9WI.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.QU.A6IN.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.A6AO.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.KK.A7B3.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CH.5788.01 3 0.0707 0.978 0.00 0.00 0.98 0.02
#> TCGA.KK.A8I5.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.YL.A8S9.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.CH.5761.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.KK.A7AZ.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.HC.7819.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.J9.A8CL.01 3 0.1637 0.941 0.00 0.00 0.94 0.06
#> TCGA.EJ.A7NF.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.XK.AAJA.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.KK.A6E8.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.HC.7821.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.8474.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.7075.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.KC.A7F6.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.8213.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9LZ.01 1 0.3172 0.812 0.84 0.00 0.16 0.00
#> TCGA.CH.5765.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.V1.A8WW.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.A48F.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.V1.A9OQ.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.YL.A8HM.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.G9.6377.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.M7.A722.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.G9.6361.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.EJ.5511.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.ZG.A9KY.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.YJ.A8SW.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.A46F.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.HC.7077.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.5519.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.VN.A88R.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.H9.A6BY.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.5517.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.J4.AAU2.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.Y6.A9XI.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.CH.5737.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.G9.6338.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.2A.AAYF.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.M7.A71Z.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.CH.5750.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9ND.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.EJ.8469.01 1 0.0707 0.978 0.98 0.00 0.02 0.00
#> TCGA.EJ.7315.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SP.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CH.5791.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A8IF.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.EJ.A65D.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.A4ZV.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.KK.A7AP.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.VP.A87D.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A8II.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.J9.A52B.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CH.5767.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.CH.5752.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.YL.A9WK.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.HC.7078.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.FC.A5OB.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.J4.AATZ.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.V1.A9OL.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.J9.A52D.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.EJ.7788.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.J9.A8CN.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.ZG.A9L1.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.VP.A875.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.KK.A59Y.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.G9.6362.11 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.A631.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SA.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KC.A7FD.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.EJ.7784.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.J4.A83I.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.G9.6373.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.G9.6371.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.XQ.A8TA.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.ZG.A9L9.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.M7.A724.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.VN.A88K.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A8ID.01 4 0.2345 0.888 0.00 0.10 0.00 0.90
#> TCGA.CH.5790.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.7231.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9L5.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.HC.7230.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CH.5741.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A59V.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A7AQ.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.HC.A6AL.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.HC.8264.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.HI.7171.01 1 0.0707 0.978 0.98 0.00 0.02 0.00
#> TCGA.XK.AAJP.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.HC.7212.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.2A.A8VO.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.HC.8259.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VN.A88P.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.G9.6369.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.KK.A6E1.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.XJ.A83F.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VP.A87B.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.YL.A8SR.01 2 0.3801 0.713 0.00 0.78 0.00 0.22
#> TCGA.KK.A7AY.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.2A.AAYU.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.G9.7525.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.KK.A8IK.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.KK.A7AU.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VN.A943.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.KK.A59X.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.EJ.5494.01 3 0.0707 0.978 0.00 0.00 0.98 0.02
#> TCGA.HC.7213.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.CH.5772.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.EJ.7325.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.7789.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.HC.8257.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.2A.AAYO.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A5A1.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.YL.A9WL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.7080.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.V1.A9O5.06 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.KC.A7F5.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.EJ.A8FS.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.YL.A8HL.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.CH.5753.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SH.01 3 0.2011 0.920 0.00 0.00 0.92 0.08
#> TCGA.G9.6362.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.5530.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VN.A88M.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.7782.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.KK.A6E2.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.7744.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.XK.AAJ3.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.HC.A8CY.01 3 0.1637 0.941 0.00 0.00 0.94 0.06
#> TCGA.KK.A6E0.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.XK.AAK1.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.XK.AAIW.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.TP.A8TV.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.FC.A6HD.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.EJ.8472.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.WW.A8ZI.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.J4.A83N.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.A6AN.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.QU.A6IL.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.V1.A9ZI.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SQ.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.KK.A7B4.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.J4.A83J.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.M7.A725.01 4 0.3172 0.812 0.00 0.16 0.00 0.84
#> TCGA.J4.A67N.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.VP.A876.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A8IH.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VP.A87K.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HC.A632.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
#> TCGA.G9.6496.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.2A.A8VV.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.5525.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KK.A59Z.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.HC.7752.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.EJ.A65J.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.2A.A8VX.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.V1.A9OT.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.KC.A7FA.01 4 0.0707 0.971 0.00 0.00 0.02 0.98
#> TCGA.HC.7738.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.J4.8198.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.EJ.7123.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.2A.A8W1.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.CH.5768.01 3 0.0000 0.994 0.00 0.00 1.00 0.00
#> TCGA.G9.6332.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.A46G.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EJ.7312.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.V1.A8MM.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.EJ.A65F.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.G9.6498.01 4 0.0000 0.990 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.KK.A8IA.01 3 0.2280 0.74490 0.00 0.00 0.88 0.00 0.12
#> TCGA.KK.A6E4.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.H9.7775.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A9DX.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OF.01 5 0.0000 0.76378 0.00 0.00 0.00 0.00 1.00
#> TCGA.EJ.7125.01 4 0.3561 0.62901 0.00 0.26 0.00 0.74 0.00
#> TCGA.YL.A9WI.01 4 0.3796 0.57826 0.00 0.30 0.00 0.70 0.00
#> TCGA.QU.A6IN.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AO.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A7B3.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5788.01 5 0.0000 0.76378 0.00 0.00 0.00 0.00 1.00
#> TCGA.KK.A8I5.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8S9.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.CH.5761.01 2 0.3684 0.55049 0.00 0.72 0.00 0.28 0.00
#> TCGA.KK.A7AZ.01 5 0.3274 0.57059 0.00 0.00 0.22 0.00 0.78
#> TCGA.HC.7819.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CL.01 5 0.0000 0.76378 0.00 0.00 0.00 0.00 1.00
#> TCGA.EJ.A7NF.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJA.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7821.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8474.01 1 0.2516 0.84013 0.86 0.00 0.14 0.00 0.00
#> TCGA.HC.7075.01 5 0.4302 -0.14765 0.00 0.00 0.48 0.00 0.52
#> TCGA.KC.A7F6.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8213.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LZ.01 3 0.0609 0.75078 0.02 0.00 0.98 0.00 0.00
#> TCGA.CH.5765.01 1 0.1043 0.94116 0.96 0.00 0.04 0.00 0.00
#> TCGA.V1.A8WW.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A48F.01 1 0.1410 0.92522 0.94 0.00 0.06 0.00 0.00
#> TCGA.V1.A9OQ.01 2 0.4287 0.01431 0.00 0.54 0.00 0.46 0.00
#> TCGA.YL.A8HM.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6377.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.M7.A722.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6361.01 3 0.0609 0.75615 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.5511.01 3 0.3684 0.65608 0.00 0.00 0.72 0.00 0.28
#> TCGA.ZG.A9KY.01 4 0.1410 0.72994 0.00 0.00 0.00 0.94 0.06
#> TCGA.YJ.A8SW.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A46F.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.7077.01 1 0.4287 0.11968 0.54 0.00 0.46 0.00 0.00
#> TCGA.EJ.5519.01 5 0.3983 0.61891 0.00 0.00 0.00 0.34 0.66
#> TCGA.VN.A88R.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.H9.A6BY.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5517.01 3 0.3274 0.71408 0.00 0.00 0.78 0.00 0.22
#> TCGA.J4.AAU2.01 3 0.2280 0.74006 0.00 0.00 0.88 0.00 0.12
#> TCGA.Y6.A9XI.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5737.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6338.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.2A.AAYF.01 3 0.4182 0.34835 0.40 0.00 0.60 0.00 0.00
#> TCGA.M7.A71Z.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 3 0.4262 0.12173 0.00 0.00 0.56 0.00 0.44
#> TCGA.CH.5750.01 1 0.1732 0.90654 0.92 0.00 0.08 0.00 0.00
#> TCGA.ZG.A9ND.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.EJ.8469.01 3 0.3109 0.61531 0.20 0.00 0.80 0.00 0.00
#> TCGA.EJ.7315.01 5 0.2929 0.69870 0.00 0.00 0.18 0.00 0.82
#> TCGA.YL.A8SP.01 1 0.1043 0.94116 0.96 0.00 0.04 0.00 0.00
#> TCGA.CH.5791.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IF.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A65D.01 1 0.4307 0.00705 0.50 0.00 0.50 0.00 0.00
#> TCGA.HC.A4ZV.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.KK.A7AP.01 5 0.3796 0.67217 0.00 0.00 0.00 0.30 0.70
#> TCGA.VP.A87D.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8II.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52B.01 3 0.4182 0.34835 0.40 0.00 0.60 0.00 0.00
#> TCGA.CH.5767.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5752.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WK.01 5 0.3274 0.57059 0.00 0.00 0.22 0.00 0.78
#> TCGA.HC.7078.01 3 0.3109 0.72628 0.00 0.00 0.80 0.00 0.20
#> TCGA.FC.A5OB.01 3 0.2280 0.74006 0.00 0.00 0.88 0.00 0.12
#> TCGA.J4.AATZ.01 2 0.3796 0.50659 0.00 0.70 0.00 0.30 0.00
#> TCGA.V1.A9OL.01 4 0.2516 0.63935 0.00 0.00 0.00 0.86 0.14
#> TCGA.J9.A52D.01 3 0.3424 0.69958 0.00 0.00 0.76 0.00 0.24
#> TCGA.EJ.7788.01 3 0.0609 0.75500 0.00 0.00 0.98 0.00 0.02
#> TCGA.J9.A8CN.01 5 0.3424 0.70601 0.00 0.00 0.00 0.24 0.76
#> TCGA.ZG.A9L1.01 3 0.1732 0.76014 0.00 0.00 0.92 0.00 0.08
#> TCGA.VP.A875.01 3 0.4126 0.31286 0.00 0.00 0.62 0.00 0.38
#> TCGA.KK.A59Y.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6362.11 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A631.01 3 0.4262 0.22887 0.44 0.00 0.56 0.00 0.00
#> TCGA.YL.A8SA.01 1 0.1043 0.94116 0.96 0.00 0.04 0.00 0.00
#> TCGA.KC.A7FD.01 5 0.4227 0.07042 0.00 0.00 0.42 0.00 0.58
#> TCGA.EJ.7784.01 1 0.1732 0.90654 0.92 0.00 0.08 0.00 0.00
#> TCGA.J4.A83I.01 3 0.2020 0.75204 0.00 0.00 0.90 0.00 0.10
#> TCGA.G9.6373.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6371.01 5 0.3424 0.70601 0.00 0.00 0.00 0.24 0.76
#> TCGA.XQ.A8TA.01 3 0.2280 0.74490 0.00 0.00 0.88 0.00 0.12
#> TCGA.ZG.A9L9.01 3 0.4126 0.39787 0.38 0.00 0.62 0.00 0.00
#> TCGA.M7.A724.01 5 0.3424 0.70601 0.00 0.00 0.00 0.24 0.76
#> TCGA.VN.A88K.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8ID.01 4 0.0609 0.77391 0.00 0.02 0.00 0.98 0.00
#> TCGA.CH.5790.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7231.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L5.01 4 0.4302 0.15536 0.00 0.48 0.00 0.52 0.00
#> TCGA.HC.7230.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5741.01 1 0.0609 0.95456 0.98 0.00 0.02 0.00 0.00
#> TCGA.KK.A59V.01 3 0.4126 0.39787 0.38 0.00 0.62 0.00 0.00
#> TCGA.KK.A7AQ.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.A6AL.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.8264.01 5 0.3424 0.70601 0.00 0.00 0.00 0.24 0.76
#> TCGA.HI.7171.01 3 0.3274 0.60452 0.22 0.00 0.78 0.00 0.00
#> TCGA.XK.AAJP.01 4 0.4302 -0.16031 0.00 0.00 0.00 0.52 0.48
#> TCGA.HC.7212.01 3 0.0000 0.75186 0.00 0.00 1.00 0.00 0.00
#> TCGA.2A.A8VO.01 3 0.2516 0.74041 0.00 0.00 0.86 0.00 0.14
#> TCGA.HC.8259.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88P.01 5 0.3274 0.57081 0.00 0.00 0.22 0.00 0.78
#> TCGA.G9.6369.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.KK.A6E1.01 5 0.3796 0.67217 0.00 0.00 0.00 0.30 0.70
#> TCGA.XJ.A83F.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87B.01 4 0.4302 -0.16031 0.00 0.00 0.00 0.52 0.48
#> TCGA.YL.A8SR.01 4 0.3109 0.69206 0.00 0.20 0.00 0.80 0.00
#> TCGA.KK.A7AY.01 3 0.0000 0.75186 0.00 0.00 1.00 0.00 0.00
#> TCGA.2A.AAYU.01 3 0.3895 0.53698 0.00 0.00 0.68 0.00 0.32
#> TCGA.G9.7525.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 5 0.3561 0.69717 0.00 0.00 0.00 0.26 0.74
#> TCGA.KK.A8IK.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A943.01 5 0.3424 0.70601 0.00 0.00 0.00 0.24 0.76
#> TCGA.KK.A59X.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5494.01 5 0.0000 0.76378 0.00 0.00 0.00 0.00 1.00
#> TCGA.HC.7213.01 3 0.2280 0.75331 0.00 0.00 0.88 0.00 0.12
#> TCGA.CH.5772.01 5 0.3109 0.59743 0.00 0.00 0.20 0.00 0.80
#> TCGA.EJ.7325.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7789.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.8257.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.AAYO.01 3 0.2280 0.74006 0.00 0.00 0.88 0.00 0.12
#> TCGA.YL.A8SL.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A5A1.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.YL.A9WL.01 1 0.2020 0.88636 0.90 0.00 0.10 0.00 0.00
#> TCGA.HC.7080.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A9O5.06 4 0.3796 0.57826 0.00 0.30 0.00 0.70 0.00
#> TCGA.KC.A7F5.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A8FS.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.YL.A8HL.01 5 0.4252 0.68045 0.00 0.00 0.02 0.28 0.70
#> TCGA.CH.5753.01 3 0.0000 0.75186 0.00 0.00 1.00 0.00 0.00
#> TCGA.YL.A8SH.01 5 0.0000 0.76378 0.00 0.00 0.00 0.00 1.00
#> TCGA.G9.6362.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5530.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88M.01 1 0.0609 0.95456 0.98 0.00 0.02 0.00 0.00
#> TCGA.EJ.7782.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A6E2.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7744.01 3 0.2280 0.74490 0.00 0.00 0.88 0.00 0.12
#> TCGA.XK.AAJ3.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 5 0.0000 0.76378 0.00 0.00 0.00 0.00 1.00
#> TCGA.KK.A6E0.01 4 0.0000 0.77616 0.00 0.00 0.00 1.00 0.00
#> TCGA.XK.AAK1.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.XK.AAIW.01 4 0.2280 0.69396 0.00 0.00 0.00 0.88 0.12
#> TCGA.TP.A8TV.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 4 0.4302 0.15473 0.00 0.48 0.00 0.52 0.00
#> TCGA.EJ.8472.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 5 0.0609 0.75847 0.00 0.00 0.02 0.00 0.98
#> TCGA.WW.A8ZI.01 5 0.3424 0.70601 0.00 0.00 0.00 0.24 0.76
#> TCGA.J4.A83N.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AN.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IL.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A9ZI.01 3 0.2280 0.75331 0.00 0.00 0.88 0.00 0.12
#> TCGA.YL.A8SQ.01 5 0.0000 0.76378 0.00 0.00 0.00 0.00 1.00
#> TCGA.KK.A7B4.01 3 0.2280 0.75331 0.00 0.00 0.88 0.00 0.12
#> TCGA.J4.A83J.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.M7.A725.01 4 0.0609 0.77391 0.00 0.02 0.00 0.98 0.00
#> TCGA.J4.A67N.01 1 0.3684 0.61335 0.72 0.00 0.28 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.VP.A876.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IH.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87K.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A632.01 5 0.3796 0.67217 0.00 0.00 0.00 0.30 0.70
#> TCGA.G9.6496.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.A8VV.01 1 0.0000 0.96671 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5525.01 3 0.3424 0.58661 0.24 0.00 0.76 0.00 0.00
#> TCGA.KK.A59Z.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7752.01 3 0.3109 0.72473 0.00 0.00 0.80 0.00 0.20
#> TCGA.EJ.A65J.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 4 0.3796 0.57826 0.00 0.30 0.00 0.70 0.00
#> TCGA.V1.A9OT.01 1 0.1043 0.94116 0.96 0.00 0.04 0.00 0.00
#> TCGA.KC.A7FA.01 5 0.1043 0.75910 0.00 0.00 0.00 0.04 0.96
#> TCGA.HC.7738.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.8198.01 3 0.1043 0.75894 0.00 0.00 0.96 0.00 0.04
#> TCGA.EJ.7123.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.A8W1.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5768.01 3 0.2516 0.74439 0.00 0.00 0.86 0.00 0.14
#> TCGA.G9.6332.01 1 0.1043 0.94116 0.96 0.00 0.04 0.00 0.00
#> TCGA.EJ.A46G.01 1 0.2732 0.81400 0.84 0.00 0.16 0.00 0.00
#> TCGA.EJ.7312.01 4 0.3424 0.65041 0.00 0.24 0.00 0.76 0.00
#> TCGA.V1.A8MM.01 2 0.0000 0.96391 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A65F.01 1 0.1043 0.94116 0.96 0.00 0.04 0.00 0.00
#> TCGA.G9.6498.01 4 0.0000 0.77616 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.KK.A8IA.01 3 0.3916 0.679386 0.00 0.00 0.68 0.00 0.02 0.30
#> TCGA.KK.A6E4.01 1 0.2048 0.797628 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.H9.7775.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A9DX.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OF.01 5 0.3076 0.761710 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.EJ.7125.01 4 0.3475 0.782414 0.00 0.14 0.00 0.80 0.00 0.06
#> TCGA.YL.A9WI.01 4 0.3829 0.765403 0.00 0.18 0.00 0.76 0.00 0.06
#> TCGA.QU.A6IN.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AO.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B3.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5788.01 5 0.3076 0.761710 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.KK.A8I5.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8S9.01 4 0.1814 0.809685 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.CH.5761.01 4 0.4845 0.419110 0.00 0.40 0.00 0.54 0.00 0.06
#> TCGA.KK.A7AZ.01 3 0.4873 0.032075 0.00 0.00 0.60 0.00 0.32 0.08
#> TCGA.HC.7819.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CL.01 5 0.3076 0.761710 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.EJ.A7NF.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJA.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7821.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8474.01 1 0.3869 0.060631 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.HC.7075.01 3 0.2350 0.628709 0.00 0.00 0.88 0.00 0.10 0.02
#> TCGA.KC.A7F6.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8213.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LZ.01 6 0.4165 0.535332 0.00 0.00 0.16 0.10 0.00 0.74
#> TCGA.CH.5765.01 1 0.3309 0.600435 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.V1.A8WW.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A48F.01 1 0.3578 0.494483 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.V1.A9OQ.01 4 0.4121 0.733889 0.00 0.22 0.00 0.72 0.00 0.06
#> TCGA.YL.A8HM.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6377.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.M7.A722.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6361.01 3 0.5235 0.486076 0.00 0.00 0.52 0.10 0.00 0.38
#> TCGA.EJ.5511.01 3 0.2350 0.679137 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.ZG.A9KY.01 4 0.3711 0.671155 0.00 0.00 0.00 0.72 0.26 0.02
#> TCGA.YJ.A8SW.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A46F.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 4 0.2981 0.771548 0.00 0.00 0.00 0.82 0.16 0.02
#> TCGA.HC.7077.01 6 0.4380 0.620885 0.22 0.00 0.08 0.00 0.00 0.70
#> TCGA.EJ.5519.01 5 0.4251 0.735494 0.00 0.00 0.06 0.10 0.78 0.06
#> TCGA.VN.A88R.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.H9.A6BY.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5517.01 3 0.3409 0.607980 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.J4.AAU2.01 6 0.3797 0.148596 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.Y6.A9XI.01 2 0.0937 0.963352 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CH.5737.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6338.01 4 0.2350 0.803889 0.00 0.00 0.00 0.88 0.10 0.02
#> TCGA.2A.AAYF.01 6 0.4723 0.626192 0.14 0.00 0.18 0.00 0.00 0.68
#> TCGA.M7.A71Z.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 3 0.3660 0.646776 0.00 0.00 0.78 0.00 0.06 0.16
#> TCGA.CH.5750.01 1 0.3647 0.452477 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.ZG.A9ND.01 4 0.1814 0.809685 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.EJ.8469.01 6 0.4756 0.651436 0.10 0.00 0.06 0.10 0.00 0.74
#> TCGA.EJ.7315.01 5 0.4873 0.707053 0.00 0.00 0.32 0.00 0.60 0.08
#> TCGA.YL.A8SP.01 1 0.5235 0.148479 0.52 0.00 0.00 0.10 0.00 0.38
#> TCGA.CH.5791.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IF.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65D.01 6 0.4328 0.642035 0.18 0.00 0.00 0.10 0.00 0.72
#> TCGA.HC.A4ZV.01 4 0.1814 0.809685 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.KK.A7AP.01 5 0.4008 0.750702 0.00 0.00 0.06 0.08 0.80 0.06
#> TCGA.VP.A87D.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8II.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52B.01 6 0.4607 0.661840 0.18 0.00 0.02 0.08 0.00 0.72
#> TCGA.CH.5767.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5752.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WK.01 3 0.3198 0.464012 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.HC.7078.01 3 0.3409 0.607980 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.FC.A5OB.01 3 0.3756 0.455281 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.J4.AATZ.01 4 0.4700 0.549203 0.00 0.34 0.00 0.60 0.00 0.06
#> TCGA.V1.A9OL.01 4 0.5115 0.120145 0.00 0.00 0.02 0.48 0.46 0.04
#> TCGA.J9.A52D.01 3 0.3409 0.607980 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.EJ.7788.01 6 0.3578 0.349969 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.J9.A8CN.01 5 0.1807 0.819817 0.00 0.00 0.06 0.02 0.92 0.00
#> TCGA.ZG.A9L1.01 3 0.3578 0.655610 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.VP.A875.01 3 0.3928 0.610040 0.00 0.00 0.76 0.00 0.08 0.16
#> TCGA.KK.A59Y.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6362.11 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A631.01 6 0.4723 0.630118 0.18 0.00 0.14 0.00 0.00 0.68
#> TCGA.YL.A8SA.01 1 0.3309 0.600435 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.KC.A7FD.01 3 0.2260 0.609903 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.EJ.7784.01 1 0.3647 0.452477 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.J4.A83I.01 3 0.5195 0.515291 0.00 0.00 0.54 0.10 0.00 0.36
#> TCGA.G9.6373.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6371.01 5 0.3045 0.814154 0.00 0.00 0.10 0.00 0.84 0.06
#> TCGA.XQ.A8TA.01 3 0.3592 0.679112 0.00 0.00 0.74 0.00 0.02 0.24
#> TCGA.ZG.A9L9.01 6 0.4737 0.636937 0.16 0.00 0.16 0.00 0.00 0.68
#> TCGA.M7.A724.01 5 0.0547 0.803782 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.VN.A88K.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8ID.01 4 0.1814 0.809685 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.CH.5790.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7231.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L5.01 4 0.4121 0.733889 0.00 0.22 0.00 0.72 0.00 0.06
#> TCGA.HC.7230.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5741.01 1 0.3309 0.600435 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.KK.A59V.01 6 0.4723 0.631680 0.14 0.00 0.18 0.00 0.00 0.68
#> TCGA.KK.A7AQ.01 2 0.1267 0.947385 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.HC.A6AL.01 4 0.1814 0.809685 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.HC.8264.01 5 0.1807 0.819817 0.00 0.00 0.06 0.02 0.92 0.00
#> TCGA.HI.7171.01 6 0.4756 0.623146 0.06 0.00 0.10 0.10 0.00 0.74
#> TCGA.XK.AAJP.01 5 0.2350 0.739982 0.00 0.00 0.00 0.10 0.88 0.02
#> TCGA.HC.7212.01 6 0.4165 0.535332 0.00 0.00 0.16 0.10 0.00 0.74
#> TCGA.2A.A8VO.01 3 0.3578 0.561907 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.HC.8259.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88P.01 3 0.3198 0.464012 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.G9.6369.01 4 0.2981 0.771548 0.00 0.00 0.00 0.82 0.16 0.02
#> TCGA.KK.A6E1.01 5 0.4251 0.735494 0.00 0.00 0.06 0.10 0.78 0.06
#> TCGA.XJ.A83F.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87B.01 5 0.2350 0.739982 0.00 0.00 0.00 0.10 0.88 0.02
#> TCGA.YL.A8SR.01 4 0.2728 0.798442 0.00 0.10 0.00 0.86 0.00 0.04
#> TCGA.KK.A7AY.01 6 0.5235 -0.155865 0.00 0.00 0.38 0.10 0.00 0.52
#> TCGA.2A.AAYU.01 3 0.3351 0.677339 0.00 0.00 0.80 0.00 0.04 0.16
#> TCGA.G9.7525.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 5 0.3420 0.775528 0.00 0.00 0.06 0.04 0.84 0.06
#> TCGA.KK.A8IK.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A943.01 5 0.1807 0.819817 0.00 0.00 0.06 0.02 0.92 0.00
#> TCGA.KK.A59X.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5494.01 5 0.3076 0.761710 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.HC.7213.01 3 0.3309 0.684642 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.CH.5772.01 3 0.3309 0.420614 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.EJ.7325.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7789.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8257.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.AAYO.01 3 0.3756 0.455281 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.YL.A8SL.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A5A1.01 2 0.1267 0.947385 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.YL.A9WL.01 1 0.5285 0.000753 0.48 0.00 0.00 0.10 0.00 0.42
#> TCGA.HC.7080.01 2 0.1267 0.947385 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.V1.A9O5.06 4 0.3829 0.765403 0.00 0.18 0.00 0.76 0.00 0.06
#> TCGA.KC.A7F5.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FS.01 4 0.1814 0.809685 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.YL.A8HL.01 5 0.3735 0.762630 0.00 0.00 0.06 0.06 0.82 0.06
#> TCGA.CH.5753.01 6 0.4475 0.468549 0.00 0.00 0.20 0.10 0.00 0.70
#> TCGA.YL.A8SH.01 5 0.2941 0.771430 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.G9.6362.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5530.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88M.01 1 0.3309 0.600435 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.EJ.7782.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E2.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7744.01 3 0.3916 0.679386 0.00 0.00 0.68 0.00 0.02 0.30
#> TCGA.XK.AAJ3.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 5 0.2793 0.781301 0.00 0.00 0.20 0.00 0.80 0.00
#> TCGA.KK.A6E0.01 4 0.1814 0.809685 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.XK.AAK1.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAIW.01 4 0.3198 0.681671 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.TP.A8TV.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 4 0.4121 0.733889 0.00 0.22 0.00 0.72 0.00 0.06
#> TCGA.EJ.8472.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 5 0.4700 0.686214 0.00 0.00 0.34 0.00 0.60 0.06
#> TCGA.WW.A8ZI.01 5 0.1807 0.819817 0.00 0.00 0.06 0.02 0.92 0.00
#> TCGA.J4.A83N.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AN.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IL.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZI.01 3 0.3309 0.684642 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.YL.A8SQ.01 5 0.3198 0.739969 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.KK.A7B4.01 3 0.3499 0.665029 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.J4.A83J.01 2 0.0937 0.963352 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.M7.A725.01 4 0.2728 0.806261 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.J4.A67N.01 6 0.5144 0.457004 0.34 0.00 0.00 0.10 0.00 0.56
#> TCGA.XJ.A83G.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A876.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IH.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87K.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A632.01 5 0.4251 0.735494 0.00 0.00 0.06 0.10 0.78 0.06
#> TCGA.G9.6496.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VV.01 1 0.0000 0.903833 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5525.01 6 0.4667 0.656960 0.12 0.00 0.04 0.10 0.00 0.74
#> TCGA.KK.A59Z.01 2 0.1267 0.947385 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.HC.7752.01 3 0.3499 0.587127 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.EJ.A65J.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 4 0.3829 0.765403 0.00 0.18 0.00 0.76 0.00 0.06
#> TCGA.V1.A9OT.01 1 0.3076 0.657108 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.KC.A7FA.01 5 0.2454 0.792859 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.HC.7738.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.8198.01 3 0.3647 0.556597 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.EJ.7123.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8W1.01 2 0.0547 0.976872 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CH.5768.01 3 0.3409 0.677017 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.G9.6332.01 1 0.5144 0.272030 0.56 0.00 0.00 0.10 0.00 0.34
#> TCGA.EJ.A46G.01 1 0.3869 0.060631 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.EJ.7312.01 4 0.2728 0.798442 0.00 0.10 0.00 0.86 0.00 0.04
#> TCGA.V1.A8MM.01 2 0.0000 0.989076 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65F.01 1 0.3578 0.494483 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.G9.6498.01 4 0.1814 0.809685 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.KK.A8IA.01 3 0.4970 0.5193 0.00 0.00 0.58 0.00 0.00 0.24 0.18
#> TCGA.KK.A6E4.01 1 0.2081 0.7903 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.H9.7775.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A9DX.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OF.01 5 0.3052 0.5710 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.EJ.7125.01 4 0.0863 0.8454 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.YL.A9WI.01 4 0.1433 0.8377 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.QU.A6IN.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AO.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B3.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5788.01 5 0.3307 0.5278 0.00 0.00 0.24 0.00 0.74 0.00 0.02
#> TCGA.KK.A8I5.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8S9.01 4 0.3199 0.7946 0.00 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.CH.5761.01 4 0.4499 0.6261 0.00 0.16 0.02 0.70 0.00 0.00 0.12
#> TCGA.KK.A7AZ.01 3 0.5232 -0.2814 0.00 0.00 0.46 0.00 0.38 0.00 0.16
#> TCGA.HC.7819.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CL.01 5 0.3052 0.5710 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.EJ.A7NF.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJA.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7821.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8474.01 6 0.4681 0.4791 0.32 0.00 0.00 0.00 0.00 0.58 0.10
#> TCGA.HC.7075.01 3 0.2569 0.4931 0.00 0.00 0.84 0.00 0.14 0.02 0.00
#> TCGA.KC.A7F6.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8213.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LZ.01 6 0.1664 0.5630 0.02 0.00 0.06 0.00 0.00 0.92 0.00
#> TCGA.CH.5765.01 1 0.3358 0.4530 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.V1.A8WW.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A48F.01 1 0.3294 0.4906 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.V1.A9OQ.01 4 0.1166 0.8422 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.YL.A8HM.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6377.01 1 0.0863 0.8888 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.M7.A722.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6361.01 6 0.5086 -0.1854 0.00 0.00 0.36 0.00 0.00 0.50 0.14
#> TCGA.EJ.5511.01 3 0.2163 0.5918 0.00 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.ZG.A9KY.01 4 0.5293 0.5163 0.00 0.00 0.02 0.58 0.24 0.00 0.16
#> TCGA.YJ.A8SW.01 1 0.0863 0.8888 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.EJ.A46F.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 4 0.4001 0.7588 0.00 0.00 0.06 0.74 0.00 0.02 0.18
#> TCGA.HC.7077.01 6 0.3965 0.5852 0.12 0.00 0.02 0.00 0.00 0.76 0.10
#> TCGA.EJ.5519.01 5 0.3417 0.1886 0.00 0.00 0.00 0.02 0.72 0.00 0.26
#> TCGA.VN.A88R.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H9.A6BY.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5517.01 3 0.4783 0.5239 0.00 0.00 0.54 0.00 0.00 0.36 0.10
#> TCGA.J4.AAU2.01 3 0.4848 0.4846 0.00 0.00 0.50 0.00 0.00 0.40 0.10
#> TCGA.Y6.A9XI.01 2 0.1363 0.9255 0.00 0.94 0.00 0.04 0.00 0.00 0.02
#> TCGA.CH.5737.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6338.01 4 0.3289 0.8070 0.00 0.00 0.06 0.82 0.00 0.02 0.10
#> TCGA.2A.AAYF.01 6 0.4620 0.5237 0.08 0.00 0.10 0.00 0.00 0.72 0.10
#> TCGA.M7.A71Z.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 3 0.4338 0.3633 0.00 0.00 0.64 0.00 0.00 0.08 0.28
#> TCGA.CH.5750.01 1 0.3294 0.4906 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.ZG.A9ND.01 4 0.2654 0.8292 0.00 0.00 0.02 0.86 0.00 0.02 0.10
#> TCGA.EJ.8469.01 6 0.3914 0.5800 0.10 0.00 0.06 0.00 0.00 0.78 0.06
#> TCGA.EJ.7315.01 7 0.5341 0.4069 0.00 0.00 0.24 0.00 0.26 0.00 0.50
#> TCGA.YL.A8SP.01 1 0.4278 0.0392 0.50 0.00 0.00 0.00 0.00 0.46 0.04
#> TCGA.CH.5791.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IF.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65D.01 6 0.3863 0.5689 0.20 0.00 0.02 0.00 0.00 0.74 0.04
#> TCGA.HC.A4ZV.01 4 0.1928 0.8413 0.00 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.KK.A7AP.01 5 0.3358 -0.1971 0.00 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.VP.A87D.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8II.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52B.01 6 0.1433 0.6158 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.CH.5767.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5752.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WK.01 3 0.3685 0.1964 0.00 0.00 0.66 0.00 0.32 0.00 0.02
#> TCGA.HC.7078.01 3 0.3927 0.5808 0.00 0.00 0.66 0.00 0.00 0.30 0.04
#> TCGA.FC.A5OB.01 3 0.4848 0.4846 0.00 0.00 0.50 0.00 0.00 0.40 0.10
#> TCGA.J4.AATZ.01 4 0.3744 0.7322 0.00 0.08 0.02 0.78 0.00 0.00 0.12
#> TCGA.V1.A9OL.01 5 0.5539 -0.2404 0.00 0.00 0.00 0.38 0.38 0.00 0.24
#> TCGA.J9.A52D.01 3 0.4547 0.5512 0.00 0.00 0.58 0.00 0.00 0.34 0.08
#> TCGA.EJ.7788.01 3 0.4848 0.4846 0.00 0.00 0.50 0.00 0.00 0.40 0.10
#> TCGA.J9.A8CN.01 5 0.0504 0.5841 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZG.A9L1.01 3 0.3221 0.5892 0.00 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.VP.A875.01 3 0.4705 0.0821 0.00 0.00 0.48 0.00 0.00 0.08 0.44
#> TCGA.KK.A59Y.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6362.11 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A631.01 6 0.4161 0.5482 0.06 0.00 0.08 0.00 0.00 0.76 0.10
#> TCGA.YL.A8SA.01 1 0.3358 0.4530 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.KC.A7FD.01 3 0.3386 0.4356 0.00 0.00 0.78 0.00 0.18 0.02 0.02
#> TCGA.EJ.7784.01 1 0.3294 0.4906 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.J4.A83I.01 6 0.5485 -0.3309 0.00 0.00 0.38 0.00 0.00 0.40 0.22
#> TCGA.G9.6373.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6371.01 5 0.3011 0.5093 0.00 0.00 0.06 0.00 0.82 0.00 0.12
#> TCGA.XQ.A8TA.01 3 0.4873 0.4584 0.00 0.00 0.60 0.00 0.00 0.18 0.22
#> TCGA.ZG.A9L9.01 6 0.4161 0.5482 0.06 0.00 0.08 0.00 0.00 0.76 0.10
#> TCGA.M7.A724.01 5 0.1166 0.5656 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.VN.A88K.01 1 0.0863 0.8888 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.KK.A8ID.01 4 0.0504 0.8479 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CH.5790.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7231.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L5.01 4 0.2654 0.8051 0.00 0.00 0.02 0.86 0.00 0.02 0.10
#> TCGA.HC.7230.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5741.01 1 0.3358 0.4530 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.KK.A59V.01 6 0.4161 0.5482 0.06 0.00 0.08 0.00 0.00 0.76 0.10
#> TCGA.KK.A7AQ.01 2 0.4340 0.7031 0.00 0.72 0.02 0.14 0.00 0.00 0.12
#> TCGA.HC.A6AL.01 4 0.1671 0.8373 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.HC.8264.01 5 0.0504 0.5841 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HI.7171.01 6 0.2509 0.5959 0.06 0.00 0.02 0.00 0.00 0.88 0.04
#> TCGA.XK.AAJP.01 5 0.4158 0.4171 0.00 0.00 0.06 0.02 0.76 0.02 0.14
#> TCGA.HC.7212.01 6 0.3670 0.4356 0.00 0.00 0.14 0.00 0.00 0.76 0.10
#> TCGA.2A.A8VO.01 3 0.4848 0.4846 0.00 0.00 0.50 0.00 0.00 0.40 0.10
#> TCGA.HC.8259.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88P.01 3 0.3517 0.2856 0.00 0.00 0.70 0.00 0.28 0.00 0.02
#> TCGA.G9.6369.01 4 0.4708 0.7212 0.00 0.00 0.08 0.64 0.00 0.02 0.26
#> TCGA.KK.A6E1.01 7 0.3525 0.6867 0.00 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.XJ.A83F.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87B.01 5 0.3208 0.4660 0.00 0.00 0.04 0.02 0.82 0.00 0.12
#> TCGA.YL.A8SR.01 4 0.0504 0.8461 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.KK.A7AY.01 6 0.4108 0.1086 0.00 0.00 0.28 0.00 0.00 0.66 0.06
#> TCGA.2A.AAYU.01 3 0.4594 0.4581 0.00 0.00 0.64 0.00 0.00 0.14 0.22
#> TCGA.G9.7525.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 5 0.3815 -0.1980 0.00 0.00 0.02 0.00 0.62 0.00 0.36
#> TCGA.KK.A8IK.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A943.01 5 0.0504 0.5841 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.KK.A59X.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5494.01 5 0.3052 0.5710 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.HC.7213.01 3 0.3221 0.5892 0.00 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.CH.5772.01 3 0.4244 -0.1064 0.00 0.00 0.54 0.00 0.42 0.00 0.04
#> TCGA.EJ.7325.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7789.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8257.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.AAYO.01 3 0.4848 0.4846 0.00 0.00 0.50 0.00 0.00 0.40 0.10
#> TCGA.YL.A8SL.01 1 0.0863 0.8888 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.KK.A5A1.01 2 0.2016 0.8930 0.00 0.90 0.00 0.06 0.00 0.00 0.04
#> TCGA.YL.A9WL.01 6 0.3558 -0.0385 0.48 0.00 0.00 0.00 0.00 0.52 0.00
#> TCGA.HC.7080.01 2 0.3370 0.7684 0.00 0.78 0.00 0.16 0.00 0.00 0.06
#> TCGA.V1.A9O5.06 4 0.2654 0.8051 0.00 0.00 0.02 0.86 0.00 0.02 0.10
#> TCGA.KC.A7F5.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FS.01 4 0.3744 0.7851 0.00 0.00 0.02 0.78 0.08 0.00 0.12
#> TCGA.YL.A8HL.01 7 0.4214 0.7009 0.00 0.00 0.04 0.00 0.40 0.00 0.56
#> TCGA.CH.5753.01 6 0.3086 0.4393 0.00 0.00 0.16 0.00 0.00 0.80 0.04
#> TCGA.YL.A8SH.01 5 0.3244 0.5730 0.00 0.00 0.18 0.00 0.78 0.00 0.04
#> TCGA.G9.6362.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5530.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88M.01 1 0.3358 0.4530 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.EJ.7782.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E2.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7744.01 3 0.3637 0.5868 0.00 0.00 0.72 0.00 0.00 0.24 0.04
#> TCGA.XK.AAJ3.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 5 0.2722 0.5896 0.00 0.00 0.12 0.00 0.84 0.00 0.04
#> TCGA.KK.A6E0.01 4 0.2376 0.8204 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.XK.AAK1.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAIW.01 4 0.4902 0.3911 0.00 0.00 0.00 0.54 0.34 0.00 0.12
#> TCGA.TP.A8TV.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 4 0.1166 0.8422 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.EJ.8472.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 5 0.4615 0.3568 0.00 0.00 0.30 0.00 0.60 0.00 0.10
#> TCGA.WW.A8ZI.01 5 0.0504 0.5841 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.J4.A83N.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AN.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IL.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZI.01 3 0.3221 0.5892 0.00 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.YL.A8SQ.01 5 0.3517 0.4724 0.00 0.00 0.28 0.00 0.70 0.00 0.02
#> TCGA.KK.A7B4.01 3 0.3221 0.5892 0.00 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.J4.A83J.01 2 0.1664 0.9092 0.00 0.92 0.00 0.06 0.00 0.00 0.02
#> TCGA.M7.A725.01 4 0.0504 0.8461 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.J4.A67N.01 6 0.3047 0.5306 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.XJ.A83G.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A876.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IH.01 1 0.0863 0.8888 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.VP.A87K.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A632.01 7 0.3496 0.6968 0.00 0.00 0.00 0.00 0.42 0.00 0.58
#> TCGA.G9.6496.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VV.01 1 0.0000 0.9165 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5525.01 6 0.1664 0.6071 0.06 0.00 0.02 0.00 0.00 0.92 0.00
#> TCGA.KK.A59Z.01 2 0.4499 0.6758 0.00 0.70 0.02 0.16 0.00 0.00 0.12
#> TCGA.HC.7752.01 3 0.4737 0.5358 0.00 0.00 0.56 0.00 0.00 0.34 0.10
#> TCGA.EJ.A65J.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 4 0.0863 0.8454 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.V1.A9OT.01 1 0.2572 0.7159 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.KC.A7FA.01 5 0.1664 0.5996 0.00 0.00 0.06 0.00 0.92 0.00 0.02
#> TCGA.HC.7738.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.8198.01 3 0.4848 0.4846 0.00 0.00 0.50 0.00 0.00 0.40 0.10
#> TCGA.EJ.7123.01 2 0.0504 0.9540 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.2A.A8W1.01 2 0.0504 0.9540 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CH.5768.01 3 0.3047 0.5986 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.G9.6332.01 1 0.3558 0.1258 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.EJ.A46G.01 6 0.4820 0.3372 0.38 0.00 0.00 0.00 0.00 0.52 0.10
#> TCGA.EJ.7312.01 4 0.3000 0.7990 0.00 0.00 0.04 0.84 0.00 0.02 0.10
#> TCGA.V1.A8MM.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65F.01 1 0.3358 0.4530 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.G9.6498.01 4 0.2722 0.8175 0.00 0.00 0.00 0.84 0.04 0.00 0.12
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.KK.A8IA.01 3 0.1091 0.6395 0.00 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.KK.A6E4.01 1 0.5109 0.2934 0.58 0.00 0.00 0.00 0.00 0.24 0.14 0.04
#> TCGA.H9.7775.01 1 0.1804 0.8322 0.90 0.00 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.XJ.A9DX.01 1 0.2224 0.7976 0.86 0.00 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.V1.A9OF.01 5 0.1091 0.6251 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EJ.7125.01 4 0.0471 0.8247 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.YL.A9WI.01 4 0.1557 0.8229 0.00 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.QU.A6IN.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AO.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B3.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5788.01 5 0.2756 0.4596 0.00 0.00 0.26 0.00 0.74 0.00 0.00 0.00
#> TCGA.KK.A8I5.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8S9.01 4 0.2025 0.7623 0.00 0.00 0.00 0.88 0.02 0.00 0.10 0.00
#> TCGA.CH.5761.01 4 0.4896 0.6974 0.00 0.12 0.00 0.68 0.00 0.02 0.06 0.12
#> TCGA.KK.A7AZ.01 3 0.4557 0.4079 0.00 0.00 0.58 0.00 0.28 0.00 0.14 0.00
#> TCGA.HC.7819.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CL.01 5 0.1091 0.6251 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EJ.A7NF.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJA.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7821.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8474.01 6 0.5816 0.3067 0.08 0.00 0.00 0.00 0.00 0.42 0.14 0.36
#> TCGA.HC.7075.01 3 0.5178 0.1460 0.00 0.00 0.40 0.00 0.24 0.00 0.00 0.36
#> TCGA.KC.A7F6.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8213.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LZ.01 6 0.2224 0.4577 0.00 0.00 0.12 0.00 0.00 0.86 0.00 0.02
#> TCGA.CH.5765.01 6 0.5448 0.3001 0.38 0.00 0.00 0.00 0.00 0.44 0.14 0.04
#> TCGA.V1.A8WW.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A48F.01 1 0.5458 -0.2357 0.42 0.00 0.00 0.00 0.00 0.40 0.14 0.04
#> TCGA.V1.A9OQ.01 4 0.1741 0.8133 0.00 0.04 0.00 0.92 0.00 0.00 0.02 0.02
#> TCGA.YL.A8HM.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6377.01 1 0.2725 0.7566 0.82 0.00 0.00 0.00 0.00 0.00 0.14 0.04
#> TCGA.M7.A722.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6361.01 3 0.4077 0.2899 0.00 0.00 0.56 0.00 0.00 0.40 0.02 0.02
#> TCGA.EJ.5511.01 3 0.3729 0.5329 0.00 0.00 0.72 0.00 0.10 0.00 0.00 0.18
#> TCGA.ZG.A9KY.01 4 0.5922 -0.0129 0.00 0.00 0.00 0.46 0.20 0.08 0.26 0.00
#> TCGA.YJ.A8SW.01 1 0.2725 0.7566 0.82 0.00 0.00 0.00 0.00 0.00 0.14 0.04
#> TCGA.EJ.A46F.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 4 0.4529 0.7271 0.00 0.00 0.00 0.68 0.00 0.08 0.18 0.06
#> TCGA.HC.7077.01 6 0.5429 0.2560 0.04 0.00 0.00 0.00 0.00 0.46 0.14 0.36
#> TCGA.EJ.5519.01 7 0.4004 0.6349 0.00 0.00 0.00 0.04 0.46 0.00 0.50 0.00
#> TCGA.VN.A88R.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H9.A6BY.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5517.01 8 0.3504 0.7382 0.00 0.00 0.26 0.00 0.00 0.04 0.00 0.70
#> TCGA.J4.AAU2.01 8 0.3434 0.7906 0.00 0.00 0.14 0.00 0.00 0.10 0.00 0.76
#> TCGA.Y6.A9XI.01 2 0.0471 0.9565 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CH.5737.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6338.01 4 0.4394 0.7444 0.00 0.00 0.00 0.70 0.00 0.08 0.16 0.06
#> TCGA.2A.AAYF.01 8 0.3198 0.5193 0.00 0.00 0.02 0.00 0.00 0.26 0.00 0.72
#> TCGA.M7.A71Z.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 3 0.0471 0.6469 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CH.5750.01 6 0.5947 0.3737 0.34 0.00 0.00 0.00 0.00 0.42 0.14 0.10
#> TCGA.ZG.A9ND.01 4 0.0941 0.8210 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.EJ.8469.01 6 0.2859 0.4413 0.00 0.00 0.14 0.00 0.00 0.82 0.02 0.02
#> TCGA.EJ.7315.01 3 0.4813 -0.1574 0.00 0.00 0.44 0.00 0.14 0.00 0.42 0.00
#> TCGA.YL.A8SP.01 6 0.3637 0.5095 0.26 0.00 0.00 0.00 0.00 0.70 0.02 0.02
#> TCGA.CH.5791.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IF.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65D.01 6 0.3262 0.4820 0.04 0.00 0.10 0.00 0.00 0.82 0.02 0.02
#> TCGA.HC.A4ZV.01 4 0.2591 0.8214 0.00 0.00 0.00 0.86 0.00 0.02 0.08 0.04
#> TCGA.KK.A7AP.01 7 0.3658 0.7892 0.00 0.00 0.00 0.02 0.40 0.00 0.58 0.00
#> TCGA.VP.A87D.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8II.01 1 0.1341 0.8475 0.92 0.00 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.J9.A52B.01 6 0.4371 0.4133 0.00 0.00 0.02 0.00 0.00 0.68 0.14 0.16
#> TCGA.CH.5767.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5752.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WK.01 3 0.4302 0.4234 0.00 0.00 0.56 0.00 0.36 0.00 0.00 0.08
#> TCGA.HC.7078.01 8 0.3746 0.6434 0.00 0.00 0.32 0.00 0.00 0.04 0.00 0.64
#> TCGA.FC.A5OB.01 8 0.3434 0.7906 0.00 0.00 0.14 0.00 0.00 0.10 0.00 0.76
#> TCGA.J4.AATZ.01 4 0.4720 0.7195 0.00 0.10 0.00 0.70 0.00 0.02 0.06 0.12
#> TCGA.V1.A9OL.01 7 0.5033 0.5366 0.00 0.00 0.00 0.22 0.30 0.00 0.48 0.00
#> TCGA.J9.A52D.01 8 0.3594 0.7121 0.00 0.00 0.28 0.00 0.00 0.04 0.00 0.68
#> TCGA.EJ.7788.01 8 0.3263 0.7612 0.00 0.00 0.10 0.00 0.00 0.12 0.00 0.78
#> TCGA.J9.A8CN.01 5 0.2569 0.5528 0.00 0.00 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.ZG.A9L1.01 3 0.2623 0.6216 0.00 0.00 0.84 0.00 0.00 0.06 0.00 0.10
#> TCGA.VP.A875.01 3 0.2224 0.5980 0.00 0.00 0.86 0.00 0.00 0.00 0.12 0.02
#> TCGA.KK.A59Y.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6362.11 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A631.01 8 0.5080 -0.1029 0.00 0.00 0.02 0.00 0.00 0.40 0.12 0.46
#> TCGA.YL.A8SA.01 6 0.5448 0.3001 0.38 0.00 0.00 0.00 0.00 0.44 0.14 0.04
#> TCGA.KC.A7FD.01 3 0.4433 0.4436 0.00 0.00 0.56 0.00 0.34 0.00 0.00 0.10
#> TCGA.EJ.7784.01 1 0.5661 -0.2843 0.40 0.00 0.00 0.00 0.00 0.40 0.14 0.06
#> TCGA.J4.A83I.01 3 0.4040 0.3204 0.00 0.00 0.58 0.00 0.00 0.38 0.02 0.02
#> TCGA.G9.6373.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6371.01 5 0.2856 0.3161 0.00 0.00 0.02 0.00 0.78 0.00 0.20 0.00
#> TCGA.XQ.A8TA.01 3 0.1408 0.6379 0.00 0.00 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.ZG.A9L9.01 6 0.5089 0.0908 0.00 0.00 0.02 0.00 0.00 0.44 0.12 0.42
#> TCGA.M7.A724.01 5 0.2725 0.5115 0.00 0.00 0.00 0.00 0.82 0.04 0.14 0.00
#> TCGA.VN.A88K.01 1 0.2725 0.7566 0.82 0.00 0.00 0.00 0.00 0.00 0.14 0.04
#> TCGA.KK.A8ID.01 4 0.0471 0.8257 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CH.5790.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7231.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L5.01 4 0.4119 0.7788 0.00 0.02 0.00 0.74 0.00 0.02 0.08 0.14
#> TCGA.HC.7230.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5741.01 1 0.5448 -0.1760 0.44 0.00 0.00 0.00 0.00 0.38 0.14 0.04
#> TCGA.KK.A59V.01 6 0.5089 0.0908 0.00 0.00 0.02 0.00 0.00 0.44 0.12 0.42
#> TCGA.KK.A7AQ.01 2 0.4339 0.7197 0.00 0.74 0.00 0.08 0.00 0.02 0.06 0.10
#> TCGA.HC.A6AL.01 4 0.0471 0.8178 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HC.8264.01 5 0.2569 0.5528 0.00 0.00 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.HI.7171.01 6 0.2547 0.4515 0.00 0.00 0.12 0.00 0.00 0.84 0.00 0.04
#> TCGA.XK.AAJP.01 5 0.4487 0.3166 0.00 0.00 0.00 0.00 0.62 0.08 0.28 0.02
#> TCGA.HC.7212.01 6 0.3995 0.1240 0.00 0.00 0.36 0.00 0.00 0.60 0.02 0.02
#> TCGA.2A.A8VO.01 8 0.3385 0.7872 0.00 0.00 0.16 0.00 0.00 0.08 0.00 0.76
#> TCGA.HC.8259.01 1 0.2224 0.7973 0.86 0.00 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.VN.A88P.01 3 0.4302 0.4234 0.00 0.00 0.56 0.00 0.36 0.00 0.00 0.08
#> TCGA.G9.6369.01 4 0.4937 0.7071 0.00 0.00 0.00 0.64 0.00 0.10 0.18 0.08
#> TCGA.KK.A6E1.01 7 0.4518 0.8060 0.00 0.00 0.06 0.02 0.36 0.00 0.56 0.00
#> TCGA.XJ.A83F.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87B.01 5 0.4406 0.3387 0.00 0.00 0.00 0.00 0.64 0.08 0.26 0.02
#> TCGA.YL.A8SR.01 4 0.2348 0.8253 0.00 0.00 0.00 0.88 0.00 0.02 0.04 0.06
#> TCGA.KK.A7AY.01 6 0.4125 -0.1096 0.00 0.00 0.44 0.00 0.00 0.52 0.02 0.02
#> TCGA.2A.AAYU.01 3 0.0000 0.6509 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7525.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 7 0.3299 0.7482 0.00 0.00 0.00 0.00 0.44 0.00 0.56 0.00
#> TCGA.KK.A8IK.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A943.01 5 0.2569 0.5528 0.00 0.00 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.KK.A59X.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5494.01 5 0.1091 0.6251 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.HC.7213.01 3 0.2818 0.6067 0.00 0.00 0.82 0.00 0.00 0.06 0.00 0.12
#> TCGA.CH.5772.01 3 0.3272 0.3317 0.00 0.00 0.58 0.00 0.42 0.00 0.00 0.00
#> TCGA.EJ.7325.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7789.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8257.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.AAYO.01 8 0.3434 0.7906 0.00 0.00 0.14 0.00 0.00 0.10 0.00 0.76
#> TCGA.YL.A8SL.01 1 0.3444 0.7030 0.78 0.00 0.00 0.00 0.00 0.06 0.14 0.02
#> TCGA.KK.A5A1.01 2 0.2265 0.8730 0.00 0.88 0.00 0.02 0.00 0.00 0.02 0.08
#> TCGA.YL.A9WL.01 6 0.2981 0.5322 0.22 0.00 0.00 0.00 0.00 0.76 0.02 0.00
#> TCGA.HC.7080.01 2 0.3102 0.8094 0.00 0.82 0.00 0.08 0.00 0.00 0.02 0.08
#> TCGA.V1.A9O5.06 4 0.3675 0.7877 0.00 0.00 0.00 0.76 0.00 0.02 0.08 0.14
#> TCGA.KC.A7F5.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FS.01 4 0.2484 0.7473 0.00 0.00 0.00 0.86 0.02 0.02 0.10 0.00
#> TCGA.YL.A8HL.01 7 0.4628 0.7578 0.00 0.00 0.12 0.00 0.36 0.00 0.52 0.00
#> TCGA.CH.5753.01 6 0.3995 0.1115 0.00 0.00 0.36 0.00 0.00 0.60 0.02 0.02
#> TCGA.YL.A8SH.01 5 0.1091 0.6251 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.G9.6362.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5530.01 1 0.1804 0.8322 0.90 0.00 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.VN.A88M.01 1 0.5458 -0.2351 0.42 0.00 0.00 0.00 0.00 0.40 0.14 0.04
#> TCGA.EJ.7782.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E2.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7744.01 3 0.1887 0.6337 0.00 0.00 0.90 0.00 0.00 0.06 0.00 0.04
#> TCGA.XK.AAJ3.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 5 0.1275 0.6090 0.00 0.00 0.04 0.00 0.94 0.00 0.02 0.00
#> TCGA.KK.A6E0.01 4 0.2591 0.8214 0.00 0.00 0.00 0.86 0.00 0.02 0.08 0.04
#> TCGA.XK.AAK1.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAIW.01 4 0.5069 0.1409 0.00 0.00 0.00 0.56 0.24 0.02 0.18 0.00
#> TCGA.TP.A8TV.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 4 0.1741 0.8133 0.00 0.04 0.00 0.92 0.00 0.00 0.02 0.02
#> TCGA.EJ.8472.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 5 0.4622 0.2606 0.00 0.00 0.30 0.00 0.56 0.00 0.14 0.00
#> TCGA.WW.A8ZI.01 5 0.2569 0.5528 0.00 0.00 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.J4.A83N.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AN.01 1 0.0808 0.8754 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.QU.A6IL.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZI.01 3 0.2623 0.6216 0.00 0.00 0.84 0.00 0.00 0.06 0.00 0.10
#> TCGA.YL.A8SQ.01 5 0.3015 0.3689 0.00 0.00 0.32 0.00 0.68 0.00 0.00 0.00
#> TCGA.KK.A7B4.01 3 0.2623 0.6216 0.00 0.00 0.84 0.00 0.00 0.06 0.00 0.10
#> TCGA.J4.A83J.01 2 0.0471 0.9565 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.M7.A725.01 4 0.2071 0.8257 0.00 0.00 0.00 0.90 0.00 0.02 0.04 0.04
#> TCGA.J4.A67N.01 6 0.1947 0.5268 0.14 0.00 0.00 0.00 0.00 0.86 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A876.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.1091 0.8617 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.KK.A8IH.01 1 0.3178 0.7324 0.80 0.00 0.00 0.00 0.00 0.02 0.14 0.04
#> TCGA.VP.A87K.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A632.01 7 0.4717 0.7996 0.00 0.00 0.08 0.02 0.36 0.00 0.54 0.00
#> TCGA.G9.6496.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VV.01 1 0.0000 0.8984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5525.01 6 0.2680 0.4624 0.00 0.00 0.12 0.00 0.00 0.84 0.02 0.02
#> TCGA.KK.A59Z.01 2 0.4940 0.6341 0.00 0.68 0.00 0.10 0.00 0.02 0.08 0.12
#> TCGA.HC.7752.01 8 0.3504 0.7382 0.00 0.00 0.26 0.00 0.00 0.04 0.00 0.70
#> TCGA.EJ.A65J.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 4 0.0471 0.8247 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.V1.A9OT.01 1 0.5539 0.0437 0.50 0.00 0.00 0.00 0.00 0.30 0.14 0.06
#> TCGA.KC.A7FA.01 5 0.2114 0.5633 0.00 0.00 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.HC.7738.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.8198.01 8 0.3757 0.7393 0.00 0.00 0.26 0.00 0.00 0.06 0.00 0.68
#> TCGA.EJ.7123.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8W1.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5768.01 3 0.2623 0.6216 0.00 0.00 0.84 0.00 0.00 0.06 0.00 0.10
#> TCGA.G9.6332.01 6 0.3594 0.5090 0.28 0.00 0.00 0.00 0.00 0.68 0.04 0.00
#> TCGA.EJ.A46G.01 6 0.5816 0.3067 0.08 0.00 0.00 0.00 0.00 0.42 0.14 0.36
#> TCGA.EJ.7312.01 4 0.4022 0.7871 0.00 0.00 0.00 0.74 0.00 0.04 0.10 0.12
#> TCGA.V1.A8MM.01 2 0.0000 0.9709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65F.01 6 0.5458 0.2432 0.40 0.00 0.00 0.00 0.00 0.42 0.14 0.04
#> TCGA.G9.6498.01 4 0.1557 0.7889 0.00 0.00 0.00 0.92 0.02 0.00 0.06 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-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 78 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.974 0.989 0.4953 0.502 0.502
#> 3 3 0.970 0.966 0.974 0.3305 0.706 0.483
#> 4 4 0.771 0.812 0.868 0.1175 0.876 0.654
#> 5 5 0.769 0.742 0.830 0.0668 0.989 0.958
#> 6 6 0.715 0.526 0.718 0.0379 0.930 0.744
#> 7 7 0.732 0.606 0.752 0.0247 0.913 0.630
#> 8 8 0.745 0.529 0.681 0.0226 0.934 0.625
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.KK.A6E4.01 1 0.000 0.974 1.00 0.00
#> TCGA.H9.7775.01 2 0.000 0.999 0.00 1.00
#> TCGA.XJ.A9DX.01 1 0.000 0.974 1.00 0.00
#> TCGA.QU.A6IN.01 2 0.000 0.999 0.00 1.00
#> TCGA.KK.A7B3.01 1 0.000 0.974 1.00 0.00
#> TCGA.KK.A8I5.01 1 0.000 0.974 1.00 0.00
#> TCGA.HC.7819.01 1 0.000 0.974 1.00 0.00
#> TCGA.EJ.A7NF.01 2 0.000 0.999 0.00 1.00
#> TCGA.HC.7821.01 1 0.000 0.974 1.00 0.00
#> TCGA.EJ.8474.01 1 0.000 0.974 1.00 0.00
#> TCGA.KC.A7F6.01 1 0.000 0.974 1.00 0.00
#> TCGA.V1.A8WS.01 1 0.000 0.974 1.00 0.00
#> TCGA.HC.8213.01 2 0.000 0.999 0.00 1.00
#> TCGA.ZG.A9LZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.CH.5765.01 1 0.000 0.974 1.00 0.00
#> TCGA.V1.A8WW.01 2 0.000 0.999 0.00 1.00
#> TCGA.HC.A48F.01 2 0.000 0.999 0.00 1.00
#> TCGA.G9.6377.01 2 0.000 0.999 0.00 1.00
#> TCGA.YJ.A8SW.01 1 0.000 0.974 1.00 0.00
#> TCGA.EJ.A46F.01 1 0.000 0.974 1.00 0.00
#> TCGA.MG.AAMC.01 1 0.529 0.861 0.88 0.12
#> TCGA.HC.7077.01 1 0.000 0.974 1.00 0.00
#> TCGA.H9.A6BY.01 2 0.000 0.999 0.00 1.00
#> TCGA.2A.AAYF.01 2 0.000 0.999 0.00 1.00
#> TCGA.M7.A71Z.01 1 0.000 0.974 1.00 0.00
#> TCGA.CH.5750.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.8469.01 1 0.000 0.974 1.00 0.00
#> TCGA.YL.A8SP.01 2 0.000 0.999 0.00 1.00
#> TCGA.CH.5791.01 2 0.000 0.999 0.00 1.00
#> TCGA.HC.A76X.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.A65D.01 2 0.000 0.999 0.00 1.00
#> TCGA.VP.A87D.01 2 0.000 0.999 0.00 1.00
#> TCGA.KK.A8II.01 1 0.827 0.665 0.74 0.26
#> TCGA.J9.A52B.01 2 0.000 0.999 0.00 1.00
#> TCGA.CH.5752.01 1 0.000 0.974 1.00 0.00
#> TCGA.KK.A59Y.01 2 0.000 0.999 0.00 1.00
#> TCGA.G9.6362.11 2 0.000 0.999 0.00 1.00
#> TCGA.HC.A631.01 1 0.000 0.974 1.00 0.00
#> TCGA.YL.A8SA.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.7784.01 1 0.000 0.974 1.00 0.00
#> TCGA.G9.6373.01 2 0.000 0.999 0.00 1.00
#> TCGA.ZG.A9L9.01 2 0.000 0.999 0.00 1.00
#> TCGA.VN.A88K.01 2 0.000 0.999 0.00 1.00
#> TCGA.CH.5790.01 2 0.000 0.999 0.00 1.00
#> TCGA.HC.7231.01 1 0.402 0.903 0.92 0.08
#> TCGA.HC.7230.01 2 0.000 0.999 0.00 1.00
#> TCGA.CH.5741.01 2 0.000 0.999 0.00 1.00
#> TCGA.KK.A59V.01 1 0.000 0.974 1.00 0.00
#> TCGA.HI.7171.01 1 0.000 0.974 1.00 0.00
#> TCGA.HC.8259.01 2 0.000 0.999 0.00 1.00
#> TCGA.XJ.A83F.01 2 0.000 0.999 0.00 1.00
#> TCGA.G9.A9S4.01 1 0.000 0.974 1.00 0.00
#> TCGA.G9.7525.01 2 0.000 0.999 0.00 1.00
#> TCGA.KK.A7AU.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.7325.01 1 0.000 0.974 1.00 0.00
#> TCGA.HC.8257.01 1 0.000 0.974 1.00 0.00
#> TCGA.YL.A8SL.01 1 0.000 0.974 1.00 0.00
#> TCGA.YL.A9WL.01 2 0.000 0.999 0.00 1.00
#> TCGA.G9.6362.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.5530.01 2 0.000 0.999 0.00 1.00
#> TCGA.VN.A88M.01 2 0.000 0.999 0.00 1.00
#> TCGA.KK.A6E2.01 1 0.000 0.974 1.00 0.00
#> TCGA.J4.A6M7.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.8472.01 1 0.000 0.974 1.00 0.00
#> TCGA.YL.A9WH.01 1 0.000 0.974 1.00 0.00
#> TCGA.J4.A83N.01 2 0.000 0.999 0.00 1.00
#> TCGA.HC.A6AN.01 1 0.000 0.974 1.00 0.00
#> TCGA.J4.A67N.01 2 0.000 0.999 0.00 1.00
#> TCGA.VP.A876.01 2 0.000 0.999 0.00 1.00
#> TCGA.CH.5739.01 1 0.958 0.414 0.62 0.38
#> TCGA.KK.A8IH.01 2 0.000 0.999 0.00 1.00
#> TCGA.VP.A87K.01 2 0.000 0.999 0.00 1.00
#> TCGA.2A.A8VV.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.5525.01 2 0.000 0.999 0.00 1.00
#> TCGA.V1.A9OT.01 1 0.000 0.974 1.00 0.00
#> TCGA.G9.6332.01 2 0.000 0.999 0.00 1.00
#> TCGA.EJ.A46G.01 2 0.242 0.957 0.04 0.96
#> TCGA.EJ.A65F.01 1 0.000 0.974 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.KK.A6E4.01 1 0.153 0.961 0.96 0.04 0.00
#> TCGA.H9.7775.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.XJ.A9DX.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.QU.A6IN.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.KK.A7B3.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.KK.A8I5.01 1 0.254 0.926 0.92 0.08 0.00
#> TCGA.HC.7819.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.EJ.A7NF.01 2 0.207 0.951 0.00 0.94 0.06
#> TCGA.HC.7821.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.EJ.8474.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.KC.A7F6.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.V1.A8WS.01 2 0.254 0.911 0.08 0.92 0.00
#> TCGA.HC.8213.01 3 0.153 0.955 0.00 0.04 0.96
#> TCGA.ZG.A9LZ.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.CH.5765.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.V1.A8WW.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.HC.A48F.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.G9.6377.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.YJ.A8SW.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.EJ.A46F.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.MG.AAMC.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.HC.7077.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.H9.A6BY.01 2 0.207 0.951 0.00 0.94 0.06
#> TCGA.2A.AAYF.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.M7.A71Z.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.CH.5750.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.EJ.8469.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.YL.A8SP.01 2 0.207 0.951 0.00 0.94 0.06
#> TCGA.CH.5791.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.HC.A76X.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.EJ.A65D.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.VP.A87D.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.KK.A8II.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.J9.A52B.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.CH.5752.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.KK.A59Y.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.G9.6362.11 2 0.296 0.935 0.00 0.90 0.10
#> TCGA.HC.A631.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.YL.A8SA.01 2 0.556 0.662 0.00 0.70 0.30
#> TCGA.EJ.7784.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.G9.6373.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.ZG.A9L9.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.VN.A88K.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.CH.5790.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.HC.7231.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.HC.7230.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.CH.5741.01 3 0.207 0.931 0.00 0.06 0.94
#> TCGA.KK.A59V.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HI.7171.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.HC.8259.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.XJ.A83F.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.G9.A9S4.01 2 0.153 0.933 0.04 0.96 0.00
#> TCGA.G9.7525.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.KK.A7AU.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.EJ.7325.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.HC.8257.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.YL.A8SL.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.YL.A9WL.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.G9.6362.01 2 0.296 0.935 0.00 0.90 0.10
#> TCGA.EJ.5530.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.VN.A88M.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.KK.A6E2.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.J4.A6M7.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.EJ.8472.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.J4.A83N.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.HC.A6AN.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.J4.A67N.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.VP.A876.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.CH.5739.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.KK.A8IH.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.VP.A87K.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.2A.A8VV.01 3 0.000 0.994 0.00 0.00 1.00
#> TCGA.EJ.5525.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.V1.A9OT.01 1 0.254 0.926 0.92 0.08 0.00
#> TCGA.G9.6332.01 2 0.254 0.949 0.00 0.92 0.08
#> TCGA.EJ.A46G.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.EJ.A65F.01 1 0.000 0.992 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.KK.A6E4.01 1 0.5489 0.6601 0.70 0.06 0.00 0.24
#> TCGA.H9.7775.01 2 0.4790 0.7664 0.00 0.62 0.00 0.38
#> TCGA.XJ.A9DX.01 1 0.2921 0.8650 0.86 0.14 0.00 0.00
#> TCGA.QU.A6IN.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.KK.A7B3.01 1 0.2011 0.8897 0.92 0.08 0.00 0.00
#> TCGA.KK.A8I5.01 4 0.5392 0.3993 0.28 0.04 0.00 0.68
#> TCGA.HC.7819.01 1 0.0707 0.9071 0.98 0.02 0.00 0.00
#> TCGA.EJ.A7NF.01 4 0.5767 0.1881 0.00 0.28 0.06 0.66
#> TCGA.HC.7821.01 1 0.0000 0.9075 1.00 0.00 0.00 0.00
#> TCGA.EJ.8474.01 1 0.2011 0.8897 0.92 0.08 0.00 0.00
#> TCGA.KC.A7F6.01 1 0.0707 0.9071 0.98 0.02 0.00 0.00
#> TCGA.V1.A8WS.01 2 0.3972 0.6262 0.08 0.84 0.00 0.08
#> TCGA.HC.8213.01 3 0.4790 0.3808 0.00 0.00 0.62 0.38
#> TCGA.ZG.A9LZ.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.CH.5765.01 1 0.2921 0.8786 0.86 0.14 0.00 0.00
#> TCGA.V1.A8WW.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.HC.A48F.01 3 0.0707 0.9354 0.00 0.02 0.98 0.00
#> TCGA.G9.6377.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.YJ.A8SW.01 1 0.2921 0.8650 0.86 0.14 0.00 0.00
#> TCGA.EJ.A46F.01 1 0.2921 0.8786 0.86 0.14 0.00 0.00
#> TCGA.MG.AAMC.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.HC.7077.01 1 0.2011 0.8897 0.92 0.08 0.00 0.00
#> TCGA.H9.A6BY.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.2A.AAYF.01 3 0.0707 0.9354 0.00 0.02 0.98 0.00
#> TCGA.M7.A71Z.01 1 0.2921 0.8786 0.86 0.14 0.00 0.00
#> TCGA.CH.5750.01 3 0.0707 0.9354 0.00 0.02 0.98 0.00
#> TCGA.EJ.8469.01 1 0.2921 0.8786 0.86 0.14 0.00 0.00
#> TCGA.YL.A8SP.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.CH.5791.01 2 0.5512 0.8589 0.00 0.66 0.04 0.30
#> TCGA.HC.A76X.01 2 0.6074 0.8068 0.00 0.60 0.06 0.34
#> TCGA.EJ.A65D.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.VP.A87D.01 3 0.0707 0.9354 0.00 0.02 0.98 0.00
#> TCGA.KK.A8II.01 2 0.4977 0.6206 0.00 0.54 0.00 0.46
#> TCGA.J9.A52B.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.CH.5752.01 1 0.2921 0.8786 0.86 0.14 0.00 0.00
#> TCGA.KK.A59Y.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.G9.6362.11 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.HC.A631.01 1 0.2011 0.8897 0.92 0.08 0.00 0.00
#> TCGA.YL.A8SA.01 3 0.7550 -0.1807 0.00 0.22 0.48 0.30
#> TCGA.EJ.7784.01 1 0.2921 0.8786 0.86 0.14 0.00 0.00
#> TCGA.G9.6373.01 3 0.0707 0.9354 0.00 0.02 0.98 0.00
#> TCGA.ZG.A9L9.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.VN.A88K.01 3 0.0707 0.9354 0.00 0.02 0.98 0.00
#> TCGA.CH.5790.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.HC.7231.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.HC.7230.01 2 0.5883 0.8500 0.00 0.64 0.06 0.30
#> TCGA.CH.5741.01 2 0.5392 0.5622 0.00 0.68 0.28 0.04
#> TCGA.KK.A59V.01 1 0.0000 0.9075 1.00 0.00 0.00 0.00
#> TCGA.HI.7171.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.HC.8259.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.XJ.A83F.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.G9.A9S4.01 2 0.3821 0.6830 0.04 0.84 0.00 0.12
#> TCGA.G9.7525.01 2 0.6299 0.6643 0.00 0.52 0.06 0.42
#> TCGA.KK.A7AU.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.EJ.7325.01 4 0.3400 0.5969 0.00 0.18 0.00 0.82
#> TCGA.HC.8257.01 1 0.0000 0.9075 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SL.01 1 0.0000 0.9075 1.00 0.00 0.00 0.00
#> TCGA.YL.A9WL.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.G9.6362.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.EJ.5530.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.VN.A88M.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.KK.A6E2.01 1 0.2647 0.8850 0.88 0.12 0.00 0.00
#> TCGA.J4.A6M7.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.EJ.8472.01 1 0.2921 0.8786 0.86 0.14 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.2011 0.8897 0.92 0.08 0.00 0.00
#> TCGA.J4.A83N.01 4 0.6074 -0.0951 0.00 0.34 0.06 0.60
#> TCGA.HC.A6AN.01 1 0.0000 0.9075 1.00 0.00 0.00 0.00
#> TCGA.J4.A67N.01 3 0.0707 0.9354 0.00 0.02 0.98 0.00
#> TCGA.VP.A876.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.CH.5739.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.KK.A8IH.01 4 0.0000 0.8401 0.00 0.00 0.00 1.00
#> TCGA.VP.A87K.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.2A.A8VV.01 3 0.0000 0.9381 0.00 0.00 1.00 0.00
#> TCGA.EJ.5525.01 2 0.5256 0.8834 0.00 0.70 0.04 0.26
#> TCGA.V1.A9OT.01 1 0.5767 0.5953 0.66 0.06 0.00 0.28
#> TCGA.G9.6332.01 2 0.5883 0.8500 0.00 0.64 0.06 0.30
#> TCGA.EJ.A46G.01 4 0.3172 0.7391 0.00 0.16 0.00 0.84
#> TCGA.EJ.A65F.01 1 0.0707 0.9071 0.98 0.02 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.KK.A6E4.01 1 0.4096 0.51478 0.76 0.04 0.00 0.20 0.00
#> TCGA.H9.7775.01 5 0.5759 0.69287 0.00 0.20 0.00 0.18 0.62
#> TCGA.XJ.A9DX.01 1 0.1410 0.72237 0.94 0.06 0.00 0.00 0.00
#> TCGA.QU.A6IN.01 4 0.0000 0.80654 0.00 0.00 0.00 1.00 0.00
#> TCGA.KK.A7B3.01 1 0.0000 0.75454 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8I5.01 4 0.3521 0.69424 0.14 0.04 0.00 0.82 0.00
#> TCGA.HC.7819.01 1 0.3895 0.82417 0.68 0.32 0.00 0.00 0.00
#> TCGA.EJ.A7NF.01 4 0.5659 0.37487 0.00 0.10 0.00 0.58 0.32
#> TCGA.HC.7821.01 1 0.3561 0.82717 0.74 0.26 0.00 0.00 0.00
#> TCGA.EJ.8474.01 1 0.0000 0.75454 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F6.01 1 0.3796 0.82705 0.70 0.30 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 5 0.5173 0.30838 0.04 0.46 0.00 0.00 0.50
#> TCGA.HC.8213.01 4 0.5607 0.29047 0.00 0.08 0.38 0.54 0.00
#> TCGA.ZG.A9LZ.01 4 0.1732 0.78581 0.00 0.08 0.00 0.92 0.00
#> TCGA.CH.5765.01 1 0.4182 0.80271 0.60 0.40 0.00 0.00 0.00
#> TCGA.V1.A8WW.01 4 0.1043 0.79364 0.00 0.04 0.00 0.96 0.00
#> TCGA.HC.A48F.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.6377.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.YJ.A8SW.01 1 0.1410 0.72237 0.94 0.06 0.00 0.00 0.00
#> TCGA.EJ.A46F.01 1 0.4798 0.76804 0.54 0.44 0.00 0.00 0.02
#> TCGA.MG.AAMC.01 4 0.0609 0.80501 0.00 0.02 0.00 0.98 0.00
#> TCGA.HC.7077.01 1 0.0000 0.75454 1.00 0.00 0.00 0.00 0.00
#> TCGA.H9.A6BY.01 5 0.2331 0.73774 0.00 0.02 0.00 0.08 0.90
#> TCGA.2A.AAYF.01 3 0.1732 0.89753 0.00 0.08 0.92 0.00 0.00
#> TCGA.M7.A71Z.01 1 0.4227 0.79420 0.58 0.42 0.00 0.00 0.00
#> TCGA.CH.5750.01 3 0.2280 0.87169 0.00 0.12 0.88 0.00 0.00
#> TCGA.EJ.8469.01 1 0.5157 0.74793 0.52 0.44 0.00 0.00 0.04
#> TCGA.YL.A8SP.01 5 0.4426 0.75241 0.00 0.22 0.02 0.02 0.74
#> TCGA.CH.5791.01 5 0.2616 0.73450 0.00 0.00 0.02 0.10 0.88
#> TCGA.HC.A76X.01 5 0.5156 0.64236 0.00 0.06 0.02 0.22 0.70
#> TCGA.EJ.A65D.01 5 0.4426 0.75241 0.00 0.22 0.02 0.02 0.74
#> TCGA.VP.A87D.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.KK.A8II.01 5 0.6200 0.43538 0.00 0.16 0.00 0.32 0.52
#> TCGA.J9.A52B.01 5 0.4426 0.75241 0.00 0.22 0.02 0.02 0.74
#> TCGA.CH.5752.01 1 0.4798 0.76804 0.54 0.44 0.00 0.00 0.02
#> TCGA.KK.A59Y.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.6362.11 5 0.4268 0.74470 0.00 0.20 0.02 0.02 0.76
#> TCGA.HC.A631.01 1 0.0000 0.75454 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SA.01 3 0.6903 -0.17486 0.00 0.04 0.44 0.12 0.40
#> TCGA.EJ.7784.01 1 0.5447 0.73009 0.50 0.44 0.00 0.00 0.06
#> TCGA.G9.6373.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZG.A9L9.01 4 0.1043 0.80124 0.00 0.04 0.00 0.96 0.00
#> TCGA.VN.A88K.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.CH.5790.01 3 0.1043 0.92763 0.00 0.04 0.96 0.00 0.00
#> TCGA.HC.7231.01 4 0.0000 0.80654 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.7230.01 5 0.3903 0.70289 0.00 0.02 0.02 0.16 0.80
#> TCGA.CH.5741.01 5 0.5050 0.68067 0.00 0.12 0.18 0.00 0.70
#> TCGA.KK.A59V.01 1 0.3561 0.82717 0.74 0.26 0.00 0.00 0.00
#> TCGA.HI.7171.01 4 0.1410 0.79555 0.00 0.06 0.00 0.94 0.00
#> TCGA.HC.8259.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.XJ.A83F.01 3 0.1216 0.92454 0.00 0.02 0.96 0.02 0.00
#> TCGA.G9.A9S4.01 5 0.4540 0.51237 0.02 0.34 0.00 0.00 0.64
#> TCGA.G9.7525.01 5 0.6124 0.41630 0.00 0.10 0.02 0.30 0.58
#> TCGA.KK.A7AU.01 5 0.1410 0.75206 0.00 0.06 0.00 0.00 0.94
#> TCGA.EJ.7325.01 4 0.5136 0.53111 0.00 0.08 0.00 0.66 0.26
#> TCGA.HC.8257.01 1 0.3796 0.82705 0.70 0.30 0.00 0.00 0.00
#> TCGA.YL.A8SL.01 1 0.3561 0.82717 0.74 0.26 0.00 0.00 0.00
#> TCGA.YL.A9WL.01 5 0.3977 0.75667 0.00 0.10 0.02 0.06 0.82
#> TCGA.G9.6362.01 5 0.4268 0.74470 0.00 0.20 0.02 0.02 0.76
#> TCGA.EJ.5530.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.VN.A88M.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.KK.A6E2.01 1 0.4126 0.80938 0.62 0.38 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.8472.01 1 0.4126 0.80938 0.62 0.38 0.00 0.00 0.00
#> TCGA.YL.A9WH.01 1 0.0000 0.75454 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A83N.01 4 0.6205 -0.00836 0.00 0.08 0.02 0.46 0.44
#> TCGA.HC.A6AN.01 1 0.3561 0.82717 0.74 0.26 0.00 0.00 0.00
#> TCGA.J4.A67N.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.VP.A876.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.CH.5739.01 4 0.0609 0.80551 0.00 0.02 0.00 0.98 0.00
#> TCGA.KK.A8IH.01 4 0.0000 0.80654 0.00 0.00 0.00 1.00 0.00
#> TCGA.VP.A87K.01 5 0.3903 0.75579 0.00 0.16 0.02 0.02 0.80
#> TCGA.2A.A8VV.01 3 0.0000 0.95023 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5525.01 5 0.4268 0.75676 0.00 0.20 0.02 0.02 0.76
#> TCGA.V1.A9OT.01 1 0.4728 0.42625 0.70 0.06 0.00 0.24 0.00
#> TCGA.G9.6332.01 5 0.4653 0.70367 0.00 0.06 0.02 0.16 0.76
#> TCGA.EJ.A46G.01 4 0.5083 0.65119 0.00 0.16 0.00 0.70 0.14
#> TCGA.EJ.A65F.01 1 0.3796 0.82705 0.70 0.30 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.KK.A6E4.01 6 0.5882 0.9121 0.38 0.00 0.00 0.20 0.00 0.42
#> TCGA.H9.7775.01 5 0.6167 0.4897 0.00 0.26 0.00 0.16 0.54 0.04
#> TCGA.XJ.A9DX.01 1 0.4938 -0.1735 0.58 0.08 0.00 0.00 0.00 0.34
#> TCGA.QU.A6IN.01 4 0.0000 0.8346 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.KK.A7B3.01 1 0.3797 -0.2120 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.KK.A8I5.01 4 0.3928 0.5720 0.08 0.00 0.00 0.76 0.00 0.16
#> TCGA.HC.7819.01 1 0.1480 0.5757 0.94 0.04 0.00 0.00 0.00 0.02
#> TCGA.EJ.A7NF.01 5 0.6862 0.0579 0.00 0.08 0.00 0.36 0.40 0.16
#> TCGA.HC.7821.01 1 0.1267 0.5427 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EJ.8474.01 1 0.4246 -0.1970 0.58 0.02 0.00 0.00 0.00 0.40
#> TCGA.KC.A7F6.01 1 0.1092 0.5671 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.V1.A8WS.01 2 0.7351 0.6526 0.24 0.44 0.00 0.02 0.22 0.08
#> TCGA.HC.8213.01 3 0.6900 0.0846 0.00 0.06 0.38 0.34 0.00 0.22
#> TCGA.ZG.A9LZ.01 4 0.2403 0.8047 0.00 0.04 0.00 0.90 0.02 0.04
#> TCGA.CH.5765.01 1 0.2474 0.5688 0.88 0.08 0.00 0.00 0.00 0.04
#> TCGA.V1.A8WW.01 4 0.1635 0.8173 0.00 0.02 0.00 0.94 0.02 0.02
#> TCGA.HC.A48F.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6377.01 3 0.0937 0.9038 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.YJ.A8SW.01 1 0.4938 -0.1735 0.58 0.08 0.00 0.00 0.00 0.34
#> TCGA.EJ.A46F.01 1 0.4798 0.3042 0.62 0.30 0.00 0.00 0.00 0.08
#> TCGA.MG.AAMC.01 4 0.1267 0.8248 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.HC.7077.01 1 0.3797 -0.2120 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.H9.A6BY.01 5 0.4462 0.1864 0.00 0.28 0.00 0.06 0.66 0.00
#> TCGA.2A.AAYF.01 3 0.4121 0.7303 0.00 0.06 0.72 0.00 0.00 0.22
#> TCGA.M7.A71Z.01 1 0.3544 0.5363 0.80 0.12 0.00 0.00 0.00 0.08
#> TCGA.CH.5750.01 3 0.4983 0.6937 0.00 0.06 0.68 0.04 0.00 0.22
#> TCGA.EJ.8469.01 1 0.4993 0.1784 0.56 0.36 0.00 0.00 0.00 0.08
#> TCGA.YL.A8SP.01 5 0.3499 0.5029 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.CH.5791.01 5 0.4502 0.4119 0.00 0.14 0.00 0.10 0.74 0.02
#> TCGA.HC.A76X.01 5 0.4195 0.4725 0.00 0.00 0.02 0.20 0.74 0.04
#> TCGA.EJ.A65D.01 5 0.3499 0.5029 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.VP.A87D.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A8II.01 5 0.6851 0.2575 0.00 0.22 0.00 0.30 0.42 0.06
#> TCGA.J9.A52B.01 5 0.3499 0.5029 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.CH.5752.01 1 0.4873 0.2724 0.60 0.32 0.00 0.00 0.00 0.08
#> TCGA.KK.A59Y.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6362.11 5 0.5569 0.3940 0.00 0.32 0.00 0.00 0.52 0.16
#> TCGA.HC.A631.01 1 0.4246 -0.1970 0.58 0.02 0.00 0.00 0.00 0.40
#> TCGA.YL.A8SA.01 5 0.6769 0.2474 0.00 0.04 0.36 0.10 0.46 0.04
#> TCGA.EJ.7784.01 1 0.5474 0.1368 0.54 0.36 0.00 0.00 0.02 0.08
#> TCGA.G9.6373.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9L9.01 4 0.2020 0.8222 0.00 0.02 0.00 0.92 0.02 0.04
#> TCGA.VN.A88K.01 3 0.0547 0.9079 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CH.5790.01 3 0.2020 0.8634 0.00 0.00 0.92 0.02 0.04 0.02
#> TCGA.HC.7231.01 4 0.0000 0.8346 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.7230.01 5 0.3318 0.4765 0.00 0.02 0.02 0.14 0.82 0.00
#> TCGA.CH.5741.01 5 0.3873 0.4731 0.00 0.04 0.16 0.00 0.78 0.02
#> TCGA.KK.A59V.01 1 0.0937 0.5501 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.HI.7171.01 4 0.3007 0.7924 0.00 0.02 0.00 0.86 0.04 0.08
#> TCGA.HC.8259.01 3 0.0937 0.9038 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.XJ.A83F.01 3 0.3045 0.8506 0.00 0.02 0.86 0.06 0.00 0.06
#> TCGA.G9.A9S4.01 2 0.6857 0.5457 0.06 0.44 0.00 0.04 0.38 0.08
#> TCGA.G9.7525.01 5 0.7054 0.2846 0.00 0.06 0.04 0.22 0.52 0.16
#> TCGA.KK.A7AU.01 5 0.3156 0.3919 0.00 0.18 0.00 0.02 0.80 0.00
#> TCGA.EJ.7325.01 4 0.6347 -0.0311 0.00 0.22 0.00 0.44 0.32 0.02
#> TCGA.HC.8257.01 1 0.1092 0.5772 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.YL.A8SL.01 1 0.0937 0.5655 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.YL.A9WL.01 5 0.0937 0.5126 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.G9.6362.01 5 0.5569 0.3940 0.00 0.32 0.00 0.00 0.52 0.16
#> TCGA.EJ.5530.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VN.A88M.01 3 0.0937 0.9038 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.KK.A6E2.01 1 0.2190 0.5729 0.90 0.04 0.00 0.00 0.00 0.06
#> TCGA.J4.A6M7.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.8472.01 1 0.3163 0.5445 0.82 0.14 0.00 0.00 0.00 0.04
#> TCGA.YL.A9WH.01 1 0.4078 -0.0629 0.64 0.02 0.00 0.00 0.00 0.34
#> TCGA.J4.A83N.01 5 0.7063 0.2428 0.00 0.06 0.04 0.30 0.48 0.12
#> TCGA.HC.A6AN.01 1 0.1814 0.5009 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.J4.A67N.01 3 0.1807 0.8873 0.00 0.02 0.92 0.00 0.00 0.06
#> TCGA.VP.A876.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 4 0.0547 0.8320 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.KK.A8IH.01 4 0.0000 0.8346 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VP.A87K.01 5 0.3499 0.5015 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.2A.A8VV.01 3 0.0000 0.9101 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5525.01 5 0.4002 0.5060 0.00 0.32 0.00 0.00 0.66 0.02
#> TCGA.V1.A9OT.01 6 0.5945 0.9146 0.36 0.00 0.00 0.22 0.00 0.42
#> TCGA.G9.6332.01 5 0.4055 0.4911 0.00 0.00 0.04 0.14 0.78 0.04
#> TCGA.EJ.A46G.01 4 0.6649 0.4289 0.00 0.12 0.00 0.52 0.12 0.24
#> TCGA.EJ.A65F.01 1 0.0547 0.5730 0.98 0.00 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.KK.A6E4.01 6 0.5995 0.459047 0.16 0.02 0.00 0.32 0.00 0.48 0.02
#> TCGA.H9.7775.01 5 0.4505 -0.445906 0.00 0.06 0.00 0.00 0.50 0.00 0.44
#> TCGA.XJ.A9DX.01 6 0.4765 0.662672 0.28 0.04 0.00 0.00 0.02 0.64 0.02
#> TCGA.QU.A6IN.01 4 0.0863 0.857402 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.KK.A7B3.01 6 0.3909 0.702542 0.40 0.02 0.00 0.00 0.00 0.58 0.00
#> TCGA.KK.A8I5.01 4 0.1928 0.792991 0.00 0.02 0.00 0.90 0.00 0.08 0.00
#> TCGA.HC.7819.01 1 0.1928 0.730713 0.90 0.02 0.00 0.00 0.00 0.08 0.00
#> TCGA.EJ.A7NF.01 5 0.5600 0.427416 0.00 0.16 0.00 0.16 0.62 0.04 0.02
#> TCGA.HC.7821.01 1 0.1886 0.702104 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.EJ.8474.01 6 0.3459 0.705447 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.KC.A7F6.01 1 0.2163 0.715356 0.88 0.02 0.00 0.00 0.00 0.10 0.00
#> TCGA.V1.A8WS.01 2 0.4737 0.220057 0.34 0.56 0.00 0.00 0.10 0.00 0.00
#> TCGA.HC.8213.01 3 0.7357 0.401332 0.00 0.08 0.50 0.20 0.08 0.10 0.04
#> TCGA.ZG.A9LZ.01 4 0.2421 0.826582 0.00 0.02 0.00 0.88 0.00 0.02 0.08
#> TCGA.CH.5765.01 1 0.0000 0.751597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WW.01 4 0.3680 0.741716 0.00 0.02 0.00 0.78 0.14 0.00 0.06
#> TCGA.HC.A48F.01 3 0.0504 0.895470 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.G9.6377.01 3 0.0504 0.896015 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.YJ.A8SW.01 6 0.4765 0.662672 0.28 0.04 0.00 0.00 0.02 0.64 0.02
#> TCGA.EJ.A46F.01 1 0.2945 0.588029 0.74 0.26 0.00 0.00 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 4 0.0504 0.855990 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.HC.7077.01 6 0.3909 0.702542 0.40 0.02 0.00 0.00 0.00 0.58 0.00
#> TCGA.H9.A6BY.01 5 0.3909 0.311243 0.00 0.40 0.00 0.02 0.58 0.00 0.00
#> TCGA.2A.AAYF.01 3 0.5536 0.683225 0.00 0.08 0.68 0.02 0.02 0.12 0.08
#> TCGA.M7.A71Z.01 1 0.0863 0.736013 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5750.01 3 0.7056 0.511660 0.00 0.10 0.54 0.02 0.08 0.12 0.14
#> TCGA.EJ.8469.01 1 0.3413 0.422332 0.62 0.38 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SP.01 7 0.2945 0.714490 0.00 0.00 0.00 0.00 0.26 0.00 0.74
#> TCGA.CH.5791.01 5 0.4461 0.464476 0.00 0.22 0.00 0.04 0.70 0.02 0.02
#> TCGA.HC.A76X.01 5 0.1860 0.504800 0.00 0.00 0.02 0.02 0.92 0.00 0.04
#> TCGA.EJ.A65D.01 7 0.2945 0.714490 0.00 0.00 0.00 0.00 0.26 0.00 0.74
#> TCGA.VP.A87D.01 3 0.0504 0.893462 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.KK.A8II.01 7 0.7624 0.102998 0.00 0.18 0.00 0.24 0.24 0.04 0.30
#> TCGA.J9.A52B.01 7 0.2945 0.714490 0.00 0.00 0.00 0.00 0.26 0.00 0.74
#> TCGA.CH.5752.01 1 0.3047 0.574366 0.72 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A59Y.01 3 0.0504 0.893462 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.G9.6362.11 2 0.6809 -0.012159 0.00 0.34 0.00 0.00 0.24 0.12 0.30
#> TCGA.HC.A631.01 6 0.3909 0.704800 0.40 0.00 0.00 0.00 0.00 0.58 0.02
#> TCGA.YL.A8SA.01 5 0.5582 0.247153 0.00 0.04 0.24 0.02 0.60 0.00 0.10
#> TCGA.EJ.7784.01 1 0.4244 0.353291 0.54 0.42 0.00 0.00 0.00 0.04 0.00
#> TCGA.G9.6373.01 3 0.0504 0.895470 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.ZG.A9L9.01 4 0.2159 0.835814 0.00 0.02 0.00 0.90 0.00 0.02 0.06
#> TCGA.VN.A88K.01 3 0.0504 0.895470 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CH.5790.01 3 0.2906 0.732434 0.00 0.00 0.80 0.00 0.18 0.00 0.02
#> TCGA.HC.7231.01 4 0.0863 0.857402 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.HC.7230.01 5 0.2912 0.538637 0.00 0.14 0.00 0.04 0.82 0.00 0.00
#> TCGA.CH.5741.01 5 0.4177 0.271085 0.00 0.00 0.12 0.00 0.70 0.00 0.18
#> TCGA.KK.A59V.01 1 0.2376 0.697534 0.86 0.02 0.00 0.00 0.00 0.12 0.00
#> TCGA.HI.7171.01 4 0.2563 0.812511 0.00 0.04 0.00 0.88 0.00 0.04 0.04
#> TCGA.HC.8259.01 3 0.0504 0.896015 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.XJ.A83F.01 3 0.2355 0.861912 0.00 0.04 0.90 0.00 0.02 0.02 0.02
#> TCGA.G9.A9S4.01 2 0.5417 0.261110 0.18 0.56 0.00 0.00 0.24 0.00 0.02
#> TCGA.G9.7525.01 5 0.5448 0.464628 0.00 0.14 0.00 0.08 0.66 0.10 0.02
#> TCGA.KK.A7AU.01 5 0.5438 0.247758 0.00 0.32 0.00 0.00 0.52 0.02 0.14
#> TCGA.EJ.7325.01 2 0.5930 0.023934 0.00 0.42 0.00 0.30 0.26 0.02 0.00
#> TCGA.HC.8257.01 1 0.0863 0.748992 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.YL.A8SL.01 1 0.1886 0.702104 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.YL.A9WL.01 5 0.3991 0.352981 0.00 0.04 0.00 0.02 0.72 0.00 0.22
#> TCGA.G9.6362.01 2 0.6809 -0.012159 0.00 0.34 0.00 0.00 0.24 0.12 0.30
#> TCGA.EJ.5530.01 3 0.0000 0.896490 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88M.01 3 0.0504 0.896015 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.KK.A6E2.01 1 0.0000 0.751597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 3 0.0000 0.896490 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8472.01 1 0.2163 0.726130 0.88 0.10 0.00 0.00 0.00 0.02 0.00
#> TCGA.YL.A9WH.01 6 0.3985 0.624558 0.46 0.00 0.00 0.00 0.00 0.52 0.02
#> TCGA.J4.A83N.01 5 0.4575 0.508601 0.00 0.10 0.00 0.10 0.74 0.04 0.02
#> TCGA.HC.A6AN.01 1 0.2422 0.608859 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.J4.A67N.01 3 0.2355 0.865225 0.00 0.02 0.90 0.00 0.02 0.02 0.04
#> TCGA.VP.A876.01 3 0.0504 0.893462 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CH.5739.01 4 0.0863 0.857402 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.KK.A8IH.01 4 0.1363 0.854674 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.VP.A87K.01 7 0.4127 0.597389 0.00 0.04 0.00 0.00 0.36 0.00 0.60
#> TCGA.2A.A8VV.01 3 0.0504 0.893462 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EJ.5525.01 7 0.3546 0.409999 0.00 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.V1.A9OT.01 6 0.6351 0.317542 0.12 0.04 0.00 0.34 0.00 0.46 0.04
#> TCGA.G9.6332.01 5 0.3000 0.444104 0.00 0.00 0.04 0.02 0.84 0.00 0.10
#> TCGA.EJ.A46G.01 4 0.7858 0.000826 0.00 0.14 0.00 0.32 0.18 0.26 0.10
#> TCGA.EJ.A65F.01 1 0.1166 0.744595 0.94 0.00 0.00 0.00 0.00 0.06 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.KK.A6E4.01 1 0.6949 -0.42585 0.30 0.00 0.00 0.28 0.06 0.28 0.00 0.08
#> TCGA.H9.7775.01 7 0.6422 0.17320 0.00 0.08 0.00 0.10 0.36 0.00 0.40 0.06
#> TCGA.XJ.A9DX.01 6 0.4169 0.58940 0.18 0.00 0.00 0.00 0.02 0.70 0.00 0.10
#> TCGA.QU.A6IN.01 4 0.0471 0.78812 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.KK.A7B3.01 6 0.4383 0.76794 0.42 0.00 0.00 0.00 0.02 0.52 0.00 0.04
#> TCGA.KK.A8I5.01 4 0.3402 0.72821 0.06 0.00 0.00 0.82 0.04 0.06 0.00 0.02
#> TCGA.HC.7819.01 1 0.0471 0.74661 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NF.01 5 0.6758 0.48488 0.00 0.12 0.00 0.10 0.46 0.00 0.10 0.22
#> TCGA.HC.7821.01 1 0.0471 0.75686 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.EJ.8474.01 6 0.3299 0.78099 0.44 0.00 0.00 0.00 0.00 0.56 0.00 0.00
#> TCGA.KC.A7F6.01 1 0.0000 0.75601 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 2 0.3021 0.54664 0.16 0.80 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.HC.8213.01 8 0.5677 0.08720 0.00 0.00 0.34 0.12 0.08 0.00 0.00 0.46
#> TCGA.ZG.A9LZ.01 4 0.4767 0.67860 0.00 0.06 0.00 0.70 0.14 0.04 0.00 0.06
#> TCGA.CH.5765.01 1 0.2404 0.70704 0.84 0.14 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.V1.A8WW.01 4 0.4544 0.56226 0.00 0.06 0.00 0.66 0.22 0.00 0.00 0.06
#> TCGA.HC.A48F.01 3 0.0000 0.87386 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6377.01 3 0.2404 0.82118 0.00 0.00 0.84 0.00 0.02 0.00 0.00 0.14
#> TCGA.YJ.A8SW.01 6 0.3970 0.59491 0.18 0.00 0.00 0.00 0.02 0.72 0.00 0.08
#> TCGA.EJ.A46F.01 1 0.3737 -0.14283 0.50 0.48 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 4 0.1275 0.78613 0.00 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.HC.7077.01 6 0.3714 0.77584 0.44 0.00 0.00 0.00 0.00 0.54 0.00 0.02
#> TCGA.H9.A6BY.01 5 0.5703 0.34230 0.00 0.38 0.00 0.04 0.38 0.00 0.20 0.00
#> TCGA.2A.AAYF.01 3 0.3329 0.21724 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.M7.A71Z.01 1 0.2719 0.65303 0.80 0.18 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CH.5750.01 8 0.5242 -0.03075 0.00 0.00 0.38 0.02 0.06 0.00 0.04 0.50
#> TCGA.EJ.8469.01 2 0.3514 0.37929 0.34 0.64 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.YL.A8SP.01 7 0.0471 0.58625 0.00 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.CH.5791.01 5 0.5922 0.43340 0.00 0.26 0.00 0.04 0.48 0.00 0.20 0.02
#> TCGA.HC.A76X.01 5 0.3991 0.47184 0.00 0.02 0.00 0.06 0.70 0.00 0.22 0.00
#> TCGA.EJ.A65D.01 7 0.0000 0.58935 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VP.A87D.01 3 0.0471 0.87178 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.KK.A8II.01 2 0.7963 -0.18427 0.00 0.26 0.00 0.22 0.18 0.04 0.22 0.08
#> TCGA.J9.A52B.01 7 0.0471 0.58806 0.00 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.CH.5752.01 2 0.3737 0.00619 0.48 0.50 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.KK.A59Y.01 3 0.1557 0.85697 0.00 0.00 0.92 0.00 0.02 0.00 0.00 0.06
#> TCGA.G9.6362.11 8 0.7526 -0.01136 0.00 0.14 0.00 0.00 0.24 0.12 0.24 0.26
#> TCGA.HC.A631.01 6 0.3272 0.78472 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.YL.A8SA.01 5 0.6762 0.15186 0.00 0.06 0.14 0.10 0.54 0.00 0.10 0.06
#> TCGA.EJ.7784.01 2 0.3449 0.43508 0.32 0.66 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G9.6373.01 3 0.0000 0.87386 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L9.01 4 0.3131 0.75260 0.00 0.04 0.00 0.84 0.04 0.02 0.00 0.06
#> TCGA.VN.A88K.01 3 0.0000 0.87386 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5790.01 3 0.4294 0.53789 0.00 0.00 0.68 0.00 0.22 0.00 0.04 0.06
#> TCGA.HC.7231.01 4 0.0000 0.79144 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7230.01 5 0.5671 0.48375 0.00 0.12 0.00 0.04 0.56 0.00 0.24 0.04
#> TCGA.CH.5741.01 5 0.4199 0.33425 0.00 0.00 0.08 0.00 0.60 0.00 0.32 0.00
#> TCGA.KK.A59V.01 1 0.0000 0.75601 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7171.01 4 0.3402 0.74720 0.00 0.04 0.00 0.82 0.06 0.02 0.00 0.06
#> TCGA.HC.8259.01 3 0.2224 0.83272 0.00 0.00 0.86 0.00 0.02 0.00 0.00 0.12
#> TCGA.XJ.A83F.01 3 0.3154 0.76572 0.00 0.00 0.78 0.00 0.06 0.00 0.00 0.16
#> TCGA.G9.A9S4.01 2 0.3319 0.47108 0.08 0.82 0.00 0.02 0.02 0.00 0.06 0.00
#> TCGA.G9.7525.01 5 0.6020 0.40942 0.00 0.04 0.00 0.06 0.46 0.00 0.10 0.34
#> TCGA.KK.A7AU.01 7 0.5970 -0.25426 0.00 0.18 0.00 0.00 0.32 0.02 0.44 0.04
#> TCGA.EJ.7325.01 2 0.5837 -0.13864 0.00 0.46 0.00 0.30 0.16 0.00 0.08 0.00
#> TCGA.HC.8257.01 1 0.0808 0.76137 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SL.01 1 0.0000 0.75601 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WL.01 7 0.4533 -0.22847 0.00 0.02 0.00 0.00 0.44 0.02 0.50 0.02
#> TCGA.G9.6362.01 8 0.7526 -0.01136 0.00 0.14 0.00 0.00 0.24 0.12 0.24 0.26
#> TCGA.EJ.5530.01 3 0.0000 0.87386 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88M.01 3 0.2224 0.83272 0.00 0.00 0.86 0.00 0.02 0.00 0.00 0.12
#> TCGA.KK.A6E2.01 1 0.2025 0.73793 0.88 0.10 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.J4.A6M7.01 3 0.0000 0.87386 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8472.01 1 0.2114 0.70233 0.84 0.16 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WH.01 6 0.3329 0.72022 0.48 0.00 0.00 0.00 0.00 0.52 0.00 0.00
#> TCGA.J4.A83N.01 5 0.5862 0.50678 0.00 0.04 0.00 0.08 0.56 0.00 0.10 0.22
#> TCGA.HC.A6AN.01 1 0.0471 0.73133 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.J4.A67N.01 3 0.1563 0.83203 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.VP.A876.01 3 0.0000 0.87386 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 4 0.1275 0.78544 0.02 0.00 0.00 0.94 0.04 0.00 0.00 0.00
#> TCGA.KK.A8IH.01 4 0.0941 0.78352 0.00 0.00 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.VP.A87K.01 7 0.2265 0.54194 0.00 0.00 0.00 0.00 0.08 0.02 0.88 0.02
#> TCGA.2A.A8VV.01 3 0.0471 0.87178 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.EJ.5525.01 7 0.4898 0.39584 0.00 0.12 0.00 0.00 0.20 0.02 0.64 0.02
#> TCGA.V1.A9OT.01 4 0.7282 -0.21812 0.26 0.02 0.00 0.32 0.06 0.26 0.00 0.08
#> TCGA.G9.6332.01 5 0.3977 0.47816 0.00 0.02 0.00 0.02 0.70 0.00 0.24 0.02
#> TCGA.EJ.A46G.01 8 0.6558 0.09140 0.00 0.04 0.00 0.16 0.10 0.26 0.00 0.44
#> TCGA.EJ.A65F.01 1 0.0471 0.76200 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node05121-leaf , Node05122-leaf , Node05123-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0212"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 33 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.733 0.894 0.944 0.4717 0.496 0.496
#> 3 3 1.000 0.987 0.992 0.3995 0.750 0.538
#> 4 4 0.768 0.725 0.836 0.0984 0.900 0.712
#> 5 5 0.714 0.606 0.810 0.0732 0.956 0.838
#> 6 6 0.742 0.750 0.812 0.0450 0.877 0.522
#> 7 7 0.778 0.769 0.830 0.0362 0.981 0.886
#> 8 8 0.822 0.798 0.805 0.0178 0.966 0.783
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.H9.7775.01 1 0.000 0.995 1.00 0.00
#> TCGA.QU.A6IN.01 1 0.000 0.995 1.00 0.00
#> TCGA.EJ.A7NF.01 1 0.000 0.995 1.00 0.00
#> TCGA.V1.A8WS.01 2 0.958 0.566 0.38 0.62
#> TCGA.ZG.A9LZ.01 2 0.000 0.854 0.00 1.00
#> TCGA.V1.A8WW.01 1 0.000 0.995 1.00 0.00
#> TCGA.MG.AAMC.01 1 0.000 0.995 1.00 0.00
#> TCGA.H9.A6BY.01 1 0.000 0.995 1.00 0.00
#> TCGA.YL.A8SP.01 2 0.000 0.854 0.00 1.00
#> TCGA.CH.5791.01 1 0.000 0.995 1.00 0.00
#> TCGA.HC.A76X.01 1 0.000 0.995 1.00 0.00
#> TCGA.EJ.A65D.01 2 0.000 0.854 0.00 1.00
#> TCGA.KK.A8II.01 1 0.000 0.995 1.00 0.00
#> TCGA.J9.A52B.01 2 0.000 0.854 0.00 1.00
#> TCGA.G9.6362.11 2 0.881 0.673 0.30 0.70
#> TCGA.YL.A8SA.01 2 0.000 0.854 0.00 1.00
#> TCGA.ZG.A9L9.01 1 0.000 0.995 1.00 0.00
#> TCGA.HC.7231.01 1 0.000 0.995 1.00 0.00
#> TCGA.HC.7230.01 1 0.000 0.995 1.00 0.00
#> TCGA.HI.7171.01 2 0.000 0.854 0.00 1.00
#> TCGA.G9.A9S4.01 2 0.958 0.566 0.38 0.62
#> TCGA.G9.7525.01 1 0.000 0.995 1.00 0.00
#> TCGA.KK.A7AU.01 2 0.881 0.673 0.30 0.70
#> TCGA.EJ.7325.01 1 0.000 0.995 1.00 0.00
#> TCGA.YL.A9WL.01 2 0.000 0.854 0.00 1.00
#> TCGA.G9.6362.01 2 0.958 0.566 0.38 0.62
#> TCGA.J4.A83N.01 1 0.000 0.995 1.00 0.00
#> TCGA.CH.5739.01 1 0.000 0.995 1.00 0.00
#> TCGA.KK.A8IH.01 1 0.000 0.995 1.00 0.00
#> TCGA.VP.A87K.01 1 0.402 0.893 0.92 0.08
#> TCGA.EJ.5525.01 2 0.000 0.854 0.00 1.00
#> TCGA.G9.6332.01 2 0.242 0.841 0.04 0.96
#> TCGA.EJ.A46G.01 1 0.000 0.995 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.H9.7775.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.QU.A6IN.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EJ.A7NF.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.V1.A8WS.01 3 0.0000 0.978 0.00 0.00 1.00
#> TCGA.ZG.A9LZ.01 2 0.0892 0.995 0.00 0.98 0.02
#> TCGA.V1.A8WW.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.H9.A6BY.01 3 0.0892 0.966 0.02 0.00 0.98
#> TCGA.YL.A8SP.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.CH.5791.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HC.A76X.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EJ.A65D.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.KK.A8II.01 3 0.0892 0.966 0.02 0.00 0.98
#> TCGA.J9.A52B.01 2 0.0892 0.995 0.00 0.98 0.02
#> TCGA.G9.6362.11 3 0.0000 0.978 0.00 0.00 1.00
#> TCGA.YL.A8SA.01 2 0.0892 0.995 0.00 0.98 0.02
#> TCGA.ZG.A9L9.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HC.7231.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HC.7230.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HI.7171.01 2 0.0892 0.995 0.00 0.98 0.02
#> TCGA.G9.A9S4.01 3 0.0000 0.978 0.00 0.00 1.00
#> TCGA.G9.7525.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.KK.A7AU.01 3 0.0000 0.978 0.00 0.00 1.00
#> TCGA.EJ.7325.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.YL.A9WL.01 2 0.0892 0.995 0.00 0.98 0.02
#> TCGA.G9.6362.01 3 0.0000 0.978 0.00 0.00 1.00
#> TCGA.J4.A83N.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.KK.A8IH.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VP.A87K.01 3 0.0000 0.978 0.00 0.00 1.00
#> TCGA.EJ.5525.01 2 0.0892 0.995 0.00 0.98 0.02
#> TCGA.G9.6332.01 3 0.0000 0.978 0.00 0.00 1.00
#> TCGA.EJ.A46G.01 3 0.3340 0.858 0.12 0.00 0.88
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.H9.7775.01 4 0.485 0.1050 0.40 0.00 0.00 0.60
#> TCGA.QU.A6IN.01 1 0.000 0.8413 1.00 0.00 0.00 0.00
#> TCGA.EJ.A7NF.01 1 0.340 0.8273 0.82 0.00 0.00 0.18
#> TCGA.V1.A8WS.01 3 0.121 0.8849 0.00 0.00 0.96 0.04
#> TCGA.ZG.A9LZ.01 2 0.000 0.9221 0.00 1.00 0.00 0.00
#> TCGA.V1.A8WW.01 1 0.000 0.8413 1.00 0.00 0.00 0.00
#> TCGA.MG.AAMC.01 1 0.000 0.8413 1.00 0.00 0.00 0.00
#> TCGA.H9.A6BY.01 4 0.498 0.1661 0.00 0.00 0.46 0.54
#> TCGA.YL.A8SP.01 2 0.462 0.7419 0.00 0.66 0.00 0.34
#> TCGA.CH.5791.01 1 0.340 0.8273 0.82 0.00 0.00 0.18
#> TCGA.HC.A76X.01 4 0.495 -0.0384 0.44 0.00 0.00 0.56
#> TCGA.EJ.A65D.01 2 0.462 0.7419 0.00 0.66 0.00 0.34
#> TCGA.KK.A8II.01 4 0.500 0.0288 0.00 0.00 0.50 0.50
#> TCGA.J9.A52B.01 2 0.000 0.9221 0.00 1.00 0.00 0.00
#> TCGA.G9.6362.11 3 0.000 0.9000 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SA.01 2 0.000 0.9221 0.00 1.00 0.00 0.00
#> TCGA.ZG.A9L9.01 1 0.334 0.7374 0.86 0.02 0.00 0.12
#> TCGA.HC.7231.01 1 0.340 0.8273 0.82 0.00 0.00 0.18
#> TCGA.HC.7230.01 1 0.340 0.8273 0.82 0.00 0.00 0.18
#> TCGA.HI.7171.01 2 0.000 0.9221 0.00 1.00 0.00 0.00
#> TCGA.G9.A9S4.01 3 0.000 0.9000 0.00 0.00 1.00 0.00
#> TCGA.G9.7525.01 1 0.340 0.8273 0.82 0.00 0.00 0.18
#> TCGA.KK.A7AU.01 3 0.000 0.9000 0.00 0.00 1.00 0.00
#> TCGA.EJ.7325.01 1 0.164 0.8120 0.94 0.00 0.00 0.06
#> TCGA.YL.A9WL.01 2 0.000 0.9221 0.00 1.00 0.00 0.00
#> TCGA.G9.6362.01 3 0.000 0.9000 0.00 0.00 1.00 0.00
#> TCGA.J4.A83N.01 1 0.340 0.8273 0.82 0.00 0.00 0.18
#> TCGA.CH.5739.01 1 0.201 0.7985 0.92 0.00 0.00 0.08
#> TCGA.KK.A8IH.01 1 0.000 0.8413 1.00 0.00 0.00 0.00
#> TCGA.VP.A87K.01 3 0.471 0.2601 0.00 0.00 0.64 0.36
#> TCGA.EJ.5525.01 2 0.000 0.9221 0.00 1.00 0.00 0.00
#> TCGA.G9.6332.01 3 0.121 0.8849 0.00 0.00 0.96 0.04
#> TCGA.EJ.A46G.01 4 0.630 0.3522 0.08 0.00 0.32 0.60
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.H9.7775.01 4 0.342 0.547 0.24 0.00 0.00 0.76 0.00
#> TCGA.QU.A6IN.01 1 0.389 0.500 0.68 0.00 0.00 0.00 0.32
#> TCGA.EJ.A7NF.01 1 0.000 0.662 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 3 0.342 0.608 0.00 0.00 0.76 0.24 0.00
#> TCGA.ZG.A9LZ.01 2 0.000 0.877 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A8WW.01 1 0.389 0.500 0.68 0.00 0.00 0.00 0.32
#> TCGA.MG.AAMC.01 1 0.389 0.500 0.68 0.00 0.00 0.00 0.32
#> TCGA.H9.A6BY.01 4 0.513 0.666 0.10 0.00 0.22 0.68 0.00
#> TCGA.YL.A8SP.01 2 0.556 0.618 0.00 0.56 0.00 0.08 0.36
#> TCGA.CH.5791.01 1 0.000 0.662 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 4 0.453 0.473 0.26 0.00 0.00 0.70 0.04
#> TCGA.EJ.A65D.01 2 0.556 0.618 0.00 0.56 0.00 0.08 0.36
#> TCGA.KK.A8II.01 4 0.473 0.669 0.08 0.00 0.20 0.72 0.00
#> TCGA.J9.A52B.01 2 0.104 0.869 0.00 0.96 0.00 0.04 0.00
#> TCGA.G9.6362.11 3 0.000 0.896 0.00 0.00 1.00 0.00 0.00
#> TCGA.YL.A8SA.01 2 0.000 0.877 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9L9.01 5 0.788 0.000 0.22 0.08 0.00 0.32 0.38
#> TCGA.HC.7231.01 1 0.000 0.662 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7230.01 1 0.000 0.662 1.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7171.01 2 0.000 0.877 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 3 0.000 0.896 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.7525.01 1 0.000 0.662 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 3 0.244 0.866 0.00 0.00 0.90 0.04 0.06
#> TCGA.EJ.7325.01 1 0.618 -0.191 0.48 0.00 0.00 0.14 0.38
#> TCGA.YL.A9WL.01 2 0.104 0.869 0.00 0.96 0.00 0.04 0.00
#> TCGA.G9.6362.01 3 0.000 0.896 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.A83N.01 1 0.000 0.662 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 1 0.655 -0.439 0.42 0.00 0.00 0.20 0.38
#> TCGA.KK.A8IH.01 1 0.389 0.500 0.68 0.00 0.00 0.00 0.32
#> TCGA.VP.A87K.01 4 0.413 0.403 0.00 0.00 0.38 0.62 0.00
#> TCGA.EJ.5525.01 2 0.000 0.877 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6332.01 3 0.311 0.857 0.00 0.00 0.86 0.08 0.06
#> TCGA.EJ.A46G.01 4 0.805 0.403 0.32 0.00 0.12 0.38 0.18
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.H9.7775.01 4 0.3198 0.680 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.QU.A6IN.01 5 0.3864 0.644 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.EJ.A7NF.01 1 0.0000 0.845 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 3 0.4002 0.475 0.00 0.00 0.66 0.32 0.00 0.02
#> TCGA.ZG.A9LZ.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WW.01 5 0.3864 0.644 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.MG.AAMC.01 5 0.3864 0.644 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.H9.A6BY.01 4 0.3787 0.756 0.10 0.00 0.12 0.78 0.00 0.00
#> TCGA.YL.A8SP.01 6 0.2793 0.987 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.CH.5791.01 1 0.0000 0.845 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 4 0.4608 0.635 0.22 0.00 0.00 0.68 0.10 0.00
#> TCGA.EJ.A65D.01 6 0.3315 0.987 0.00 0.20 0.00 0.00 0.02 0.78
#> TCGA.KK.A8II.01 4 0.3475 0.744 0.06 0.00 0.14 0.80 0.00 0.00
#> TCGA.J9.A52B.01 2 0.1480 0.945 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.G9.6362.11 3 0.0000 0.846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SA.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L9.01 5 0.6431 0.387 0.10 0.06 0.00 0.26 0.56 0.02
#> TCGA.HC.7231.01 1 0.0000 0.845 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7230.01 1 0.0000 0.845 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7171.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 3 0.0547 0.845 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.G9.7525.01 1 0.0000 0.845 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 3 0.3045 0.801 0.00 0.00 0.84 0.00 0.06 0.10
#> TCGA.EJ.7325.01 5 0.5919 0.589 0.28 0.00 0.00 0.16 0.54 0.02
#> TCGA.YL.A9WL.01 2 0.1480 0.945 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.G9.6362.01 3 0.0000 0.846 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A83N.01 1 0.0000 0.845 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 5 0.6086 0.570 0.26 0.00 0.00 0.20 0.52 0.02
#> TCGA.KK.A8IH.01 5 0.3864 0.644 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.VP.A87K.01 4 0.3309 0.544 0.00 0.00 0.28 0.72 0.00 0.00
#> TCGA.EJ.5525.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6332.01 3 0.4879 0.752 0.00 0.00 0.72 0.12 0.04 0.12
#> TCGA.EJ.A46G.01 1 0.6564 -0.123 0.42 0.00 0.00 0.38 0.14 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.H9.7775.01 4 0.2569 0.735 0.14 0.00 0.00 0.84 0.00 0.02 0.00
#> TCGA.QU.A6IN.01 5 0.2832 0.703 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.EJ.A7NF.01 1 0.0000 0.910 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WS.01 4 0.3909 0.335 0.00 0.00 0.40 0.58 0.00 0.02 0.00
#> TCGA.ZG.A9LZ.01 2 0.0504 0.943 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.V1.A8WW.01 5 0.2832 0.703 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.MG.AAMC.01 5 0.2832 0.703 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.H9.A6BY.01 4 0.2829 0.786 0.08 0.00 0.08 0.84 0.00 0.00 0.00
#> TCGA.YL.A8SP.01 7 0.1664 0.988 0.00 0.06 0.00 0.00 0.00 0.02 0.92
#> TCGA.CH.5791.01 1 0.0000 0.910 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 4 0.4079 0.681 0.12 0.00 0.00 0.76 0.08 0.04 0.00
#> TCGA.EJ.A65D.01 7 0.1166 0.988 0.00 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.KK.A8II.01 4 0.2803 0.784 0.06 0.00 0.10 0.84 0.00 0.00 0.00
#> TCGA.J9.A52B.01 2 0.2509 0.902 0.00 0.88 0.00 0.02 0.04 0.06 0.00
#> TCGA.G9.6362.11 3 0.0000 0.811 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SA.01 2 0.0000 0.946 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L9.01 5 0.5517 0.367 0.02 0.00 0.00 0.14 0.48 0.36 0.00
#> TCGA.HC.7231.01 1 0.0000 0.910 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7230.01 1 0.0000 0.910 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7171.01 2 0.0000 0.946 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 3 0.0000 0.811 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7525.01 1 0.0000 0.910 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 3 0.4305 0.694 0.00 0.00 0.66 0.02 0.00 0.28 0.04
#> TCGA.EJ.7325.01 5 0.6405 0.570 0.18 0.00 0.00 0.10 0.46 0.26 0.00
#> TCGA.YL.A9WL.01 2 0.2509 0.902 0.00 0.88 0.00 0.02 0.04 0.06 0.00
#> TCGA.G9.6362.01 3 0.0000 0.811 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A83N.01 1 0.0000 0.910 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5739.01 5 0.6465 0.554 0.14 0.00 0.00 0.14 0.46 0.26 0.00
#> TCGA.KK.A8IH.01 5 0.2832 0.703 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.VP.A87K.01 4 0.2906 0.716 0.00 0.00 0.18 0.80 0.00 0.02 0.00
#> TCGA.EJ.5525.01 2 0.0504 0.943 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G9.6332.01 3 0.5861 0.534 0.00 0.00 0.50 0.18 0.00 0.28 0.04
#> TCGA.EJ.A46G.01 1 0.5604 0.359 0.52 0.00 0.00 0.20 0.00 0.26 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.H9.7775.01 4 0.2994 0.71351 0.06 0.00 0.00 0.80 0.00 0.14 0.00 0.00
#> TCGA.QU.A6IN.01 5 0.4537 1.00000 0.40 0.00 0.00 0.00 0.50 0.10 0.00 0.00
#> TCGA.EJ.A7NF.01 1 0.0471 0.81082 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.V1.A8WS.01 4 0.4186 0.57684 0.00 0.00 0.18 0.72 0.02 0.00 0.02 0.06
#> TCGA.ZG.A9LZ.01 2 0.0808 0.87718 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.V1.A8WW.01 5 0.4537 1.00000 0.40 0.00 0.00 0.00 0.50 0.10 0.00 0.00
#> TCGA.MG.AAMC.01 5 0.4537 1.00000 0.40 0.00 0.00 0.00 0.50 0.10 0.00 0.00
#> TCGA.H9.A6BY.01 4 0.0471 0.78993 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SP.01 7 0.0808 0.95800 0.00 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.CH.5791.01 1 0.0000 0.81984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76X.01 4 0.3449 0.54840 0.02 0.00 0.00 0.66 0.00 0.32 0.00 0.00
#> TCGA.EJ.A65D.01 7 0.2204 0.95800 0.00 0.04 0.00 0.02 0.02 0.00 0.90 0.02
#> TCGA.KK.A8II.01 4 0.1741 0.78517 0.00 0.00 0.00 0.92 0.00 0.02 0.02 0.04
#> TCGA.J9.A52B.01 2 0.3710 0.79590 0.00 0.76 0.02 0.00 0.10 0.00 0.00 0.12
#> TCGA.G9.6362.11 3 0.0808 0.95562 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SA.01 2 0.0000 0.88615 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L9.01 6 0.1557 0.59608 0.00 0.00 0.00 0.00 0.02 0.92 0.00 0.06
#> TCGA.HC.7231.01 1 0.0000 0.81984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7230.01 1 0.0000 0.81984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7171.01 2 0.0000 0.88615 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S4.01 3 0.2071 0.90883 0.00 0.00 0.90 0.04 0.04 0.00 0.02 0.00
#> TCGA.G9.7525.01 1 0.0000 0.81984 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AU.01 8 0.4004 0.56081 0.00 0.00 0.46 0.00 0.04 0.00 0.00 0.50
#> TCGA.EJ.7325.01 6 0.3879 0.80026 0.14 0.00 0.00 0.02 0.10 0.74 0.00 0.00
#> TCGA.YL.A9WL.01 2 0.3710 0.79590 0.00 0.76 0.02 0.00 0.10 0.00 0.00 0.12
#> TCGA.G9.6362.01 3 0.0808 0.95562 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.J4.A83N.01 1 0.0471 0.81082 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CH.5739.01 6 0.3879 0.80026 0.14 0.00 0.00 0.02 0.10 0.74 0.00 0.00
#> TCGA.KK.A8IH.01 5 0.4537 1.00000 0.40 0.00 0.00 0.00 0.50 0.10 0.00 0.00
#> TCGA.VP.A87K.01 4 0.1408 0.77678 0.00 0.00 0.02 0.94 0.00 0.00 0.02 0.02
#> TCGA.EJ.5525.01 2 0.1341 0.86507 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.G9.6332.01 8 0.4622 0.64271 0.00 0.00 0.30 0.14 0.00 0.00 0.00 0.56
#> TCGA.EJ.A46G.01 1 0.6749 -0.00287 0.34 0.00 0.02 0.20 0.30 0.00 0.00 0.14
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-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 43 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 0.998 0.999 0.4646 0.535 0.535
#> 3 3 0.962 0.960 0.983 0.3865 0.731 0.537
#> 4 4 0.751 0.733 0.856 0.1396 0.835 0.568
#> 5 5 0.710 0.611 0.766 0.0541 0.924 0.711
#> 6 6 0.800 0.599 0.779 0.0492 0.938 0.736
#> 7 7 0.790 0.496 0.693 0.0334 0.905 0.585
#> 8 8 0.812 0.762 0.853 0.0197 0.907 0.531
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.EJ.7125.01 2 0.000 0.996 0.00 1.00
#> TCGA.YL.A9WI.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.A6AO.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5761.01 2 0.141 0.983 0.02 0.98
#> TCGA.XK.AAJA.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A6E8.01 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A9OQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.YL.A8HM.01 2 0.000 0.996 0.00 1.00
#> TCGA.M7.A722.01 2 0.000 0.996 0.00 1.00
#> TCGA.VN.A88R.01 1 0.000 1.000 1.00 0.00
#> TCGA.Y6.A9XI.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5737.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A8IF.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5767.01 1 0.000 1.000 1.00 0.00
#> TCGA.J4.AATZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZG.A9L5.01 2 0.000 0.996 0.00 1.00
#> TCGA.KK.A7AQ.01 2 0.141 0.983 0.02 0.98
#> TCGA.YL.A8SR.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A8IK.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A59X.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.7789.01 2 0.000 0.996 0.00 1.00
#> TCGA.FC.A4JI.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A5A1.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.7080.01 2 0.000 0.996 0.00 1.00
#> TCGA.V1.A9O5.06 2 0.000 0.996 0.00 1.00
#> TCGA.KC.A7F5.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.7782.01 1 0.000 1.000 1.00 0.00
#> TCGA.XK.AAJ3.01 1 0.000 1.000 1.00 0.00
#> TCGA.XK.AAK1.01 1 0.000 1.000 1.00 0.00
#> TCGA.TP.A8TV.01 1 0.000 1.000 1.00 0.00
#> TCGA.FC.A6HD.01 1 0.000 1.000 1.00 0.00
#> TCGA.QU.A6IL.01 1 0.000 1.000 1.00 0.00
#> TCGA.J4.A83J.01 1 0.000 1.000 1.00 0.00
#> TCGA.XJ.A83G.01 1 0.000 1.000 1.00 0.00
#> TCGA.G9.6496.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A59Z.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.A65J.01 1 0.000 1.000 1.00 0.00
#> TCGA.2A.A8VX.01 2 0.141 0.983 0.02 0.98
#> TCGA.HC.7738.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.7123.01 1 0.000 1.000 1.00 0.00
#> TCGA.2A.A8W1.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.7312.01 2 0.000 0.996 0.00 1.00
#> TCGA.V1.A8MM.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.EJ.7125.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.YL.A9WI.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.HC.A6AO.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.CH.5761.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.XK.AAJA.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.KK.A6E8.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.V1.A9OQ.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.YL.A8HM.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.M7.A722.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.VN.A88R.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.Y6.A9XI.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.CH.5737.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.KK.A8IF.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.CH.5767.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.J4.AATZ.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.ZG.A9L5.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.KK.A7AQ.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.YL.A8SR.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.KK.A8IK.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.KK.A59X.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.7789.01 3 0.455 0.742 0.00 0.2 0.80
#> TCGA.FC.A4JI.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.KK.A5A1.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.HC.7080.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.V1.A9O5.06 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.KC.A7F5.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.EJ.7782.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.XK.AAJ3.01 3 0.334 0.834 0.12 0.0 0.88
#> TCGA.XK.AAK1.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.TP.A8TV.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.FC.A6HD.01 1 0.522 0.659 0.74 0.0 0.26
#> TCGA.QU.A6IL.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.J4.A83J.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.XJ.A83G.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.G9.6496.01 1 0.400 0.810 0.84 0.0 0.16
#> TCGA.KK.A59Z.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.A65J.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.2A.A8VX.01 3 0.000 0.970 0.00 0.0 1.00
#> TCGA.HC.7738.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.EJ.7123.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.2A.A8W1.01 1 0.000 0.978 1.00 0.0 0.00
#> TCGA.EJ.7312.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.V1.A8MM.01 3 0.000 0.970 0.00 0.0 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EJ.7125.01 3 0.3172 0.71327 0.00 0.00 0.84 0.16
#> TCGA.YL.A9WI.01 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.HC.A6AO.01 4 0.4948 0.23072 0.00 0.00 0.44 0.56
#> TCGA.CH.5761.01 3 0.3172 0.73549 0.00 0.00 0.84 0.16
#> TCGA.XK.AAJA.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.V1.A9OQ.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.YL.A8HM.01 3 0.2011 0.77799 0.00 0.00 0.92 0.08
#> TCGA.M7.A722.01 2 0.3172 0.85373 0.00 0.84 0.00 0.16
#> TCGA.VN.A88R.01 1 0.1211 0.90906 0.96 0.00 0.00 0.04
#> TCGA.Y6.A9XI.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.CH.5737.01 1 0.1211 0.90906 0.96 0.00 0.00 0.04
#> TCGA.KK.A8IF.01 3 0.4994 -0.12977 0.00 0.00 0.52 0.48
#> TCGA.CH.5767.01 4 0.4977 0.44621 0.46 0.00 0.00 0.54
#> TCGA.J4.AATZ.01 4 0.4277 0.68699 0.28 0.00 0.00 0.72
#> TCGA.ZG.A9L5.01 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.KK.A7AQ.01 3 0.2011 0.77799 0.00 0.00 0.92 0.08
#> TCGA.YL.A8SR.01 3 0.0707 0.76788 0.00 0.00 0.98 0.02
#> TCGA.KK.A8IK.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.KK.A59X.01 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.EJ.7789.01 3 0.3172 0.71327 0.00 0.00 0.84 0.16
#> TCGA.FC.A4JI.01 4 0.4406 0.67675 0.30 0.00 0.00 0.70
#> TCGA.KK.A5A1.01 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.HC.7080.01 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.V1.A9O5.06 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.KC.A7F5.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.EJ.7782.01 4 0.4948 0.23072 0.00 0.00 0.44 0.56
#> TCGA.XK.AAJ3.01 4 0.3853 0.52663 0.02 0.00 0.16 0.82
#> TCGA.XK.AAK1.01 1 0.5000 -0.43194 0.50 0.00 0.00 0.50
#> TCGA.TP.A8TV.01 3 0.4948 0.00698 0.00 0.00 0.56 0.44
#> TCGA.FC.A6HD.01 4 0.5677 0.67271 0.14 0.00 0.14 0.72
#> TCGA.QU.A6IL.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.J4.A83J.01 1 0.1211 0.90906 0.96 0.00 0.00 0.04
#> TCGA.XJ.A83G.01 1 0.1211 0.90906 0.96 0.00 0.00 0.04
#> TCGA.G9.6496.01 4 0.5677 0.66961 0.14 0.00 0.14 0.72
#> TCGA.KK.A59Z.01 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.EJ.A65J.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 3 0.2345 0.77214 0.00 0.00 0.90 0.10
#> TCGA.HC.7738.01 1 0.0000 0.92988 1.00 0.00 0.00 0.00
#> TCGA.EJ.7123.01 4 0.4948 0.49112 0.44 0.00 0.00 0.56
#> TCGA.2A.A8W1.01 4 0.4406 0.67205 0.30 0.00 0.00 0.70
#> TCGA.EJ.7312.01 2 0.0000 0.98324 0.00 1.00 0.00 0.00
#> TCGA.V1.A8MM.01 3 0.0707 0.76788 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.EJ.7125.01 5 0.4287 -0.2933 0.00 0.00 0.46 0.00 0.54
#> TCGA.YL.A9WI.01 2 0.2249 0.9154 0.00 0.92 0.04 0.02 0.02
#> TCGA.HC.A6AO.01 5 0.5895 0.4657 0.00 0.00 0.10 0.44 0.46
#> TCGA.CH.5761.01 3 0.2438 0.6391 0.00 0.00 0.90 0.06 0.04
#> TCGA.XK.AAJA.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OQ.01 1 0.2616 0.8118 0.88 0.00 0.00 0.10 0.02
#> TCGA.YL.A8HM.01 3 0.0609 0.6424 0.00 0.00 0.98 0.00 0.02
#> TCGA.M7.A722.01 2 0.4126 0.5766 0.00 0.62 0.00 0.00 0.38
#> TCGA.VN.A88R.01 1 0.3106 0.7926 0.84 0.00 0.00 0.14 0.02
#> TCGA.Y6.A9XI.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5737.01 1 0.3106 0.7926 0.84 0.00 0.00 0.14 0.02
#> TCGA.KK.A8IF.01 5 0.6064 0.4812 0.00 0.00 0.12 0.42 0.46
#> TCGA.CH.5767.01 1 0.5689 -0.0858 0.48 0.00 0.00 0.44 0.08
#> TCGA.J4.AATZ.01 4 0.3109 0.6359 0.20 0.00 0.00 0.80 0.00
#> TCGA.ZG.A9L5.01 2 0.0000 0.9324 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A7AQ.01 3 0.1648 0.6580 0.00 0.00 0.94 0.04 0.02
#> TCGA.YL.A8SR.01 3 0.6705 0.0488 0.00 0.00 0.42 0.26 0.32
#> TCGA.KK.A8IK.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A59X.01 2 0.0000 0.9324 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7789.01 5 0.4287 -0.2933 0.00 0.00 0.46 0.00 0.54
#> TCGA.FC.A4JI.01 4 0.4216 0.5992 0.12 0.00 0.00 0.78 0.10
#> TCGA.KK.A5A1.01 2 0.2249 0.9154 0.00 0.92 0.04 0.02 0.02
#> TCGA.HC.7080.01 2 0.2249 0.9154 0.00 0.92 0.04 0.02 0.02
#> TCGA.V1.A9O5.06 2 0.0000 0.9324 0.00 1.00 0.00 0.00 0.00
#> TCGA.KC.A7F5.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7782.01 5 0.5895 0.4657 0.00 0.00 0.10 0.44 0.46
#> TCGA.XK.AAJ3.01 4 0.5048 0.1070 0.00 0.00 0.38 0.58 0.04
#> TCGA.XK.AAK1.01 1 0.5558 0.2233 0.56 0.00 0.00 0.36 0.08
#> TCGA.TP.A8TV.01 5 0.6207 0.4823 0.00 0.00 0.14 0.40 0.46
#> TCGA.FC.A6HD.01 4 0.1043 0.5634 0.04 0.00 0.00 0.96 0.00
#> TCGA.QU.A6IL.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A83J.01 1 0.3106 0.7926 0.84 0.00 0.00 0.14 0.02
#> TCGA.XJ.A83G.01 1 0.3106 0.7926 0.84 0.00 0.00 0.14 0.02
#> TCGA.G9.6496.01 4 0.3922 0.4063 0.04 0.00 0.00 0.78 0.18
#> TCGA.KK.A59Z.01 2 0.0000 0.9324 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A65J.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 3 0.1410 0.6576 0.00 0.00 0.94 0.06 0.00
#> TCGA.HC.7738.01 1 0.0000 0.8454 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7123.01 4 0.5579 0.4562 0.30 0.00 0.00 0.60 0.10
#> TCGA.2A.A8W1.01 4 0.4132 0.5630 0.26 0.00 0.00 0.72 0.02
#> TCGA.EJ.7312.01 2 0.0000 0.9324 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A8MM.01 3 0.6638 0.1022 0.00 0.00 0.44 0.24 0.32
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EJ.7125.01 6 0.4246 1.00000 0.00 0.00 0.40 0.00 0.02 0.58
#> TCGA.YL.A9WI.01 2 0.4279 0.80952 0.00 0.78 0.08 0.06 0.00 0.08
#> TCGA.HC.A6AO.01 5 0.1092 0.61681 0.00 0.00 0.02 0.02 0.96 0.00
#> TCGA.CH.5761.01 3 0.4334 0.59385 0.00 0.00 0.72 0.04 0.02 0.22
#> TCGA.XK.AAJA.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OQ.01 1 0.4754 0.60032 0.68 0.00 0.00 0.24 0.02 0.06
#> TCGA.YL.A8HM.01 3 0.0937 0.77459 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.M7.A722.01 2 0.3756 0.39583 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.VN.A88R.01 1 0.5625 0.52922 0.58 0.00 0.00 0.30 0.04 0.08
#> TCGA.Y6.A9XI.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5737.01 1 0.5625 0.52922 0.58 0.00 0.00 0.30 0.04 0.08
#> TCGA.KK.A8IF.01 5 0.1480 0.61446 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.CH.5767.01 4 0.7165 -0.12778 0.32 0.00 0.00 0.34 0.26 0.08
#> TCGA.J4.AATZ.01 4 0.2725 0.65045 0.02 0.00 0.00 0.88 0.06 0.04
#> TCGA.ZG.A9L5.01 2 0.0000 0.87548 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AQ.01 3 0.0937 0.77459 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.YL.A8SR.01 5 0.5736 0.03594 0.00 0.00 0.34 0.00 0.48 0.18
#> TCGA.KK.A8IK.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A59X.01 2 0.0000 0.87548 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7789.01 6 0.4246 1.00000 0.00 0.00 0.40 0.00 0.02 0.58
#> TCGA.FC.A4JI.01 4 0.4179 0.61230 0.02 0.00 0.00 0.76 0.16 0.06
#> TCGA.KK.A5A1.01 2 0.4008 0.81809 0.00 0.80 0.06 0.06 0.00 0.08
#> TCGA.HC.7080.01 2 0.4279 0.80952 0.00 0.78 0.08 0.06 0.00 0.08
#> TCGA.V1.A9O5.06 2 0.0000 0.87548 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F5.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7782.01 5 0.0547 0.60146 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.XK.AAJ3.01 4 0.5292 0.17558 0.00 0.00 0.18 0.60 0.00 0.22
#> TCGA.XK.AAK1.01 1 0.7165 -0.01869 0.34 0.00 0.00 0.32 0.26 0.08
#> TCGA.TP.A8TV.01 5 0.1480 0.61446 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.FC.A6HD.01 4 0.2794 0.64260 0.00 0.00 0.00 0.86 0.08 0.06
#> TCGA.QU.A6IL.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A83J.01 1 0.5625 0.52922 0.58 0.00 0.00 0.30 0.04 0.08
#> TCGA.XJ.A83G.01 1 0.5625 0.52922 0.58 0.00 0.00 0.30 0.04 0.08
#> TCGA.G9.6496.01 4 0.5110 0.21934 0.00 0.00 0.00 0.48 0.44 0.08
#> TCGA.KK.A59Z.01 2 0.0000 0.87548 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65J.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 3 0.2350 0.74539 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.HC.7738.01 1 0.0000 0.75061 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7123.01 5 0.7023 -0.31055 0.20 0.00 0.00 0.34 0.38 0.08
#> TCGA.2A.A8W1.01 4 0.1865 0.63875 0.04 0.00 0.00 0.92 0.04 0.00
#> TCGA.EJ.7312.01 2 0.0000 0.87548 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MM.01 5 0.5769 -0.00867 0.00 0.00 0.36 0.00 0.46 0.18
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EJ.7125.01 7 0.5451 0.2063 0.00 0.00 0.16 0.00 0.02 0.28 0.54
#> TCGA.YL.A9WI.01 2 0.1006 0.7775 0.00 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.HC.A6AO.01 5 0.1664 0.6546 0.00 0.00 0.00 0.06 0.92 0.02 0.00
#> TCGA.CH.5761.01 3 0.2572 0.7910 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.XK.AAJA.01 1 0.0000 0.7415 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E8.01 1 0.0000 0.7415 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OQ.01 1 0.5619 -0.1581 0.38 0.00 0.00 0.30 0.00 0.00 0.32
#> TCGA.YL.A8HM.01 3 0.0504 0.9007 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.M7.A722.01 7 0.5378 -0.0417 0.00 0.30 0.00 0.00 0.00 0.22 0.48
#> TCGA.VN.A88R.01 1 0.5631 -0.1864 0.36 0.00 0.00 0.30 0.00 0.00 0.34
#> TCGA.Y6.A9XI.01 1 0.0504 0.7405 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CH.5737.01 4 0.5631 0.1471 0.30 0.00 0.00 0.36 0.00 0.00 0.34
#> TCGA.KK.A8IF.01 5 0.0863 0.6738 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.CH.5767.01 4 0.6991 0.3734 0.16 0.00 0.00 0.36 0.12 0.02 0.34
#> TCGA.J4.AATZ.01 4 0.0000 0.4646 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9L5.01 2 0.2945 0.8740 0.00 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.KK.A7AQ.01 3 0.0504 0.9007 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.YL.A8SR.01 5 0.6257 0.3525 0.00 0.00 0.28 0.00 0.48 0.12 0.12
#> TCGA.KK.A8IK.01 1 0.0504 0.7405 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.KK.A59X.01 2 0.2945 0.8740 0.00 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.EJ.7789.01 7 0.5052 0.2362 0.00 0.02 0.14 0.00 0.00 0.22 0.62
#> TCGA.FC.A4JI.01 4 0.5404 0.2362 0.00 0.00 0.00 0.62 0.16 0.16 0.06
#> TCGA.KK.A5A1.01 2 0.1006 0.7775 0.00 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.HC.7080.01 2 0.1006 0.7775 0.00 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.V1.A9O5.06 2 0.2945 0.8740 0.00 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.KC.A7F5.01 1 0.0000 0.7415 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7782.01 5 0.0000 0.6685 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XK.AAJ3.01 4 0.5128 -0.0943 0.00 0.00 0.18 0.54 0.00 0.28 0.00
#> TCGA.XK.AAK1.01 4 0.6669 0.3522 0.18 0.00 0.00 0.36 0.12 0.00 0.34
#> TCGA.TP.A8TV.01 5 0.0863 0.6738 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.FC.A6HD.01 4 0.0863 0.4465 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.QU.A6IL.01 1 0.0000 0.7415 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A83J.01 7 0.5644 -0.4756 0.34 0.00 0.00 0.32 0.00 0.00 0.34
#> TCGA.XJ.A83G.01 1 0.5644 -0.2152 0.34 0.00 0.00 0.32 0.00 0.00 0.34
#> TCGA.G9.6496.01 5 0.5976 -0.2849 0.00 0.00 0.00 0.34 0.38 0.02 0.26
#> TCGA.KK.A59Z.01 2 0.2945 0.8740 0.00 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.EJ.A65J.01 1 0.0504 0.7405 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.2A.A8VX.01 3 0.1433 0.8835 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.HC.7738.01 1 0.0504 0.7405 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EJ.7123.01 4 0.6756 0.3590 0.06 0.00 0.00 0.36 0.22 0.02 0.34
#> TCGA.2A.A8W1.01 4 0.1363 0.4684 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.EJ.7312.01 2 0.2945 0.8740 0.00 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.V1.A8MM.01 5 0.6257 0.3525 0.00 0.00 0.28 0.00 0.48 0.12 0.12
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EJ.7125.01 7 0.1874 0.7934 0.02 0.00 0.00 0.02 0.02 0.02 0.92 0.00
#> TCGA.YL.A9WI.01 2 0.4028 0.7405 0.00 0.66 0.04 0.00 0.00 0.28 0.02 0.00
#> TCGA.HC.A6AO.01 5 0.2680 0.7546 0.00 0.00 0.02 0.00 0.84 0.12 0.00 0.02
#> TCGA.CH.5761.01 3 0.3021 0.7097 0.02 0.00 0.80 0.02 0.00 0.00 0.00 0.16
#> TCGA.XK.AAJA.01 1 0.2224 0.9890 0.86 0.00 0.00 0.12 0.00 0.02 0.00 0.00
#> TCGA.KK.A6E8.01 1 0.2224 0.9890 0.86 0.00 0.00 0.12 0.00 0.02 0.00 0.00
#> TCGA.V1.A9OQ.01 4 0.2025 0.8180 0.10 0.00 0.00 0.88 0.00 0.02 0.00 0.00
#> TCGA.YL.A8HM.01 3 0.2864 0.8360 0.00 0.00 0.84 0.00 0.06 0.02 0.08 0.00
#> TCGA.M7.A722.01 7 0.2719 0.6741 0.00 0.18 0.00 0.00 0.00 0.02 0.80 0.00
#> TCGA.VN.A88R.01 4 0.0808 0.9020 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.Y6.A9XI.01 1 0.1765 0.9890 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.CH.5737.01 4 0.0808 0.9020 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IF.01 5 0.0000 0.8148 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5767.01 4 0.0808 0.8906 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.J4.AATZ.01 8 0.4342 0.2608 0.00 0.00 0.00 0.18 0.00 0.18 0.00 0.64
#> TCGA.ZG.A9L5.01 2 0.0000 0.8587 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AQ.01 3 0.2648 0.8344 0.00 0.00 0.84 0.00 0.08 0.00 0.08 0.00
#> TCGA.YL.A8SR.01 5 0.4948 0.6936 0.02 0.00 0.12 0.00 0.66 0.04 0.16 0.00
#> TCGA.KK.A8IK.01 1 0.1765 0.9890 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.KK.A59X.01 2 0.0808 0.8517 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.EJ.7789.01 7 0.0000 0.8111 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FC.A4JI.01 6 0.4559 0.0000 0.00 0.00 0.00 0.08 0.02 0.60 0.00 0.30
#> TCGA.KK.A5A1.01 2 0.3843 0.7581 0.04 0.70 0.00 0.00 0.00 0.24 0.02 0.00
#> TCGA.HC.7080.01 2 0.4028 0.7405 0.00 0.66 0.04 0.00 0.00 0.28 0.02 0.00
#> TCGA.V1.A9O5.06 2 0.0000 0.8587 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F5.01 1 0.2224 0.9890 0.86 0.00 0.00 0.12 0.00 0.02 0.00 0.00
#> TCGA.EJ.7782.01 5 0.0808 0.8009 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.XK.AAJ3.01 8 0.3262 0.0763 0.02 0.00 0.10 0.02 0.00 0.04 0.00 0.82
#> TCGA.XK.AAK1.01 4 0.0808 0.8906 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.TP.A8TV.01 5 0.0000 0.8148 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 8 0.3729 0.2322 0.00 0.00 0.00 0.10 0.00 0.18 0.00 0.72
#> TCGA.QU.A6IL.01 1 0.2224 0.9890 0.86 0.00 0.00 0.12 0.00 0.02 0.00 0.00
#> TCGA.J4.A83J.01 4 0.0808 0.9020 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.XJ.A83G.01 4 0.0808 0.9020 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.G9.6496.01 4 0.4838 0.4287 0.00 0.00 0.00 0.66 0.08 0.14 0.00 0.12
#> TCGA.KK.A59Z.01 2 0.0000 0.8587 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65J.01 1 0.1765 0.9890 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VX.01 3 0.2858 0.7896 0.04 0.00 0.86 0.00 0.00 0.04 0.04 0.02
#> TCGA.HC.7738.01 1 0.1765 0.9890 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.EJ.7123.01 4 0.1091 0.8688 0.00 0.00 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.2A.A8W1.01 8 0.3237 0.2325 0.00 0.00 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.EJ.7312.01 2 0.0000 0.8587 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MM.01 5 0.5103 0.6735 0.02 0.00 0.14 0.00 0.64 0.04 0.16 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node05121-leaf , Node05122-leaf , Node05123-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 21 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.900 0.942 0.974 0.2913 0.743 0.743
#> 3 3 1.000 1.000 1.000 1.0610 0.657 0.538
#> 4 4 1.000 0.993 0.995 0.0620 0.962 0.905
#> 5 5 0.853 0.786 0.915 0.0492 0.986 0.961
#> 6 6 0.852 0.763 0.923 0.0301 0.990 0.973
#> 7 7 0.858 0.568 0.841 0.0411 0.924 0.781
#> 8 8 0.921 0.639 0.910 0.0401 0.986 0.950
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.XK.AAJA.01 2 0.000 0.967 0.00 1.00
#> TCGA.KK.A6E8.01 2 0.855 0.635 0.28 0.72
#> TCGA.V1.A9OQ.01 2 0.000 0.967 0.00 1.00
#> TCGA.VN.A88R.01 2 0.000 0.967 0.00 1.00
#> TCGA.Y6.A9XI.01 2 0.000 0.967 0.00 1.00
#> TCGA.CH.5737.01 2 0.000 0.967 0.00 1.00
#> TCGA.CH.5767.01 2 0.000 0.967 0.00 1.00
#> TCGA.J4.AATZ.01 2 0.000 0.967 0.00 1.00
#> TCGA.KK.A8IK.01 1 0.000 1.000 1.00 0.00
#> TCGA.FC.A4JI.01 1 0.000 1.000 1.00 0.00
#> TCGA.KC.A7F5.01 2 0.827 0.667 0.26 0.74
#> TCGA.XK.AAK1.01 2 0.000 0.967 0.00 1.00
#> TCGA.FC.A6HD.01 2 0.000 0.967 0.00 1.00
#> TCGA.QU.A6IL.01 2 0.000 0.967 0.00 1.00
#> TCGA.J4.A83J.01 2 0.000 0.967 0.00 1.00
#> TCGA.XJ.A83G.01 2 0.000 0.967 0.00 1.00
#> TCGA.G9.6496.01 2 0.000 0.967 0.00 1.00
#> TCGA.EJ.A65J.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.7738.01 2 0.000 0.967 0.00 1.00
#> TCGA.EJ.7123.01 2 0.000 0.967 0.00 1.00
#> TCGA.2A.A8W1.01 2 0.000 0.967 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.XK.AAJA.01 2 0 1 0 1 0
#> TCGA.KK.A6E8.01 3 0 1 0 0 1
#> TCGA.V1.A9OQ.01 2 0 1 0 1 0
#> TCGA.VN.A88R.01 2 0 1 0 1 0
#> TCGA.Y6.A9XI.01 3 0 1 0 0 1
#> TCGA.CH.5737.01 2 0 1 0 1 0
#> TCGA.CH.5767.01 2 0 1 0 1 0
#> TCGA.J4.AATZ.01 3 0 1 0 0 1
#> TCGA.KK.A8IK.01 1 0 1 1 0 0
#> TCGA.FC.A4JI.01 1 0 1 1 0 0
#> TCGA.KC.A7F5.01 3 0 1 0 0 1
#> TCGA.XK.AAK1.01 2 0 1 0 1 0
#> TCGA.FC.A6HD.01 2 0 1 0 1 0
#> TCGA.QU.A6IL.01 3 0 1 0 0 1
#> TCGA.J4.A83J.01 2 0 1 0 1 0
#> TCGA.XJ.A83G.01 2 0 1 0 1 0
#> TCGA.G9.6496.01 2 0 1 0 1 0
#> TCGA.EJ.A65J.01 1 0 1 1 0 0
#> TCGA.HC.7738.01 3 0 1 0 0 1
#> TCGA.EJ.7123.01 2 0 1 0 1 0
#> TCGA.2A.A8W1.01 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.XK.AAJA.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.KK.A6E8.01 3 0.000 0.967 0 0.00 1.00 0.00
#> TCGA.V1.A9OQ.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.VN.A88R.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.Y6.A9XI.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.CH.5737.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.CH.5767.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.J4.AATZ.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.KK.A8IK.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.KC.A7F5.01 3 0.000 0.967 0 0.00 1.00 0.00
#> TCGA.XK.AAK1.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.FC.A6HD.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.QU.A6IL.01 3 0.121 0.961 0 0.00 0.96 0.04
#> TCGA.J4.A83J.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.G9.6496.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.EJ.A65J.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.HC.7738.01 3 0.191 0.949 0 0.02 0.94 0.04
#> TCGA.EJ.7123.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.2A.A8W1.01 2 0.000 1.000 0 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.XK.AAJA.01 2 0.410 0.732 0.00 0.76 0.20 0.00 0.04
#> TCGA.KK.A6E8.01 3 0.380 -0.190 0.00 0.00 0.70 0.00 0.30
#> TCGA.V1.A9OQ.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.VN.A88R.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.Y6.A9XI.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.CH.5737.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5767.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.AATZ.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.KK.A8IK.01 1 0.000 0.848 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 1 0.000 0.848 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F5.01 5 0.423 0.000 0.00 0.00 0.42 0.00 0.58
#> TCGA.XK.AAK1.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.QU.A6IL.01 3 0.000 0.616 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.A83J.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6496.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A65J.01 1 0.406 0.673 0.64 0.00 0.00 0.00 0.36
#> TCGA.HC.7738.01 3 0.165 0.596 0.00 0.02 0.94 0.00 0.04
#> TCGA.EJ.7123.01 2 0.000 0.960 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.A8W1.01 2 0.411 0.785 0.00 0.80 0.14 0.02 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.XK.AAJA.01 2 0.511 0.600 0.0 0.66 0.22 0.00 0.02 0.10
#> TCGA.KK.A6E8.01 3 0.458 0.172 0.0 0.00 0.56 0.00 0.40 0.04
#> TCGA.V1.A9OQ.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88R.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.Y6.A9XI.01 4 0.279 0.882 0.0 0.00 0.00 0.86 0.06 0.08
#> TCGA.CH.5737.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5767.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.AATZ.01 4 0.000 0.882 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.KK.A8IK.01 1 0.000 1.000 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 1 0.000 1.000 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F5.01 5 0.205 0.000 0.0 0.00 0.12 0.00 0.88 0.00
#> TCGA.XK.AAK1.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 2 0.109 0.919 0.0 0.96 0.00 0.00 0.02 0.02
#> TCGA.QU.A6IL.01 3 0.156 0.680 0.0 0.00 0.92 0.00 0.08 0.00
#> TCGA.J4.A83J.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6496.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65J.01 6 0.331 0.000 0.2 0.00 0.02 0.00 0.00 0.78
#> TCGA.HC.7738.01 3 0.000 0.670 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7123.01 2 0.000 0.944 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8W1.01 2 0.509 0.718 0.0 0.74 0.08 0.04 0.04 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.XK.AAJA.01 2 0.5055 0.1221 0 0.56 0.18 0.00 0.00 0.00 0.26
#> TCGA.KK.A6E8.01 4 0.3815 -0.4212 0 0.00 0.36 0.62 0.00 0.02 0.00
#> TCGA.V1.A9OQ.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88R.01 2 0.0504 0.9252 0 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.Y6.A9XI.01 7 0.5589 -0.5424 0 0.00 0.00 0.28 0.32 0.00 0.40
#> TCGA.CH.5737.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5767.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.AATZ.01 4 0.5612 -0.3541 0 0.00 0.00 0.36 0.36 0.00 0.28
#> TCGA.KK.A8IK.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A4JI.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F5.01 5 0.3358 0.0000 0 0.00 0.00 0.36 0.64 0.00 0.00
#> TCGA.XK.AAK1.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A6HD.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IL.01 3 0.1664 0.8929 0 0.00 0.92 0.06 0.02 0.00 0.00
#> TCGA.J4.A83J.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6496.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65J.01 6 0.0000 0.0000 0 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.7738.01 3 0.0504 0.8939 0 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EJ.7123.01 2 0.0000 0.9439 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8W1.01 7 0.4175 -0.0939 0 0.38 0.04 0.00 0.00 0.00 0.58
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.XK.AAJA.01 2 0.5455 -0.358 0 0.40 0.20 0.02 0.00 0 0.00 0.38
#> TCGA.KK.A6E8.01 4 0.4669 0.000 0 0.00 0.22 0.58 0.20 0 0.00 0.00
#> TCGA.V1.A9OQ.01 2 0.0000 0.918 0 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.VN.A88R.01 2 0.0000 0.918 0 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.Y6.A9XI.01 7 0.4302 0.570 0 0.00 0.00 0.36 0.00 0 0.56 0.08
#> TCGA.CH.5737.01 2 0.0471 0.908 0 0.98 0.00 0.02 0.00 0 0.00 0.00
#> TCGA.CH.5767.01 2 0.0000 0.918 0 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.J4.AATZ.01 7 0.0471 0.570 0 0.00 0.00 0.00 0.00 0 0.98 0.02
#> TCGA.KK.A8IK.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.FC.A4JI.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.KC.A7F5.01 5 0.0000 0.000 0 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.XK.AAK1.01 2 0.0000 0.918 0 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.FC.A6HD.01 2 0.1275 0.877 0 0.94 0.00 0.02 0.00 0 0.00 0.04
#> TCGA.QU.A6IL.01 3 0.3002 0.752 0 0.00 0.82 0.12 0.02 0 0.00 0.04
#> TCGA.J4.A83J.01 2 0.0000 0.918 0 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.XJ.A83G.01 2 0.0000 0.918 0 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.G9.6496.01 2 0.0941 0.896 0 0.96 0.00 0.02 0.00 0 0.00 0.02
#> TCGA.EJ.A65J.01 6 0.0000 0.000 0 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.HC.7738.01 3 0.0000 0.769 0 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EJ.7123.01 2 0.0000 0.918 0 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.2A.A8W1.01 8 0.1765 0.000 0 0.12 0.00 0.00 0.00 0 0.00 0.88
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-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 42 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5115 0.489 0.489
#> 3 3 1.000 0.967 0.987 0.3021 0.791 0.596
#> 4 4 0.728 0.625 0.813 0.1205 0.959 0.880
#> 5 5 0.806 0.727 0.846 0.0691 0.862 0.558
#> 6 6 0.823 0.793 0.869 0.0397 0.919 0.617
#> 7 7 0.867 0.844 0.912 0.0263 0.991 0.941
#> 8 8 0.879 0.744 0.859 0.0216 0.992 0.945
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.KK.A8IA.01 1 0 1 1 0
#> TCGA.V1.A9OF.01 2 0 1 0 1
#> TCGA.CH.5788.01 2 0 1 0 1
#> TCGA.KK.A7AZ.01 2 0 1 0 1
#> TCGA.J9.A8CL.01 1 0 1 1 0
#> TCGA.HC.7075.01 2 0 1 0 1
#> TCGA.G9.6361.01 1 0 1 1 0
#> TCGA.EJ.5511.01 2 0 1 0 1
#> TCGA.EJ.5517.01 2 0 1 0 1
#> TCGA.J4.AAU2.01 2 0 1 0 1
#> TCGA.KC.A4BV.01 1 0 1 1 0
#> TCGA.EJ.7315.01 1 0 1 1 0
#> TCGA.YL.A9WK.01 1 0 1 1 0
#> TCGA.HC.7078.01 1 0 1 1 0
#> TCGA.FC.A5OB.01 1 0 1 1 0
#> TCGA.J9.A52D.01 1 0 1 1 0
#> TCGA.EJ.7788.01 1 0 1 1 0
#> TCGA.ZG.A9L1.01 2 0 1 0 1
#> TCGA.VP.A875.01 1 0 1 1 0
#> TCGA.KC.A7FD.01 2 0 1 0 1
#> TCGA.J4.A83I.01 1 0 1 1 0
#> TCGA.XQ.A8TA.01 1 0 1 1 0
#> TCGA.HC.7212.01 2 0 1 0 1
#> TCGA.2A.A8VO.01 2 0 1 0 1
#> TCGA.VN.A88P.01 2 0 1 0 1
#> TCGA.KK.A7AY.01 1 0 1 1 0
#> TCGA.2A.AAYU.01 2 0 1 0 1
#> TCGA.EJ.5494.01 1 0 1 1 0
#> TCGA.HC.7213.01 2 0 1 0 1
#> TCGA.CH.5772.01 1 0 1 1 0
#> TCGA.2A.AAYO.01 2 0 1 0 1
#> TCGA.CH.5753.01 2 0 1 0 1
#> TCGA.YL.A8SH.01 1 0 1 1 0
#> TCGA.HC.7744.01 2 0 1 0 1
#> TCGA.HC.A8CY.01 1 0 1 1 0
#> TCGA.KK.A7AW.01 1 0 1 1 0
#> TCGA.V1.A9ZI.01 2 0 1 0 1
#> TCGA.YL.A8SQ.01 1 0 1 1 0
#> TCGA.KK.A7B4.01 2 0 1 0 1
#> TCGA.HC.7752.01 2 0 1 0 1
#> TCGA.J4.8198.01 2 0 1 0 1
#> TCGA.CH.5768.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.KK.A8IA.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.V1.A9OF.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CH.5788.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.KK.A7AZ.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.J9.A8CL.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HC.7075.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.G9.6361.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.EJ.5511.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.EJ.5517.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.J4.AAU2.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.KC.A4BV.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.EJ.7315.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.YL.A9WK.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HC.7078.01 1 0.6126 0.353 0.60 0.40 0.00
#> TCGA.FC.A5OB.01 1 0.3340 0.850 0.88 0.12 0.00
#> TCGA.J9.A52D.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.EJ.7788.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.ZG.A9L1.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.VP.A875.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.KC.A7FD.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.J4.A83I.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.XQ.A8TA.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HC.7212.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.2A.A8VO.01 3 0.0892 0.979 0.00 0.02 0.98
#> TCGA.VN.A88P.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.KK.A7AY.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.2A.AAYU.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.EJ.5494.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HC.7213.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.CH.5772.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.2A.AAYO.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.CH.5753.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.YL.A8SH.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HC.7744.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HC.A8CY.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.KK.A7AW.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.V1.A9ZI.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.YL.A8SQ.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.KK.A7B4.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HC.7752.01 3 0.0000 0.998 0.00 0.00 1.00
#> TCGA.J4.8198.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CH.5768.01 2 0.0000 1.000 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.KK.A8IA.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.V1.A9OF.01 4 0.7497 0.403 0.26 0.24 0.00 0.50
#> TCGA.CH.5788.01 2 0.0000 0.723 0.00 1.00 0.00 0.00
#> TCGA.KK.A7AZ.01 3 0.0000 0.939 0.00 0.00 1.00 0.00
#> TCGA.J9.A8CL.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.HC.7075.01 4 0.4994 0.278 0.00 0.48 0.00 0.52
#> TCGA.G9.6361.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.EJ.5511.01 3 0.0000 0.939 0.00 0.00 1.00 0.00
#> TCGA.EJ.5517.01 3 0.0000 0.939 0.00 0.00 1.00 0.00
#> TCGA.J4.AAU2.01 3 0.4406 0.554 0.00 0.00 0.70 0.30
#> TCGA.KC.A4BV.01 1 0.0000 0.608 1.00 0.00 0.00 0.00
#> TCGA.EJ.7315.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.YL.A9WK.01 1 0.4134 0.703 0.74 0.00 0.00 0.26
#> TCGA.HC.7078.01 1 0.4472 0.315 0.76 0.02 0.00 0.22
#> TCGA.FC.A5OB.01 1 0.4642 0.275 0.74 0.02 0.00 0.24
#> TCGA.J9.A52D.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.EJ.7788.01 2 0.4948 0.198 0.44 0.56 0.00 0.00
#> TCGA.ZG.A9L1.01 3 0.0000 0.939 0.00 0.00 1.00 0.00
#> TCGA.VP.A875.01 2 0.4948 0.198 0.44 0.56 0.00 0.00
#> TCGA.KC.A7FD.01 2 0.0000 0.723 0.00 1.00 0.00 0.00
#> TCGA.J4.A83I.01 1 0.0707 0.619 0.98 0.00 0.00 0.02
#> TCGA.XQ.A8TA.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.HC.7212.01 2 0.0000 0.723 0.00 1.00 0.00 0.00
#> TCGA.2A.A8VO.01 4 0.7816 0.368 0.00 0.26 0.34 0.40
#> TCGA.VN.A88P.01 2 0.4855 -0.237 0.00 0.60 0.00 0.40
#> TCGA.KK.A7AY.01 1 0.3801 0.693 0.78 0.00 0.00 0.22
#> TCGA.2A.AAYU.01 3 0.0000 0.939 0.00 0.00 1.00 0.00
#> TCGA.EJ.5494.01 1 0.2647 0.496 0.88 0.00 0.00 0.12
#> TCGA.HC.7213.01 3 0.0000 0.939 0.00 0.00 1.00 0.00
#> TCGA.CH.5772.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.2A.AAYO.01 3 0.2647 0.832 0.00 0.00 0.88 0.12
#> TCGA.CH.5753.01 2 0.0000 0.723 0.00 1.00 0.00 0.00
#> TCGA.YL.A8SH.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.HC.7744.01 2 0.0000 0.723 0.00 1.00 0.00 0.00
#> TCGA.HC.A8CY.01 1 0.0707 0.619 0.98 0.00 0.00 0.02
#> TCGA.KK.A7AW.01 1 0.0000 0.608 1.00 0.00 0.00 0.00
#> TCGA.V1.A9ZI.01 2 0.4855 -0.237 0.00 0.60 0.00 0.40
#> TCGA.YL.A8SQ.01 1 0.4994 0.735 0.52 0.00 0.00 0.48
#> TCGA.KK.A7B4.01 2 0.0707 0.701 0.00 0.98 0.00 0.02
#> TCGA.HC.7752.01 3 0.0000 0.939 0.00 0.00 1.00 0.00
#> TCGA.J4.8198.01 2 0.0000 0.723 0.00 1.00 0.00 0.00
#> TCGA.CH.5768.01 2 0.0000 0.723 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.KK.A8IA.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.V1.A9OF.01 4 0.5005 0.4450 0.06 0.02 0.00 0.72 0.20
#> TCGA.CH.5788.01 2 0.2331 0.8468 0.00 0.90 0.00 0.02 0.08
#> TCGA.KK.A7AZ.01 3 0.0000 0.9257 0.00 0.00 1.00 0.00 0.00
#> TCGA.J9.A8CL.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.HC.7075.01 4 0.1732 0.7035 0.00 0.08 0.00 0.92 0.00
#> TCGA.G9.6361.01 1 0.4302 -0.5452 0.52 0.00 0.00 0.00 0.48
#> TCGA.EJ.5511.01 3 0.0000 0.9257 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5517.01 3 0.0000 0.9257 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.AAU2.01 4 0.3684 0.5221 0.00 0.00 0.28 0.72 0.00
#> TCGA.KC.A4BV.01 1 0.0000 0.6553 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7315.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.YL.A9WK.01 1 0.3983 0.0580 0.66 0.00 0.00 0.00 0.34
#> TCGA.HC.7078.01 1 0.6244 0.4512 0.54 0.00 0.00 0.26 0.20
#> TCGA.FC.A5OB.01 1 0.6327 0.4167 0.52 0.00 0.00 0.28 0.20
#> TCGA.J9.A52D.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.EJ.7788.01 2 0.3999 0.6790 0.24 0.74 0.00 0.00 0.02
#> TCGA.ZG.A9L1.01 3 0.0000 0.9257 0.00 0.00 1.00 0.00 0.00
#> TCGA.VP.A875.01 2 0.4613 0.5186 0.36 0.62 0.00 0.00 0.02
#> TCGA.KC.A7FD.01 2 0.0609 0.8924 0.00 0.98 0.00 0.00 0.02
#> TCGA.J4.A83I.01 1 0.0609 0.6425 0.98 0.00 0.00 0.00 0.02
#> TCGA.XQ.A8TA.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.HC.7212.01 2 0.0000 0.8967 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.A8VO.01 4 0.4433 0.6364 0.00 0.06 0.20 0.74 0.00
#> TCGA.VN.A88P.01 4 0.3895 0.6321 0.00 0.32 0.00 0.68 0.00
#> TCGA.KK.A7AY.01 1 0.1410 0.6015 0.94 0.00 0.00 0.00 0.06
#> TCGA.2A.AAYU.01 3 0.0000 0.9257 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5494.01 1 0.6146 0.4745 0.56 0.00 0.00 0.24 0.20
#> TCGA.HC.7213.01 3 0.0000 0.9257 0.00 0.00 1.00 0.00 0.00
#> TCGA.CH.5772.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.2A.AAYO.01 3 0.4262 0.0865 0.00 0.00 0.56 0.44 0.00
#> TCGA.CH.5753.01 2 0.0609 0.8924 0.00 0.98 0.00 0.00 0.02
#> TCGA.YL.A8SH.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.HC.7744.01 2 0.0000 0.8967 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 1 0.0000 0.6553 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 1 0.0000 0.6553 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZI.01 4 0.3895 0.6321 0.00 0.32 0.00 0.68 0.00
#> TCGA.YL.A8SQ.01 5 0.3684 1.0000 0.28 0.00 0.00 0.00 0.72
#> TCGA.KK.A7B4.01 2 0.0000 0.8967 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7752.01 3 0.0000 0.9257 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.8198.01 2 0.0000 0.8967 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5768.01 2 0.0000 0.8967 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.KK.A8IA.01 5 0.0547 0.936 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.V1.A9OF.01 6 0.3315 0.443 0.02 0.00 0.00 0.20 0.00 0.78
#> TCGA.CH.5788.01 2 0.6768 0.294 0.12 0.44 0.00 0.10 0.00 0.34
#> TCGA.KK.A7AZ.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J9.A8CL.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.7075.01 4 0.2474 0.731 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.G9.6361.01 1 0.3851 0.302 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.EJ.5511.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5517.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.AAU2.01 4 0.2048 0.728 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.KC.A4BV.01 1 0.2048 0.785 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.EJ.7315.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.YL.A9WK.01 5 0.3409 0.432 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.HC.7078.01 6 0.3578 0.823 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.FC.A5OB.01 6 0.3578 0.823 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.J9.A52D.01 5 0.0547 0.936 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.EJ.7788.01 2 0.4700 0.404 0.34 0.60 0.00 0.00 0.00 0.06
#> TCGA.ZG.A9L1.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VP.A875.01 1 0.4552 0.331 0.64 0.30 0.00 0.00 0.00 0.06
#> TCGA.KC.A7FD.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A83I.01 1 0.2048 0.785 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.XQ.A8TA.01 5 0.0547 0.936 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.HC.7212.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VO.01 4 0.2725 0.747 0.00 0.04 0.06 0.88 0.00 0.02
#> TCGA.VN.A88P.01 4 0.5977 0.646 0.04 0.22 0.00 0.58 0.00 0.16
#> TCGA.KK.A7AY.01 1 0.2260 0.772 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.2A.AAYU.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5494.01 6 0.4078 0.809 0.34 0.00 0.00 0.00 0.02 0.64
#> TCGA.HC.7213.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5772.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.2A.AAYO.01 4 0.3309 0.593 0.00 0.00 0.28 0.72 0.00 0.00
#> TCGA.CH.5753.01 2 0.0547 0.864 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SH.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.7744.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 1 0.2048 0.785 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.KK.A7AW.01 1 0.2048 0.785 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.V1.A9ZI.01 4 0.5977 0.646 0.04 0.22 0.00 0.58 0.00 0.16
#> TCGA.YL.A8SQ.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.KK.A7B4.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7752.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.8198.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5768.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.KK.A8IA.01 5 0.2376 0.893 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.V1.A9OF.01 6 0.0863 0.807 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.CH.5788.01 7 0.2864 0.000 0.02 0.12 0.00 0.02 0.00 0.00 0.84
#> TCGA.KK.A7AZ.01 3 0.0504 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.J9.A8CL.01 5 0.0000 0.916 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.7075.01 4 0.0504 0.816 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.G9.6361.01 1 0.2832 0.788 0.76 0.00 0.00 0.00 0.24 0.00 0.00
#> TCGA.EJ.5511.01 3 0.0504 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EJ.5517.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.AAU2.01 4 0.1006 0.814 0.02 0.00 0.02 0.96 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 1 0.1928 0.877 0.90 0.00 0.00 0.00 0.08 0.00 0.02
#> TCGA.EJ.7315.01 5 0.0504 0.906 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.YL.A9WK.01 5 0.1886 0.809 0.12 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.HC.7078.01 6 0.1886 0.930 0.12 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.FC.A5OB.01 6 0.1886 0.930 0.12 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.J9.A52D.01 5 0.2376 0.893 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.EJ.7788.01 2 0.4718 0.399 0.32 0.60 0.00 0.00 0.00 0.02 0.06
#> TCGA.ZG.A9L1.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A875.01 1 0.2769 0.681 0.86 0.08 0.00 0.00 0.00 0.02 0.04
#> TCGA.KC.A7FD.01 2 0.1363 0.873 0.04 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.J4.A83I.01 1 0.1671 0.882 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.XQ.A8TA.01 5 0.2376 0.893 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.HC.7212.01 2 0.0504 0.892 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8VO.01 4 0.0504 0.816 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.VN.A88P.01 4 0.4702 0.643 0.00 0.04 0.00 0.68 0.00 0.08 0.20
#> TCGA.KK.A7AY.01 1 0.2422 0.852 0.82 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.2A.AAYU.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5494.01 6 0.2376 0.915 0.12 0.00 0.00 0.00 0.02 0.86 0.00
#> TCGA.HC.7213.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5772.01 5 0.0000 0.916 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.2A.AAYO.01 4 0.2421 0.763 0.02 0.00 0.08 0.88 0.00 0.00 0.02
#> TCGA.CH.5753.01 2 0.2509 0.827 0.06 0.88 0.00 0.00 0.00 0.02 0.04
#> TCGA.YL.A8SH.01 5 0.1664 0.907 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.HC.7744.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 1 0.1928 0.877 0.90 0.00 0.00 0.00 0.08 0.00 0.02
#> TCGA.KK.A7AW.01 1 0.2081 0.872 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.V1.A9ZI.01 4 0.4702 0.643 0.00 0.04 0.00 0.68 0.00 0.08 0.20
#> TCGA.YL.A8SQ.01 5 0.0000 0.916 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.KK.A7B4.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7752.01 3 0.0504 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.J4.8198.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5768.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.KK.A8IA.01 5 0.3015 0.729 0.00 0.00 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.V1.A9OF.01 6 0.1765 0.869 0.00 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.CH.5788.01 7 0.0471 0.000 0.00 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.KK.A7AZ.01 3 0.0471 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.J9.A8CL.01 5 0.0000 0.819 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7075.01 4 0.0941 0.777 0.02 0.00 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.G9.6361.01 1 0.2114 0.813 0.84 0.00 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.EJ.5511.01 3 0.0471 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EJ.5517.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.AAU2.01 4 0.0000 0.774 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 1 0.0941 0.823 0.96 0.00 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.EJ.7315.01 5 0.0471 0.808 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.YL.A9WK.01 5 0.3036 0.600 0.18 0.00 0.00 0.00 0.78 0.04 0.00 0.00
#> TCGA.HC.7078.01 6 0.0471 0.949 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.FC.A5OB.01 6 0.0941 0.945 0.02 0.00 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.J9.A52D.01 5 0.3015 0.729 0.00 0.00 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.EJ.7788.01 8 0.5577 0.000 0.26 0.32 0.00 0.00 0.00 0.00 0.02 0.40
#> TCGA.ZG.A9L1.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A875.01 1 0.2981 0.507 0.76 0.02 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.KC.A7FD.01 2 0.3449 0.393 0.00 0.66 0.00 0.00 0.00 0.00 0.02 0.32
#> TCGA.J4.A83I.01 1 0.0808 0.835 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.XQ.A8TA.01 5 0.3015 0.729 0.00 0.00 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.HC.7212.01 2 0.2406 0.608 0.00 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.2A.A8VO.01 4 0.0941 0.777 0.02 0.00 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.VN.A88P.01 4 0.6034 0.501 0.00 0.14 0.00 0.54 0.00 0.02 0.16 0.14
#> TCGA.KK.A7AY.01 1 0.2404 0.817 0.84 0.00 0.00 0.00 0.14 0.02 0.00 0.00
#> TCGA.2A.AAYU.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5494.01 6 0.0471 0.949 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.HC.7213.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5772.01 5 0.0000 0.819 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.AAYO.01 4 0.0941 0.761 0.00 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.CH.5753.01 2 0.3570 0.278 0.00 0.62 0.00 0.00 0.00 0.00 0.02 0.36
#> TCGA.YL.A8SH.01 5 0.1765 0.794 0.00 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.HC.7744.01 2 0.0471 0.746 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HC.A8CY.01 1 0.1275 0.812 0.94 0.00 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.KK.A7AW.01 1 0.2725 0.805 0.82 0.00 0.00 0.00 0.14 0.04 0.00 0.00
#> TCGA.V1.A9ZI.01 4 0.6034 0.501 0.00 0.14 0.00 0.54 0.00 0.02 0.16 0.14
#> TCGA.YL.A8SQ.01 5 0.0000 0.819 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A7B4.01 2 0.0000 0.749 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7752.01 3 0.0471 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.J4.8198.01 2 0.0000 0.749 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5768.01 2 0.0000 0.749 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node023. Child nodes: Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node05121-leaf , Node05122-leaf , Node05123-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 18 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.998 0.999 0.5041 0.497 0.497
#> 3 3 1.000 0.998 0.999 0.1953 0.889 0.779
#> 4 4 0.863 0.787 0.924 0.0895 0.928 0.823
#> 5 5 0.902 0.734 0.923 0.0687 0.948 0.846
#> 6 6 0.915 0.605 0.897 0.0308 0.954 0.851
#> 7 7 0.961 0.722 0.926 0.0270 0.961 0.864
#> 8 8 0.974 0.639 0.862 0.0145 0.993 0.974
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 5
There is also optional best \(k\) = 2 3 5 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.KK.A8IA.01 1 0.000 1.000 1.00 0.00
#> TCGA.J9.A8CL.01 2 0.000 0.998 0.00 1.00
#> TCGA.G9.6361.01 1 0.000 1.000 1.00 0.00
#> TCGA.KC.A4BV.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.7315.01 1 0.000 1.000 1.00 0.00
#> TCGA.YL.A9WK.01 2 0.000 0.998 0.00 1.00
#> TCGA.HC.7078.01 2 0.000 0.998 0.00 1.00
#> TCGA.FC.A5OB.01 2 0.000 0.998 0.00 1.00
#> TCGA.J9.A52D.01 2 0.000 0.998 0.00 1.00
#> TCGA.J4.A83I.01 1 0.000 1.000 1.00 0.00
#> TCGA.XQ.A8TA.01 2 0.000 0.998 0.00 1.00
#> TCGA.KK.A7AY.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.5494.01 2 0.000 0.998 0.00 1.00
#> TCGA.CH.5772.01 2 0.000 0.998 0.00 1.00
#> TCGA.YL.A8SH.01 2 0.000 0.998 0.00 1.00
#> TCGA.HC.A8CY.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A7AW.01 2 0.141 0.980 0.02 0.98
#> TCGA.YL.A8SQ.01 2 0.000 0.998 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.KK.A8IA.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.J9.A8CL.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.G9.6361.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.KC.A4BV.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.EJ.7315.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.YL.A9WK.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HC.7078.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.FC.A5OB.01 2 0.0892 0.980 0 0.98 0.02
#> TCGA.J9.A52D.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.J4.A83I.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.XQ.A8TA.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.KK.A7AY.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.EJ.5494.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.CH.5772.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.YL.A8SH.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HC.A8CY.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.KK.A7AW.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.YL.A8SQ.01 2 0.0000 0.998 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.KK.A8IA.01 1 0.2345 0.824 0.90 0.00 0.00 0.10
#> TCGA.J9.A8CL.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.G9.6361.01 1 0.0000 0.873 1.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 1 0.4134 0.769 0.74 0.00 0.00 0.26
#> TCGA.EJ.7315.01 1 0.4134 0.769 0.74 0.00 0.00 0.26
#> TCGA.YL.A9WK.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.HC.7078.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FC.A5OB.01 3 0.4713 0.308 0.00 0.36 0.64 0.00
#> TCGA.J9.A52D.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.J4.A83I.01 1 0.0000 0.873 1.00 0.00 0.00 0.00
#> TCGA.XQ.A8TA.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.KK.A7AY.01 1 0.0707 0.868 0.98 0.00 0.00 0.02
#> TCGA.EJ.5494.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.CH.5772.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.YL.A8SH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.HC.A8CY.01 4 0.4713 0.000 0.00 0.00 0.36 0.64
#> TCGA.KK.A7AW.01 3 0.0000 -0.111 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SQ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.KK.A8IA.01 5 0.202 0.432 0.10 0.00 0.00 0.0 0.90
#> TCGA.J9.A8CL.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.G9.6361.01 1 0.398 0.440 0.66 0.00 0.00 0.0 0.34
#> TCGA.KC.A4BV.01 1 0.141 0.591 0.94 0.00 0.00 0.0 0.06
#> TCGA.EJ.7315.01 1 0.000 0.555 1.00 0.00 0.00 0.0 0.00
#> TCGA.YL.A9WK.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.HC.7078.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.FC.A5OB.01 3 0.104 0.858 0.00 0.04 0.96 0.0 0.00
#> TCGA.J9.A52D.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.J4.A83I.01 1 0.418 0.306 0.60 0.00 0.00 0.0 0.40
#> TCGA.XQ.A8TA.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.KK.A7AY.01 5 0.446 0.179 0.32 0.00 0.02 0.0 0.66
#> TCGA.EJ.5494.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.CH.5772.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.YL.A8SH.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
#> TCGA.HC.A8CY.01 4 0.000 0.000 0.00 0.00 0.00 1.0 0.00
#> TCGA.KK.A7AW.01 3 0.202 0.851 0.00 0.00 0.90 0.1 0.00
#> TCGA.YL.A8SQ.01 2 0.000 1.000 0.00 1.00 0.00 0.0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.KK.A8IA.01 5 0.5801 0.000 0.24 0.00 0.00 0.00 0.50 0.26
#> TCGA.J9.A8CL.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6361.01 1 0.1092 0.487 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.KC.A4BV.01 1 0.4806 -0.629 0.48 0.00 0.02 0.00 0.02 0.48
#> TCGA.EJ.7315.01 6 0.3409 0.000 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.YL.A9WK.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7078.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A5OB.01 3 0.3324 0.711 0.00 0.06 0.84 0.00 0.08 0.02
#> TCGA.J9.A52D.01 2 0.0547 0.982 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.J4.A83I.01 1 0.0000 0.500 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XQ.A8TA.01 2 0.0547 0.982 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.KK.A7AY.01 1 0.3828 0.201 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.EJ.5494.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5772.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SH.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.KK.A7AW.01 3 0.2048 0.689 0.00 0.00 0.88 0.12 0.00 0.00
#> TCGA.YL.A8SQ.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.KK.A8IA.01 5 0.1433 0.000 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.J9.A8CL.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6361.01 1 0.0504 0.959 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.KC.A4BV.01 6 0.4901 0.370 0.40 0.00 0.00 0.00 0.02 0.52 0.06
#> TCGA.EJ.7315.01 6 0.1433 0.523 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.YL.A9WK.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7078.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.A5OB.01 3 0.4831 0.680 0.00 0.02 0.72 0.00 0.06 0.08 0.12
#> TCGA.J9.A52D.01 2 0.1006 0.970 0.00 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.J4.A83I.01 1 0.0504 0.959 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.XQ.A8TA.01 2 0.1006 0.970 0.00 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.KK.A7AY.01 7 0.2906 0.000 0.18 0.00 0.00 0.00 0.02 0.00 0.80
#> TCGA.EJ.5494.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5772.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SH.01 2 0.0504 0.980 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 3 0.1433 0.664 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.YL.A8SQ.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.KK.A8IA.01 5 0.0000 0.000 0.00 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.J9.A8CL.01 2 0.0471 0.981 0.00 0.98 0.02 0 0.00 0.00 0.00 0.00
#> TCGA.G9.6361.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BV.01 6 0.6386 0.306 0.26 0.00 0.22 0 0.02 0.42 0.08 0.00
#> TCGA.EJ.7315.01 6 0.1341 0.374 0.08 0.00 0.00 0 0.00 0.92 0.00 0.00
#> TCGA.YL.A9WK.01 2 0.0000 0.985 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.HC.7078.01 2 0.0471 0.981 0.00 0.98 0.02 0 0.00 0.00 0.00 0.00
#> TCGA.FC.A5OB.01 3 0.2650 0.000 0.00 0.00 0.76 0 0.00 0.00 0.00 0.24
#> TCGA.J9.A52D.01 2 0.0471 0.977 0.00 0.98 0.00 0 0.00 0.02 0.00 0.00
#> TCGA.J4.A83I.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.XQ.A8TA.01 2 0.0941 0.963 0.00 0.96 0.02 0 0.00 0.02 0.00 0.00
#> TCGA.KK.A7AY.01 7 0.1091 0.000 0.06 0.00 0.00 0 0.00 0.00 0.94 0.00
#> TCGA.EJ.5494.01 2 0.0471 0.981 0.00 0.98 0.02 0 0.00 0.00 0.00 0.00
#> TCGA.CH.5772.01 2 0.0000 0.985 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SH.01 2 0.0000 0.985 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.HC.A8CY.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.KK.A7AW.01 8 0.0000 0.000 0.00 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.YL.A8SQ.01 2 0.0000 0.985 0.00 1.00 0.00 0 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: Node02. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["024"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 30 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.4603 0.540 0.540
#> 3 3 0.725 0.933 0.915 0.4357 0.772 0.579
#> 4 4 0.799 0.893 0.848 0.1192 0.945 0.824
#> 5 5 0.724 0.732 0.745 0.0631 0.901 0.632
#> 6 6 0.749 0.805 0.795 0.0346 0.936 0.678
#> 7 7 0.746 0.750 0.814 0.0326 1.000 1.000
#> 8 8 0.728 0.696 0.813 0.0192 0.989 0.925
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.YL.A8S9.01 2 0 1 0 1
#> TCGA.ZG.A9KY.01 2 0 1 0 1
#> TCGA.ZG.A9L0.01 2 0 1 0 1
#> TCGA.EJ.5519.01 1 0 1 1 0
#> TCGA.G9.6338.01 2 0 1 0 1
#> TCGA.ZG.A9ND.01 2 0 1 0 1
#> TCGA.HC.A4ZV.01 1 0 1 1 0
#> TCGA.KK.A7AP.01 2 0 1 0 1
#> TCGA.V1.A9OL.01 1 0 1 1 0
#> TCGA.J9.A8CN.01 2 0 1 0 1
#> TCGA.G9.6371.01 2 0 1 0 1
#> TCGA.M7.A724.01 2 0 1 0 1
#> TCGA.KK.A8ID.01 2 0 1 0 1
#> TCGA.HC.A6AL.01 1 0 1 1 0
#> TCGA.HC.8264.01 2 0 1 0 1
#> TCGA.XK.AAJP.01 2 0 1 0 1
#> TCGA.G9.6369.01 2 0 1 0 1
#> TCGA.KK.A6E1.01 1 0 1 1 0
#> TCGA.VP.A87B.01 2 0 1 0 1
#> TCGA.VP.A87J.01 1 0 1 1 0
#> TCGA.VN.A943.01 2 0 1 0 1
#> TCGA.EJ.A8FS.01 2 0 1 0 1
#> TCGA.YL.A8HL.01 1 0 1 1 0
#> TCGA.KK.A6E0.01 2 0 1 0 1
#> TCGA.XK.AAIW.01 2 0 1 0 1
#> TCGA.WW.A8ZI.01 2 0 1 0 1
#> TCGA.M7.A725.01 1 0 1 1 0
#> TCGA.HC.A632.01 1 0 1 1 0
#> TCGA.KC.A7FA.01 1 0 1 1 0
#> TCGA.G9.6498.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.YL.A8S9.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.ZG.A9KY.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.ZG.A9L0.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.EJ.5519.01 1 0.455 0.888 0.8 0.00 0.20
#> TCGA.G9.6338.01 2 0.334 0.822 0.0 0.88 0.12
#> TCGA.ZG.A9ND.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.HC.A4ZV.01 1 0.455 0.888 0.8 0.00 0.20
#> TCGA.KK.A7AP.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.V1.A9OL.01 1 0.000 0.928 1.0 0.00 0.00
#> TCGA.J9.A8CN.01 3 0.455 0.945 0.0 0.20 0.80
#> TCGA.G9.6371.01 3 0.000 0.732 0.0 0.00 1.00
#> TCGA.M7.A724.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.KK.A8ID.01 3 0.455 0.945 0.0 0.20 0.80
#> TCGA.HC.A6AL.01 1 0.455 0.888 0.8 0.00 0.20
#> TCGA.HC.8264.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.XK.AAJP.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.G9.6369.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.KK.A6E1.01 1 0.000 0.928 1.0 0.00 0.00
#> TCGA.VP.A87B.01 2 0.000 0.985 0.0 1.00 0.00
#> TCGA.VP.A87J.01 1 0.000 0.928 1.0 0.00 0.00
#> TCGA.VN.A943.01 3 0.455 0.945 0.0 0.20 0.80
#> TCGA.EJ.A8FS.01 3 0.522 0.885 0.0 0.26 0.74
#> TCGA.YL.A8HL.01 1 0.000 0.928 1.0 0.00 0.00
#> TCGA.KK.A6E0.01 3 0.480 0.931 0.0 0.22 0.78
#> TCGA.XK.AAIW.01 3 0.455 0.945 0.0 0.20 0.80
#> TCGA.WW.A8ZI.01 3 0.429 0.937 0.0 0.18 0.82
#> TCGA.M7.A725.01 1 0.000 0.928 1.0 0.00 0.00
#> TCGA.HC.A632.01 1 0.455 0.888 0.8 0.00 0.20
#> TCGA.KC.A7FA.01 1 0.000 0.928 1.0 0.00 0.00
#> TCGA.G9.6498.01 3 0.429 0.937 0.0 0.18 0.82
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.YL.A8S9.01 2 0.2921 0.870 0.00 0.86 0.00 0.14
#> TCGA.ZG.A9KY.01 2 0.0000 0.898 0.00 1.00 0.00 0.00
#> TCGA.ZG.A9L0.01 2 0.2921 0.870 0.00 0.86 0.00 0.14
#> TCGA.EJ.5519.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.G9.6338.01 2 0.6686 0.581 0.00 0.62 0.20 0.18
#> TCGA.ZG.A9ND.01 2 0.0000 0.898 0.00 1.00 0.00 0.00
#> TCGA.HC.A4ZV.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.KK.A7AP.01 2 0.4624 0.733 0.00 0.66 0.00 0.34
#> TCGA.V1.A9OL.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.J9.A8CN.01 3 0.1211 0.899 0.00 0.00 0.96 0.04
#> TCGA.G9.6371.01 3 0.0707 0.891 0.00 0.00 0.98 0.02
#> TCGA.M7.A724.01 2 0.0000 0.898 0.00 1.00 0.00 0.00
#> TCGA.KK.A8ID.01 3 0.4790 0.711 0.00 0.00 0.62 0.38
#> TCGA.HC.A6AL.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.HC.8264.01 2 0.2921 0.870 0.00 0.86 0.00 0.14
#> TCGA.XK.AAJP.01 2 0.0000 0.898 0.00 1.00 0.00 0.00
#> TCGA.G9.6369.01 2 0.0000 0.898 0.00 1.00 0.00 0.00
#> TCGA.KK.A6E1.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.VP.A87B.01 2 0.0000 0.898 0.00 1.00 0.00 0.00
#> TCGA.VP.A87J.01 1 0.1637 0.870 0.94 0.00 0.00 0.06
#> TCGA.VN.A943.01 3 0.1211 0.899 0.00 0.00 0.96 0.04
#> TCGA.EJ.A8FS.01 3 0.4079 0.837 0.00 0.02 0.80 0.18
#> TCGA.YL.A8HL.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.KK.A6E0.01 3 0.3400 0.848 0.00 0.00 0.82 0.18
#> TCGA.XK.AAIW.01 3 0.0000 0.897 0.00 0.00 1.00 0.00
#> TCGA.WW.A8ZI.01 3 0.2345 0.851 0.00 0.00 0.90 0.10
#> TCGA.M7.A725.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.HC.A632.01 4 0.4994 1.000 0.48 0.00 0.00 0.52
#> TCGA.KC.A7FA.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.G9.6498.01 3 0.0000 0.897 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.YL.A8S9.01 5 0.4307 0.5817 0.00 0.50 0.00 0.00 0.50
#> TCGA.ZG.A9KY.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 5 0.4307 0.5817 0.00 0.50 0.00 0.00 0.50
#> TCGA.EJ.5519.01 4 0.3684 0.8850 0.28 0.00 0.00 0.72 0.00
#> TCGA.G9.6338.01 5 0.7304 0.5074 0.00 0.28 0.22 0.04 0.46
#> TCGA.ZG.A9ND.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.A4ZV.01 4 0.6054 0.8859 0.28 0.00 0.00 0.56 0.16
#> TCGA.KK.A7AP.01 5 0.5979 0.5116 0.00 0.36 0.00 0.12 0.52
#> TCGA.V1.A9OL.01 1 0.0000 0.9144 1.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CN.01 3 0.0609 0.7623 0.00 0.00 0.98 0.00 0.02
#> TCGA.G9.6371.01 3 0.2732 0.6906 0.00 0.00 0.84 0.16 0.00
#> TCGA.M7.A724.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A8ID.01 5 0.5927 -0.0601 0.00 0.00 0.34 0.12 0.54
#> TCGA.HC.A6AL.01 4 0.3684 0.8850 0.28 0.00 0.00 0.72 0.00
#> TCGA.HC.8264.01 5 0.4307 0.5817 0.00 0.50 0.00 0.00 0.50
#> TCGA.XK.AAJP.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6369.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A6E1.01 1 0.0000 0.9144 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87B.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 1 0.4637 0.6292 0.74 0.00 0.00 0.16 0.10
#> TCGA.VN.A943.01 3 0.0609 0.7623 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.A8FS.01 3 0.5695 0.0787 0.00 0.02 0.48 0.04 0.46
#> TCGA.YL.A8HL.01 1 0.0000 0.9144 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E0.01 3 0.5695 0.0787 0.00 0.02 0.48 0.04 0.46
#> TCGA.XK.AAIW.01 3 0.1043 0.7556 0.00 0.00 0.96 0.04 0.00
#> TCGA.WW.A8ZI.01 3 0.3946 0.6931 0.00 0.00 0.80 0.12 0.08
#> TCGA.M7.A725.01 1 0.2020 0.8540 0.90 0.00 0.00 0.00 0.10
#> TCGA.HC.A632.01 4 0.6054 0.8859 0.28 0.00 0.00 0.56 0.16
#> TCGA.KC.A7FA.01 1 0.0000 0.9144 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6498.01 3 0.0000 0.7629 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.YL.A8S9.01 5 0.4534 0.635 0.00 0.38 0.00 0.00 0.58 0.04
#> TCGA.ZG.A9KY.01 2 0.0937 0.946 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.ZG.A9L0.01 5 0.4534 0.635 0.00 0.38 0.00 0.00 0.58 0.04
#> TCGA.EJ.5519.01 4 0.2094 0.910 0.00 0.00 0.00 0.90 0.08 0.02
#> TCGA.G9.6338.01 5 0.4863 0.597 0.00 0.20 0.14 0.00 0.66 0.00
#> TCGA.ZG.A9ND.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A4ZV.01 4 0.0937 0.898 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.KK.A7AP.01 6 0.4094 0.754 0.00 0.08 0.00 0.00 0.18 0.74
#> TCGA.V1.A9OL.01 1 0.3309 0.920 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.J9.A8CN.01 3 0.0937 0.834 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.G9.6371.01 3 0.3324 0.724 0.00 0.00 0.84 0.06 0.08 0.02
#> TCGA.M7.A724.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8ID.01 6 0.5356 0.773 0.08 0.00 0.08 0.00 0.16 0.68
#> TCGA.HC.A6AL.01 4 0.2094 0.910 0.00 0.00 0.00 0.90 0.08 0.02
#> TCGA.HC.8264.01 5 0.4576 0.616 0.00 0.40 0.00 0.00 0.56 0.04
#> TCGA.XK.AAJP.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6369.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E1.01 1 0.3819 0.920 0.70 0.00 0.00 0.28 0.02 0.00
#> TCGA.VP.A87B.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 1 0.5544 0.716 0.50 0.00 0.00 0.40 0.02 0.08
#> TCGA.VN.A943.01 3 0.0937 0.834 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EJ.A8FS.01 5 0.4265 0.468 0.00 0.04 0.30 0.00 0.66 0.00
#> TCGA.YL.A8HL.01 1 0.3819 0.920 0.70 0.00 0.00 0.28 0.02 0.00
#> TCGA.KK.A6E0.01 5 0.4002 0.437 0.00 0.02 0.32 0.00 0.66 0.00
#> TCGA.XK.AAIW.01 3 0.0547 0.837 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.WW.A8ZI.01 3 0.6873 0.373 0.20 0.00 0.50 0.00 0.18 0.12
#> TCGA.M7.A725.01 1 0.5208 0.872 0.62 0.00 0.00 0.28 0.02 0.08
#> TCGA.HC.A632.01 4 0.0547 0.906 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.KC.A7FA.01 1 0.3309 0.920 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.G9.6498.01 3 0.0000 0.838 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.YL.A8S9.01 5 0.5234 0.586 0.12 0.30 0.00 0.00 0.56 0.02 0.00
#> TCGA.ZG.A9KY.01 2 0.1886 0.862 0.12 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 5 0.5234 0.586 0.12 0.30 0.00 0.00 0.56 0.02 0.00
#> TCGA.EJ.5519.01 4 0.1886 0.807 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.G9.6338.01 5 0.1166 0.571 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.ZG.A9ND.01 2 0.0863 0.942 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A4ZV.01 4 0.6283 0.799 0.16 0.00 0.04 0.58 0.00 0.10 0.12
#> TCGA.KK.A7AP.01 6 0.5818 0.730 0.12 0.06 0.00 0.06 0.12 0.64 0.00
#> TCGA.V1.A9OL.01 7 0.0000 0.904 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.J9.A8CN.01 3 0.3047 0.757 0.00 0.00 0.72 0.00 0.28 0.00 0.00
#> TCGA.G9.6371.01 3 0.3755 0.484 0.00 0.00 0.64 0.34 0.02 0.00 0.00
#> TCGA.M7.A724.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8ID.01 6 0.2259 0.747 0.00 0.00 0.00 0.00 0.16 0.84 0.00
#> TCGA.HC.A6AL.01 4 0.1886 0.807 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.HC.8264.01 5 0.5234 0.586 0.12 0.30 0.00 0.00 0.56 0.02 0.00
#> TCGA.XK.AAJP.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6369.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E1.01 7 0.0000 0.904 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.VP.A87B.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 7 0.3795 0.748 0.22 0.00 0.00 0.06 0.00 0.00 0.72
#> TCGA.VN.A943.01 3 0.3047 0.757 0.00 0.00 0.72 0.00 0.28 0.00 0.00
#> TCGA.EJ.A8FS.01 5 0.0504 0.538 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.YL.A8HL.01 7 0.0000 0.904 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.KK.A6E0.01 5 0.0504 0.538 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.XK.AAIW.01 3 0.4461 0.707 0.02 0.00 0.70 0.02 0.22 0.04 0.00
#> TCGA.WW.A8ZI.01 3 0.5639 0.133 0.42 0.00 0.46 0.04 0.06 0.02 0.00
#> TCGA.M7.A725.01 7 0.2708 0.799 0.22 0.00 0.00 0.00 0.00 0.00 0.78
#> TCGA.HC.A632.01 4 0.6217 0.799 0.18 0.00 0.04 0.58 0.00 0.08 0.12
#> TCGA.KC.A7FA.01 7 0.0000 0.904 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G9.6498.01 3 0.3047 0.757 0.00 0.00 0.72 0.00 0.28 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.YL.A8S9.01 5 0.527 0.604 0.22 0.18 0.00 0.00 0.56 0.04 0.00 0.00
#> TCGA.ZG.A9KY.01 2 0.227 0.786 0.18 0.82 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L0.01 5 0.527 0.604 0.22 0.18 0.00 0.00 0.56 0.04 0.00 0.00
#> TCGA.EJ.5519.01 4 0.156 0.756 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.G9.6338.01 5 0.255 0.607 0.00 0.04 0.12 0.00 0.84 0.00 0.00 0.00
#> TCGA.ZG.A9ND.01 2 0.109 0.911 0.06 0.94 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A4ZV.01 4 0.616 0.676 0.30 0.00 0.00 0.48 0.00 0.06 0.10 0.06
#> TCGA.KK.A7AP.01 6 0.697 0.531 0.22 0.10 0.00 0.04 0.08 0.48 0.00 0.08
#> TCGA.V1.A9OL.01 7 0.000 0.818 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.J9.A8CN.01 3 0.000 0.811 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6371.01 3 0.276 0.509 0.00 0.00 0.74 0.26 0.00 0.00 0.00 0.00
#> TCGA.M7.A724.01 2 0.000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8ID.01 6 0.286 0.486 0.00 0.00 0.10 0.00 0.08 0.82 0.00 0.00
#> TCGA.HC.A6AL.01 4 0.156 0.756 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.HC.8264.01 5 0.527 0.604 0.22 0.18 0.00 0.00 0.56 0.04 0.00 0.00
#> TCGA.XK.AAJP.01 2 0.000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6369.01 2 0.000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E1.01 7 0.109 0.816 0.00 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.VP.A87B.01 2 0.000 0.944 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A87J.01 7 0.686 0.469 0.08 0.00 0.00 0.14 0.16 0.02 0.50 0.10
#> TCGA.VN.A943.01 3 0.000 0.811 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FS.01 5 0.211 0.587 0.00 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.YL.A8HL.01 7 0.109 0.816 0.00 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.KK.A6E0.01 5 0.211 0.587 0.00 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.XK.AAIW.01 3 0.374 0.557 0.18 0.00 0.74 0.06 0.00 0.02 0.00 0.00
#> TCGA.WW.A8ZI.01 8 0.265 0.000 0.00 0.00 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.M7.A725.01 7 0.524 0.655 0.08 0.00 0.00 0.00 0.12 0.04 0.66 0.10
#> TCGA.HC.A632.01 4 0.480 0.719 0.32 0.00 0.00 0.56 0.00 0.00 0.10 0.02
#> TCGA.KC.A7FA.01 7 0.000 0.818 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6498.01 3 0.000 0.811 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: Node0. Child nodes: Node011-leaf , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 , Node053-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 50 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.995 0.998 0.4912 0.510 0.510
#> 3 3 0.879 0.867 0.954 0.3190 0.673 0.448
#> 4 4 1.000 0.975 0.989 0.1236 0.775 0.466
#> 5 5 0.768 0.670 0.806 0.0872 0.888 0.619
#> 6 6 0.761 0.715 0.846 0.0473 0.922 0.646
#> 7 7 0.761 0.699 0.823 0.0230 0.978 0.870
#> 8 8 0.788 0.655 0.793 0.0115 0.956 0.746
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.EJ.AB27.01 2 0.000 0.996 0.00 1.00
#> TCGA.KC.A4BL.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.A46B.01 1 0.000 1.000 1.00 0.00
#> TCGA.X4.A8KS.01 1 0.000 1.000 1.00 0.00
#> TCGA.KC.A7FE.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.7817.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.A8D0.01 2 0.000 0.996 0.00 1.00
#> TCGA.SU.A7E7.01 2 0.000 0.996 0.00 1.00
#> TCGA.G9.6342.11 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.A65B.01 2 0.000 0.996 0.00 1.00
#> TCGA.ZG.A9LU.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.5506.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.A8FO.01 1 0.000 1.000 1.00 0.00
#> TCGA.J4.AATV.01 2 0.000 0.996 0.00 1.00
#> TCGA.KK.A8I7.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.7791.01 2 0.000 0.996 0.00 1.00
#> TCGA.KK.A8IC.01 2 0.000 0.996 0.00 1.00
#> TCGA.CH.5765.11 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A9O7.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.5498.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.A46D.01 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A8MK.01 2 0.529 0.864 0.12 0.88
#> TCGA.YL.A8HJ.01 2 0.000 0.996 0.00 1.00
#> TCGA.G9.6353.01 1 0.000 1.000 1.00 0.00
#> TCGA.XJ.A9DQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZG.A9MC.01 2 0.000 0.996 0.00 1.00
#> TCGA.G9.6378.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.7079.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.A8D1.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.A7NG.01 1 0.000 1.000 1.00 0.00
#> TCGA.KC.A4BR.01 2 0.000 0.996 0.00 1.00
#> TCGA.CH.5768.11 1 0.000 1.000 1.00 0.00
#> TCGA.HC.A6HX.01 1 0.000 1.000 1.00 0.00
#> TCGA.M7.A71Y.01 1 0.000 1.000 1.00 0.00
#> TCGA.VN.A88I.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.5531.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.8258.01 2 0.000 0.996 0.00 1.00
#> TCGA.J4.A6G1.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.8260.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.7740.01 2 0.000 0.996 0.00 1.00
#> TCGA.KK.A7B2.01 2 0.000 0.996 0.00 1.00
#> TCGA.HC.7742.11 1 0.000 1.000 1.00 0.00
#> TCGA.G9.6351.11 1 0.000 1.000 1.00 0.00
#> TCGA.YL.A9WX.01 2 0.000 0.996 0.00 1.00
#> TCGA.ZG.A9L6.01 2 0.000 0.996 0.00 1.00
#> TCGA.M7.A723.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5771.01 2 0.000 0.996 0.00 1.00
#> TCGA.EJ.A6RA.01 1 0.000 1.000 1.00 0.00
#> TCGA.J4.A6G3.01 2 0.000 0.996 0.00 1.00
#> TCGA.G9.6329.01 2 0.000 0.996 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EJ.AB27.01 2 0.630 0.0135 0.0 0.52 0.48
#> TCGA.KC.A4BL.01 3 0.624 0.1923 0.0 0.44 0.56
#> TCGA.EJ.A46B.01 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.X4.A8KS.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.KC.A7FE.01 3 0.624 0.1923 0.0 0.44 0.56
#> TCGA.HC.7817.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.HC.A8D0.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.SU.A7E7.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.G9.6342.11 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.EJ.A65B.01 2 0.502 0.6541 0.0 0.76 0.24
#> TCGA.ZG.A9LU.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.EJ.5506.01 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.EJ.A8FO.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.J4.AATV.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.KK.A8I7.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.EJ.7791.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.KK.A8IC.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.CH.5765.11 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.V1.A9O7.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.EJ.5498.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.EJ.A46D.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.V1.A8MK.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.YL.A8HJ.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.G9.6353.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.XJ.A9DQ.01 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.ZG.A9MC.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.G9.6378.01 3 0.296 0.8226 0.1 0.00 0.90
#> TCGA.HC.7079.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.HC.A8D1.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.EJ.A7NG.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.KC.A4BR.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.CH.5768.11 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.HC.A6HX.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.M7.A71Y.01 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.VN.A88I.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.EJ.5531.01 3 0.254 0.8524 0.0 0.08 0.92
#> TCGA.HC.8258.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.J4.A6G1.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.HC.8260.01 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.HC.7740.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.KK.A7B2.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.HC.7742.11 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.G9.6351.11 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.YL.A9WX.01 3 0.000 0.9296 0.0 0.00 1.00
#> TCGA.ZG.A9L6.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.M7.A723.01 1 0.631 0.0469 0.5 0.00 0.50
#> TCGA.CH.5771.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.EJ.A6RA.01 1 0.000 0.9431 1.0 0.00 0.00
#> TCGA.J4.A6G3.01 2 0.000 0.9557 0.0 1.00 0.00
#> TCGA.G9.6329.01 3 0.000 0.9296 0.0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EJ.AB27.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.KC.A4BL.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.EJ.A46B.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.X4.A8KS.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.KC.A7FE.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.HC.7817.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.HC.A8D0.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.SU.A7E7.01 2 0.0707 0.974 0 0.98 0.02 0.00
#> TCGA.G9.6342.11 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.EJ.A65B.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.ZG.A9LU.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.EJ.5506.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EJ.A8FO.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.J4.AATV.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.KK.A8I7.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.EJ.7791.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.KK.A8IC.01 3 0.2345 0.873 0 0.10 0.90 0.00
#> TCGA.CH.5765.11 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.V1.A9O7.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.EJ.5498.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.EJ.A46D.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.V1.A8MK.01 3 0.0707 0.953 0 0.02 0.98 0.00
#> TCGA.YL.A8HJ.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.G9.6353.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.XJ.A9DQ.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ZG.A9MC.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.G9.6378.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.HC.7079.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.HC.A8D1.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.EJ.A7NG.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.KC.A4BR.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.CH.5768.11 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.HC.A6HX.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.M7.A71Y.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.VN.A88I.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.EJ.5531.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.HC.8258.01 2 0.1211 0.959 0 0.96 0.00 0.04
#> TCGA.J4.A6G1.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.HC.8260.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.HC.7740.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.KK.A7B2.01 3 0.0707 0.953 0 0.02 0.98 0.00
#> TCGA.HC.7742.11 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.G9.6351.11 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.YL.A9WX.01 2 0.1211 0.954 0 0.96 0.04 0.00
#> TCGA.ZG.A9L6.01 2 0.1211 0.958 0 0.96 0.00 0.04
#> TCGA.M7.A723.01 3 0.0000 0.967 0 0.00 1.00 0.00
#> TCGA.CH.5771.01 2 0.0000 0.989 0 1.00 0.00 0.00
#> TCGA.EJ.A6RA.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.J4.A6G3.01 2 0.1211 0.959 0 0.96 0.00 0.04
#> TCGA.G9.6329.01 3 0.3975 0.689 0 0.24 0.76 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EJ.AB27.01 2 0.3684 0.727 0.00 0.72 0.00 0.00 0.28
#> TCGA.KC.A4BL.01 2 0.4262 0.754 0.00 0.56 0.00 0.00 0.44
#> TCGA.EJ.A46B.01 3 0.4302 -0.208 0.48 0.00 0.52 0.00 0.00
#> TCGA.X4.A8KS.01 3 0.1410 0.744 0.00 0.00 0.94 0.00 0.06
#> TCGA.KC.A7FE.01 2 0.4262 0.754 0.00 0.56 0.00 0.00 0.44
#> TCGA.HC.7817.01 2 0.4262 0.754 0.00 0.56 0.00 0.00 0.44
#> TCGA.HC.A8D0.01 2 0.1410 0.630 0.00 0.94 0.00 0.00 0.06
#> TCGA.SU.A7E7.01 5 0.3868 0.471 0.00 0.14 0.06 0.00 0.80
#> TCGA.G9.6342.11 3 0.1043 0.768 0.00 0.00 0.96 0.00 0.04
#> TCGA.EJ.A65B.01 2 0.4262 0.754 0.00 0.56 0.00 0.00 0.44
#> TCGA.ZG.A9LU.01 3 0.4302 -0.309 0.00 0.00 0.52 0.00 0.48
#> TCGA.EJ.5506.01 1 0.0000 0.956 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FO.01 5 0.4262 0.364 0.00 0.00 0.44 0.00 0.56
#> TCGA.J4.AATV.01 5 0.4287 -0.730 0.00 0.46 0.00 0.00 0.54
#> TCGA.KK.A8I7.01 2 0.4182 0.757 0.00 0.60 0.00 0.00 0.40
#> TCGA.EJ.7791.01 2 0.4262 0.754 0.00 0.56 0.00 0.00 0.44
#> TCGA.KK.A8IC.01 5 0.4456 0.536 0.00 0.02 0.32 0.00 0.66
#> TCGA.CH.5765.11 1 0.0000 0.956 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O7.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.EJ.5498.01 2 0.1043 0.644 0.00 0.96 0.00 0.00 0.04
#> TCGA.EJ.A46D.01 5 0.4302 0.267 0.00 0.00 0.48 0.00 0.52
#> TCGA.V1.A8MK.01 5 0.4227 0.422 0.00 0.00 0.42 0.00 0.58
#> TCGA.YL.A8HJ.01 4 0.3983 0.646 0.00 0.34 0.00 0.66 0.00
#> TCGA.G9.6353.01 3 0.0609 0.779 0.00 0.00 0.98 0.00 0.02
#> TCGA.XJ.A9DQ.01 1 0.1732 0.948 0.92 0.00 0.08 0.00 0.00
#> TCGA.ZG.A9MC.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6378.01 3 0.0000 0.771 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.7079.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.A8D1.01 2 0.2732 0.516 0.00 0.84 0.00 0.00 0.16
#> TCGA.EJ.A7NG.01 3 0.0609 0.779 0.00 0.00 0.98 0.00 0.02
#> TCGA.KC.A4BR.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.CH.5768.11 1 0.0000 0.956 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HX.01 3 0.3109 0.555 0.00 0.00 0.80 0.00 0.20
#> TCGA.M7.A71Y.01 1 0.1732 0.948 0.92 0.00 0.08 0.00 0.00
#> TCGA.VN.A88I.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.EJ.5531.01 2 0.4060 0.715 0.00 0.64 0.00 0.00 0.36
#> TCGA.HC.8258.01 2 0.4227 0.756 0.00 0.58 0.00 0.00 0.42
#> TCGA.J4.A6G1.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.HC.8260.01 1 0.1732 0.948 0.92 0.00 0.08 0.00 0.00
#> TCGA.HC.7740.01 2 0.4262 0.754 0.00 0.56 0.00 0.00 0.44
#> TCGA.KK.A7B2.01 5 0.3983 0.522 0.00 0.00 0.34 0.00 0.66
#> TCGA.HC.7742.11 1 0.0000 0.956 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6351.11 3 0.0609 0.779 0.00 0.00 0.98 0.00 0.02
#> TCGA.YL.A9WX.01 5 0.2438 0.489 0.00 0.04 0.06 0.00 0.90
#> TCGA.ZG.A9L6.01 2 0.2012 0.616 0.00 0.92 0.00 0.02 0.06
#> TCGA.M7.A723.01 3 0.0609 0.757 0.02 0.00 0.98 0.00 0.00
#> TCGA.CH.5771.01 2 0.2020 0.655 0.00 0.90 0.00 0.00 0.10
#> TCGA.EJ.A6RA.01 1 0.1410 0.954 0.94 0.00 0.06 0.00 0.00
#> TCGA.J4.A6G3.01 2 0.2280 0.707 0.00 0.88 0.00 0.00 0.12
#> TCGA.G9.6329.01 5 0.3999 0.557 0.00 0.02 0.24 0.00 0.74
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EJ.AB27.01 2 0.5110 -0.2962 0.00 0.48 0.00 0.00 0.08 0.44
#> TCGA.KC.A4BL.01 2 0.0000 0.8037 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A46B.01 3 0.4420 0.0640 0.34 0.00 0.62 0.00 0.00 0.04
#> TCGA.X4.A8KS.01 3 0.4873 0.5047 0.00 0.00 0.60 0.00 0.32 0.08
#> TCGA.KC.A7FE.01 2 0.0000 0.8037 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7817.01 2 0.0547 0.7975 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.HC.A8D0.01 6 0.3523 0.8209 0.00 0.18 0.00 0.00 0.04 0.78
#> TCGA.SU.A7E7.01 5 0.3746 0.7453 0.00 0.08 0.00 0.00 0.78 0.14
#> TCGA.G9.6342.11 3 0.2631 0.7601 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.EJ.A65B.01 2 0.0000 0.8037 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LU.01 5 0.3499 0.3859 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.EJ.5506.01 1 0.0000 0.8474 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FO.01 5 0.1480 0.8541 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.J4.AATV.01 2 0.2956 0.6767 0.00 0.84 0.00 0.00 0.12 0.04
#> TCGA.KK.A8I7.01 2 0.2941 0.5575 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.EJ.7791.01 2 0.0000 0.8037 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IC.01 5 0.1480 0.8610 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.CH.5765.11 1 0.0000 0.8474 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O7.01 4 0.0000 0.9188 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5498.01 6 0.2941 0.8122 0.00 0.22 0.00 0.00 0.00 0.78
#> TCGA.EJ.A46D.01 5 0.1267 0.8405 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.V1.A8MK.01 5 0.1092 0.8661 0.00 0.02 0.02 0.00 0.96 0.00
#> TCGA.YL.A8HJ.01 4 0.3864 0.1761 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.G9.6353.01 3 0.2793 0.7547 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.XJ.A9DQ.01 1 0.3660 0.8262 0.78 0.00 0.16 0.00 0.00 0.06
#> TCGA.ZG.A9MC.01 4 0.0000 0.9188 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.6378.01 3 0.2094 0.6807 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.HC.7079.01 4 0.0000 0.9188 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.A8D1.01 6 0.3746 0.7960 0.00 0.14 0.00 0.00 0.08 0.78
#> TCGA.EJ.A7NG.01 3 0.2631 0.7601 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.KC.A4BR.01 4 0.0000 0.9188 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CH.5768.11 1 0.0000 0.8474 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HX.01 3 0.3756 0.4720 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.M7.A71Y.01 1 0.3982 0.8090 0.74 0.00 0.20 0.00 0.00 0.06
#> TCGA.VN.A88I.01 4 0.0000 0.9188 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5531.01 2 0.5801 0.0652 0.00 0.50 0.00 0.00 0.24 0.26
#> TCGA.HC.8258.01 2 0.0547 0.7941 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.J4.A6G1.01 4 0.0000 0.9188 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.8260.01 1 0.4247 0.7623 0.70 0.00 0.24 0.00 0.00 0.06
#> TCGA.HC.7740.01 2 0.0547 0.7941 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.KK.A7B2.01 5 0.1865 0.8616 0.00 0.04 0.04 0.00 0.92 0.00
#> TCGA.HC.7742.11 1 0.0000 0.8474 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6351.11 3 0.2793 0.7547 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.YL.A9WX.01 5 0.2350 0.8392 0.00 0.10 0.00 0.00 0.88 0.02
#> TCGA.ZG.A9L6.01 6 0.2581 0.7633 0.00 0.12 0.00 0.00 0.02 0.86
#> TCGA.M7.A723.01 3 0.0547 0.7007 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CH.5771.01 6 0.4067 0.7731 0.00 0.26 0.00 0.00 0.04 0.70
#> TCGA.EJ.A6RA.01 1 0.3982 0.8092 0.74 0.00 0.20 0.00 0.00 0.06
#> TCGA.J4.A6G3.01 6 0.4337 0.3212 0.00 0.48 0.00 0.02 0.00 0.50
#> TCGA.G9.6329.01 5 0.2345 0.8627 0.00 0.06 0.02 0.00 0.90 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EJ.AB27.01 2 0.6226 0.074 0.00 0.40 0.14 0.00 0.08 0.38 0.00
#> TCGA.KC.A4BL.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A46B.01 7 0.4030 0.397 0.16 0.00 0.12 0.00 0.00 0.00 0.72
#> TCGA.X4.A8KS.01 7 0.5490 0.293 0.00 0.00 0.24 0.00 0.32 0.00 0.44
#> TCGA.KC.A7FE.01 2 0.2159 0.751 0.00 0.90 0.06 0.00 0.02 0.02 0.00
#> TCGA.HC.7817.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8D0.01 6 0.1664 0.774 0.00 0.06 0.00 0.00 0.02 0.92 0.00
#> TCGA.SU.A7E7.01 5 0.4984 0.646 0.00 0.08 0.14 0.00 0.68 0.10 0.00
#> TCGA.G9.6342.11 7 0.2906 0.697 0.00 0.00 0.02 0.00 0.18 0.00 0.80
#> TCGA.EJ.A65B.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LU.01 5 0.3519 0.604 0.00 0.00 0.04 0.00 0.74 0.00 0.22
#> TCGA.EJ.5506.01 1 0.0000 0.786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FO.01 5 0.2016 0.805 0.00 0.00 0.06 0.00 0.90 0.04 0.00
#> TCGA.J4.AATV.01 2 0.5276 0.554 0.00 0.64 0.10 0.00 0.18 0.08 0.00
#> TCGA.KK.A8I7.01 2 0.2422 0.678 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.EJ.7791.01 2 0.0504 0.783 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IC.01 5 0.1718 0.822 0.00 0.00 0.04 0.00 0.92 0.04 0.00
#> TCGA.CH.5765.11 1 0.0000 0.786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O7.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5498.01 6 0.1671 0.767 0.00 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.EJ.A46D.01 5 0.0504 0.827 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.V1.A8MK.01 5 0.0504 0.829 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.YL.A8HJ.01 6 0.3525 0.186 0.00 0.00 0.00 0.44 0.00 0.56 0.00
#> TCGA.G9.6353.01 7 0.3052 0.688 0.00 0.00 0.02 0.00 0.20 0.00 0.78
#> TCGA.XJ.A9DQ.01 1 0.4883 0.737 0.60 0.00 0.20 0.00 0.00 0.00 0.20
#> TCGA.ZG.A9MC.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6378.01 7 0.3755 0.531 0.00 0.00 0.34 0.00 0.02 0.00 0.64
#> TCGA.HC.7079.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.A8D1.01 6 0.1928 0.771 0.00 0.08 0.00 0.00 0.02 0.90 0.00
#> TCGA.EJ.A7NG.01 7 0.2081 0.703 0.00 0.00 0.00 0.00 0.14 0.00 0.86
#> TCGA.KC.A4BR.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5768.11 1 0.0000 0.786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HX.01 7 0.3985 0.207 0.00 0.00 0.02 0.00 0.46 0.00 0.52
#> TCGA.M7.A71Y.01 1 0.4990 0.728 0.58 0.00 0.20 0.00 0.00 0.00 0.22
#> TCGA.VN.A88I.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5531.01 2 0.6357 0.360 0.00 0.50 0.14 0.00 0.16 0.20 0.00
#> TCGA.HC.8258.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A6G1.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.8260.01 1 0.4990 0.728 0.58 0.00 0.20 0.00 0.00 0.00 0.22
#> TCGA.HC.7740.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B2.01 5 0.3000 0.773 0.00 0.02 0.04 0.00 0.84 0.00 0.10
#> TCGA.HC.7742.11 1 0.0504 0.788 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.G9.6351.11 7 0.3307 0.656 0.00 0.00 0.02 0.00 0.24 0.00 0.74
#> TCGA.YL.A9WX.01 5 0.4110 0.751 0.00 0.06 0.10 0.00 0.78 0.04 0.02
#> TCGA.ZG.A9L6.01 6 0.3047 0.644 0.00 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.M7.A723.01 7 0.2278 0.661 0.00 0.00 0.08 0.00 0.04 0.00 0.88
#> TCGA.CH.5771.01 6 0.3388 0.649 0.00 0.20 0.04 0.00 0.00 0.76 0.00
#> TCGA.EJ.A6RA.01 1 0.4429 0.737 0.66 0.00 0.12 0.00 0.00 0.00 0.22
#> TCGA.J4.A6G3.01 2 0.3909 0.217 0.00 0.58 0.02 0.00 0.00 0.40 0.00
#> TCGA.G9.6329.01 5 0.2355 0.822 0.00 0.02 0.04 0.00 0.90 0.02 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.EJ.AB27.01 2 0.5860 0.321 0.00 0.50 0.00 0.00 0.10 0.22 0.18 0.00
#> TCGA.KC.A4BL.01 2 0.0000 0.771 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A46B.01 1 0.5246 0.194 0.48 0.00 0.38 0.00 0.00 0.00 0.06 0.08
#> TCGA.X4.A8KS.01 5 0.7354 -0.130 0.10 0.00 0.26 0.00 0.30 0.00 0.22 0.12
#> TCGA.KC.A7FE.01 2 0.0941 0.758 0.02 0.96 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HC.7817.01 2 0.1275 0.756 0.00 0.94 0.00 0.00 0.00 0.04 0.02 0.00
#> TCGA.HC.A8D0.01 6 0.2407 0.687 0.00 0.08 0.00 0.00 0.06 0.86 0.00 0.00
#> TCGA.SU.A7E7.01 5 0.0808 0.815 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.G9.6342.11 3 0.1557 0.803 0.02 0.00 0.92 0.00 0.06 0.00 0.00 0.00
#> TCGA.EJ.A65B.01 2 0.0000 0.771 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LU.01 5 0.3154 0.708 0.00 0.00 0.16 0.00 0.78 0.00 0.06 0.00
#> TCGA.EJ.5506.01 8 0.3142 0.664 0.36 0.00 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.EJ.A8FO.01 5 0.2807 0.793 0.00 0.00 0.02 0.00 0.84 0.00 0.10 0.04
#> TCGA.J4.AATV.01 2 0.4983 0.365 0.02 0.54 0.00 0.00 0.36 0.04 0.04 0.00
#> TCGA.KK.A8I7.01 2 0.3198 0.571 0.00 0.72 0.00 0.00 0.00 0.26 0.02 0.00
#> TCGA.EJ.7791.01 2 0.0000 0.771 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IC.01 5 0.2224 0.812 0.00 0.00 0.02 0.00 0.86 0.00 0.12 0.00
#> TCGA.CH.5765.11 8 0.3142 0.664 0.36 0.00 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.V1.A9O7.01 4 0.0471 0.981 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EJ.5498.01 6 0.2114 0.644 0.00 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.EJ.A46D.01 5 0.3002 0.781 0.00 0.00 0.12 0.00 0.82 0.00 0.04 0.02
#> TCGA.V1.A8MK.01 5 0.1275 0.830 0.00 0.00 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.YL.A8HJ.01 6 0.3299 0.129 0.00 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.G9.6353.01 3 0.1887 0.803 0.04 0.00 0.90 0.00 0.06 0.00 0.00 0.00
#> TCGA.XJ.A9DQ.01 1 0.1275 0.733 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZG.A9MC.01 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6378.01 8 0.6552 -0.261 0.08 0.00 0.30 0.00 0.02 0.00 0.28 0.32
#> TCGA.HC.7079.01 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A8D1.01 6 0.2407 0.684 0.00 0.06 0.00 0.00 0.08 0.86 0.00 0.00
#> TCGA.EJ.A7NG.01 3 0.2020 0.800 0.02 0.00 0.90 0.00 0.06 0.00 0.00 0.02
#> TCGA.KC.A4BR.01 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5768.11 8 0.3142 0.664 0.36 0.00 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.HC.A6HX.01 3 0.3514 0.462 0.02 0.00 0.64 0.00 0.34 0.00 0.00 0.00
#> TCGA.M7.A71Y.01 1 0.1091 0.737 0.94 0.00 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88I.01 4 0.0471 0.981 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EJ.5531.01 2 0.6146 0.206 0.00 0.42 0.00 0.00 0.26 0.22 0.10 0.00
#> TCGA.HC.8258.01 2 0.0471 0.766 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.J4.A6G1.01 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8260.01 1 0.1275 0.737 0.94 0.00 0.04 0.00 0.00 0.00 0.02 0.00
#> TCGA.HC.7740.01 2 0.0000 0.771 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B2.01 5 0.1091 0.821 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.HC.7742.11 8 0.3142 0.664 0.36 0.00 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.G9.6351.11 3 0.2623 0.782 0.06 0.00 0.84 0.00 0.10 0.00 0.00 0.00
#> TCGA.YL.A9WX.01 5 0.1275 0.816 0.00 0.04 0.02 0.00 0.94 0.00 0.00 0.00
#> TCGA.ZG.A9L6.01 6 0.3333 0.374 0.00 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.M7.A723.01 3 0.4644 0.350 0.24 0.00 0.64 0.00 0.00 0.00 0.06 0.06
#> TCGA.CH.5771.01 6 0.3941 0.481 0.00 0.26 0.00 0.00 0.02 0.68 0.04 0.00
#> TCGA.EJ.A6RA.01 1 0.3314 0.634 0.80 0.00 0.08 0.00 0.00 0.00 0.02 0.10
#> TCGA.J4.A6G3.01 2 0.3594 0.516 0.00 0.68 0.00 0.04 0.00 0.28 0.00 0.00
#> TCGA.G9.6329.01 5 0.0471 0.828 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011-leaf , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 , Node053-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["04"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 155 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 0.996 0.998 0.4727 0.529 0.529
#> 3 3 1.000 0.996 0.998 0.3403 0.747 0.559
#> 4 4 1.000 0.970 0.988 0.1499 0.808 0.538
#> 5 5 0.864 0.904 0.922 0.0728 0.892 0.634
#> 6 6 0.904 0.820 0.905 0.0346 0.998 0.990
#> 7 7 0.896 0.774 0.874 0.0206 0.962 0.819
#> 8 8 0.837 0.699 0.831 0.0175 0.993 0.963
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.G9.6343.01 2 0.000 1.000 0.00 1.00
#> TCGA.KK.A6E6.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.6339.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.5509.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5521.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5754.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7314.01 1 0.000 0.997 1.00 0.00
#> TCGA.XA.A8JR.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.7781.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5751.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A8WL.01 2 0.000 1.000 0.00 1.00
#> TCGA.XK.AAJT.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6366.01 1 0.000 0.997 1.00 0.00
#> TCGA.KC.A4BN.01 1 0.000 0.997 1.00 0.00
#> TCGA.KK.A8IG.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7786.01 1 0.000 0.997 1.00 0.00
#> TCGA.J4.A83K.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.8470.01 1 0.242 0.957 0.96 0.04
#> TCGA.VP.AA1N.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5524.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7209.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7742.01 1 0.000 0.997 1.00 0.00
#> TCGA.J9.A8CP.01 2 0.000 1.000 0.00 1.00
#> TCGA.V1.A9O5.01 2 0.000 1.000 0.00 1.00
#> TCGA.VP.A879.01 1 0.000 0.997 1.00 0.00
#> TCGA.VN.A88Q.01 1 0.000 0.997 1.00 0.00
#> TCGA.M7.A721.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5514.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5526.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.5542.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5769.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7748.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.6365.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.7510.01 2 0.000 1.000 0.00 1.00
#> TCGA.V1.A8MG.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.A7NN.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.8265.01 2 0.000 1.000 0.00 1.00
#> TCGA.KK.A7AV.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7218.01 2 0.000 1.000 0.00 1.00
#> TCGA.YL.A8SC.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A8X3.01 1 0.000 0.997 1.00 0.00
#> TCGA.KK.A6DY.01 1 0.000 0.997 1.00 0.00
#> TCGA.KK.A8I8.01 1 0.000 0.997 1.00 0.00
#> TCGA.QU.A6IO.01 2 0.000 1.000 0.00 1.00
#> TCGA.XJ.A83H.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZG.A8QY.01 2 0.000 1.000 0.00 1.00
#> TCGA.YL.A8SO.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5522.01 1 0.000 0.997 1.00 0.00
#> TCGA.ZG.A9M4.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.A9S0.01 2 0.000 1.000 0.00 1.00
#> TCGA.TP.A8TT.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A9Z9.01 2 0.000 1.000 0.00 1.00
#> TCGA.HC.7232.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7081.01 1 0.000 0.997 1.00 0.00
#> TCGA.VP.A87H.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.7521.01 2 0.000 1.000 0.00 1.00
#> TCGA.YL.A8HO.01 2 0.000 1.000 0.00 1.00
#> TCGA.J4.A83M.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7736.01 2 0.000 1.000 0.00 1.00
#> TCGA.VN.A88N.01 1 0.000 0.997 1.00 0.00
#> TCGA.QU.A6IP.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A9O9.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7210.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZG.A9LB.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.8468.01 1 0.000 0.997 1.00 0.00
#> TCGA.KK.A7B1.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.8262.01 1 0.000 0.997 1.00 0.00
#> TCGA.HI.7170.01 1 0.000 0.997 1.00 0.00
#> TCGA.J4.A67L.01 1 0.000 0.997 1.00 0.00
#> TCGA.KC.A7F3.01 2 0.000 1.000 0.00 1.00
#> TCGA.HC.8256.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5769.11 1 0.000 0.997 1.00 0.00
#> TCGA.G9.6499.11 2 0.000 1.000 0.00 1.00
#> TCGA.KK.A8I9.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7317.01 2 0.000 1.000 0.00 1.00
#> TCGA.YL.A8S8.01 2 0.000 1.000 0.00 1.00
#> TCGA.Y6.A8TL.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A8MF.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.A65E.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZG.A8QX.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6342.01 1 0.000 0.997 1.00 0.00
#> TCGA.J4.8200.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.5532.01 1 0.000 0.997 1.00 0.00
#> TCGA.HI.7168.01 2 0.000 1.000 0.00 1.00
#> TCGA.HC.7233.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.A65M.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.A8FN.01 2 0.000 1.000 0.00 1.00
#> TCGA.J4.A83L.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.5507.01 1 0.000 0.997 1.00 0.00
#> TCGA.J9.A8CK.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5744.01 1 0.000 0.997 1.00 0.00
#> TCGA.ZG.A9N3.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6354.01 1 0.000 0.997 1.00 0.00
#> TCGA.VN.A88O.01 2 0.000 1.000 0.00 1.00
#> TCGA.HC.7211.01 2 0.000 1.000 0.00 1.00
#> TCGA.KK.A8I6.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7327.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.A65G.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.A76W.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.A9S7.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.8216.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5794.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A9OA.01 1 0.000 0.997 1.00 0.00
#> TCGA.J9.A52E.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7818.01 1 0.000 0.997 1.00 0.00
#> TCGA.FC.7961.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5504.01 2 0.000 1.000 0.00 1.00
#> TCGA.J4.A67S.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.A6AQ.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5766.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7321.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.7523.01 2 0.000 1.000 0.00 1.00
#> TCGA.2A.A8VT.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.7519.01 1 0.000 0.997 1.00 0.00
#> TCGA.ZG.A9LM.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.7318.01 1 0.000 0.997 1.00 0.00
#> TCGA.J9.A8CM.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6364.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.7331.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6494.01 1 0.000 0.997 1.00 0.00
#> TCGA.HI.7169.01 1 0.000 0.997 1.00 0.00
#> TCGA.J4.A67K.01 1 0.000 0.997 1.00 0.00
#> TCGA.QU.A6IM.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.A9TE.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7115.01 2 0.000 1.000 0.00 1.00
#> TCGA.YL.A8SF.01 1 0.000 0.997 1.00 0.00
#> TCGA.VP.A872.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A8ML.01 2 0.000 1.000 0.00 1.00
#> TCGA.CH.5745.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5740.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.7509.01 1 0.000 0.997 1.00 0.00
#> TCGA.KK.A8IJ.01 1 0.000 0.997 1.00 0.00
#> TCGA.CH.5748.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A8MU.01 2 0.000 1.000 0.00 1.00
#> TCGA.V1.A9Z7.01 1 0.760 0.719 0.78 0.22
#> TCGA.KK.A6E5.01 2 0.000 1.000 0.00 1.00
#> TCGA.KK.A8IL.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7820.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.5518.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZG.A9NI.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.A6HY.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.A7NM.01 2 0.000 1.000 0.00 1.00
#> TCGA.CH.5764.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.A6RC.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.A9TH.01 2 0.000 1.000 0.00 1.00
#> TCGA.V1.A8WV.01 2 0.000 1.000 0.00 1.00
#> TCGA.YL.A8SJ.01 1 0.000 0.997 1.00 0.00
#> TCGA.G9.6363.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.7749.01 1 0.000 0.997 1.00 0.00
#> TCGA.KK.A6E7.01 1 0.000 0.997 1.00 0.00
#> TCGA.V1.A9OX.01 2 0.000 1.000 0.00 1.00
#> TCGA.VN.A88L.01 1 0.000 0.997 1.00 0.00
#> TCGA.HC.8261.01 1 0.000 0.997 1.00 0.00
#> TCGA.XQ.A8TB.01 1 0.000 0.997 1.00 0.00
#> TCGA.EJ.5496.01 1 0.000 0.997 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.G9.6343.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.KK.A6E6.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.G9.6339.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.5509.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.5521.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.CH.5754.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.EJ.7314.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.XA.A8JR.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.7781.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.CH.5751.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.V1.A8WL.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.XK.AAJT.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.G9.6366.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.KC.A4BN.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.KK.A8IG.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.7786.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.J4.A83K.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.8470.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.VP.AA1N.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.5524.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7209.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7742.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.J9.A8CP.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.V1.A9O5.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.VP.A879.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.VN.A88Q.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.M7.A721.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.5514.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.5526.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.5542.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.CH.5769.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7748.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.G9.6365.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.G9.7510.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.V1.A8MG.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.A7NN.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.HC.8265.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.KK.A7AV.01 3 0.296 0.889 0.00 0.1 0.90
#> TCGA.EJ.7218.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.YL.A8SC.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.V1.A8X3.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.KK.A6DY.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.KK.A8I8.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.QU.A6IO.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.XJ.A83H.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.ZG.A8QY.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.YL.A8SO.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.5522.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.ZG.A9M4.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.G9.A9S0.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.TP.A8TT.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.V1.A9Z9.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.HC.7232.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7081.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.VP.A87H.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.G9.7521.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.YL.A8HO.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.J4.A83M.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7736.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.VN.A88N.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.QU.A6IP.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.V1.A9O9.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7210.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.ZG.A9LB.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.8468.01 1 0.400 0.811 0.84 0.0 0.16
#> TCGA.KK.A7B1.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.8262.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HI.7170.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.J4.A67L.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.KC.A7F3.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.HC.8256.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.CH.5769.11 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.G9.6499.11 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.KK.A8I9.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.EJ.7317.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.YL.A8S8.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.Y6.A8TL.01 1 0.153 0.955 0.96 0.0 0.04
#> TCGA.V1.A8MF.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.A65E.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.ZG.A8QX.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.G9.6342.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.J4.8200.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.5532.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.HI.7168.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.HC.7233.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.A65M.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.EJ.A8FN.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.J4.A83L.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.5507.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.J9.A8CK.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.CH.5744.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.ZG.A9N3.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.G9.6354.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.VN.A88O.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.HC.7211.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.KK.A8I6.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.EJ.7327.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.A65G.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.A76W.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.G9.A9S7.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.8216.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.CH.5794.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.V1.A9OA.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.J9.A52E.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7818.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.FC.7961.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.EJ.5504.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.J4.A67S.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.A6AQ.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.CH.5766.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.EJ.7321.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.G9.7523.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.2A.A8VT.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.G9.7519.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.ZG.A9LM.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.EJ.7318.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.J9.A8CM.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.G9.6364.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.7331.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.G9.6494.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.HI.7169.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.J4.A67K.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.QU.A6IM.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.HC.A9TE.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.EJ.7115.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.YL.A8SF.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.VP.A872.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.V1.A8ML.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.CH.5745.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.CH.5740.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.G9.7509.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.KK.A8IJ.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.CH.5748.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.V1.A8MU.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.V1.A9Z7.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.KK.A6E5.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.KK.A8IL.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7820.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.5518.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.ZG.A9NI.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.A6HY.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.A7NM.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.CH.5764.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.A6RC.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.A9TH.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.V1.A8WV.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.YL.A8SJ.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.G9.6363.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.7749.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.KK.A6E7.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.V1.A9OX.01 2 0.000 1.000 0.00 1.0 0.00
#> TCGA.VN.A88L.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.HC.8261.01 3 0.000 0.998 0.00 0.0 1.00
#> TCGA.XQ.A8TB.01 1 0.000 0.997 1.00 0.0 0.00
#> TCGA.EJ.5496.01 1 0.000 0.997 1.00 0.0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.G9.6343.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.KK.A6E6.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G9.6339.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.5509.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EJ.5521.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.CH.5754.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EJ.7314.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.XA.A8JR.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.EJ.7781.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.CH.5751.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.V1.A8WL.01 3 0.2345 0.871 0.00 0.00 0.90 0.10
#> TCGA.XK.AAJT.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.G9.6366.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.KC.A4BN.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.KK.A8IG.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EJ.7786.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.J4.A83K.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.8470.01 3 0.2011 0.891 0.00 0.00 0.92 0.08
#> TCGA.VP.AA1N.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EJ.5524.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7209.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7742.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.J9.A8CP.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.V1.A9O5.01 4 0.3172 0.809 0.00 0.16 0.00 0.84
#> TCGA.VP.A879.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VN.A88Q.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.M7.A721.01 4 0.3975 0.689 0.00 0.24 0.00 0.76
#> TCGA.EJ.5514.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EJ.5526.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.5542.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CH.5769.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.HC.7748.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G9.6365.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G9.7510.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.V1.A8MG.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EJ.A7NN.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.HC.8265.01 2 0.1211 0.958 0.00 0.96 0.00 0.04
#> TCGA.KK.A7AV.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EJ.7218.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.YL.A8SC.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.V1.A8X3.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.KK.A6DY.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.KK.A8I8.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.QU.A6IO.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.XJ.A83H.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.ZG.A8QY.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.YL.A8SO.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EJ.5522.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9M4.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.G9.A9S0.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.TP.A8TT.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.HC.7232.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7081.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VP.A87H.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.G9.7521.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.YL.A8HO.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.J4.A83M.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7736.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.VN.A88N.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.QU.A6IP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.V1.A9O9.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7210.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.ZG.A9LB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.8468.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.KK.A7B1.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.8262.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HI.7170.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.J4.A67L.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.KC.A7F3.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.HC.8256.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.CH.5769.11 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.G9.6499.11 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.KK.A8I9.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EJ.7317.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.YL.A8S8.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.Y6.A8TL.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.V1.A8MF.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.EJ.A65E.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.ZG.A8QX.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.G9.6342.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.J4.8200.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.5532.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.HI.7168.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.HC.7233.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.A65M.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EJ.A8FN.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.J4.A83L.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.5507.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.J9.A8CK.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CH.5744.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9N3.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.G9.6354.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.HC.7211.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.KK.A8I6.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EJ.7327.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.A65G.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.HC.A76W.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.G9.A9S7.01 3 0.4522 0.538 0.32 0.00 0.68 0.00
#> TCGA.HC.8216.01 3 0.1637 0.899 0.06 0.00 0.94 0.00
#> TCGA.CH.5794.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.V1.A9OA.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.J9.A52E.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7818.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.FC.7961.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EJ.5504.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.J4.A67S.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.A6AQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CH.5766.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EJ.7321.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.2A.A8VT.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.G9.7519.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9LM.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.EJ.7318.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.J9.A8CM.01 4 0.0707 0.965 0.00 0.00 0.02 0.98
#> TCGA.G9.6364.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.7331.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.G9.6494.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.HI.7169.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.J4.A67K.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.QU.A6IM.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.HC.A9TE.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EJ.7115.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.YL.A8SF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VP.A872.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.V1.A8ML.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.CH.5745.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CH.5740.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G9.7509.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.KK.A8IJ.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.CH.5748.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.V1.A8MU.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.V1.A9Z7.01 3 0.3400 0.777 0.00 0.00 0.82 0.18
#> TCGA.KK.A6E5.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.KK.A8IL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7820.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.5518.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.ZG.A9NI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.A7NM.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.CH.5764.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 3 0.4977 0.168 0.46 0.00 0.54 0.00
#> TCGA.HC.A9TH.01 3 0.3975 0.688 0.00 0.00 0.76 0.24
#> TCGA.V1.A8WV.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.YL.A8SJ.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.G9.6363.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.7749.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.KK.A6E7.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.V1.A9OX.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.VN.A88L.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HC.8261.01 3 0.0000 0.959 0.00 0.00 1.00 0.00
#> TCGA.XQ.A8TB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EJ.5496.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.G9.6343.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.KK.A6E6.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6339.01 1 0.0609 0.976 0.98 0.00 0.00 0.00 0.02
#> TCGA.EJ.5509.01 2 0.4676 0.745 0.00 0.74 0.12 0.14 0.00
#> TCGA.EJ.5521.01 5 0.3274 0.422 0.00 0.00 0.22 0.00 0.78
#> TCGA.CH.5754.01 4 0.1732 0.905 0.00 0.00 0.08 0.92 0.00
#> TCGA.EJ.7314.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.XA.A8JR.01 5 0.1410 0.775 0.00 0.00 0.06 0.00 0.94
#> TCGA.EJ.7781.01 5 0.1410 0.775 0.00 0.00 0.06 0.00 0.94
#> TCGA.CH.5751.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.V1.A8WL.01 3 0.3291 0.821 0.00 0.00 0.84 0.12 0.04
#> TCGA.XK.AAJT.01 4 0.2280 0.903 0.00 0.00 0.12 0.88 0.00
#> TCGA.G9.6366.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BN.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IG.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7786.01 5 0.1410 0.775 0.00 0.00 0.06 0.00 0.94
#> TCGA.J4.A83K.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8470.01 3 0.3641 0.833 0.00 0.00 0.82 0.12 0.06
#> TCGA.VP.AA1N.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5524.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7209.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7742.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.J9.A8CP.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A9O5.01 4 0.2280 0.903 0.00 0.00 0.12 0.88 0.00
#> TCGA.VP.A879.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88Q.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.M7.A721.01 4 0.2280 0.903 0.00 0.00 0.12 0.88 0.00
#> TCGA.EJ.5514.01 2 0.1043 0.962 0.00 0.96 0.04 0.00 0.00
#> TCGA.EJ.5526.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5542.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5769.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.HC.7748.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.G9.6365.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7510.01 4 0.2280 0.903 0.00 0.00 0.12 0.88 0.00
#> TCGA.V1.A8MG.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A7NN.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.HC.8265.01 4 0.5864 0.406 0.00 0.32 0.12 0.56 0.00
#> TCGA.KK.A7AV.01 4 0.1732 0.918 0.00 0.00 0.08 0.92 0.00
#> TCGA.EJ.7218.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SC.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.V1.A8X3.01 3 0.2929 0.899 0.00 0.00 0.82 0.00 0.18
#> TCGA.KK.A6DY.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.KK.A8I8.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IO.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.XJ.A83H.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZG.A8QY.01 4 0.0609 0.930 0.00 0.00 0.02 0.98 0.00
#> TCGA.YL.A8SO.01 2 0.1043 0.962 0.00 0.96 0.04 0.00 0.00
#> TCGA.EJ.5522.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9M4.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.TP.A8TT.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7232.01 5 0.3274 0.741 0.22 0.00 0.00 0.00 0.78
#> TCGA.HC.7081.01 5 0.3561 0.736 0.26 0.00 0.00 0.00 0.74
#> TCGA.VP.A87H.01 3 0.3424 0.698 0.00 0.00 0.76 0.24 0.00
#> TCGA.G9.7521.01 2 0.0609 0.967 0.00 0.98 0.02 0.00 0.00
#> TCGA.YL.A8HO.01 2 0.2280 0.913 0.00 0.88 0.12 0.00 0.00
#> TCGA.J4.A83M.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7736.01 4 0.1410 0.913 0.00 0.00 0.06 0.94 0.00
#> TCGA.VN.A88N.01 5 0.1410 0.775 0.00 0.00 0.06 0.00 0.94
#> TCGA.QU.A6IP.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O9.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7210.01 2 0.2280 0.913 0.00 0.88 0.12 0.00 0.00
#> TCGA.ZG.A9LB.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.EJ.8468.01 5 0.1732 0.756 0.00 0.00 0.08 0.00 0.92
#> TCGA.KK.A7B1.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8262.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7170.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.J4.A67L.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F3.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.8256.01 3 0.3684 0.848 0.00 0.00 0.72 0.00 0.28
#> TCGA.CH.5769.11 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.G9.6499.11 4 0.1410 0.924 0.00 0.00 0.06 0.94 0.00
#> TCGA.KK.A8I9.01 4 0.0609 0.930 0.00 0.00 0.02 0.98 0.00
#> TCGA.EJ.7317.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.YL.A8S8.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.Y6.A8TL.01 5 0.1410 0.775 0.00 0.00 0.06 0.00 0.94
#> TCGA.V1.A8MF.01 5 0.1410 0.775 0.00 0.00 0.06 0.00 0.94
#> TCGA.EJ.A65E.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZG.A8QX.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6342.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.8200.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.EJ.5532.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.HI.7168.01 4 0.2280 0.903 0.00 0.00 0.12 0.88 0.00
#> TCGA.HC.7233.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65M.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.EJ.A8FN.01 2 0.1043 0.962 0.00 0.96 0.04 0.00 0.00
#> TCGA.J4.A83L.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5507.01 3 0.3561 0.893 0.00 0.00 0.74 0.00 0.26
#> TCGA.J9.A8CK.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5744.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9N3.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6354.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 2 0.1043 0.962 0.00 0.96 0.04 0.00 0.00
#> TCGA.HC.7211.01 4 0.1043 0.930 0.00 0.00 0.04 0.96 0.00
#> TCGA.KK.A8I6.01 4 0.2020 0.894 0.00 0.00 0.10 0.90 0.00
#> TCGA.EJ.7327.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65G.01 5 0.1410 0.775 0.00 0.00 0.06 0.00 0.94
#> TCGA.HC.A76W.01 3 0.3684 0.883 0.00 0.00 0.72 0.00 0.28
#> TCGA.G9.A9S7.01 5 0.0609 0.786 0.02 0.00 0.00 0.00 0.98
#> TCGA.HC.8216.01 5 0.1648 0.789 0.04 0.00 0.02 0.00 0.94
#> TCGA.CH.5794.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.V1.A9OA.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52E.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.HC.7818.01 3 0.3561 0.884 0.00 0.00 0.74 0.00 0.26
#> TCGA.FC.7961.01 2 0.2280 0.913 0.00 0.88 0.12 0.00 0.00
#> TCGA.EJ.5504.01 4 0.2280 0.903 0.00 0.00 0.12 0.88 0.00
#> TCGA.J4.A67S.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AQ.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5766.01 4 0.2020 0.894 0.00 0.00 0.10 0.90 0.00
#> TCGA.EJ.7321.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.2A.A8VT.01 3 0.3697 0.804 0.00 0.00 0.82 0.08 0.10
#> TCGA.G9.7519.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.ZG.A9LM.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.EJ.7318.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.J9.A8CM.01 3 0.3641 0.770 0.00 0.00 0.82 0.12 0.06
#> TCGA.G9.6364.01 5 0.3684 0.728 0.28 0.00 0.00 0.00 0.72
#> TCGA.EJ.7331.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6494.01 3 0.2929 0.899 0.00 0.00 0.82 0.00 0.18
#> TCGA.HI.7169.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67K.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IM.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.HC.A9TE.01 4 0.2020 0.894 0.00 0.00 0.10 0.90 0.00
#> TCGA.EJ.7115.01 4 0.2280 0.903 0.00 0.00 0.12 0.88 0.00
#> TCGA.YL.A8SF.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A872.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.V1.A8ML.01 4 0.0609 0.930 0.00 0.00 0.02 0.98 0.00
#> TCGA.CH.5745.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5740.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7509.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IJ.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.CH.5748.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.V1.A8MU.01 2 0.1043 0.962 0.00 0.96 0.04 0.00 0.00
#> TCGA.V1.A9Z7.01 3 0.3641 0.833 0.00 0.00 0.82 0.12 0.06
#> TCGA.KK.A6E5.01 2 0.0609 0.967 0.00 0.98 0.02 0.00 0.00
#> TCGA.KK.A8IL.01 5 0.3561 0.739 0.26 0.00 0.00 0.00 0.74
#> TCGA.HC.7820.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5518.01 4 0.0000 0.936 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZG.A9NI.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NM.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.CH.5764.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 5 0.1648 0.789 0.04 0.00 0.02 0.00 0.94
#> TCGA.HC.A9TH.01 3 0.2280 0.792 0.00 0.00 0.88 0.12 0.00
#> TCGA.V1.A8WV.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SJ.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.G9.6363.01 1 0.1410 0.926 0.94 0.00 0.00 0.00 0.06
#> TCGA.HC.7749.01 3 0.3684 0.883 0.00 0.00 0.72 0.00 0.28
#> TCGA.KK.A6E7.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.V1.A9OX.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00
#> TCGA.VN.A88L.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8261.01 3 0.3274 0.907 0.00 0.00 0.78 0.00 0.22
#> TCGA.XQ.A8TB.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5496.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.G9.6343.01 4 0.0547 0.865 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.KK.A6E6.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6339.01 1 0.1092 0.945 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EJ.5509.01 2 0.5963 0.252 0.00 0.44 0.00 0.32 0.00 0.24
#> TCGA.EJ.5521.01 5 0.6039 0.220 0.00 0.00 0.28 0.00 0.42 0.30
#> TCGA.CH.5754.01 4 0.3309 0.671 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.EJ.7314.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XA.A8JR.01 5 0.0547 0.825 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.EJ.7781.01 5 0.0937 0.814 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.CH.5751.01 3 0.0937 0.784 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.V1.A8WL.01 3 0.0547 0.760 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.XK.AAJT.01 4 0.3460 0.765 0.00 0.00 0.00 0.76 0.02 0.22
#> TCGA.G9.6366.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KC.A4BN.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IG.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7786.01 5 0.0547 0.825 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.J4.A83K.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8470.01 3 0.1480 0.732 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.VP.AA1N.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5524.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7209.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7742.01 3 0.0547 0.797 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.J9.A8CP.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O5.01 4 0.3460 0.765 0.00 0.00 0.00 0.76 0.02 0.22
#> TCGA.VP.A879.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88Q.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.M7.A721.01 4 0.3076 0.762 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.EJ.5514.01 2 0.2454 0.867 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.EJ.5526.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5542.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5769.01 5 0.3592 0.777 0.00 0.00 0.02 0.00 0.74 0.24
#> TCGA.HC.7748.01 5 0.4348 0.729 0.04 0.00 0.00 0.00 0.64 0.32
#> TCGA.G9.6365.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7510.01 4 0.3076 0.762 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.V1.A8MG.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NN.01 3 0.0937 0.784 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.HC.8265.01 4 0.4834 0.645 0.00 0.10 0.00 0.64 0.00 0.26
#> TCGA.KK.A7AV.01 4 0.0937 0.861 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EJ.7218.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SC.01 5 0.3592 0.777 0.00 0.00 0.02 0.00 0.74 0.24
#> TCGA.V1.A8X3.01 3 0.0937 0.762 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.KK.A6DY.01 5 0.4246 0.689 0.00 0.00 0.02 0.00 0.58 0.40
#> TCGA.KK.A8I8.01 1 0.2454 0.821 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.QU.A6IO.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A83H.01 4 0.0547 0.865 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZG.A8QY.01 4 0.2094 0.831 0.00 0.00 0.02 0.90 0.00 0.08
#> TCGA.YL.A8SO.01 2 0.2260 0.876 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.EJ.5522.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9M4.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 4 0.0000 0.867 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TP.A8TT.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7232.01 5 0.4246 0.684 0.02 0.00 0.00 0.00 0.58 0.40
#> TCGA.HC.7081.01 5 0.4078 0.731 0.02 0.00 0.00 0.00 0.64 0.34
#> TCGA.VP.A87H.01 3 0.3567 0.380 0.00 0.00 0.80 0.10 0.00 0.10
#> TCGA.G9.7521.01 2 0.1556 0.894 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.YL.A8HO.01 2 0.3076 0.810 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.J4.A83M.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7736.01 4 0.2094 0.835 0.00 0.00 0.02 0.90 0.00 0.08
#> TCGA.VN.A88N.01 5 0.0547 0.825 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.QU.A6IP.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O9.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7210.01 2 0.3592 0.791 0.00 0.74 0.00 0.02 0.00 0.24
#> TCGA.ZG.A9LB.01 5 0.1480 0.820 0.04 0.00 0.00 0.00 0.94 0.02
#> TCGA.EJ.8468.01 5 0.2260 0.712 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.KK.A7B1.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8262.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7170.01 5 0.1480 0.820 0.04 0.00 0.00 0.00 0.94 0.02
#> TCGA.J4.A67L.01 1 0.0547 0.964 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.KC.A7F3.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8256.01 3 0.3499 0.122 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.CH.5769.11 5 0.3711 0.776 0.00 0.00 0.02 0.00 0.72 0.26
#> TCGA.G9.6499.11 4 0.0547 0.865 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.KK.A8I9.01 4 0.2094 0.831 0.00 0.00 0.02 0.90 0.00 0.08
#> TCGA.EJ.7317.01 4 0.0547 0.864 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.YL.A8S8.01 2 0.0547 0.905 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.Y6.A8TL.01 5 0.1556 0.783 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.V1.A8MF.01 5 0.0547 0.825 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.EJ.A65E.01 4 0.0000 0.867 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZG.A8QX.01 4 0.0000 0.867 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.6342.01 1 0.3315 0.749 0.78 0.00 0.00 0.00 0.02 0.20
#> TCGA.J4.8200.01 5 0.1480 0.820 0.04 0.00 0.00 0.00 0.94 0.02
#> TCGA.EJ.5532.01 3 0.0937 0.784 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.HI.7168.01 4 0.2260 0.832 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.HC.7233.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65M.01 4 0.0000 0.867 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.A8FN.01 2 0.2454 0.867 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.J4.A83L.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5507.01 3 0.2094 0.668 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.J9.A8CK.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5744.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9N3.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6354.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 2 0.2454 0.867 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.HC.7211.01 4 0.0937 0.866 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.KK.A8I6.01 4 0.3819 0.657 0.00 0.00 0.02 0.70 0.00 0.28
#> TCGA.EJ.7327.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65G.01 5 0.0547 0.825 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.HC.A76W.01 3 0.2048 0.676 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.G9.A9S7.01 5 0.4246 0.689 0.00 0.00 0.02 0.00 0.58 0.40
#> TCGA.HC.8216.01 5 0.0547 0.825 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.CH.5794.01 5 0.4199 0.688 0.00 0.00 0.02 0.00 0.60 0.38
#> TCGA.V1.A9OA.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52E.01 5 0.1480 0.820 0.04 0.00 0.00 0.00 0.94 0.02
#> TCGA.HC.7818.01 3 0.2048 0.676 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.FC.7961.01 2 0.3076 0.810 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.EJ.5504.01 4 0.3076 0.762 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.J4.A67S.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AQ.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5766.01 4 0.3819 0.657 0.00 0.00 0.02 0.70 0.00 0.28
#> TCGA.EJ.7321.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 4 0.0547 0.864 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.2A.A8VT.01 6 0.4337 0.000 0.00 0.00 0.48 0.02 0.00 0.50
#> TCGA.G9.7519.01 5 0.1480 0.820 0.04 0.00 0.00 0.00 0.94 0.02
#> TCGA.ZG.A9LM.01 3 0.0547 0.797 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EJ.7318.01 5 0.1480 0.820 0.04 0.00 0.00 0.00 0.94 0.02
#> TCGA.J9.A8CM.01 3 0.4845 -0.698 0.00 0.00 0.54 0.06 0.00 0.40
#> TCGA.G9.6364.01 5 0.4078 0.731 0.02 0.00 0.00 0.00 0.64 0.34
#> TCGA.EJ.7331.01 4 0.0547 0.864 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.G9.6494.01 3 0.0937 0.762 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HI.7169.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67K.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IM.01 3 0.0547 0.797 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.HC.A9TE.01 4 0.3819 0.657 0.00 0.00 0.02 0.70 0.00 0.28
#> TCGA.EJ.7115.01 4 0.3460 0.765 0.00 0.00 0.00 0.76 0.02 0.22
#> TCGA.YL.A8SF.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A872.01 5 0.3592 0.777 0.00 0.00 0.02 0.00 0.74 0.24
#> TCGA.V1.A8ML.01 4 0.1092 0.861 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.CH.5745.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5740.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7509.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IJ.01 3 0.0547 0.797 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.CH.5748.01 3 0.0937 0.784 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.V1.A8MU.01 2 0.2260 0.876 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.V1.A9Z7.01 3 0.2094 0.679 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.KK.A6E5.01 2 0.1814 0.889 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.KK.A8IL.01 5 0.1092 0.825 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.HC.7820.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5518.01 4 0.0000 0.867 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZG.A9NI.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NM.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5764.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 5 0.1092 0.825 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.HC.A9TH.01 3 0.2981 0.443 0.00 0.00 0.82 0.02 0.00 0.16
#> TCGA.V1.A8WV.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SJ.01 3 0.0547 0.797 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.G9.6363.01 1 0.4926 0.521 0.64 0.00 0.00 0.00 0.12 0.24
#> TCGA.HC.7749.01 3 0.3156 0.450 0.00 0.00 0.80 0.00 0.02 0.18
#> TCGA.KK.A6E7.01 3 0.0547 0.797 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.V1.A9OX.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88L.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8261.01 3 0.0547 0.797 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.XQ.A8TB.01 1 0.1556 0.911 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.EJ.5496.01 1 0.0000 0.981 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.G9.6343.01 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.KK.A6E6.01 1 0.0504 0.9586 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G9.6339.01 1 0.1166 0.9209 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.EJ.5509.01 4 0.3685 0.0377 0.00 0.32 0.00 0.66 0.00 0.00 0.02
#> TCGA.EJ.5521.01 7 0.6909 0.2755 0.00 0.00 0.16 0.00 0.22 0.26 0.36
#> TCGA.CH.5754.01 6 0.4939 0.5991 0.00 0.00 0.00 0.30 0.00 0.56 0.14
#> TCGA.EJ.7314.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XA.A8JR.01 5 0.0000 0.8335 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.7781.01 5 0.0504 0.8202 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CH.5751.01 3 0.3149 0.8243 0.00 0.00 0.84 0.00 0.06 0.06 0.04
#> TCGA.V1.A8WL.01 3 0.0504 0.8490 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.XK.AAJT.01 4 0.0504 0.5737 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.G9.6366.01 1 0.0504 0.9586 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.KC.A4BN.01 1 0.0504 0.9586 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.KK.A8IG.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7786.01 5 0.0000 0.8335 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.A83K.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8470.01 3 0.0863 0.8410 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.VP.AA1N.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5524.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7209.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7742.01 3 0.1363 0.8569 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.J9.A8CP.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O5.01 4 0.0863 0.5551 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.VP.A879.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88Q.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.M7.A721.01 4 0.0504 0.5505 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EJ.5514.01 2 0.2906 0.8424 0.00 0.80 0.00 0.18 0.00 0.00 0.02
#> TCGA.EJ.5526.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5542.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5769.01 5 0.4418 0.2818 0.00 0.00 0.00 0.00 0.62 0.08 0.30
#> TCGA.HC.7748.01 7 0.3815 0.4815 0.02 0.00 0.00 0.00 0.36 0.00 0.62
#> TCGA.G9.6365.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7510.01 4 0.0000 0.5722 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A8MG.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NN.01 3 0.2213 0.8473 0.00 0.00 0.90 0.00 0.04 0.02 0.04
#> TCGA.HC.8265.01 4 0.2376 0.3756 0.00 0.12 0.00 0.86 0.00 0.00 0.02
#> TCGA.KK.A7AV.01 4 0.3139 0.7439 0.00 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.EJ.7218.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SC.01 5 0.4108 0.3730 0.00 0.00 0.00 0.00 0.66 0.06 0.28
#> TCGA.V1.A8X3.01 3 0.1363 0.8507 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.KK.A6DY.01 7 0.3517 0.5652 0.00 0.00 0.00 0.00 0.28 0.02 0.70
#> TCGA.KK.A8I8.01 1 0.3496 0.2167 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.QU.A6IO.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A83H.01 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.ZG.A8QY.01 4 0.4577 0.6633 0.00 0.00 0.02 0.58 0.00 0.36 0.04
#> TCGA.YL.A8SO.01 2 0.2906 0.8424 0.00 0.80 0.00 0.18 0.00 0.00 0.02
#> TCGA.EJ.5522.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9M4.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.TP.A8TT.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7232.01 7 0.3887 0.5727 0.02 0.00 0.00 0.00 0.26 0.02 0.70
#> TCGA.HC.7081.01 7 0.3755 0.5056 0.02 0.00 0.00 0.00 0.34 0.00 0.64
#> TCGA.VP.A87H.01 3 0.3667 0.6201 0.00 0.00 0.74 0.00 0.00 0.20 0.06
#> TCGA.G9.7521.01 2 0.1928 0.8838 0.00 0.90 0.00 0.08 0.00 0.00 0.02
#> TCGA.YL.A8HO.01 2 0.3685 0.7189 0.00 0.66 0.00 0.32 0.00 0.00 0.02
#> TCGA.J4.A83M.01 1 0.0504 0.9586 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HC.7736.01 4 0.3546 0.5554 0.00 0.00 0.00 0.54 0.00 0.46 0.00
#> TCGA.VN.A88N.01 5 0.0000 0.8335 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QU.A6IP.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O9.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7210.01 2 0.3685 0.7189 0.00 0.66 0.00 0.32 0.00 0.00 0.02
#> TCGA.ZG.A9LB.01 5 0.1363 0.8238 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.EJ.8468.01 5 0.3149 0.6884 0.00 0.00 0.06 0.00 0.84 0.06 0.04
#> TCGA.KK.A7B1.01 1 0.1433 0.9011 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.HC.8262.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HI.7170.01 5 0.1363 0.8238 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.J4.A67L.01 1 0.0863 0.9396 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.KC.A7F3.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8256.01 3 0.4016 0.7632 0.00 0.00 0.76 0.00 0.14 0.06 0.04
#> TCGA.CH.5769.11 5 0.4328 0.2615 0.00 0.00 0.00 0.00 0.60 0.06 0.34
#> TCGA.G9.6499.11 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.KK.A8I9.01 4 0.4577 0.6633 0.00 0.00 0.02 0.58 0.00 0.36 0.04
#> TCGA.EJ.7317.01 4 0.3358 0.7317 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.YL.A8S8.01 2 0.0504 0.9011 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.Y6.A8TL.01 5 0.2509 0.7378 0.00 0.00 0.02 0.00 0.88 0.06 0.04
#> TCGA.V1.A8MF.01 5 0.0000 0.8335 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.A65E.01 4 0.3294 0.7422 0.00 0.00 0.00 0.66 0.00 0.34 0.00
#> TCGA.ZG.A8QX.01 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.G9.6342.01 7 0.3558 0.0154 0.48 0.00 0.00 0.00 0.00 0.00 0.52
#> TCGA.J4.8200.01 5 0.1363 0.8238 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.EJ.5532.01 3 0.3149 0.8243 0.00 0.00 0.84 0.00 0.06 0.06 0.04
#> TCGA.HI.7168.01 4 0.1671 0.6326 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.HC.7233.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65M.01 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.EJ.A8FN.01 2 0.2906 0.8424 0.00 0.80 0.00 0.18 0.00 0.00 0.02
#> TCGA.J4.A83L.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5507.01 3 0.5091 0.6780 0.00 0.00 0.64 0.00 0.04 0.20 0.12
#> TCGA.J9.A8CK.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5744.01 1 0.0504 0.9577 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZG.A9N3.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6354.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 2 0.2906 0.8424 0.00 0.80 0.00 0.18 0.00 0.00 0.02
#> TCGA.HC.7211.01 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.KK.A8I6.01 6 0.4939 0.5991 0.00 0.00 0.00 0.30 0.00 0.56 0.14
#> TCGA.EJ.7327.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65G.01 5 0.0504 0.8356 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HC.A76W.01 3 0.5218 0.6373 0.00 0.00 0.60 0.00 0.02 0.20 0.18
#> TCGA.G9.A9S7.01 7 0.3517 0.5652 0.00 0.00 0.00 0.00 0.28 0.02 0.70
#> TCGA.HC.8216.01 5 0.0504 0.8356 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CH.5794.01 7 0.5341 0.3984 0.00 0.00 0.00 0.00 0.26 0.24 0.50
#> TCGA.V1.A9OA.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52E.01 5 0.1363 0.8238 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.HC.7818.01 3 0.5324 0.6235 0.00 0.00 0.58 0.00 0.02 0.22 0.18
#> TCGA.FC.7961.01 2 0.3685 0.7189 0.00 0.66 0.00 0.32 0.00 0.00 0.02
#> TCGA.EJ.5504.01 4 0.0000 0.5722 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67S.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AQ.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5766.01 6 0.4939 0.5991 0.00 0.00 0.00 0.30 0.00 0.56 0.14
#> TCGA.EJ.7321.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 4 0.3358 0.7317 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.2A.A8VT.01 6 0.4681 0.2840 0.00 0.00 0.10 0.00 0.00 0.58 0.32
#> TCGA.G9.7519.01 5 0.1363 0.8238 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.ZG.A9LM.01 3 0.0504 0.8576 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EJ.7318.01 5 0.1363 0.8238 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.J9.A8CM.01 6 0.4629 0.3897 0.00 0.00 0.16 0.00 0.00 0.64 0.20
#> TCGA.G9.6364.01 7 0.3815 0.4815 0.02 0.00 0.00 0.00 0.36 0.00 0.62
#> TCGA.EJ.7331.01 4 0.3358 0.7317 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.G9.6494.01 3 0.1363 0.8507 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.HI.7169.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67K.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IM.01 3 0.0504 0.8576 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.HC.A9TE.01 6 0.4939 0.5991 0.00 0.00 0.00 0.30 0.00 0.56 0.14
#> TCGA.EJ.7115.01 4 0.1006 0.5682 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.YL.A8SF.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A872.01 5 0.4681 0.1805 0.00 0.00 0.00 0.00 0.58 0.10 0.32
#> TCGA.V1.A8ML.01 4 0.3755 0.7248 0.00 0.00 0.00 0.64 0.00 0.34 0.02
#> TCGA.CH.5745.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5740.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7509.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IJ.01 3 0.0504 0.8576 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CH.5748.01 3 0.3149 0.8243 0.00 0.00 0.84 0.00 0.06 0.06 0.04
#> TCGA.V1.A8MU.01 2 0.2569 0.8618 0.00 0.84 0.00 0.14 0.00 0.00 0.02
#> TCGA.V1.A9Z7.01 3 0.1664 0.8225 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.KK.A6E5.01 2 0.2163 0.8775 0.00 0.88 0.00 0.10 0.00 0.00 0.02
#> TCGA.KK.A8IL.01 5 0.1006 0.8287 0.02 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.HC.7820.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5518.01 4 0.3221 0.7482 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.ZG.A9NI.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NM.01 2 0.0504 0.9021 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CH.5764.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 5 0.0504 0.8356 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HC.A9TH.01 3 0.3199 0.7454 0.00 0.00 0.80 0.00 0.00 0.14 0.06
#> TCGA.V1.A8WV.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SJ.01 3 0.0504 0.8576 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.G9.6363.01 7 0.4426 0.3359 0.38 0.00 0.00 0.00 0.06 0.00 0.56
#> TCGA.HC.7749.01 3 0.6166 0.3978 0.00 0.00 0.42 0.00 0.04 0.26 0.28
#> TCGA.KK.A6E7.01 3 0.1006 0.8585 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.V1.A9OX.01 2 0.0000 0.9050 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88L.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8261.01 3 0.1363 0.8569 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.XQ.A8TB.01 1 0.3358 0.4153 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.EJ.5496.01 1 0.0000 0.9735 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.G9.6343.01 4 0.0000 0.7339 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E6.01 1 0.0471 0.9084 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G9.6339.01 1 0.2864 0.7816 0.84 0.00 0.00 0.00 0.06 0.00 0.02 0.08
#> TCGA.EJ.5509.01 8 0.5211 0.0000 0.00 0.26 0.00 0.34 0.00 0.00 0.00 0.40
#> TCGA.EJ.5521.01 7 0.7312 0.0611 0.00 0.00 0.18 0.00 0.06 0.26 0.26 0.24
#> TCGA.CH.5754.01 6 0.3237 0.7026 0.00 0.00 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.EJ.7314.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.XA.A8JR.01 5 0.1887 0.7508 0.00 0.00 0.06 0.00 0.90 0.00 0.00 0.04
#> TCGA.EJ.7781.01 5 0.1887 0.7508 0.00 0.00 0.06 0.00 0.90 0.00 0.00 0.04
#> TCGA.CH.5751.01 3 0.4034 0.7048 0.00 0.00 0.76 0.00 0.06 0.04 0.02 0.12
#> TCGA.V1.A8WL.01 3 0.2071 0.7481 0.00 0.00 0.90 0.04 0.00 0.04 0.00 0.02
#> TCGA.XK.AAJT.01 4 0.4775 0.3161 0.00 0.00 0.00 0.60 0.02 0.02 0.06 0.30
#> TCGA.G9.6366.01 1 0.1341 0.8686 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.KC.A4BN.01 1 0.0808 0.8973 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.KK.A8IG.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7786.01 5 0.1887 0.7508 0.00 0.00 0.06 0.00 0.90 0.00 0.00 0.04
#> TCGA.J4.A83K.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.EJ.8470.01 3 0.2071 0.7383 0.00 0.00 0.90 0.02 0.00 0.00 0.04 0.04
#> TCGA.VP.AA1N.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5524.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.HC.7209.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.HC.7742.01 3 0.0471 0.7803 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.J9.A8CP.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9O5.01 4 0.4599 0.3139 0.00 0.00 0.00 0.60 0.02 0.02 0.04 0.32
#> TCGA.VP.A879.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88Q.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.M7.A721.01 4 0.3618 0.2326 0.00 0.00 0.00 0.60 0.00 0.00 0.02 0.38
#> TCGA.EJ.5514.01 2 0.2888 0.7697 0.00 0.80 0.00 0.00 0.04 0.00 0.00 0.16
#> TCGA.EJ.5526.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.EJ.5542.01 1 0.1091 0.9146 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.CH.5769.01 5 0.6982 0.1496 0.00 0.00 0.06 0.00 0.36 0.10 0.24 0.24
#> TCGA.HC.7748.01 7 0.4019 0.6532 0.06 0.00 0.00 0.00 0.14 0.00 0.74 0.06
#> TCGA.G9.6365.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.G9.7510.01 4 0.3995 0.2684 0.00 0.00 0.00 0.60 0.00 0.02 0.02 0.36
#> TCGA.V1.A8MG.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NN.01 3 0.2348 0.7592 0.00 0.00 0.88 0.00 0.00 0.04 0.02 0.06
#> TCGA.HC.8265.01 4 0.4325 -0.0839 0.00 0.04 0.00 0.56 0.02 0.00 0.00 0.38
#> TCGA.KK.A7AV.01 4 0.1408 0.7239 0.00 0.00 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.EJ.7218.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SC.01 5 0.6731 0.2198 0.00 0.00 0.06 0.00 0.42 0.08 0.20 0.24
#> TCGA.V1.A8X3.01 3 0.0808 0.7756 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.KK.A6DY.01 7 0.2623 0.6115 0.00 0.00 0.06 0.00 0.10 0.00 0.84 0.00
#> TCGA.KK.A8I8.01 7 0.3142 0.4249 0.36 0.00 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.QU.A6IO.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XJ.A83H.01 4 0.0000 0.7339 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A8QY.01 4 0.3894 0.5817 0.00 0.00 0.00 0.76 0.00 0.08 0.06 0.10
#> TCGA.YL.A8SO.01 2 0.2888 0.7697 0.00 0.80 0.00 0.00 0.04 0.00 0.00 0.16
#> TCGA.EJ.5522.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.ZG.A9M4.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 4 0.1275 0.7259 0.00 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.TP.A8TT.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7232.01 7 0.2623 0.6617 0.06 0.00 0.00 0.00 0.10 0.00 0.84 0.00
#> TCGA.HC.7081.01 7 0.4019 0.6532 0.06 0.00 0.00 0.00 0.14 0.00 0.74 0.06
#> TCGA.VP.A87H.01 3 0.5936 0.4075 0.00 0.00 0.58 0.16 0.00 0.08 0.06 0.12
#> TCGA.G9.7521.01 2 0.2725 0.7851 0.00 0.82 0.00 0.00 0.04 0.00 0.00 0.14
#> TCGA.YL.A8HO.01 2 0.3862 0.4076 0.00 0.60 0.00 0.00 0.04 0.00 0.00 0.36
#> TCGA.J4.A83M.01 1 0.1091 0.8853 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.HC.7736.01 4 0.1563 0.6487 0.00 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.VN.A88N.01 5 0.1887 0.7508 0.00 0.00 0.06 0.00 0.90 0.00 0.00 0.04
#> TCGA.QU.A6IP.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.V1.A9O9.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7210.01 2 0.4325 0.2200 0.00 0.56 0.00 0.04 0.02 0.00 0.00 0.38
#> TCGA.ZG.A9LB.01 5 0.2407 0.6985 0.06 0.00 0.00 0.00 0.86 0.00 0.00 0.08
#> TCGA.EJ.8468.01 5 0.4896 0.6057 0.00 0.00 0.12 0.00 0.68 0.06 0.02 0.12
#> TCGA.KK.A7B1.01 1 0.1887 0.8484 0.90 0.00 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.HC.8262.01 1 0.0808 0.9161 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HI.7170.01 5 0.2648 0.6861 0.08 0.00 0.00 0.00 0.84 0.00 0.00 0.08
#> TCGA.J4.A67L.01 1 0.2132 0.8300 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.KC.A7F3.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8256.01 3 0.4720 0.6615 0.00 0.00 0.70 0.00 0.10 0.06 0.02 0.12
#> TCGA.CH.5769.11 5 0.6795 0.1705 0.00 0.00 0.06 0.00 0.40 0.08 0.24 0.22
#> TCGA.G9.6499.11 4 0.0941 0.7292 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.KK.A8I9.01 4 0.3894 0.5817 0.00 0.00 0.00 0.76 0.00 0.08 0.06 0.10
#> TCGA.EJ.7317.01 4 0.1804 0.6971 0.00 0.00 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.YL.A8S8.01 2 0.0471 0.8407 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.Y6.A8TL.01 5 0.4896 0.6057 0.00 0.00 0.12 0.00 0.68 0.06 0.02 0.12
#> TCGA.V1.A8MF.01 5 0.1091 0.7556 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EJ.A65E.01 4 0.1275 0.7259 0.00 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.ZG.A8QX.01 4 0.0000 0.7339 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6342.01 7 0.3374 0.5145 0.30 0.00 0.00 0.00 0.00 0.00 0.68 0.02
#> TCGA.J4.8200.01 5 0.2648 0.6861 0.08 0.00 0.00 0.00 0.84 0.00 0.00 0.08
#> TCGA.EJ.5532.01 3 0.4295 0.6941 0.00 0.00 0.74 0.00 0.06 0.06 0.02 0.12
#> TCGA.HI.7168.01 4 0.3843 0.4735 0.00 0.00 0.00 0.70 0.00 0.02 0.04 0.24
#> TCGA.HC.7233.01 1 0.0808 0.8985 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EJ.A65M.01 4 0.0000 0.7339 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A8FN.01 2 0.3170 0.7252 0.00 0.76 0.00 0.00 0.04 0.00 0.00 0.20
#> TCGA.J4.A83L.01 1 0.0808 0.8985 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EJ.5507.01 3 0.6055 0.3704 0.00 0.00 0.42 0.00 0.00 0.24 0.08 0.26
#> TCGA.J9.A8CK.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5744.01 1 0.0471 0.9092 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ZG.A9N3.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6354.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 2 0.3170 0.7252 0.00 0.76 0.00 0.00 0.04 0.00 0.00 0.20
#> TCGA.HC.7211.01 4 0.0941 0.7292 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.KK.A8I6.01 6 0.3237 0.7026 0.00 0.00 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.EJ.7327.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.EJ.A65G.01 5 0.1091 0.7556 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.HC.A76W.01 3 0.5755 0.5142 0.00 0.00 0.52 0.00 0.00 0.22 0.10 0.16
#> TCGA.G9.A9S7.01 7 0.2623 0.6115 0.00 0.00 0.06 0.00 0.10 0.00 0.84 0.00
#> TCGA.HC.8216.01 5 0.1091 0.7556 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CH.5794.01 7 0.6739 0.2964 0.00 0.00 0.06 0.00 0.08 0.22 0.42 0.22
#> TCGA.V1.A9OA.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.J9.A52E.01 5 0.2648 0.6861 0.08 0.00 0.00 0.00 0.84 0.00 0.00 0.08
#> TCGA.HC.7818.01 3 0.5896 0.4761 0.00 0.00 0.48 0.00 0.00 0.26 0.10 0.16
#> TCGA.FC.7961.01 2 0.3862 0.4076 0.00 0.60 0.00 0.00 0.04 0.00 0.00 0.36
#> TCGA.EJ.5504.01 4 0.3995 0.2684 0.00 0.00 0.00 0.60 0.00 0.02 0.02 0.36
#> TCGA.J4.A67S.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AQ.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5766.01 6 0.3237 0.7026 0.00 0.00 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.EJ.7321.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.G9.7523.01 4 0.1804 0.6971 0.00 0.00 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.2A.A8VT.01 6 0.1887 0.4640 0.00 0.00 0.04 0.00 0.00 0.90 0.06 0.00
#> TCGA.G9.7519.01 5 0.2165 0.7084 0.06 0.00 0.00 0.00 0.88 0.00 0.00 0.06
#> TCGA.ZG.A9LM.01 3 0.0808 0.7759 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.EJ.7318.01 5 0.2648 0.6861 0.08 0.00 0.00 0.00 0.84 0.00 0.00 0.08
#> TCGA.J9.A8CM.01 6 0.2350 0.4856 0.00 0.00 0.10 0.00 0.00 0.86 0.04 0.00
#> TCGA.G9.6364.01 7 0.4019 0.6532 0.06 0.00 0.00 0.00 0.14 0.00 0.74 0.06
#> TCGA.EJ.7331.01 4 0.1804 0.6971 0.00 0.00 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.G9.6494.01 3 0.0808 0.7756 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.HI.7169.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67K.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.QU.A6IM.01 3 0.0471 0.7775 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HC.A9TE.01 6 0.3237 0.7026 0.00 0.00 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.EJ.7115.01 4 0.4599 0.3139 0.00 0.00 0.00 0.60 0.02 0.02 0.04 0.32
#> TCGA.YL.A8SF.01 1 0.1341 0.9118 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.VP.A872.01 5 0.7133 0.0119 0.00 0.00 0.06 0.00 0.30 0.12 0.28 0.24
#> TCGA.V1.A8ML.01 4 0.1804 0.7012 0.00 0.00 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.CH.5745.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.CH.5740.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.G9.7509.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IJ.01 3 0.0471 0.7780 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CH.5748.01 3 0.4295 0.6941 0.00 0.00 0.74 0.00 0.06 0.06 0.02 0.12
#> TCGA.V1.A8MU.01 2 0.2725 0.7851 0.00 0.82 0.00 0.00 0.04 0.00 0.00 0.14
#> TCGA.V1.A9Z7.01 3 0.5047 0.5671 0.00 0.00 0.68 0.04 0.00 0.08 0.08 0.12
#> TCGA.KK.A6E5.01 2 0.2725 0.7851 0.00 0.82 0.00 0.00 0.04 0.00 0.00 0.14
#> TCGA.KK.A8IL.01 5 0.2071 0.7316 0.04 0.00 0.02 0.00 0.90 0.00 0.00 0.04
#> TCGA.HC.7820.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.EJ.5518.01 4 0.0000 0.7339 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9NI.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NM.01 2 0.1887 0.8203 0.00 0.90 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.CH.5764.01 1 0.0000 0.9159 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 5 0.1091 0.7556 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.HC.A9TH.01 3 0.3404 0.5894 0.00 0.00 0.72 0.00 0.00 0.24 0.00 0.04
#> TCGA.V1.A8WV.01 2 0.0471 0.8431 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.YL.A8SJ.01 3 0.0471 0.7780 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.G9.6363.01 7 0.4041 0.5875 0.22 0.00 0.00 0.00 0.04 0.00 0.70 0.04
#> TCGA.HC.7749.01 3 0.6424 0.2672 0.00 0.00 0.36 0.00 0.00 0.26 0.14 0.24
#> TCGA.KK.A6E7.01 3 0.0471 0.7803 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.V1.A9OX.01 2 0.0000 0.8464 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88L.01 1 0.1765 0.9036 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.HC.8261.01 3 0.0471 0.7803 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.XQ.A8TB.01 1 0.3971 -0.0274 0.54 0.00 0.00 0.00 0.00 0.00 0.42 0.04
#> TCGA.EJ.5496.01 1 0.1091 0.9146 0.94 0.00 0.00 0.00 0.00 0.00 0.00 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: Node04. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["041"]
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 58 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 0.977 0.990 0.3249 0.687 0.687
#> 3 3 1.000 0.998 0.999 0.9797 0.670 0.519
#> 4 4 0.821 0.885 0.915 0.1168 0.823 0.557
#> 5 5 0.809 0.808 0.872 0.0817 1.000 1.000
#> 6 6 0.769 0.711 0.820 0.0302 0.917 0.700
#> 7 7 0.785 0.552 0.801 0.0389 0.932 0.690
#> 8 8 0.785 0.583 0.776 0.0181 0.921 0.618
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.KK.A6E6.01 2 0.855 0.620 0.28 0.72
#> TCGA.G9.6339.01 2 0.000 0.988 0.00 1.00
#> TCGA.EJ.7314.01 1 0.000 1.000 1.00 0.00
#> TCGA.G9.6366.01 2 0.000 0.988 0.00 1.00
#> TCGA.KC.A4BN.01 2 0.000 0.988 0.00 1.00
#> TCGA.J4.A83K.01 2 0.000 0.988 0.00 1.00
#> TCGA.EJ.5524.01 2 0.000 0.988 0.00 1.00
#> TCGA.HC.7209.01 2 0.000 0.988 0.00 1.00
#> TCGA.VP.A879.01 2 0.000 0.988 0.00 1.00
#> TCGA.VN.A88Q.01 2 0.000 0.988 0.00 1.00
#> TCGA.EJ.5526.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.5542.01 2 0.000 0.988 0.00 1.00
#> TCGA.HC.7748.01 2 0.000 0.988 0.00 1.00
#> TCGA.G9.6365.01 2 0.000 0.988 0.00 1.00
#> TCGA.KK.A8I8.01 2 0.000 0.988 0.00 1.00
#> TCGA.EJ.5522.01 2 0.000 0.988 0.00 1.00
#> TCGA.TP.A8TT.01 2 0.000 0.988 0.00 1.00
#> TCGA.HC.7232.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.7081.01 2 0.000 0.988 0.00 1.00
#> TCGA.J4.A83M.01 2 0.000 0.988 0.00 1.00
#> TCGA.QU.A6IP.01 2 0.000 0.988 0.00 1.00
#> TCGA.V1.A9O9.01 2 0.000 0.988 0.00 1.00
#> TCGA.ZG.A9LB.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A7B1.01 2 0.000 0.988 0.00 1.00
#> TCGA.HC.8262.01 1 0.000 1.000 1.00 0.00
#> TCGA.HI.7170.01 2 0.000 0.988 0.00 1.00
#> TCGA.J4.A67L.01 2 0.000 0.988 0.00 1.00
#> TCGA.G9.6342.01 2 0.000 0.988 0.00 1.00
#> TCGA.J4.8200.01 2 0.000 0.988 0.00 1.00
#> TCGA.HC.7233.01 2 0.000 0.988 0.00 1.00
#> TCGA.J4.A83L.01 2 0.000 0.988 0.00 1.00
#> TCGA.J9.A8CK.01 2 0.000 0.988 0.00 1.00
#> TCGA.CH.5744.01 2 0.000 0.988 0.00 1.00
#> TCGA.G9.6354.01 2 0.000 0.988 0.00 1.00
#> TCGA.EJ.7327.01 2 0.000 0.988 0.00 1.00
#> TCGA.V1.A9OA.01 1 0.000 1.000 1.00 0.00
#> TCGA.J9.A52E.01 2 0.000 0.988 0.00 1.00
#> TCGA.J4.A67S.01 2 0.000 0.988 0.00 1.00
#> TCGA.HC.A6AQ.01 2 0.000 0.988 0.00 1.00
#> TCGA.EJ.7321.01 1 0.000 1.000 1.00 0.00
#> TCGA.G9.7519.01 2 0.000 0.988 0.00 1.00
#> TCGA.EJ.7318.01 2 0.000 0.988 0.00 1.00
#> TCGA.G9.6364.01 2 0.000 0.988 0.00 1.00
#> TCGA.HI.7169.01 2 0.000 0.988 0.00 1.00
#> TCGA.J4.A67K.01 2 0.000 0.988 0.00 1.00
#> TCGA.YL.A8SF.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5745.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5740.01 2 0.855 0.620 0.28 0.72
#> TCGA.G9.7509.01 2 0.000 0.988 0.00 1.00
#> TCGA.KK.A8IL.01 2 0.000 0.988 0.00 1.00
#> TCGA.HC.7820.01 2 0.000 0.988 0.00 1.00
#> TCGA.ZG.A9NI.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.A6HY.01 2 0.000 0.988 0.00 1.00
#> TCGA.CH.5764.01 2 0.000 0.988 0.00 1.00
#> TCGA.G9.6363.01 2 0.000 0.988 0.00 1.00
#> TCGA.VN.A88L.01 2 0.000 0.988 0.00 1.00
#> TCGA.XQ.A8TB.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.5496.01 2 0.000 0.988 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.KK.A6E6.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.G9.6339.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.EJ.7314.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.G9.6366.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.KC.A4BN.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.J4.A83K.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.EJ.5524.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.HC.7209.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.VP.A879.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.VN.A88Q.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.EJ.5526.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.EJ.5542.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.HC.7748.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.G9.6365.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.KK.A8I8.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.EJ.5522.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.TP.A8TT.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.HC.7232.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.HC.7081.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.J4.A83M.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.QU.A6IP.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.V1.A9O9.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.ZG.A9LB.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.KK.A7B1.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.HC.8262.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.HI.7170.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.J4.A67L.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.G9.6342.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.J4.8200.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.HC.7233.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.J4.A83L.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.J9.A8CK.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.CH.5744.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.G9.6354.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.EJ.7327.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.V1.A9OA.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.J9.A52E.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.J4.A67S.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.HC.A6AQ.01 3 0.153 0.950 0 0.04 0.96
#> TCGA.EJ.7321.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.G9.7519.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.EJ.7318.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.G9.6364.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.HI.7169.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.J4.A67K.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.YL.A8SF.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CH.5745.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CH.5740.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.G9.7509.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.KK.A8IL.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.HC.7820.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.ZG.A9NI.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.HC.A6HY.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.CH.5764.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.G9.6363.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.VN.A88L.01 3 0.000 0.998 0 0.00 1.00
#> TCGA.XQ.A8TB.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.EJ.5496.01 2 0.000 1.000 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.KK.A6E6.01 4 0.3801 0.882 0.00 0.00 0.22 0.78
#> TCGA.G9.6339.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.EJ.7314.01 1 0.0000 0.940 1.00 0.00 0.00 0.00
#> TCGA.G9.6366.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.KC.A4BN.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.J4.A83K.01 3 0.4134 0.679 0.00 0.26 0.74 0.00
#> TCGA.EJ.5524.01 4 0.4134 0.901 0.00 0.00 0.26 0.74
#> TCGA.HC.7209.01 4 0.4624 0.828 0.00 0.00 0.34 0.66
#> TCGA.VP.A879.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.VN.A88Q.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.EJ.5526.01 1 0.3610 0.859 0.80 0.00 0.00 0.20
#> TCGA.EJ.5542.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.HC.7748.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.G9.6365.01 3 0.4134 0.679 0.00 0.26 0.74 0.00
#> TCGA.KK.A8I8.01 4 0.4134 0.901 0.00 0.00 0.26 0.74
#> TCGA.EJ.5522.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.TP.A8TT.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.HC.7232.01 1 0.0000 0.940 1.00 0.00 0.00 0.00
#> TCGA.HC.7081.01 4 0.4134 0.901 0.00 0.00 0.26 0.74
#> TCGA.J4.A83M.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.QU.A6IP.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.V1.A9O9.01 3 0.2011 0.742 0.00 0.00 0.92 0.08
#> TCGA.ZG.A9LB.01 1 0.0000 0.940 1.00 0.00 0.00 0.00
#> TCGA.KK.A7B1.01 2 0.0707 0.974 0.00 0.98 0.02 0.00
#> TCGA.HC.8262.01 1 0.3975 0.837 0.76 0.00 0.00 0.24
#> TCGA.HI.7170.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.J4.A67L.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.G9.6342.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.J4.8200.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.HC.7233.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.J4.A83L.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.J9.A8CK.01 4 0.4713 0.800 0.00 0.00 0.36 0.64
#> TCGA.CH.5744.01 3 0.4134 0.679 0.00 0.26 0.74 0.00
#> TCGA.G9.6354.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EJ.7327.01 4 0.4134 0.901 0.00 0.00 0.26 0.74
#> TCGA.V1.A9OA.01 1 0.0000 0.940 1.00 0.00 0.00 0.00
#> TCGA.J9.A52E.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.J4.A67S.01 3 0.4797 0.657 0.00 0.26 0.72 0.02
#> TCGA.HC.A6AQ.01 3 0.0707 0.832 0.00 0.00 0.98 0.02
#> TCGA.EJ.7321.01 4 0.3975 0.228 0.24 0.00 0.00 0.76
#> TCGA.G9.7519.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.EJ.7318.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.G9.6364.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.HI.7169.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.J4.A67K.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SF.01 1 0.0000 0.940 1.00 0.00 0.00 0.00
#> TCGA.CH.5745.01 1 0.3975 0.837 0.76 0.00 0.00 0.24
#> TCGA.CH.5740.01 4 0.3610 0.868 0.00 0.00 0.20 0.80
#> TCGA.G9.7509.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.KK.A8IL.01 2 0.0707 0.987 0.00 0.98 0.00 0.02
#> TCGA.HC.7820.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.ZG.A9NI.01 1 0.0000 0.940 1.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CH.5764.01 3 0.0000 0.843 0.00 0.00 1.00 0.00
#> TCGA.G9.6363.01 3 0.4134 0.679 0.00 0.26 0.74 0.00
#> TCGA.VN.A88L.01 4 0.4134 0.901 0.00 0.00 0.26 0.74
#> TCGA.XQ.A8TB.01 1 0.0000 0.940 1.00 0.00 0.00 0.00
#> TCGA.EJ.5496.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.KK.A6E6.01 4 0.0000 0.870 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6339.01 3 0.4060 0.671 0.00 0.36 0.64 0.00 0.00
#> TCGA.EJ.7314.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6366.01 5 0.1732 0.890 0.00 0.08 0.00 0.00 0.92
#> TCGA.KC.A4BN.01 5 0.0000 0.898 0.00 0.00 0.00 0.00 1.00
#> TCGA.J4.A83K.01 3 0.3424 0.711 0.00 0.24 0.76 0.00 0.00
#> TCGA.EJ.5524.01 4 0.0609 0.869 0.00 0.02 0.00 0.98 0.00
#> TCGA.HC.7209.01 4 0.5210 0.614 0.00 0.12 0.20 0.68 0.00
#> TCGA.VP.A879.01 5 0.0000 0.898 0.00 0.00 0.00 0.00 1.00
#> TCGA.VN.A88Q.01 3 0.2873 0.756 0.00 0.12 0.86 0.02 0.00
#> TCGA.EJ.5526.01 1 0.3424 0.831 0.76 0.24 0.00 0.00 0.00
#> TCGA.EJ.5542.01 5 0.2516 0.839 0.00 0.14 0.00 0.00 0.86
#> TCGA.HC.7748.01 3 0.1410 0.786 0.00 0.06 0.94 0.00 0.00
#> TCGA.G9.6365.01 3 0.3424 0.711 0.00 0.24 0.76 0.00 0.00
#> TCGA.KK.A8I8.01 4 0.2020 0.842 0.00 0.10 0.00 0.90 0.00
#> TCGA.EJ.5522.01 5 0.0000 0.898 0.00 0.00 0.00 0.00 1.00
#> TCGA.TP.A8TT.01 3 0.2020 0.776 0.00 0.10 0.90 0.00 0.00
#> TCGA.HC.7232.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7081.01 4 0.0000 0.870 0.00 0.00 0.00 1.00 0.00
#> TCGA.J4.A83M.01 3 0.4060 0.671 0.00 0.36 0.64 0.00 0.00
#> TCGA.QU.A6IP.01 5 0.0000 0.898 0.00 0.00 0.00 0.00 1.00
#> TCGA.V1.A9O9.01 3 0.5258 0.629 0.00 0.18 0.68 0.14 0.00
#> TCGA.ZG.A9LB.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B1.01 5 0.6009 0.519 0.00 0.24 0.18 0.00 0.58
#> TCGA.HC.8262.01 1 0.3424 0.831 0.76 0.24 0.00 0.00 0.00
#> TCGA.HI.7170.01 5 0.1732 0.890 0.00 0.08 0.00 0.00 0.92
#> TCGA.J4.A67L.01 5 0.2020 0.890 0.00 0.10 0.00 0.00 0.90
#> TCGA.G9.6342.01 3 0.0000 0.788 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.8200.01 5 0.1732 0.890 0.00 0.08 0.00 0.00 0.92
#> TCGA.HC.7233.01 5 0.1732 0.890 0.00 0.08 0.00 0.00 0.92
#> TCGA.J4.A83L.01 5 0.1732 0.890 0.00 0.08 0.00 0.00 0.92
#> TCGA.J9.A8CK.01 4 0.5597 0.566 0.00 0.16 0.20 0.64 0.00
#> TCGA.CH.5744.01 3 0.3424 0.711 0.00 0.24 0.76 0.00 0.00
#> TCGA.G9.6354.01 5 0.3424 0.768 0.00 0.24 0.00 0.00 0.76
#> TCGA.EJ.7327.01 4 0.0000 0.870 0.00 0.00 0.00 1.00 0.00
#> TCGA.V1.A9OA.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52E.01 3 0.2280 0.774 0.00 0.12 0.88 0.00 0.00
#> TCGA.J4.A67S.01 3 0.3999 0.701 0.00 0.24 0.74 0.00 0.02
#> TCGA.HC.A6AQ.01 3 0.3895 0.688 0.00 0.32 0.68 0.00 0.00
#> TCGA.EJ.7321.01 4 0.5680 0.484 0.14 0.24 0.00 0.62 0.00
#> TCGA.G9.7519.01 5 0.1732 0.890 0.00 0.08 0.00 0.00 0.92
#> TCGA.EJ.7318.01 3 0.4060 0.671 0.00 0.36 0.64 0.00 0.00
#> TCGA.G9.6364.01 5 0.0000 0.898 0.00 0.00 0.00 0.00 1.00
#> TCGA.HI.7169.01 5 0.0000 0.898 0.00 0.00 0.00 0.00 1.00
#> TCGA.J4.A67K.01 3 0.0000 0.788 0.00 0.00 1.00 0.00 0.00
#> TCGA.YL.A8SF.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5745.01 1 0.3424 0.831 0.76 0.24 0.00 0.00 0.00
#> TCGA.CH.5740.01 4 0.0000 0.870 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.7509.01 5 0.3424 0.768 0.00 0.24 0.00 0.00 0.76
#> TCGA.KK.A8IL.01 5 0.1732 0.890 0.00 0.08 0.00 0.00 0.92
#> TCGA.HC.7820.01 5 0.2280 0.850 0.00 0.12 0.00 0.00 0.88
#> TCGA.ZG.A9NI.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 5 0.0000 0.898 0.00 0.00 0.00 0.00 1.00
#> TCGA.CH.5764.01 3 0.0000 0.788 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.6363.01 3 0.3424 0.711 0.00 0.24 0.76 0.00 0.00
#> TCGA.VN.A88L.01 4 0.0609 0.869 0.00 0.02 0.00 0.98 0.00
#> TCGA.XQ.A8TB.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5496.01 5 0.5263 0.653 0.00 0.24 0.10 0.00 0.66
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.KK.A6E6.01 4 0.1814 0.770 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.G9.6339.01 2 0.3309 0.987 0.00 0.72 0.28 0.00 0.00 0.00
#> TCGA.EJ.7314.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6366.01 5 0.2793 0.840 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.KC.A4BN.01 5 0.0000 0.865 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.J4.A83K.01 3 0.0000 0.615 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5524.01 4 0.0000 0.785 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.7209.01 4 0.3631 0.729 0.00 0.10 0.04 0.82 0.00 0.04
#> TCGA.VP.A879.01 5 0.0000 0.865 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VN.A88Q.01 3 0.7062 0.225 0.00 0.16 0.44 0.12 0.00 0.28
#> TCGA.EJ.5526.01 6 0.3864 0.691 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.EJ.5542.01 5 0.1814 0.821 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.HC.7748.01 3 0.3523 0.514 0.00 0.18 0.78 0.00 0.00 0.04
#> TCGA.G9.6365.01 3 0.0000 0.615 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KK.A8I8.01 4 0.4165 0.677 0.00 0.10 0.00 0.74 0.00 0.16
#> TCGA.EJ.5522.01 5 0.0000 0.865 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TP.A8TT.01 3 0.5354 0.200 0.00 0.26 0.58 0.00 0.00 0.16
#> TCGA.HC.7232.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7081.01 4 0.0547 0.786 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.J4.A83M.01 2 0.3309 0.987 0.00 0.72 0.28 0.00 0.00 0.00
#> TCGA.QU.A6IP.01 5 0.0000 0.865 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.V1.A9O9.01 4 0.7374 -0.231 0.00 0.28 0.24 0.36 0.00 0.12
#> TCGA.ZG.A9LB.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B1.01 3 0.4328 -0.240 0.00 0.00 0.52 0.00 0.46 0.02
#> TCGA.HC.8262.01 6 0.3864 0.691 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.HI.7170.01 5 0.2793 0.840 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.J4.A67L.01 5 0.3163 0.850 0.00 0.00 0.04 0.00 0.82 0.14
#> TCGA.G9.6342.01 3 0.3787 0.568 0.00 0.10 0.78 0.00 0.00 0.12
#> TCGA.J4.8200.01 5 0.2793 0.840 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.HC.7233.01 5 0.2793 0.840 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.J4.A83L.01 5 0.2793 0.840 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.J9.A8CK.01 4 0.4851 0.601 0.00 0.20 0.04 0.70 0.00 0.06
#> TCGA.CH.5744.01 3 0.0000 0.615 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6354.01 5 0.3198 0.685 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.EJ.7327.01 4 0.1267 0.779 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.V1.A9OA.01 1 0.2350 0.815 0.88 0.10 0.00 0.00 0.00 0.02
#> TCGA.J9.A52E.01 3 0.5684 0.166 0.00 0.28 0.52 0.00 0.00 0.20
#> TCGA.J4.A67S.01 3 0.1092 0.581 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.HC.A6AQ.01 2 0.3409 0.959 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.EJ.7321.01 6 0.5844 0.302 0.12 0.02 0.00 0.36 0.00 0.50
#> TCGA.G9.7519.01 5 0.2793 0.840 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.EJ.7318.01 2 0.3309 0.987 0.00 0.72 0.28 0.00 0.00 0.00
#> TCGA.G9.6364.01 5 0.0000 0.865 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HI.7169.01 5 0.0000 0.865 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.J4.A67K.01 3 0.3787 0.568 0.00 0.10 0.78 0.00 0.00 0.12
#> TCGA.YL.A8SF.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5745.01 6 0.3864 0.691 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.CH.5740.01 4 0.1814 0.770 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.G9.7509.01 5 0.3460 0.735 0.00 0.00 0.22 0.00 0.76 0.02
#> TCGA.KK.A8IL.01 5 0.2793 0.840 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.HC.7820.01 5 0.1267 0.843 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.ZG.A9NI.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 5 0.0000 0.865 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CH.5764.01 3 0.3787 0.568 0.00 0.10 0.78 0.00 0.00 0.12
#> TCGA.G9.6363.01 3 0.0000 0.615 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VN.A88L.01 4 0.1814 0.769 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.XQ.A8TB.01 1 0.0000 0.972 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5496.01 5 0.3797 0.389 0.00 0.00 0.42 0.00 0.58 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.KK.A6E6.01 4 0.1664 0.7442 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.G9.6339.01 2 0.1433 0.9625 0.00 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.EJ.7314.01 1 0.0000 0.9972 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6366.01 5 0.3562 0.0447 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.KC.A4BN.01 5 0.0000 0.7443 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.A83K.01 3 0.0000 0.7914 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5524.01 4 0.1664 0.7658 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.HC.7209.01 4 0.3487 0.6960 0.00 0.12 0.00 0.78 0.00 0.00 0.10
#> TCGA.VP.A879.01 5 0.0000 0.7443 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VN.A88Q.01 7 0.3848 0.5212 0.00 0.02 0.16 0.06 0.00 0.00 0.76
#> TCGA.EJ.5526.01 6 0.5438 -0.1989 0.42 0.02 0.00 0.00 0.00 0.44 0.12
#> TCGA.EJ.5542.01 5 0.1363 0.7156 0.00 0.00 0.04 0.00 0.94 0.00 0.02
#> TCGA.HC.7748.01 3 0.2829 0.7678 0.00 0.08 0.84 0.00 0.00 0.00 0.08
#> TCGA.G9.6365.01 3 0.0000 0.7914 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8I8.01 7 0.3139 0.1727 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.EJ.5522.01 5 0.0000 0.7443 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TP.A8TT.01 3 0.5669 0.1050 0.00 0.20 0.50 0.00 0.00 0.02 0.28
#> TCGA.HC.7232.01 1 0.0000 0.9972 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7081.01 4 0.0000 0.7717 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A83M.01 2 0.1433 0.9625 0.00 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IP.01 5 0.0000 0.7443 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.V1.A9O9.01 4 0.6980 -0.2362 0.00 0.26 0.16 0.32 0.00 0.00 0.26
#> TCGA.ZG.A9LB.01 1 0.0000 0.9972 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B1.01 3 0.2745 0.5512 0.00 0.00 0.82 0.00 0.16 0.02 0.00
#> TCGA.HC.8262.01 6 0.5438 -0.1989 0.42 0.02 0.00 0.00 0.00 0.44 0.12
#> TCGA.HI.7170.01 5 0.3562 0.0447 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.J4.A67L.01 5 0.3139 0.4509 0.00 0.00 0.00 0.00 0.70 0.30 0.00
#> TCGA.G9.6342.01 3 0.2803 0.7753 0.00 0.06 0.84 0.00 0.00 0.00 0.10
#> TCGA.J4.8200.01 6 0.3562 -0.2164 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.HC.7233.01 6 0.3562 -0.2164 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.J4.A83L.01 6 0.3562 -0.2164 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.J9.A8CK.01 4 0.3985 0.6337 0.00 0.18 0.00 0.72 0.00 0.00 0.10
#> TCGA.CH.5744.01 3 0.1166 0.7984 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.G9.6354.01 5 0.3052 0.5978 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.EJ.7327.01 4 0.0863 0.7641 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.V1.A9OA.01 1 0.0504 0.9831 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A52E.01 7 0.6268 0.1658 0.00 0.20 0.32 0.00 0.00 0.06 0.42
#> TCGA.J4.A67S.01 3 0.0504 0.7772 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HC.A6AQ.01 2 0.1886 0.9164 0.00 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.EJ.7321.01 6 0.6623 -0.1312 0.10 0.02 0.00 0.32 0.00 0.44 0.12
#> TCGA.G9.7519.01 5 0.3562 0.0447 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.EJ.7318.01 2 0.1166 0.9399 0.00 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.G9.6364.01 5 0.0000 0.7443 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HI.7169.01 5 0.0000 0.7443 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.A67K.01 3 0.3058 0.7623 0.00 0.08 0.82 0.00 0.00 0.00 0.10
#> TCGA.YL.A8SF.01 1 0.0000 0.9972 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5745.01 6 0.5438 -0.1989 0.42 0.02 0.00 0.00 0.00 0.44 0.12
#> TCGA.CH.5740.01 4 0.0863 0.7641 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.G9.7509.01 5 0.2906 0.6383 0.00 0.00 0.18 0.00 0.80 0.02 0.00
#> TCGA.KK.A8IL.01 6 0.3562 -0.2164 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.HC.7820.01 5 0.1006 0.7275 0.00 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.ZG.A9NI.01 1 0.0000 0.9972 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 5 0.0000 0.7443 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CH.5764.01 3 0.3058 0.7623 0.00 0.08 0.82 0.00 0.00 0.00 0.10
#> TCGA.G9.6363.01 3 0.1166 0.7984 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.VN.A88L.01 4 0.2163 0.7539 0.00 0.02 0.00 0.88 0.00 0.00 0.10
#> TCGA.XQ.A8TB.01 1 0.0000 0.9972 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5496.01 5 0.3968 0.1621 0.00 0.00 0.44 0.00 0.54 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.KK.A6E6.01 4 0.4073 0.357 0.00 0.00 0.00 0.66 0.00 0.00 0.24 0.10
#> TCGA.G9.6339.01 2 0.1341 1.000 0.00 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7314.01 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6366.01 5 0.0000 0.531 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KC.A4BN.01 5 0.4799 0.462 0.00 0.00 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.J4.A83K.01 3 0.3237 0.551 0.00 0.00 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.EJ.5524.01 4 0.0000 0.641 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7209.01 4 0.2132 0.597 0.00 0.08 0.04 0.88 0.00 0.00 0.00 0.00
#> TCGA.VP.A879.01 5 0.4799 0.462 0.00 0.00 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.VN.A88Q.01 3 0.4958 -0.157 0.00 0.00 0.44 0.10 0.00 0.02 0.44 0.00
#> TCGA.EJ.5526.01 6 0.2267 0.891 0.18 0.00 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.EJ.5542.01 5 0.4914 0.161 0.00 0.00 0.00 0.00 0.42 0.00 0.16 0.42
#> TCGA.HC.7748.01 3 0.2719 0.564 0.00 0.18 0.80 0.00 0.00 0.00 0.00 0.02
#> TCGA.G9.6365.01 3 0.3237 0.551 0.00 0.00 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.KK.A8I8.01 7 0.3845 0.000 0.00 0.00 0.00 0.28 0.00 0.06 0.66 0.00
#> TCGA.EJ.5522.01 5 0.4799 0.462 0.00 0.00 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.TP.A8TT.01 3 0.5020 0.408 0.00 0.06 0.68 0.00 0.00 0.06 0.14 0.06
#> TCGA.HC.7232.01 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7081.01 4 0.0808 0.640 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.J4.A83M.01 2 0.1341 1.000 0.00 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.QU.A6IP.01 5 0.4799 0.462 0.00 0.00 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.V1.A9O9.01 4 0.6509 -0.038 0.00 0.14 0.26 0.48 0.00 0.02 0.06 0.04
#> TCGA.ZG.A9LB.01 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B1.01 3 0.4562 0.280 0.00 0.00 0.46 0.00 0.10 0.00 0.00 0.44
#> TCGA.HC.8262.01 6 0.2267 0.891 0.18 0.00 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.HI.7170.01 5 0.0000 0.531 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67L.01 5 0.2981 0.435 0.00 0.00 0.00 0.00 0.76 0.00 0.02 0.22
#> TCGA.G9.6342.01 3 0.0471 0.632 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.J4.8200.01 5 0.0000 0.531 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7233.01 5 0.0000 0.531 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A83L.01 5 0.0000 0.531 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J9.A8CK.01 4 0.3319 0.539 0.00 0.08 0.06 0.82 0.00 0.02 0.02 0.00
#> TCGA.CH.5744.01 3 0.2406 0.652 0.00 0.00 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.G9.6354.01 8 0.4059 0.536 0.00 0.00 0.00 0.00 0.28 0.00 0.08 0.64
#> TCGA.EJ.7327.01 4 0.2569 0.555 0.00 0.00 0.00 0.82 0.00 0.00 0.16 0.02
#> TCGA.V1.A9OA.01 1 0.4077 0.730 0.76 0.08 0.00 0.00 0.00 0.02 0.04 0.10
#> TCGA.J9.A52E.01 3 0.5758 0.284 0.00 0.04 0.58 0.00 0.00 0.14 0.18 0.06
#> TCGA.J4.A67S.01 3 0.3943 0.515 0.00 0.00 0.56 0.00 0.04 0.00 0.00 0.40
#> TCGA.HC.A6AQ.01 2 0.1341 1.000 0.00 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7321.01 6 0.3036 0.619 0.00 0.00 0.00 0.18 0.00 0.78 0.00 0.04
#> TCGA.G9.7519.01 5 0.0000 0.531 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7318.01 2 0.1341 1.000 0.00 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6364.01 5 0.4799 0.462 0.00 0.00 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.HI.7169.01 5 0.4799 0.462 0.00 0.00 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.J4.A67K.01 3 0.0941 0.629 0.00 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.YL.A8SF.01 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5745.01 6 0.2267 0.891 0.18 0.00 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.CH.5740.01 4 0.3657 0.434 0.00 0.00 0.00 0.72 0.00 0.00 0.20 0.08
#> TCGA.G9.7509.01 8 0.3015 0.634 0.00 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.KK.A8IL.01 5 0.0000 0.531 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7820.01 5 0.4910 0.235 0.00 0.00 0.00 0.00 0.44 0.00 0.16 0.40
#> TCGA.ZG.A9NI.01 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6HY.01 5 0.4799 0.462 0.00 0.00 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.CH.5764.01 3 0.0471 0.632 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G9.6363.01 3 0.2650 0.641 0.00 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.VN.A88L.01 4 0.1275 0.629 0.00 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.XQ.A8TB.01 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5496.01 8 0.3909 0.551 0.00 0.00 0.18 0.00 0.12 0.00 0.00 0.70
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["042"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 26 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.980 0.986 0.3782 0.631 0.631
#> 3 3 1.000 1.000 1.000 0.7827 0.695 0.517
#> 4 4 0.783 0.626 0.774 0.1001 0.908 0.717
#> 5 5 0.780 0.855 0.868 0.0589 0.920 0.698
#> 6 6 0.793 0.793 0.779 0.0378 0.945 0.743
#> 7 7 0.804 0.681 0.830 0.0294 0.985 0.904
#> 8 8 0.827 0.606 0.835 0.0217 0.997 0.979
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.EJ.5509.01 2 0.000 0.981 0.00 1.00
#> TCGA.KK.A8IG.01 2 0.327 0.955 0.06 0.94
#> TCGA.VP.AA1N.01 2 0.000 0.981 0.00 1.00
#> TCGA.J9.A8CP.01 2 0.242 0.967 0.04 0.96
#> TCGA.EJ.5514.01 2 0.242 0.967 0.04 0.96
#> TCGA.V1.A8MG.01 2 0.000 0.981 0.00 1.00
#> TCGA.HC.8265.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.7218.01 2 0.327 0.955 0.06 0.94
#> TCGA.QU.A6IO.01 2 0.000 0.981 0.00 1.00
#> TCGA.YL.A8SO.01 2 0.000 0.981 0.00 1.00
#> TCGA.ZG.A9M4.01 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A9Z9.01 2 0.000 0.981 0.00 1.00
#> TCGA.G9.7521.01 1 0.000 1.000 1.00 0.00
#> TCGA.YL.A8HO.01 2 0.000 0.981 0.00 1.00
#> TCGA.HC.7210.01 2 0.000 0.981 0.00 1.00
#> TCGA.KC.A7F3.01 2 0.327 0.955 0.06 0.94
#> TCGA.YL.A8S8.01 2 0.000 0.981 0.00 1.00
#> TCGA.EJ.A8FN.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZG.A9N3.01 1 0.000 1.000 1.00 0.00
#> TCGA.VN.A88O.01 2 0.000 0.981 0.00 1.00
#> TCGA.FC.7961.01 2 0.000 0.981 0.00 1.00
#> TCGA.V1.A8MU.01 2 0.327 0.955 0.06 0.94
#> TCGA.KK.A6E5.01 2 0.000 0.981 0.00 1.00
#> TCGA.EJ.A7NM.01 2 0.000 0.981 0.00 1.00
#> TCGA.V1.A8WV.01 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A9OX.01 2 0.242 0.967 0.04 0.96
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EJ.5509.01 3 0 1 0 0 1
#> TCGA.KK.A8IG.01 2 0 1 0 1 0
#> TCGA.VP.AA1N.01 2 0 1 0 1 0
#> TCGA.J9.A8CP.01 2 0 1 0 1 0
#> TCGA.EJ.5514.01 2 0 1 0 1 0
#> TCGA.V1.A8MG.01 3 0 1 0 0 1
#> TCGA.HC.8265.01 1 0 1 1 0 0
#> TCGA.EJ.7218.01 2 0 1 0 1 0
#> TCGA.QU.A6IO.01 3 0 1 0 0 1
#> TCGA.YL.A8SO.01 3 0 1 0 0 1
#> TCGA.ZG.A9M4.01 1 0 1 1 0 0
#> TCGA.V1.A9Z9.01 3 0 1 0 0 1
#> TCGA.G9.7521.01 1 0 1 1 0 0
#> TCGA.YL.A8HO.01 3 0 1 0 0 1
#> TCGA.HC.7210.01 2 0 1 0 1 0
#> TCGA.KC.A7F3.01 2 0 1 0 1 0
#> TCGA.YL.A8S8.01 3 0 1 0 0 1
#> TCGA.EJ.A8FN.01 1 0 1 1 0 0
#> TCGA.ZG.A9N3.01 1 0 1 1 0 0
#> TCGA.VN.A88O.01 3 0 1 0 0 1
#> TCGA.FC.7961.01 3 0 1 0 0 1
#> TCGA.V1.A8MU.01 2 0 1 0 1 0
#> TCGA.KK.A6E5.01 2 0 1 0 1 0
#> TCGA.EJ.A7NM.01 2 0 1 0 1 0
#> TCGA.V1.A8WV.01 1 0 1 1 0 0
#> TCGA.V1.A9OX.01 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EJ.5509.01 3 0.000 0.847 0.0 0.00 1.00 0.00
#> TCGA.KK.A8IG.01 2 0.485 -0.271 0.0 0.60 0.00 0.40
#> TCGA.VP.AA1N.01 2 0.441 0.238 0.0 0.70 0.00 0.30
#> TCGA.J9.A8CP.01 4 0.499 0.568 0.0 0.48 0.00 0.52
#> TCGA.EJ.5514.01 2 0.000 0.399 0.0 1.00 0.00 0.00
#> TCGA.V1.A8MG.01 3 0.380 0.909 0.0 0.00 0.78 0.22
#> TCGA.HC.8265.01 1 0.361 0.879 0.8 0.00 0.00 0.20
#> TCGA.EJ.7218.01 4 0.499 0.568 0.0 0.48 0.00 0.52
#> TCGA.QU.A6IO.01 3 0.428 0.890 0.0 0.00 0.72 0.28
#> TCGA.YL.A8SO.01 3 0.361 0.910 0.0 0.00 0.80 0.20
#> TCGA.ZG.A9M4.01 1 0.000 0.941 1.0 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 3 0.428 0.890 0.0 0.00 0.72 0.28
#> TCGA.G9.7521.01 1 0.000 0.941 1.0 0.00 0.00 0.00
#> TCGA.YL.A8HO.01 3 0.361 0.910 0.0 0.00 0.80 0.20
#> TCGA.HC.7210.01 2 0.441 0.238 0.0 0.70 0.00 0.30
#> TCGA.KC.A7F3.01 4 0.499 0.568 0.0 0.48 0.00 0.52
#> TCGA.YL.A8S8.01 3 0.000 0.847 0.0 0.00 1.00 0.00
#> TCGA.EJ.A8FN.01 1 0.361 0.879 0.8 0.00 0.00 0.20
#> TCGA.ZG.A9N3.01 1 0.000 0.941 1.0 0.00 0.00 0.00
#> TCGA.VN.A88O.01 3 0.398 0.905 0.0 0.00 0.76 0.24
#> TCGA.FC.7961.01 3 0.000 0.847 0.0 0.00 1.00 0.00
#> TCGA.V1.A8MU.01 2 0.485 -0.271 0.0 0.60 0.00 0.40
#> TCGA.KK.A6E5.01 4 0.498 -0.202 0.0 0.46 0.00 0.54
#> TCGA.EJ.A7NM.01 2 0.000 0.399 0.0 1.00 0.00 0.00
#> TCGA.V1.A8WV.01 1 0.000 0.941 1.0 0.00 0.00 0.00
#> TCGA.V1.A9OX.01 4 0.499 0.568 0.0 0.48 0.00 0.52
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EJ.5509.01 3 0.4818 0.755 0.00 0.18 0.72 0.00 0.10
#> TCGA.KK.A8IG.01 4 0.0609 0.977 0.00 0.02 0.00 0.98 0.00
#> TCGA.VP.AA1N.01 2 0.3895 0.738 0.00 0.68 0.00 0.32 0.00
#> TCGA.J9.A8CP.01 4 0.0000 0.988 0.00 0.00 0.00 1.00 0.00
#> TCGA.EJ.5514.01 5 0.5599 0.935 0.00 0.26 0.00 0.12 0.62
#> TCGA.V1.A8MG.01 3 0.0609 0.847 0.00 0.00 0.98 0.00 0.02
#> TCGA.HC.8265.01 1 0.4263 0.812 0.76 0.06 0.00 0.00 0.18
#> TCGA.EJ.7218.01 4 0.0000 0.988 0.00 0.00 0.00 1.00 0.00
#> TCGA.QU.A6IO.01 3 0.2616 0.792 0.00 0.10 0.88 0.00 0.02
#> TCGA.YL.A8SO.01 3 0.0609 0.848 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZG.A9M4.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 3 0.2616 0.792 0.00 0.10 0.88 0.00 0.02
#> TCGA.G9.7521.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8HO.01 3 0.0609 0.848 0.00 0.00 0.98 0.00 0.02
#> TCGA.HC.7210.01 2 0.3895 0.738 0.00 0.68 0.00 0.32 0.00
#> TCGA.KC.A7F3.01 4 0.0000 0.988 0.00 0.00 0.00 1.00 0.00
#> TCGA.YL.A8S8.01 3 0.5050 0.746 0.00 0.18 0.70 0.00 0.12
#> TCGA.EJ.A8FN.01 1 0.4676 0.799 0.74 0.12 0.00 0.00 0.14
#> TCGA.ZG.A9N3.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 3 0.0609 0.847 0.00 0.00 0.98 0.00 0.02
#> TCGA.FC.7961.01 3 0.4818 0.755 0.00 0.18 0.72 0.00 0.10
#> TCGA.V1.A8MU.01 4 0.0609 0.977 0.00 0.02 0.00 0.98 0.00
#> TCGA.KK.A6E5.01 2 0.5555 0.487 0.00 0.64 0.22 0.14 0.00
#> TCGA.EJ.A7NM.01 5 0.5263 0.936 0.00 0.24 0.00 0.10 0.66
#> TCGA.V1.A8WV.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OX.01 4 0.0000 0.988 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.EJ.5509.01 6 0.3851 1.000 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.KK.A8IG.01 4 0.2581 0.860 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.VP.AA1N.01 2 0.3819 0.658 0.00 0.70 0.00 0.28 0.00 0.02
#> TCGA.J9.A8CP.01 4 0.0937 0.914 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EJ.5514.01 5 0.2474 0.681 0.00 0.04 0.00 0.08 0.88 0.00
#> TCGA.V1.A8MG.01 3 0.1267 0.753 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.HC.8265.01 1 0.4727 0.703 0.66 0.10 0.00 0.00 0.00 0.24
#> TCGA.EJ.7218.01 4 0.0547 0.918 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.QU.A6IO.01 3 0.1267 0.755 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.YL.A8SO.01 3 0.3942 0.628 0.00 0.04 0.80 0.00 0.06 0.10
#> TCGA.ZG.A9M4.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 3 0.1267 0.755 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.G9.7521.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8HO.01 3 0.3942 0.628 0.00 0.04 0.80 0.00 0.06 0.10
#> TCGA.HC.7210.01 2 0.3309 0.661 0.00 0.72 0.00 0.28 0.00 0.00
#> TCGA.KC.A7F3.01 4 0.0000 0.922 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.YL.A8S8.01 6 0.3851 1.000 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.EJ.A8FN.01 1 0.5545 0.703 0.66 0.14 0.00 0.00 0.06 0.14
#> TCGA.ZG.A9N3.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 3 0.0000 0.775 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FC.7961.01 6 0.3851 1.000 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.V1.A8MU.01 4 0.2048 0.865 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.KK.A6E5.01 2 0.4873 0.336 0.00 0.52 0.42 0.06 0.00 0.00
#> TCGA.EJ.A7NM.01 5 0.5390 0.690 0.00 0.18 0.00 0.02 0.64 0.16
#> TCGA.V1.A8WV.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OX.01 4 0.0000 0.922 0.00 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EJ.5509.01 6 0.3047 0.942 0.00 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.KK.A8IG.01 4 0.2278 0.898 0.00 0.00 0.00 0.88 0.08 0.04 0.00
#> TCGA.VP.AA1N.01 2 0.2081 0.688 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.J9.A8CP.01 4 0.0863 0.936 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EJ.5514.01 5 0.0504 0.583 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.V1.A8MG.01 3 0.2572 0.684 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.HC.8265.01 1 0.5837 -0.812 0.48 0.06 0.00 0.00 0.02 0.06 0.38
#> TCGA.EJ.7218.01 4 0.0504 0.940 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.QU.A6IO.01 3 0.0504 0.747 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SO.01 3 0.4033 0.647 0.00 0.00 0.70 0.00 0.00 0.22 0.08
#> TCGA.ZG.A9M4.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 3 0.0504 0.747 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.G9.7521.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8HO.01 3 0.4033 0.647 0.00 0.00 0.70 0.00 0.00 0.22 0.08
#> TCGA.HC.7210.01 2 0.2259 0.687 0.00 0.84 0.00 0.16 0.00 0.00 0.00
#> TCGA.KC.A7F3.01 4 0.0000 0.944 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.YL.A8S8.01 6 0.4569 0.886 0.00 0.02 0.28 0.00 0.00 0.64 0.06
#> TCGA.EJ.A8FN.01 7 0.3546 0.000 0.46 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.ZG.A9N3.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 3 0.0000 0.752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.7961.01 6 0.3047 0.942 0.00 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.V1.A8MU.01 4 0.1928 0.903 0.00 0.00 0.00 0.90 0.08 0.02 0.00
#> TCGA.KK.A6E5.01 2 0.3943 0.398 0.00 0.56 0.42 0.02 0.00 0.00 0.00
#> TCGA.EJ.A7NM.01 5 0.6194 0.583 0.00 0.08 0.00 0.00 0.44 0.14 0.34
#> TCGA.V1.A8WV.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OX.01 4 0.0000 0.944 0.00 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EJ.5509.01 6 0.3318 0.884 0.00 0.00 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.KK.A8IG.01 4 0.3102 0.854 0.00 0.00 0.00 0.82 0.02 0.08 0.08 0.00
#> TCGA.VP.AA1N.01 2 0.3262 0.641 0.00 0.82 0.00 0.02 0.00 0.04 0.02 0.10
#> TCGA.J9.A8CP.01 4 0.2532 0.892 0.00 0.04 0.00 0.88 0.00 0.04 0.02 0.02
#> TCGA.EJ.5514.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A8MG.01 3 0.0000 0.594 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8265.01 1 0.5753 -0.755 0.40 0.00 0.00 0.00 0.00 0.06 0.38 0.16
#> TCGA.EJ.7218.01 4 0.0941 0.925 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.QU.A6IO.01 3 0.4428 0.692 0.00 0.02 0.72 0.00 0.00 0.08 0.14 0.04
#> TCGA.YL.A8SO.01 3 0.2224 0.536 0.00 0.00 0.86 0.00 0.00 0.02 0.12 0.00
#> TCGA.ZG.A9M4.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z9.01 3 0.4428 0.692 0.00 0.02 0.72 0.00 0.00 0.08 0.14 0.04
#> TCGA.G9.7521.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8HO.01 3 0.2404 0.526 0.00 0.00 0.84 0.00 0.00 0.02 0.14 0.00
#> TCGA.HC.7210.01 2 0.0471 0.670 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.KC.A7F3.01 4 0.0000 0.932 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8S8.01 6 0.2938 0.778 0.00 0.00 0.30 0.00 0.00 0.70 0.00 0.00
#> TCGA.EJ.A8FN.01 7 0.3193 0.000 0.38 0.00 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.ZG.A9N3.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VN.A88O.01 3 0.4684 0.688 0.00 0.02 0.70 0.00 0.00 0.08 0.14 0.06
#> TCGA.FC.7961.01 6 0.3318 0.884 0.00 0.00 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.V1.A8MU.01 4 0.1275 0.915 0.00 0.00 0.00 0.94 0.02 0.04 0.00 0.00
#> TCGA.KK.A6E5.01 2 0.5352 0.462 0.00 0.64 0.12 0.00 0.00 0.06 0.14 0.04
#> TCGA.EJ.A7NM.01 8 0.3083 0.000 0.00 0.00 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.V1.A8WV.01 1 0.0000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OX.01 4 0.0000 0.932 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["043"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.698 0.944 0.968 0.4923 0.512 0.512
#> 3 3 1.000 0.962 0.986 0.3473 0.751 0.547
#> 4 4 0.780 0.922 0.934 0.1253 0.894 0.694
#> 5 5 0.791 0.862 0.910 0.0371 0.972 0.888
#> 6 6 0.830 0.779 0.889 0.0258 0.999 0.995
#> 7 7 0.764 0.680 0.851 0.0192 0.974 0.886
#> 8 8 0.810 0.523 0.839 0.0148 0.970 0.858
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.EJ.5521.01 2 0.000 0.944 0.00 1.00
#> TCGA.XA.A8JR.01 2 0.469 0.905 0.10 0.90
#> TCGA.EJ.7781.01 2 0.000 0.944 0.00 1.00
#> TCGA.CH.5751.01 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A8WL.01 2 0.000 0.944 0.00 1.00
#> TCGA.EJ.7786.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.8470.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.7742.01 2 0.000 0.944 0.00 1.00
#> TCGA.CH.5769.01 2 0.000 0.944 0.00 1.00
#> TCGA.EJ.A7NN.01 2 0.000 0.944 0.00 1.00
#> TCGA.YL.A8SC.01 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A8X3.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A6DY.01 1 0.000 1.000 1.00 0.00
#> TCGA.VN.A88N.01 2 0.000 0.944 0.00 1.00
#> TCGA.EJ.8468.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.8256.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5769.11 2 0.000 0.944 0.00 1.00
#> TCGA.Y6.A8TL.01 1 0.000 1.000 1.00 0.00
#> TCGA.V1.A8MF.01 2 0.000 0.944 0.00 1.00
#> TCGA.EJ.5532.01 2 0.469 0.905 0.10 0.90
#> TCGA.EJ.5507.01 2 0.000 0.944 0.00 1.00
#> TCGA.EJ.A65G.01 2 0.469 0.905 0.10 0.90
#> TCGA.HC.A76W.01 1 0.000 1.000 1.00 0.00
#> TCGA.G9.A9S7.01 2 0.000 0.944 0.00 1.00
#> TCGA.HC.8216.01 2 0.000 0.944 0.00 1.00
#> TCGA.CH.5794.01 2 0.000 0.944 0.00 1.00
#> TCGA.HC.7818.01 2 0.469 0.905 0.10 0.90
#> TCGA.2A.A8VT.01 2 0.881 0.652 0.30 0.70
#> TCGA.ZG.A9LM.01 2 0.000 0.944 0.00 1.00
#> TCGA.G9.6494.01 1 0.000 1.000 1.00 0.00
#> TCGA.QU.A6IM.01 2 0.469 0.905 0.10 0.90
#> TCGA.VP.A872.01 2 0.000 0.944 0.00 1.00
#> TCGA.KK.A8IJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.CH.5748.01 2 0.469 0.905 0.10 0.90
#> TCGA.V1.A9Z7.01 1 0.000 1.000 1.00 0.00
#> TCGA.EJ.A6RC.01 2 0.469 0.905 0.10 0.90
#> TCGA.HC.A9TH.01 2 0.000 0.944 0.00 1.00
#> TCGA.YL.A8SJ.01 2 0.904 0.605 0.32 0.68
#> TCGA.HC.7749.01 1 0.000 1.000 1.00 0.00
#> TCGA.KK.A6E7.01 1 0.000 1.000 1.00 0.00
#> TCGA.HC.8261.01 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.EJ.5521.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.XA.A8JR.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.EJ.7781.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.CH.5751.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.V1.A8WL.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.EJ.7786.01 2 0.6126 0.319 0.40 0.60 0.00
#> TCGA.EJ.8470.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.HC.7742.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.CH.5769.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EJ.A7NN.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.YL.A8SC.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.V1.A8X3.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.KK.A6DY.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.VN.A88N.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.EJ.8468.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.HC.8256.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.CH.5769.11 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.Y6.A8TL.01 1 0.3340 0.855 0.88 0.12 0.00
#> TCGA.V1.A8MF.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.EJ.5532.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.EJ.5507.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EJ.A65G.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.HC.A76W.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.G9.A9S7.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.HC.8216.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.CH.5794.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.HC.7818.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.2A.A8VT.01 3 0.0892 0.979 0.02 0.00 0.98
#> TCGA.ZG.A9LM.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.G9.6494.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.QU.A6IM.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.VP.A872.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.KK.A8IJ.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.CH.5748.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.V1.A9Z7.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.EJ.A6RC.01 2 0.0000 0.969 0.00 1.00 0.00
#> TCGA.HC.A9TH.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.YL.A8SJ.01 1 0.1529 0.951 0.96 0.00 0.04
#> TCGA.HC.7749.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.KK.A6E7.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.HC.8261.01 1 0.0000 0.988 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.EJ.5521.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.XA.A8JR.01 2 0.2345 0.946 0.00 0.90 0.00 0.10
#> TCGA.EJ.7781.01 4 0.0707 0.989 0.00 0.02 0.00 0.98
#> TCGA.CH.5751.01 1 0.0000 0.918 1.00 0.00 0.00 0.00
#> TCGA.V1.A8WL.01 4 0.0707 0.989 0.00 0.02 0.00 0.98
#> TCGA.EJ.7786.01 2 0.2411 0.901 0.04 0.92 0.00 0.04
#> TCGA.EJ.8470.01 1 0.3172 0.867 0.84 0.16 0.00 0.00
#> TCGA.HC.7742.01 4 0.0707 0.989 0.00 0.02 0.00 0.98
#> TCGA.CH.5769.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.EJ.A7NN.01 4 0.0707 0.989 0.00 0.02 0.00 0.98
#> TCGA.YL.A8SC.01 1 0.1637 0.898 0.94 0.06 0.00 0.00
#> TCGA.V1.A8X3.01 1 0.0000 0.918 1.00 0.00 0.00 0.00
#> TCGA.KK.A6DY.01 1 0.0000 0.918 1.00 0.00 0.00 0.00
#> TCGA.VN.A88N.01 4 0.0707 0.989 0.00 0.02 0.00 0.98
#> TCGA.EJ.8468.01 1 0.3610 0.826 0.80 0.20 0.00 0.00
#> TCGA.HC.8256.01 1 0.3172 0.867 0.84 0.16 0.00 0.00
#> TCGA.CH.5769.11 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.Y6.A8TL.01 2 0.2345 0.832 0.10 0.90 0.00 0.00
#> TCGA.V1.A8MF.01 4 0.0707 0.989 0.00 0.02 0.00 0.98
#> TCGA.EJ.5532.01 2 0.3801 0.817 0.00 0.78 0.00 0.22
#> TCGA.EJ.5507.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.EJ.A65G.01 2 0.2345 0.946 0.00 0.90 0.00 0.10
#> TCGA.HC.A76W.01 1 0.0707 0.913 0.98 0.02 0.00 0.00
#> TCGA.G9.A9S7.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.HC.8216.01 4 0.0707 0.989 0.00 0.02 0.00 0.98
#> TCGA.CH.5794.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.HC.7818.01 2 0.3037 0.932 0.02 0.88 0.00 0.10
#> TCGA.2A.A8VT.01 3 0.6122 0.660 0.16 0.16 0.68 0.00
#> TCGA.ZG.A9LM.01 4 0.1637 0.921 0.00 0.06 0.00 0.94
#> TCGA.G9.6494.01 1 0.0000 0.918 1.00 0.00 0.00 0.00
#> TCGA.QU.A6IM.01 2 0.2345 0.946 0.00 0.90 0.00 0.10
#> TCGA.VP.A872.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.KK.A8IJ.01 1 0.2345 0.901 0.90 0.10 0.00 0.00
#> TCGA.CH.5748.01 2 0.2345 0.946 0.00 0.90 0.00 0.10
#> TCGA.V1.A9Z7.01 1 0.1637 0.914 0.94 0.06 0.00 0.00
#> TCGA.EJ.A6RC.01 2 0.2345 0.946 0.00 0.90 0.00 0.10
#> TCGA.HC.A9TH.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SJ.01 1 0.4088 0.805 0.82 0.14 0.00 0.04
#> TCGA.HC.7749.01 1 0.0707 0.913 0.98 0.02 0.00 0.00
#> TCGA.KK.A6E7.01 1 0.1637 0.914 0.94 0.06 0.00 0.00
#> TCGA.HC.8261.01 1 0.3172 0.867 0.84 0.16 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EJ.5521.01 3 0.0609 0.976 0.00 0.00 0.98 0.00 0.02
#> TCGA.XA.A8JR.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7781.01 4 0.2732 0.928 0.00 0.16 0.00 0.84 0.00
#> TCGA.CH.5751.01 1 0.0609 0.854 0.98 0.00 0.00 0.00 0.02
#> TCGA.V1.A8WL.01 4 0.2929 0.921 0.00 0.18 0.00 0.82 0.00
#> TCGA.EJ.7786.01 2 0.2280 0.811 0.12 0.88 0.00 0.00 0.00
#> TCGA.EJ.8470.01 1 0.1732 0.840 0.92 0.08 0.00 0.00 0.00
#> TCGA.HC.7742.01 4 0.2873 0.926 0.00 0.12 0.00 0.86 0.02
#> TCGA.CH.5769.01 3 0.0000 0.978 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.A7NN.01 4 0.2438 0.867 0.00 0.06 0.00 0.90 0.04
#> TCGA.YL.A8SC.01 1 0.4360 0.557 0.68 0.02 0.00 0.00 0.30
#> TCGA.V1.A8X3.01 1 0.2516 0.804 0.86 0.00 0.00 0.00 0.14
#> TCGA.KK.A6DY.01 1 0.1410 0.844 0.94 0.00 0.00 0.00 0.06
#> TCGA.VN.A88N.01 4 0.2280 0.927 0.00 0.12 0.00 0.88 0.00
#> TCGA.EJ.8468.01 1 0.1732 0.840 0.92 0.08 0.00 0.00 0.00
#> TCGA.HC.8256.01 1 0.1732 0.840 0.92 0.08 0.00 0.00 0.00
#> TCGA.CH.5769.11 3 0.0000 0.978 0.00 0.00 1.00 0.00 0.00
#> TCGA.Y6.A8TL.01 2 0.2516 0.789 0.14 0.86 0.00 0.00 0.00
#> TCGA.V1.A8MF.01 4 0.2020 0.918 0.00 0.10 0.00 0.90 0.00
#> TCGA.EJ.5532.01 2 0.2732 0.722 0.00 0.84 0.00 0.16 0.00
#> TCGA.EJ.5507.01 3 0.0000 0.978 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.A65G.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.A76W.01 1 0.2929 0.769 0.82 0.00 0.00 0.00 0.18
#> TCGA.G9.A9S7.01 3 0.0609 0.976 0.00 0.00 0.98 0.00 0.02
#> TCGA.HC.8216.01 4 0.2929 0.921 0.00 0.18 0.00 0.82 0.00
#> TCGA.CH.5794.01 3 0.1043 0.969 0.00 0.00 0.96 0.00 0.04
#> TCGA.HC.7818.01 2 0.1043 0.896 0.00 0.96 0.00 0.00 0.04
#> TCGA.2A.A8VT.01 5 0.3348 0.622 0.02 0.00 0.08 0.04 0.86
#> TCGA.ZG.A9LM.01 4 0.4254 0.841 0.00 0.22 0.00 0.74 0.04
#> TCGA.G9.6494.01 1 0.2280 0.817 0.88 0.00 0.00 0.00 0.12
#> TCGA.QU.A6IM.01 2 0.0609 0.908 0.02 0.98 0.00 0.00 0.00
#> TCGA.VP.A872.01 3 0.1043 0.955 0.00 0.00 0.96 0.00 0.04
#> TCGA.KK.A8IJ.01 1 0.1043 0.857 0.96 0.04 0.00 0.00 0.00
#> TCGA.CH.5748.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A9Z7.01 1 0.0609 0.860 0.98 0.02 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.A9TH.01 3 0.1043 0.960 0.00 0.00 0.96 0.00 0.04
#> TCGA.YL.A8SJ.01 5 0.4398 0.574 0.24 0.04 0.00 0.00 0.72
#> TCGA.HC.7749.01 1 0.3109 0.748 0.80 0.00 0.00 0.00 0.20
#> TCGA.KK.A6E7.01 1 0.0609 0.860 0.98 0.02 0.00 0.00 0.00
#> TCGA.HC.8261.01 1 0.1732 0.840 0.92 0.08 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EJ.5521.01 3 0.1267 0.935 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.XA.A8JR.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7781.01 4 0.1267 0.841 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.CH.5751.01 1 0.1092 0.839 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.V1.A8WL.01 4 0.1556 0.839 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.EJ.7786.01 2 0.0937 0.898 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.EJ.8470.01 1 0.0937 0.845 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.HC.7742.01 4 0.2512 0.835 0.00 0.06 0.00 0.88 0.00 0.06
#> TCGA.CH.5769.01 3 0.0000 0.947 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A7NN.01 4 0.3578 0.506 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.YL.A8SC.01 1 0.6167 0.269 0.54 0.04 0.00 0.00 0.26 0.16
#> TCGA.V1.A8X3.01 1 0.2790 0.787 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.KK.A6DY.01 1 0.2794 0.795 0.86 0.00 0.00 0.00 0.06 0.08
#> TCGA.VN.A88N.01 4 0.1807 0.844 0.00 0.06 0.00 0.92 0.00 0.02
#> TCGA.EJ.8468.01 1 0.0937 0.845 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.HC.8256.01 1 0.0937 0.845 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.CH.5769.11 3 0.0000 0.947 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.Y6.A8TL.01 2 0.1267 0.881 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MF.01 4 0.1480 0.835 0.00 0.04 0.00 0.94 0.00 0.02
#> TCGA.EJ.5532.01 2 0.3460 0.627 0.00 0.76 0.00 0.22 0.02 0.00
#> TCGA.EJ.5507.01 3 0.0000 0.947 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.A65G.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76W.01 1 0.3679 0.717 0.76 0.00 0.00 0.00 0.04 0.20
#> TCGA.G9.A9S7.01 3 0.3045 0.870 0.00 0.00 0.84 0.00 0.06 0.10
#> TCGA.HC.8216.01 4 0.1814 0.822 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CH.5794.01 3 0.2094 0.917 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.HC.7818.01 2 0.1814 0.849 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.2A.A8VT.01 5 0.1807 0.000 0.00 0.02 0.06 0.00 0.92 0.00
#> TCGA.ZG.A9LM.01 4 0.6168 0.341 0.00 0.14 0.00 0.52 0.04 0.30
#> TCGA.G9.6494.01 1 0.2790 0.787 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.QU.A6IM.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A872.01 3 0.1480 0.917 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.KK.A8IJ.01 1 0.0547 0.850 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.CH.5748.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z7.01 1 0.0547 0.850 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A9TH.01 3 0.0547 0.946 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.YL.A8SJ.01 6 0.7753 0.000 0.12 0.06 0.00 0.10 0.36 0.36
#> TCGA.HC.7749.01 1 0.4247 0.637 0.70 0.00 0.00 0.00 0.06 0.24
#> TCGA.KK.A6E7.01 1 0.0547 0.850 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.HC.8261.01 1 0.0937 0.845 0.96 0.04 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.EJ.5521.01 3 0.1433 0.9008 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.XA.A8JR.01 2 0.0000 0.9092 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7781.01 4 0.2569 0.7738 0.00 0.14 0.00 0.84 0.00 0.02 0.00
#> TCGA.CH.5751.01 1 0.1166 0.7467 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.V1.A8WL.01 4 0.3055 0.7707 0.00 0.14 0.00 0.82 0.00 0.02 0.02
#> TCGA.EJ.7786.01 2 0.1433 0.8474 0.08 0.92 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8470.01 1 0.1433 0.7349 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7742.01 4 0.2278 0.6954 0.00 0.08 0.00 0.88 0.00 0.00 0.04
#> TCGA.CH.5769.01 3 0.0504 0.9120 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EJ.A7NN.01 7 0.3525 0.0000 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.YL.A8SC.01 6 0.7016 0.1932 0.32 0.08 0.00 0.02 0.10 0.44 0.04
#> TCGA.V1.A8X3.01 1 0.3221 0.5292 0.68 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.KK.A6DY.01 1 0.3417 0.5756 0.72 0.00 0.00 0.02 0.00 0.26 0.00
#> TCGA.VN.A88N.01 4 0.3908 0.6589 0.00 0.20 0.00 0.72 0.00 0.00 0.08
#> TCGA.EJ.8468.01 1 0.1166 0.7465 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8256.01 1 0.1433 0.7349 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5769.11 3 0.0504 0.9120 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.Y6.A8TL.01 2 0.1671 0.8235 0.10 0.90 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MF.01 4 0.4022 0.6607 0.00 0.10 0.00 0.78 0.02 0.02 0.08
#> TCGA.EJ.5532.01 2 0.3417 0.5262 0.00 0.72 0.00 0.26 0.00 0.02 0.00
#> TCGA.EJ.5507.01 3 0.0504 0.9103 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EJ.A65G.01 2 0.0000 0.9092 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76W.01 1 0.3413 0.4490 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.G9.A9S7.01 3 0.4161 0.7918 0.00 0.00 0.76 0.00 0.08 0.06 0.10
#> TCGA.HC.8216.01 4 0.2569 0.7708 0.00 0.14 0.00 0.84 0.00 0.02 0.00
#> TCGA.CH.5794.01 3 0.2572 0.8736 0.00 0.00 0.86 0.00 0.00 0.06 0.08
#> TCGA.HC.7818.01 2 0.1928 0.8462 0.00 0.90 0.00 0.00 0.02 0.08 0.00
#> TCGA.2A.A8VT.01 5 0.0863 0.0000 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.ZG.A9LM.01 4 0.5386 0.3062 0.00 0.06 0.00 0.60 0.00 0.10 0.24
#> TCGA.G9.6494.01 1 0.2832 0.6253 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.QU.A6IM.01 2 0.0000 0.9092 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A872.01 3 0.2016 0.8741 0.00 0.00 0.90 0.00 0.06 0.00 0.04
#> TCGA.KK.A8IJ.01 1 0.0504 0.7594 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5748.01 2 0.0000 0.9092 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z7.01 1 0.0000 0.7596 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 2 0.0000 0.9092 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A9TH.01 3 0.1363 0.9109 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.YL.A8SJ.01 6 0.6028 -0.0468 0.06 0.00 0.06 0.08 0.10 0.66 0.04
#> TCGA.HC.7749.01 1 0.3546 0.2489 0.54 0.00 0.00 0.00 0.00 0.46 0.00
#> TCGA.KK.A6E7.01 1 0.0000 0.7596 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8261.01 1 0.1433 0.7349 0.92 0.08 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EJ.5521.01 3 0.2265 0.8579 0.00 0.00 0.88 0.00 0.02 0.00 0.02 0.08
#> TCGA.XA.A8JR.01 2 0.0000 0.9153 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7781.01 4 0.2265 0.7284 0.00 0.08 0.00 0.88 0.00 0.02 0.02 0.00
#> TCGA.CH.5751.01 1 0.2132 0.5722 0.88 0.04 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.V1.A8WL.01 4 0.3002 0.7098 0.00 0.12 0.00 0.82 0.00 0.00 0.04 0.02
#> TCGA.EJ.7786.01 2 0.0471 0.9015 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.8470.01 1 0.1091 0.6406 0.94 0.06 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7742.01 4 0.2407 0.6931 0.00 0.06 0.00 0.86 0.00 0.00 0.08 0.00
#> TCGA.CH.5769.01 3 0.0000 0.8750 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NN.01 7 0.2267 0.0000 0.00 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.YL.A8SC.01 1 0.7042 -0.4943 0.38 0.06 0.00 0.00 0.08 0.10 0.04 0.34
#> TCGA.V1.A8X3.01 1 0.3015 -0.2618 0.68 0.00 0.00 0.00 0.00 0.00 0.00 0.32
#> TCGA.KK.A6DY.01 1 0.3615 0.1531 0.74 0.00 0.00 0.00 0.00 0.02 0.04 0.20
#> TCGA.VN.A88N.01 4 0.4041 0.5411 0.00 0.22 0.00 0.70 0.00 0.04 0.04 0.00
#> TCGA.EJ.8468.01 1 0.1341 0.6255 0.92 0.08 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8256.01 1 0.1341 0.6255 0.92 0.08 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5769.11 3 0.0000 0.8750 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Y6.A8TL.01 2 0.0808 0.8828 0.04 0.96 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MF.01 4 0.3454 0.5659 0.00 0.02 0.00 0.80 0.00 0.04 0.12 0.02
#> TCGA.EJ.5532.01 2 0.3618 0.2058 0.00 0.60 0.00 0.38 0.00 0.02 0.00 0.00
#> TCGA.EJ.5507.01 3 0.0000 0.8750 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A65G.01 2 0.0000 0.9153 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A76W.01 1 0.4004 -0.8742 0.50 0.00 0.00 0.00 0.00 0.04 0.00 0.46
#> TCGA.G9.A9S7.01 3 0.4734 0.7317 0.00 0.00 0.70 0.00 0.08 0.04 0.04 0.14
#> TCGA.HC.8216.01 4 0.2591 0.7256 0.00 0.08 0.00 0.86 0.00 0.04 0.00 0.02
#> TCGA.CH.5794.01 3 0.4661 0.7521 0.00 0.00 0.70 0.00 0.06 0.04 0.04 0.16
#> TCGA.HC.7818.01 2 0.2337 0.8445 0.02 0.90 0.00 0.02 0.02 0.00 0.02 0.02
#> TCGA.2A.A8VT.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9LM.01 4 0.4619 0.0622 0.02 0.00 0.00 0.48 0.00 0.44 0.06 0.00
#> TCGA.G9.6494.01 1 0.2938 -0.1750 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.QU.A6IM.01 2 0.0000 0.9153 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VP.A872.01 3 0.2348 0.8214 0.00 0.00 0.88 0.00 0.00 0.04 0.06 0.02
#> TCGA.KK.A8IJ.01 1 0.0808 0.6411 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5748.01 2 0.0000 0.9153 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z7.01 1 0.0808 0.6411 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A6RC.01 2 0.0000 0.9153 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A9TH.01 3 0.2484 0.8511 0.00 0.00 0.86 0.00 0.02 0.02 0.00 0.10
#> TCGA.YL.A8SJ.01 6 0.5989 0.0000 0.10 0.00 0.02 0.00 0.12 0.52 0.00 0.24
#> TCGA.HC.7749.01 8 0.3318 0.0000 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.KK.A6E7.01 1 0.0808 0.6411 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8261.01 1 0.1091 0.6406 0.94 0.06 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: Node04. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["044"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 30 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.669 0.770 0.904 0.4119 0.669 0.669
#> 3 3 1.000 1.000 1.000 0.5860 0.678 0.519
#> 4 4 0.794 0.906 0.913 0.1520 0.800 0.485
#> 5 5 0.751 0.820 0.897 0.0472 0.986 0.940
#> 6 6 0.899 0.756 0.899 0.0335 0.982 0.915
#> 7 7 0.808 0.680 0.851 0.0273 1.000 1.000
#> 8 8 0.841 0.731 0.859 0.0153 0.954 0.767
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.G9.6343.01 2 0.995 0.861 0.46 0.54
#> TCGA.CH.5754.01 1 0.995 1.000 0.54 0.46
#> TCGA.XK.AAJT.01 2 0.995 0.861 0.46 0.54
#> TCGA.V1.A9O5.01 2 0.000 0.314 0.00 1.00
#> TCGA.M7.A721.01 2 0.995 0.861 0.46 0.54
#> TCGA.G9.7510.01 2 0.995 0.861 0.46 0.54
#> TCGA.KK.A7AV.01 2 0.995 0.861 0.46 0.54
#> TCGA.XJ.A83H.01 2 0.242 0.219 0.04 0.96
#> TCGA.ZG.A8QY.01 2 0.995 0.861 0.46 0.54
#> TCGA.G9.A9S0.01 2 0.242 0.219 0.04 0.96
#> TCGA.VP.A87H.01 2 0.995 0.861 0.46 0.54
#> TCGA.HC.7736.01 2 0.995 0.861 0.46 0.54
#> TCGA.G9.6499.11 2 0.995 0.861 0.46 0.54
#> TCGA.KK.A8I9.01 2 0.995 0.861 0.46 0.54
#> TCGA.EJ.7317.01 2 0.995 0.861 0.46 0.54
#> TCGA.EJ.A65E.01 2 0.995 0.861 0.46 0.54
#> TCGA.ZG.A8QX.01 2 0.995 0.861 0.46 0.54
#> TCGA.HI.7168.01 1 0.995 1.000 0.54 0.46
#> TCGA.EJ.A65M.01 2 0.995 0.861 0.46 0.54
#> TCGA.HC.7211.01 2 0.242 0.219 0.04 0.96
#> TCGA.KK.A8I6.01 1 0.995 1.000 0.54 0.46
#> TCGA.EJ.5504.01 2 0.000 0.314 0.00 1.00
#> TCGA.CH.5766.01 1 0.995 1.000 0.54 0.46
#> TCGA.G9.7523.01 2 0.995 0.861 0.46 0.54
#> TCGA.J9.A8CM.01 1 0.995 1.000 0.54 0.46
#> TCGA.EJ.7331.01 2 0.995 0.861 0.46 0.54
#> TCGA.HC.A9TE.01 1 0.995 1.000 0.54 0.46
#> TCGA.EJ.7115.01 2 0.995 0.861 0.46 0.54
#> TCGA.V1.A8ML.01 2 0.995 0.861 0.46 0.54
#> TCGA.EJ.5518.01 2 0.000 0.314 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.G9.6343.01 3 0 1 0 0 1
#> TCGA.CH.5754.01 1 0 1 1 0 0
#> TCGA.XK.AAJT.01 3 0 1 0 0 1
#> TCGA.V1.A9O5.01 3 0 1 0 0 1
#> TCGA.M7.A721.01 3 0 1 0 0 1
#> TCGA.G9.7510.01 2 0 1 0 1 0
#> TCGA.KK.A7AV.01 2 0 1 0 1 0
#> TCGA.XJ.A83H.01 3 0 1 0 0 1
#> TCGA.ZG.A8QY.01 2 0 1 0 1 0
#> TCGA.G9.A9S0.01 3 0 1 0 0 1
#> TCGA.VP.A87H.01 2 0 1 0 1 0
#> TCGA.HC.7736.01 3 0 1 0 0 1
#> TCGA.G9.6499.11 2 0 1 0 1 0
#> TCGA.KK.A8I9.01 2 0 1 0 1 0
#> TCGA.EJ.7317.01 2 0 1 0 1 0
#> TCGA.EJ.A65E.01 2 0 1 0 1 0
#> TCGA.ZG.A8QX.01 2 0 1 0 1 0
#> TCGA.HI.7168.01 1 0 1 1 0 0
#> TCGA.EJ.A65M.01 2 0 1 0 1 0
#> TCGA.HC.7211.01 3 0 1 0 0 1
#> TCGA.KK.A8I6.01 1 0 1 1 0 0
#> TCGA.EJ.5504.01 3 0 1 0 0 1
#> TCGA.CH.5766.01 1 0 1 1 0 0
#> TCGA.G9.7523.01 2 0 1 0 1 0
#> TCGA.J9.A8CM.01 1 0 1 1 0 0
#> TCGA.EJ.7331.01 2 0 1 0 1 0
#> TCGA.HC.A9TE.01 1 0 1 1 0 0
#> TCGA.EJ.7115.01 2 0 1 0 1 0
#> TCGA.V1.A8ML.01 2 0 1 0 1 0
#> TCGA.EJ.5518.01 3 0 1 0 0 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.G9.6343.01 4 0.3172 0.716 0.00 0.00 0.16 0.84
#> TCGA.CH.5754.01 1 0.0000 0.982 1.00 0.00 0.00 0.00
#> TCGA.XK.AAJT.01 4 0.3400 0.713 0.00 0.00 0.18 0.82
#> TCGA.V1.A9O5.01 3 0.1211 0.946 0.00 0.00 0.96 0.04
#> TCGA.M7.A721.01 4 0.3610 0.711 0.00 0.00 0.20 0.80
#> TCGA.G9.7510.01 4 0.3801 0.834 0.00 0.22 0.00 0.78
#> TCGA.KK.A7AV.01 4 0.3801 0.834 0.00 0.22 0.00 0.78
#> TCGA.XJ.A83H.01 3 0.1637 0.925 0.00 0.00 0.94 0.06
#> TCGA.ZG.A8QY.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.G9.A9S0.01 3 0.0000 0.951 0.00 0.00 1.00 0.00
#> TCGA.VP.A87H.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.HC.7736.01 3 0.1211 0.946 0.00 0.00 0.96 0.04
#> TCGA.G9.6499.11 4 0.4713 0.699 0.00 0.36 0.00 0.64
#> TCGA.KK.A8I9.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EJ.7317.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EJ.A65E.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ZG.A8QX.01 4 0.3801 0.834 0.00 0.22 0.00 0.78
#> TCGA.HI.7168.01 1 0.2647 0.903 0.88 0.00 0.00 0.12
#> TCGA.EJ.A65M.01 4 0.4713 0.699 0.00 0.36 0.00 0.64
#> TCGA.HC.7211.01 3 0.3400 0.838 0.00 0.00 0.82 0.18
#> TCGA.KK.A8I6.01 1 0.0000 0.982 1.00 0.00 0.00 0.00
#> TCGA.EJ.5504.01 3 0.0707 0.950 0.00 0.00 0.98 0.02
#> TCGA.CH.5766.01 1 0.0000 0.982 1.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.J9.A8CM.01 1 0.0000 0.982 1.00 0.00 0.00 0.00
#> TCGA.EJ.7331.01 4 0.3801 0.834 0.00 0.22 0.00 0.78
#> TCGA.HC.A9TE.01 1 0.0000 0.982 1.00 0.00 0.00 0.00
#> TCGA.EJ.7115.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.V1.A8ML.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EJ.5518.01 3 0.0000 0.951 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.G9.6343.01 4 0.2616 0.772 0.00 0.00 0.02 0.88 0.10
#> TCGA.CH.5754.01 1 0.0000 0.917 1.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJT.01 4 0.5341 0.545 0.00 0.00 0.08 0.62 0.30
#> TCGA.V1.A9O5.01 3 0.3852 0.736 0.00 0.00 0.76 0.02 0.22
#> TCGA.M7.A721.01 4 0.3697 0.774 0.00 0.00 0.10 0.82 0.08
#> TCGA.G9.7510.01 4 0.2020 0.864 0.00 0.10 0.00 0.90 0.00
#> TCGA.KK.A7AV.01 4 0.2020 0.864 0.00 0.10 0.00 0.90 0.00
#> TCGA.XJ.A83H.01 3 0.2754 0.760 0.00 0.00 0.88 0.04 0.08
#> TCGA.ZG.A8QY.01 2 0.0000 0.980 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 3 0.0000 0.824 0.00 0.00 1.00 0.00 0.00
#> TCGA.VP.A87H.01 2 0.0000 0.980 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7736.01 3 0.2732 0.734 0.00 0.00 0.84 0.00 0.16
#> TCGA.G9.6499.11 4 0.2929 0.818 0.00 0.18 0.00 0.82 0.00
#> TCGA.KK.A8I9.01 2 0.0000 0.980 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7317.01 2 0.2012 0.910 0.00 0.92 0.00 0.06 0.02
#> TCGA.EJ.A65E.01 2 0.0609 0.977 0.00 0.98 0.00 0.00 0.02
#> TCGA.ZG.A8QX.01 4 0.2020 0.864 0.00 0.10 0.00 0.90 0.00
#> TCGA.HI.7168.01 1 0.4227 0.400 0.58 0.00 0.00 0.00 0.42
#> TCGA.EJ.A65M.01 4 0.2929 0.818 0.00 0.18 0.00 0.82 0.00
#> TCGA.HC.7211.01 5 0.5498 0.000 0.00 0.00 0.34 0.08 0.58
#> TCGA.KK.A8I6.01 1 0.0000 0.917 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5504.01 3 0.2280 0.815 0.00 0.00 0.88 0.00 0.12
#> TCGA.CH.5766.01 1 0.0000 0.917 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 2 0.0000 0.980 0.00 1.00 0.00 0.00 0.00
#> TCGA.J9.A8CM.01 1 0.0000 0.917 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7331.01 4 0.3697 0.850 0.00 0.10 0.00 0.82 0.08
#> TCGA.HC.A9TE.01 1 0.0000 0.917 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7115.01 2 0.0609 0.977 0.00 0.98 0.00 0.00 0.02
#> TCGA.V1.A8ML.01 2 0.0609 0.977 0.00 0.98 0.00 0.00 0.02
#> TCGA.EJ.5518.01 3 0.0000 0.824 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.G9.6343.01 4 0.4566 0.603 0.00 0.00 0.00 0.70 0.14 0.16
#> TCGA.CH.5754.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJT.01 6 0.3315 0.000 0.00 0.00 0.02 0.20 0.00 0.78
#> TCGA.V1.A9O5.01 3 0.4200 0.639 0.00 0.00 0.74 0.00 0.12 0.14
#> TCGA.M7.A721.01 4 0.4713 0.636 0.00 0.00 0.02 0.72 0.12 0.14
#> TCGA.G9.7510.01 4 0.0547 0.798 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.KK.A7AV.01 4 0.0547 0.798 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.XJ.A83H.01 3 0.0547 0.808 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.ZG.A8QY.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 3 0.0000 0.827 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VP.A87H.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7736.01 3 0.3309 0.596 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.G9.6499.11 4 0.1267 0.774 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.KK.A8I9.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7317.01 2 0.2190 0.902 0.00 0.90 0.00 0.04 0.06 0.00
#> TCGA.EJ.A65E.01 2 0.1480 0.947 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.ZG.A8QX.01 4 0.0547 0.798 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.HI.7168.01 1 0.5523 0.229 0.50 0.00 0.00 0.00 0.36 0.14
#> TCGA.EJ.A65M.01 4 0.1556 0.752 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.HC.7211.01 5 0.4144 0.000 0.00 0.00 0.36 0.02 0.62 0.00
#> TCGA.KK.A8I6.01 1 0.0547 0.888 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EJ.5504.01 3 0.0547 0.826 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CH.5766.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 2 0.0000 0.973 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CM.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7331.01 4 0.5073 0.628 0.00 0.02 0.00 0.68 0.14 0.16
#> TCGA.HC.A9TE.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7115.01 2 0.0547 0.968 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.V1.A8ML.01 2 0.1092 0.963 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.EJ.5518.01 3 0.0000 0.827 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.G9.6343.01 4 0.349 0.4102 0.0 0.00 0.12 0.78 0.10 0.00 0.00
#> TCGA.CH.5754.01 1 0.000 0.8801 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJT.01 6 0.242 0.0000 0.0 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.V1.A9O5.01 7 0.523 0.5940 0.0 0.00 0.12 0.00 0.06 0.18 0.64
#> TCGA.M7.A721.01 4 0.000 0.5585 0.0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.7510.01 4 0.341 0.6586 0.0 0.00 0.38 0.62 0.00 0.00 0.00
#> TCGA.KK.A7AV.01 4 0.314 0.6703 0.0 0.00 0.30 0.70 0.00 0.00 0.00
#> TCGA.XJ.A83H.01 7 0.172 0.8319 0.0 0.00 0.04 0.00 0.04 0.00 0.92
#> TCGA.ZG.A8QY.01 2 0.000 0.8866 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 7 0.000 0.8394 0.0 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.VP.A87H.01 2 0.000 0.8866 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7736.01 7 0.208 0.7612 0.0 0.00 0.00 0.00 0.00 0.14 0.86
#> TCGA.G9.6499.11 4 0.443 0.6260 0.0 0.06 0.38 0.56 0.00 0.00 0.00
#> TCGA.KK.A8I9.01 2 0.000 0.8866 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7317.01 2 0.319 0.7192 0.0 0.76 0.22 0.00 0.00 0.02 0.00
#> TCGA.EJ.A65E.01 2 0.384 0.7716 0.0 0.74 0.16 0.00 0.10 0.00 0.00
#> TCGA.ZG.A8QX.01 4 0.314 0.6675 0.0 0.00 0.30 0.70 0.00 0.00 0.00
#> TCGA.HI.7168.01 1 0.639 -0.0573 0.4 0.00 0.18 0.00 0.34 0.08 0.00
#> TCGA.EJ.A65M.01 4 0.443 0.6260 0.0 0.06 0.38 0.56 0.00 0.00 0.00
#> TCGA.HC.7211.01 5 0.283 0.0000 0.0 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.KK.A8I6.01 1 0.000 0.8801 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5504.01 7 0.221 0.8343 0.0 0.00 0.04 0.00 0.04 0.02 0.90
#> TCGA.CH.5766.01 1 0.000 0.8801 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 2 0.000 0.8866 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CM.01 1 0.000 0.8801 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7331.01 4 0.349 0.4102 0.0 0.00 0.12 0.78 0.10 0.00 0.00
#> TCGA.HC.A9TE.01 1 0.000 0.8801 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7115.01 2 0.238 0.8474 0.0 0.86 0.12 0.00 0.02 0.00 0.00
#> TCGA.V1.A8ML.01 2 0.291 0.8319 0.0 0.80 0.18 0.00 0.02 0.00 0.00
#> TCGA.EJ.5518.01 7 0.000 0.8394 0.0 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.G9.6343.01 8 0.0000 0.796 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CH.5754.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJT.01 6 0.0941 0.000 0.00 0.00 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.V1.A9O5.01 7 0.6478 0.455 0.00 0.00 0.14 0.12 0.14 0.08 0.52 0.00
#> TCGA.M7.A721.01 8 0.2650 0.391 0.00 0.00 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.G9.7510.01 4 0.3193 0.890 0.00 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.KK.A7AV.01 4 0.3193 0.890 0.00 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.XJ.A83H.01 7 0.2348 0.812 0.00 0.00 0.00 0.06 0.04 0.02 0.88 0.00
#> TCGA.ZG.A8QY.01 2 0.0000 0.887 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.A9S0.01 7 0.0000 0.820 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VP.A87H.01 2 0.0000 0.887 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7736.01 7 0.1765 0.752 0.00 0.00 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.G9.6499.11 4 0.4415 0.859 0.00 0.06 0.02 0.60 0.00 0.00 0.00 0.32
#> TCGA.KK.A8I9.01 2 0.0000 0.887 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7317.01 2 0.4211 0.645 0.00 0.68 0.22 0.08 0.00 0.02 0.00 0.00
#> TCGA.EJ.A65E.01 2 0.3444 0.775 0.00 0.78 0.14 0.06 0.02 0.00 0.00 0.00
#> TCGA.ZG.A8QX.01 4 0.3193 0.869 0.00 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.HI.7168.01 3 0.4952 0.000 0.20 0.00 0.50 0.00 0.30 0.00 0.00 0.00
#> TCGA.EJ.A65M.01 4 0.4415 0.859 0.00 0.06 0.02 0.60 0.00 0.00 0.00 0.32
#> TCGA.HC.7211.01 5 0.1765 0.000 0.00 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.KK.A8I6.01 1 0.0808 0.894 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.EJ.5504.01 7 0.2348 0.812 0.00 0.00 0.00 0.06 0.04 0.02 0.88 0.00
#> TCGA.CH.5766.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7523.01 2 0.0000 0.887 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J9.A8CM.01 1 0.1765 0.886 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.EJ.7331.01 8 0.0000 0.796 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HC.A9TE.01 1 0.1765 0.886 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.EJ.7115.01 2 0.1557 0.863 0.00 0.92 0.06 0.02 0.00 0.00 0.00 0.00
#> TCGA.V1.A8ML.01 2 0.3483 0.789 0.00 0.76 0.18 0.04 0.00 0.02 0.00 0.00
#> TCGA.EJ.5518.01 7 0.0000 0.820 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011-leaf , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 , Node053-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["05"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 87 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 0.989 0.996 0.3979 0.607 0.607
#> 3 3 1.000 0.973 0.980 0.5848 0.719 0.550
#> 4 4 0.903 0.875 0.935 0.1193 0.867 0.663
#> 5 5 0.825 0.792 0.899 0.0921 0.813 0.473
#> 6 6 0.802 0.770 0.853 0.0368 0.947 0.777
#> 7 7 0.854 0.837 0.889 0.0337 0.963 0.824
#> 8 8 0.861 0.742 0.841 0.0217 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> 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.YL.A8SB.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.7797.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZG.A8QW.01 1 0.000 0.994 1.00 0.00
#> TCGA.YL.A8HK.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5501.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.7330.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6351.01 1 0.000 0.994 1.00 0.00
#> TCGA.KK.A8IM.01 1 0.000 0.994 1.00 0.00
#> TCGA.G9.6348.01 1 0.000 0.994 1.00 0.00
#> TCGA.J4.A67Q.01 1 0.000 0.994 1.00 0.00
#> TCGA.2A.A8VL.01 1 0.000 0.994 1.00 0.00
#> TCGA.V1.A9ZK.01 2 0.000 1.000 0.00 1.00
#> TCGA.HC.7737.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6384.01 1 0.000 0.994 1.00 0.00
#> TCGA.V1.A9ZG.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZG.A9LN.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.7794.01 2 0.000 1.000 0.00 1.00
#> TCGA.YL.A9WJ.01 2 0.000 1.000 0.00 1.00
#> TCGA.V1.A9Z8.01 1 0.000 0.994 1.00 0.00
#> TCGA.YL.A8SK.01 1 0.000 0.994 1.00 0.00
#> TCGA.J4.A67M.01 1 0.000 0.994 1.00 0.00
#> TCGA.G9.6499.01 2 0.000 1.000 0.00 1.00
#> TCGA.J4.A67T.01 1 0.000 0.994 1.00 0.00
#> TCGA.KK.A6E3.01 1 0.000 0.994 1.00 0.00
#> TCGA.G9.6336.01 1 0.000 0.994 1.00 0.00
#> TCGA.V1.A8MJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.VP.A87C.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.5497.01 1 0.000 0.994 1.00 0.00
#> TCGA.XK.AAJR.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6363.11 1 0.000 0.994 1.00 0.00
#> TCGA.V1.A9OY.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZG.A9L4.01 1 0.000 0.994 1.00 0.00
#> TCGA.HC.7747.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZG.A9LS.01 1 0.000 0.994 1.00 0.00
#> TCGA.V1.A9OH.01 2 0.000 1.000 0.00 1.00
#> TCGA.VP.A878.01 1 0.000 0.994 1.00 0.00
#> TCGA.HC.7745.01 1 0.000 0.994 1.00 0.00
#> TCGA.G9.6379.01 1 0.000 0.994 1.00 0.00
#> TCGA.CH.5762.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.5527.01 1 0.000 0.994 1.00 0.00
#> TCGA.G9.6356.01 1 0.000 0.994 1.00 0.00
#> TCGA.G9.6333.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5495.01 1 0.000 0.994 1.00 0.00
#> TCGA.V1.A8WN.01 1 0.000 0.994 1.00 0.00
#> TCGA.HC.A6AS.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.7328.01 1 0.000 0.994 1.00 0.00
#> TCGA.YL.A8SI.01 2 0.000 1.000 0.00 1.00
#> TCGA.J4.A67O.01 1 0.000 0.994 1.00 0.00
#> TCGA.XK.AAIV.01 2 0.000 1.000 0.00 1.00
#> TCGA.KK.A8IB.01 2 0.000 1.000 0.00 1.00
#> TCGA.XK.AAIR.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7783.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.5502.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.7785.01 1 0.000 0.994 1.00 0.00
#> TCGA.4L.AA1F.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5516.01 1 0.000 0.994 1.00 0.00
#> TCGA.KK.A7B0.01 2 0.000 1.000 0.00 1.00
#> TCGA.KK.A8I4.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.5512.01 1 0.000 0.994 1.00 0.00
#> TCGA.2A.A8W3.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZG.A9LY.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.7793.01 1 0.000 0.994 1.00 0.00
#> TCGA.HC.8266.01 1 0.000 0.994 1.00 0.00
#> TCGA.CH.5792.01 2 0.000 1.000 0.00 1.00
#> TCGA.G9.6347.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.A46I.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.5508.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.A7NH.01 1 0.000 0.994 1.00 0.00
#> TCGA.J9.A52C.01 1 0.000 0.994 1.00 0.00
#> TCGA.FC.7708.01 1 0.000 0.994 1.00 0.00
#> TCGA.J4.A67R.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.5499.01 2 0.000 1.000 0.00 1.00
#> TCGA.CH.5738.01 1 0.000 0.994 1.00 0.00
#> TCGA.G9.7522.01 1 0.000 0.994 1.00 0.00
#> TCGA.HC.A6AP.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.5510.01 1 0.943 0.437 0.64 0.36
#> TCGA.CH.5746.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZG.A8QZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.TK.A8OK.01 2 0.000 1.000 0.00 1.00
#> TCGA.X4.A8KQ.01 1 0.000 0.994 1.00 0.00
#> TCGA.HC.7750.01 1 0.000 0.994 1.00 0.00
#> TCGA.YL.A9WY.01 2 0.000 1.000 0.00 1.00
#> TCGA.VP.A87E.01 1 0.000 0.994 1.00 0.00
#> TCGA.V1.A9ZR.01 2 0.000 1.000 0.00 1.00
#> TCGA.EJ.7792.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZG.A9L2.01 1 0.000 0.994 1.00 0.00
#> TCGA.EJ.5505.01 1 0.000 0.994 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.YL.A8SB.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.7797.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A8QW.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.YL.A8HK.01 3 0.0000 0.935 0.00 0.00 1.00
#> TCGA.EJ.5501.01 1 0.0892 0.979 0.98 0.00 0.02
#> TCGA.EJ.7330.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.G9.6351.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A8IM.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.6348.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.J4.A67Q.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.2A.A8VL.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A9ZK.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.HC.7737.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.G9.6384.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A9ZG.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.ZG.A9LN.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.EJ.7794.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.YL.A9WJ.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.V1.A9Z8.01 1 0.0892 0.979 0.98 0.00 0.02
#> TCGA.YL.A8SK.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.J4.A67M.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.G9.6499.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.J4.A67T.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A6E3.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.G9.6336.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A8MJ.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.VP.A87C.01 1 0.0892 0.979 0.98 0.00 0.02
#> TCGA.EJ.5497.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.XK.AAJR.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.G9.6363.11 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.V1.A9OY.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A9L4.01 3 0.0000 0.935 0.00 0.00 1.00
#> TCGA.HC.7747.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A9LS.01 3 0.0892 0.947 0.02 0.00 0.98
#> TCGA.V1.A9OH.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.VP.A878.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.HC.7745.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.6379.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.CH.5762.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.EJ.5527.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.6333.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.EJ.5495.01 3 0.0000 0.935 0.00 0.00 1.00
#> TCGA.V1.A8WN.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A6AS.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.EJ.7328.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.YL.A8SI.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.J4.A67O.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.XK.AAIV.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.KK.A8IB.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.XK.AAIR.01 3 0.0000 0.935 0.00 0.00 1.00
#> TCGA.EJ.7783.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.5502.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.7785.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.4L.AA1F.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.EJ.5516.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.KK.A7B0.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.KK.A8I4.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.EJ.5512.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.2A.A8W3.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.ZG.A9LY.01 3 0.0000 0.935 0.00 0.00 1.00
#> TCGA.EJ.7793.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.8266.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.CH.5792.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.G9.6347.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.A46I.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.EJ.5508.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.A7NH.01 3 0.5397 0.667 0.28 0.00 0.72
#> TCGA.J9.A52C.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.FC.7708.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.J4.A67R.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.EJ.5499.01 3 0.0000 0.935 0.00 0.00 1.00
#> TCGA.CH.5738.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.G9.7522.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.HC.A6AP.01 2 0.1529 0.986 0.00 0.96 0.04
#> TCGA.EJ.5510.01 3 0.0000 0.935 0.00 0.00 1.00
#> TCGA.CH.5746.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A8QZ.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.TK.A8OK.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.X4.A8KQ.01 3 0.5560 0.631 0.30 0.00 0.70
#> TCGA.HC.7750.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.YL.A9WY.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.VP.A87E.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.V1.A9ZR.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EJ.7792.01 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.ZG.A9L2.01 3 0.1529 0.957 0.04 0.00 0.96
#> TCGA.EJ.5505.01 1 0.0000 0.998 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.YL.A8SB.01 1 0.317 0.825 0.84 0.00 0.16 0.00
#> TCGA.EJ.7797.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.ZG.A8QW.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.YL.A8HK.01 4 0.000 0.855 0.00 0.00 0.00 1.00
#> TCGA.EJ.5501.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.EJ.7330.01 4 0.201 0.851 0.00 0.08 0.00 0.92
#> TCGA.G9.6351.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.KK.A8IM.01 1 0.479 0.465 0.62 0.00 0.38 0.00
#> TCGA.G9.6348.01 1 0.361 0.779 0.80 0.00 0.20 0.00
#> TCGA.J4.A67Q.01 3 0.495 0.067 0.44 0.00 0.56 0.00
#> TCGA.2A.A8VL.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.V1.A9ZK.01 2 0.361 0.858 0.00 0.80 0.00 0.20
#> TCGA.HC.7737.01 2 0.380 0.837 0.00 0.78 0.00 0.22
#> TCGA.G9.6384.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.V1.A9ZG.01 4 0.164 0.861 0.00 0.06 0.00 0.94
#> TCGA.ZG.A9LN.01 3 0.164 0.917 0.00 0.00 0.94 0.06
#> TCGA.EJ.7794.01 2 0.361 0.858 0.00 0.80 0.00 0.20
#> TCGA.YL.A9WJ.01 2 0.361 0.858 0.00 0.80 0.00 0.20
#> TCGA.V1.A9Z8.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.YL.A8SK.01 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.J4.A67M.01 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.G9.6499.01 2 0.361 0.858 0.00 0.80 0.00 0.20
#> TCGA.J4.A67T.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.KK.A6E3.01 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.G9.6336.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.V1.A8MJ.01 1 0.201 0.900 0.92 0.00 0.08 0.00
#> TCGA.VP.A87C.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.EJ.5497.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.XK.AAJR.01 2 0.000 0.873 0.00 1.00 0.00 0.00
#> TCGA.G9.6363.11 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.V1.A9OY.01 1 0.201 0.900 0.92 0.00 0.08 0.00
#> TCGA.ZG.A9L4.01 3 0.340 0.813 0.00 0.00 0.82 0.18
#> TCGA.HC.7747.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.ZG.A9LS.01 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.V1.A9OH.01 2 0.000 0.873 0.00 1.00 0.00 0.00
#> TCGA.VP.A878.01 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.HC.7745.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.G9.6379.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.CH.5762.01 3 0.164 0.917 0.00 0.00 0.94 0.06
#> TCGA.EJ.5527.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.G9.6356.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.G9.6333.01 2 0.361 0.858 0.00 0.80 0.00 0.20
#> TCGA.EJ.5495.01 4 0.398 0.612 0.00 0.00 0.24 0.76
#> TCGA.V1.A8WN.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.HC.A6AS.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.EJ.7328.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SI.01 4 0.164 0.861 0.00 0.06 0.00 0.94
#> TCGA.J4.A67O.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.XK.AAIV.01 4 0.201 0.851 0.00 0.08 0.00 0.92
#> TCGA.KK.A8IB.01 2 0.000 0.873 0.00 1.00 0.00 0.00
#> TCGA.XK.AAIR.01 4 0.000 0.855 0.00 0.00 0.00 1.00
#> TCGA.EJ.7783.01 1 0.499 0.177 0.52 0.00 0.48 0.00
#> TCGA.EJ.5502.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.EJ.7785.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.4L.AA1F.01 4 0.201 0.851 0.00 0.08 0.00 0.92
#> TCGA.EJ.5516.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.KK.A7B0.01 4 0.340 0.721 0.00 0.18 0.00 0.82
#> TCGA.KK.A8I4.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.EJ.5512.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.2A.A8W3.01 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.ZG.A9LY.01 3 0.340 0.813 0.00 0.00 0.82 0.18
#> TCGA.EJ.7793.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.HC.8266.01 3 0.201 0.912 0.00 0.00 0.92 0.08
#> TCGA.CH.5792.01 2 0.000 0.873 0.00 1.00 0.00 0.00
#> TCGA.G9.6347.01 1 0.201 0.900 0.92 0.00 0.08 0.00
#> TCGA.EJ.A46I.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.EJ.5508.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.EJ.A7NH.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.J9.A52C.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.J4.A67R.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.EJ.5499.01 4 0.000 0.855 0.00 0.00 0.00 1.00
#> TCGA.CH.5738.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.G9.7522.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.HC.A6AP.01 2 0.361 0.858 0.00 0.80 0.00 0.20
#> TCGA.EJ.5510.01 4 0.361 0.672 0.00 0.00 0.20 0.80
#> TCGA.CH.5746.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.ZG.A8QZ.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.TK.A8OK.01 2 0.000 0.873 0.00 1.00 0.00 0.00
#> TCGA.X4.A8KQ.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.HC.7750.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.YL.A9WY.01 2 0.000 0.873 0.00 1.00 0.00 0.00
#> TCGA.VP.A87E.01 1 0.000 0.951 1.00 0.00 0.00 0.00
#> TCGA.V1.A9ZR.01 2 0.000 0.873 0.00 1.00 0.00 0.00
#> TCGA.EJ.7792.01 1 0.265 0.866 0.88 0.00 0.12 0.00
#> TCGA.ZG.A9L2.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.EJ.5505.01 1 0.201 0.900 0.92 0.00 0.08 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.YL.A8SB.01 3 0.2020 0.77416 0.10 0.00 0.90 0.00 0.00
#> TCGA.EJ.7797.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A8QW.01 3 0.4287 -0.00876 0.00 0.00 0.54 0.00 0.46
#> TCGA.YL.A8HK.01 5 0.3983 0.40845 0.00 0.00 0.00 0.34 0.66
#> TCGA.EJ.5501.01 3 0.0000 0.78212 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.7330.01 4 0.0000 0.77691 0.00 0.00 0.00 1.00 0.00
#> TCGA.G9.6351.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IM.01 3 0.2012 0.78228 0.06 0.00 0.92 0.00 0.02
#> TCGA.G9.6348.01 3 0.1732 0.78229 0.08 0.00 0.92 0.00 0.00
#> TCGA.J4.A67Q.01 3 0.1043 0.78863 0.04 0.00 0.96 0.00 0.00
#> TCGA.2A.A8VL.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZK.01 4 0.3796 0.69312 0.00 0.30 0.00 0.70 0.00
#> TCGA.HC.7737.01 4 0.1410 0.77563 0.00 0.06 0.00 0.94 0.00
#> TCGA.G9.6384.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZG.01 4 0.2020 0.72078 0.00 0.00 0.00 0.90 0.10
#> TCGA.ZG.A9LN.01 5 0.4227 0.34962 0.00 0.00 0.42 0.00 0.58
#> TCGA.EJ.7794.01 4 0.3796 0.69312 0.00 0.30 0.00 0.70 0.00
#> TCGA.YL.A9WJ.01 4 0.3796 0.69312 0.00 0.30 0.00 0.70 0.00
#> TCGA.V1.A9Z8.01 3 0.0609 0.78150 0.00 0.00 0.98 0.00 0.02
#> TCGA.YL.A8SK.01 5 0.3109 0.75145 0.00 0.00 0.20 0.00 0.80
#> TCGA.J4.A67M.01 5 0.3109 0.75145 0.00 0.00 0.20 0.00 0.80
#> TCGA.G9.6499.01 4 0.3796 0.69312 0.00 0.30 0.00 0.70 0.00
#> TCGA.J4.A67T.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A6E3.01 5 0.3109 0.75145 0.00 0.00 0.20 0.00 0.80
#> TCGA.G9.6336.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MJ.01 3 0.2929 0.70132 0.18 0.00 0.82 0.00 0.00
#> TCGA.VP.A87C.01 3 0.0609 0.78150 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.5497.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJR.01 2 0.0000 0.99206 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6363.11 5 0.1043 0.77450 0.00 0.00 0.04 0.00 0.96
#> TCGA.V1.A9OY.01 3 0.3424 0.64686 0.24 0.00 0.76 0.00 0.00
#> TCGA.ZG.A9L4.01 5 0.0000 0.77131 0.00 0.00 0.00 0.00 1.00
#> TCGA.HC.7747.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LS.01 5 0.2280 0.78557 0.00 0.00 0.12 0.00 0.88
#> TCGA.V1.A9OH.01 2 0.0000 0.99206 0.00 1.00 0.00 0.00 0.00
#> TCGA.VP.A878.01 5 0.2020 0.78735 0.00 0.00 0.10 0.00 0.90
#> TCGA.HC.7745.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6379.01 3 0.4262 0.06739 0.00 0.00 0.56 0.00 0.44
#> TCGA.CH.5762.01 5 0.3895 0.55378 0.00 0.00 0.32 0.00 0.68
#> TCGA.EJ.5527.01 3 0.0609 0.77921 0.00 0.00 0.98 0.00 0.02
#> TCGA.G9.6356.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6333.01 4 0.3796 0.69312 0.00 0.30 0.00 0.70 0.00
#> TCGA.EJ.5495.01 5 0.0609 0.76617 0.00 0.00 0.00 0.02 0.98
#> TCGA.V1.A8WN.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AS.01 3 0.4262 0.06739 0.00 0.00 0.56 0.00 0.44
#> TCGA.EJ.7328.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SI.01 4 0.0609 0.77121 0.00 0.00 0.00 0.98 0.02
#> TCGA.J4.A67O.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAIV.01 4 0.0000 0.77691 0.00 0.00 0.00 1.00 0.00
#> TCGA.KK.A8IB.01 2 0.0000 0.99206 0.00 1.00 0.00 0.00 0.00
#> TCGA.XK.AAIR.01 4 0.3983 0.39141 0.00 0.00 0.00 0.66 0.34
#> TCGA.EJ.7783.01 3 0.2331 0.77510 0.08 0.00 0.90 0.00 0.02
#> TCGA.EJ.5502.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7785.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.4L.AA1F.01 4 0.0609 0.77121 0.00 0.00 0.00 0.98 0.02
#> TCGA.EJ.5516.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B0.01 4 0.0609 0.77868 0.00 0.02 0.00 0.98 0.00
#> TCGA.KK.A8I4.01 3 0.0609 0.77921 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.5512.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.2A.A8W3.01 5 0.2020 0.78707 0.00 0.00 0.10 0.00 0.90
#> TCGA.ZG.A9LY.01 5 0.1648 0.78482 0.00 0.00 0.04 0.02 0.94
#> TCGA.EJ.7793.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8266.01 5 0.2929 0.75529 0.00 0.00 0.18 0.00 0.82
#> TCGA.CH.5792.01 2 0.1043 0.95051 0.00 0.96 0.00 0.04 0.00
#> TCGA.G9.6347.01 3 0.2280 0.76186 0.12 0.00 0.88 0.00 0.00
#> TCGA.EJ.A46I.01 3 0.4287 0.04536 0.00 0.00 0.54 0.00 0.46
#> TCGA.EJ.5508.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NH.01 3 0.0609 0.78150 0.00 0.00 0.98 0.00 0.02
#> TCGA.J9.A52C.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67R.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5499.01 5 0.4287 0.09061 0.00 0.00 0.00 0.46 0.54
#> TCGA.CH.5738.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.7522.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AP.01 4 0.3796 0.69312 0.00 0.30 0.00 0.70 0.00
#> TCGA.EJ.5510.01 5 0.3561 0.53960 0.00 0.00 0.00 0.26 0.74
#> TCGA.CH.5746.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A8QZ.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.TK.A8OK.01 2 0.0000 0.99206 0.00 1.00 0.00 0.00 0.00
#> TCGA.X4.A8KQ.01 3 0.0609 0.78150 0.00 0.00 0.98 0.00 0.02
#> TCGA.HC.7750.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WY.01 2 0.0000 0.99206 0.00 1.00 0.00 0.00 0.00
#> TCGA.VP.A87E.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZR.01 2 0.0000 0.99206 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7792.01 3 0.2280 0.76186 0.12 0.00 0.88 0.00 0.00
#> TCGA.ZG.A9L2.01 3 0.0609 0.78150 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.5505.01 3 0.3983 0.51348 0.34 0.00 0.66 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.YL.A8SB.01 3 0.1267 0.739 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EJ.7797.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A8QW.01 5 0.3756 0.649 0.00 0.00 0.40 0.00 0.60 0.00
#> TCGA.YL.A8HK.01 6 0.0937 0.771 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.EJ.5501.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7330.01 4 0.2260 0.800 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.G9.6351.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IM.01 3 0.5992 0.562 0.02 0.14 0.48 0.00 0.36 0.00
#> TCGA.G9.6348.01 3 0.1267 0.739 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.J4.A67Q.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2A.A8VL.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZK.01 4 0.0000 0.836 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HC.7737.01 4 0.1814 0.819 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.G9.6384.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZG.01 6 0.3578 0.165 0.00 0.00 0.00 0.34 0.00 0.66
#> TCGA.ZG.A9LN.01 5 0.4199 0.665 0.00 0.00 0.38 0.00 0.60 0.02
#> TCGA.EJ.7794.01 4 0.0000 0.836 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.YL.A9WJ.01 4 0.0000 0.836 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.V1.A9Z8.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SK.01 5 0.5202 0.719 0.00 0.00 0.14 0.00 0.60 0.26
#> TCGA.J4.A67M.01 5 0.5202 0.719 0.00 0.00 0.14 0.00 0.60 0.26
#> TCGA.G9.6499.01 4 0.0000 0.836 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.A67T.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.KK.A6E3.01 5 0.5202 0.719 0.00 0.00 0.14 0.00 0.60 0.26
#> TCGA.G9.6336.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MJ.01 3 0.6480 0.570 0.06 0.14 0.48 0.00 0.32 0.00
#> TCGA.VP.A87C.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5497.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XK.AAJR.01 2 0.2260 0.939 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.G9.6363.11 5 0.5295 0.302 0.00 0.10 0.00 0.00 0.46 0.44
#> TCGA.V1.A9OY.01 3 0.5666 0.583 0.20 0.02 0.60 0.00 0.18 0.00
#> TCGA.ZG.A9L4.01 5 0.3851 0.419 0.00 0.00 0.00 0.00 0.54 0.46
#> TCGA.HC.7747.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9LS.01 5 0.4873 0.679 0.00 0.00 0.08 0.00 0.60 0.32
#> TCGA.V1.A9OH.01 2 0.2260 0.939 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.VP.A878.01 5 0.2956 0.353 0.00 0.12 0.00 0.00 0.84 0.04
#> TCGA.HC.7745.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6379.01 5 0.3756 0.649 0.00 0.00 0.40 0.00 0.60 0.00
#> TCGA.CH.5762.01 5 0.5150 0.712 0.00 0.00 0.22 0.00 0.62 0.16
#> TCGA.EJ.5527.01 3 0.5523 0.567 0.00 0.14 0.50 0.00 0.36 0.00
#> TCGA.G9.6356.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.G9.6333.01 4 0.0000 0.836 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5495.01 6 0.3076 0.393 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.V1.A8WN.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AS.01 5 0.3756 0.649 0.00 0.00 0.40 0.00 0.60 0.00
#> TCGA.EJ.7328.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SI.01 4 0.3756 0.445 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.J4.A67O.01 1 0.1092 0.957 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.XK.AAIV.01 4 0.2631 0.771 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.KK.A8IB.01 2 0.2260 0.939 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.XK.AAIR.01 6 0.2581 0.702 0.00 0.00 0.00 0.12 0.02 0.86
#> TCGA.EJ.7783.01 3 0.5992 0.562 0.02 0.14 0.48 0.00 0.36 0.00
#> TCGA.EJ.5502.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.EJ.7785.01 1 0.1092 0.957 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.4L.AA1F.01 4 0.3869 0.205 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.EJ.5516.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.KK.A7B0.01 4 0.2260 0.800 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.KK.A8I4.01 3 0.5481 0.576 0.00 0.14 0.52 0.00 0.34 0.00
#> TCGA.EJ.5512.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.2A.A8W3.01 5 0.4002 0.634 0.00 0.00 0.02 0.00 0.66 0.32
#> TCGA.ZG.A9LY.01 5 0.4631 0.660 0.00 0.00 0.06 0.00 0.62 0.32
#> TCGA.EJ.7793.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.8266.01 5 0.4834 0.708 0.00 0.00 0.10 0.00 0.64 0.26
#> TCGA.CH.5792.01 2 0.3851 0.480 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.G9.6347.01 3 0.2094 0.727 0.08 0.00 0.90 0.00 0.00 0.02
#> TCGA.EJ.A46I.01 5 0.3706 0.652 0.00 0.00 0.38 0.00 0.62 0.00
#> TCGA.EJ.5508.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.A7NH.01 3 0.0547 0.716 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.J9.A52C.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.J4.A67R.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5499.01 6 0.0547 0.775 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.CH.5738.01 1 0.1092 0.957 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.G9.7522.01 1 0.1092 0.957 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.HC.A6AP.01 4 0.0000 0.836 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5510.01 6 0.0937 0.771 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.CH.5746.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZG.A8QZ.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.TK.A8OK.01 2 0.2260 0.939 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.X4.A8KQ.01 3 0.0547 0.716 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.HC.7750.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.YL.A9WY.01 2 0.2260 0.939 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.VP.A87E.01 1 0.2558 0.936 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.V1.A9ZR.01 2 0.2260 0.939 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.EJ.7792.01 3 0.2094 0.727 0.08 0.00 0.90 0.00 0.00 0.02
#> TCGA.ZG.A9L2.01 3 0.0547 0.716 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EJ.5505.01 3 0.5337 0.463 0.32 0.02 0.60 0.00 0.04 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.YL.A8SB.01 3 0.0504 0.9222 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.EJ.7797.01 1 0.2163 0.8942 0.88 0.10 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZG.A8QW.01 5 0.1718 0.9140 0.00 0.00 0.04 0.00 0.92 0.00 0.04
#> TCGA.YL.A8HK.01 6 0.0863 0.8305 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.EJ.5501.01 3 0.0504 0.9270 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EJ.7330.01 4 0.1886 0.7887 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.G9.6351.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.KK.A8IM.01 7 0.2708 0.8093 0.00 0.00 0.22 0.00 0.00 0.00 0.78
#> TCGA.G9.6348.01 3 0.0504 0.9222 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.J4.A67Q.01 3 0.1006 0.9256 0.00 0.02 0.96 0.00 0.02 0.00 0.00
#> TCGA.2A.A8VL.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.V1.A9ZK.01 4 0.0000 0.8404 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7737.01 4 0.1671 0.8020 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.G9.6384.01 1 0.2163 0.8942 0.88 0.10 0.00 0.00 0.00 0.00 0.02
#> TCGA.V1.A9ZG.01 6 0.1718 0.8152 0.00 0.00 0.00 0.04 0.00 0.92 0.04
#> TCGA.ZG.A9LN.01 5 0.0863 0.9229 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.EJ.7794.01 4 0.0000 0.8404 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.YL.A9WJ.01 4 0.0000 0.8404 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A9Z8.01 3 0.0504 0.9270 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.YL.A8SK.01 5 0.0000 0.9326 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J4.A67M.01 5 0.0000 0.9326 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.6499.01 4 0.0000 0.8404 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67T.01 1 0.1860 0.8756 0.92 0.00 0.02 0.00 0.00 0.04 0.02
#> TCGA.KK.A6E3.01 5 0.0000 0.9326 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G9.6336.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.V1.A8MJ.01 7 0.4993 0.6517 0.12 0.00 0.24 0.00 0.00 0.02 0.62
#> TCGA.VP.A87C.01 3 0.1006 0.9256 0.00 0.02 0.96 0.00 0.02 0.00 0.00
#> TCGA.EJ.5497.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.XK.AAJR.01 2 0.2376 0.9876 0.00 0.86 0.00 0.12 0.00 0.00 0.02
#> TCGA.G9.6363.11 7 0.4640 0.4965 0.00 0.00 0.00 0.00 0.18 0.18 0.64
#> TCGA.V1.A9OY.01 3 0.4260 0.6327 0.14 0.00 0.74 0.00 0.00 0.04 0.08
#> TCGA.ZG.A9L4.01 5 0.3745 0.5716 0.00 0.00 0.00 0.00 0.70 0.26 0.04
#> TCGA.HC.7747.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.ZG.A9LS.01 5 0.0504 0.9281 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.V1.A9OH.01 2 0.1886 0.9938 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.VP.A878.01 7 0.3052 0.6138 0.00 0.00 0.00 0.00 0.20 0.02 0.78
#> TCGA.HC.7745.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.G9.6379.01 5 0.1671 0.8782 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CH.5762.01 5 0.0863 0.9239 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EJ.5527.01 7 0.2708 0.8093 0.00 0.00 0.22 0.00 0.00 0.00 0.78
#> TCGA.G9.6356.01 1 0.2016 0.8629 0.90 0.00 0.00 0.00 0.00 0.04 0.06
#> TCGA.G9.6333.01 4 0.0000 0.8404 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5495.01 6 0.3388 0.6274 0.00 0.00 0.00 0.00 0.20 0.76 0.04
#> TCGA.V1.A8WN.01 1 0.2163 0.8942 0.88 0.10 0.00 0.00 0.00 0.00 0.02
#> TCGA.HC.A6AS.01 5 0.1166 0.9130 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.EJ.7328.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.YL.A8SI.01 4 0.4923 0.0688 0.00 0.00 0.02 0.50 0.00 0.42 0.06
#> TCGA.J4.A67O.01 1 0.1363 0.8819 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.XK.AAIV.01 4 0.3494 0.7310 0.00 0.00 0.02 0.80 0.00 0.12 0.06
#> TCGA.KK.A8IB.01 2 0.1886 0.9938 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.XK.AAIR.01 6 0.2509 0.8021 0.00 0.00 0.02 0.04 0.00 0.88 0.06
#> TCGA.EJ.7783.01 7 0.2572 0.8175 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.EJ.5502.01 1 0.1860 0.8756 0.92 0.00 0.02 0.00 0.00 0.04 0.02
#> TCGA.EJ.7785.01 1 0.1363 0.8819 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.4L.AA1F.01 6 0.4869 0.1664 0.00 0.00 0.02 0.38 0.00 0.54 0.06
#> TCGA.EJ.5516.01 1 0.1860 0.8756 0.92 0.00 0.02 0.00 0.00 0.04 0.02
#> TCGA.KK.A7B0.01 4 0.1886 0.7887 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.KK.A8I4.01 7 0.2572 0.8175 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.EJ.5512.01 1 0.1860 0.8756 0.92 0.00 0.02 0.00 0.00 0.04 0.02
#> TCGA.2A.A8W3.01 5 0.0504 0.9277 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZG.A9LY.01 5 0.0504 0.9281 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.7793.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.HC.8266.01 5 0.0863 0.9239 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CH.5792.01 4 0.3496 -0.0296 0.00 0.42 0.00 0.58 0.00 0.00 0.00
#> TCGA.G9.6347.01 3 0.1006 0.9214 0.02 0.02 0.96 0.00 0.00 0.00 0.00
#> TCGA.EJ.A46I.01 5 0.1718 0.9140 0.00 0.00 0.04 0.00 0.92 0.00 0.04
#> TCGA.EJ.5508.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.EJ.A7NH.01 3 0.0504 0.9270 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.J9.A52C.01 1 0.0863 0.8929 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 1 0.2213 0.8645 0.90 0.00 0.02 0.00 0.00 0.04 0.04
#> TCGA.J4.A67R.01 1 0.2163 0.8942 0.88 0.10 0.00 0.00 0.00 0.00 0.02
#> TCGA.EJ.5499.01 6 0.0863 0.8305 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.CH.5738.01 1 0.1363 0.8819 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.G9.7522.01 1 0.1363 0.8819 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.HC.A6AP.01 4 0.0000 0.8404 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5510.01 6 0.0863 0.8305 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.CH.5746.01 1 0.2512 0.8913 0.86 0.10 0.00 0.00 0.00 0.00 0.04
#> TCGA.ZG.A8QZ.01 1 0.2769 0.8323 0.86 0.00 0.02 0.00 0.00 0.04 0.08
#> TCGA.TK.A8OK.01 2 0.1886 0.9938 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.X4.A8KQ.01 3 0.0863 0.9093 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.HC.7750.01 1 0.1860 0.8756 0.92 0.00 0.02 0.00 0.00 0.04 0.02
#> TCGA.YL.A9WY.01 2 0.1886 0.9938 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.VP.A87E.01 1 0.2355 0.8655 0.90 0.02 0.02 0.00 0.00 0.04 0.02
#> TCGA.V1.A9ZR.01 2 0.2376 0.9876 0.00 0.86 0.00 0.12 0.00 0.00 0.02
#> TCGA.EJ.7792.01 3 0.1006 0.9214 0.02 0.02 0.96 0.00 0.00 0.00 0.00
#> TCGA.ZG.A9L2.01 3 0.1363 0.9084 0.00 0.02 0.94 0.00 0.04 0.00 0.00
#> TCGA.EJ.5505.01 3 0.3000 0.7636 0.10 0.00 0.84 0.00 0.00 0.04 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.YL.A8SB.01 3 0.1557 0.8012 0.00 0.00 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.EJ.7797.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.ZG.A8QW.01 5 0.2071 0.8919 0.02 0.00 0.04 0.00 0.90 0.00 0.04 0.00
#> TCGA.YL.A8HK.01 6 0.0471 0.7675 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.EJ.5501.01 3 0.0471 0.7983 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EJ.7330.01 4 0.1741 0.8386 0.04 0.00 0.00 0.92 0.00 0.02 0.02 0.00
#> TCGA.G9.6351.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.KK.A8IM.01 7 0.2406 0.6972 0.00 0.00 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.G9.6348.01 3 0.1275 0.8059 0.00 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.J4.A67Q.01 3 0.3319 0.7959 0.08 0.02 0.82 0.00 0.00 0.00 0.02 0.06
#> TCGA.2A.A8VL.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.V1.A9ZK.01 4 0.0471 0.8600 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HC.7737.01 4 0.0471 0.8572 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.G9.6384.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.V1.A9ZG.01 6 0.3299 0.7211 0.18 0.00 0.00 0.00 0.00 0.76 0.06 0.00
#> TCGA.ZG.A9LN.01 5 0.0471 0.9074 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.EJ.7794.01 4 0.0000 0.8656 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A9WJ.01 4 0.0000 0.8656 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9Z8.01 3 0.0471 0.7994 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.YL.A8SK.01 5 0.0000 0.9098 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67M.01 5 0.0000 0.9098 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6499.01 4 0.0000 0.8656 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67T.01 8 0.0471 0.7024 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.KK.A6E3.01 5 0.0000 0.9098 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6336.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.V1.A8MJ.01 7 0.5698 0.2295 0.04 0.00 0.20 0.00 0.00 0.00 0.40 0.36
#> TCGA.VP.A87C.01 3 0.2265 0.7945 0.08 0.02 0.88 0.00 0.02 0.00 0.00 0.00
#> TCGA.EJ.5497.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.XK.AAJR.01 2 0.0941 0.9806 0.02 0.96 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.G9.6363.11 7 0.5534 0.1425 0.02 0.00 0.02 0.00 0.14 0.34 0.48 0.00
#> TCGA.V1.A9OY.01 3 0.5827 0.0823 0.06 0.00 0.40 0.00 0.00 0.00 0.18 0.36
#> TCGA.ZG.A9L4.01 5 0.5242 0.2183 0.04 0.00 0.02 0.00 0.50 0.38 0.06 0.00
#> TCGA.HC.7747.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.ZG.A9LS.01 5 0.0941 0.8994 0.02 0.00 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.V1.A9OH.01 2 0.0471 0.9857 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VP.A878.01 7 0.5241 0.4730 0.12 0.00 0.04 0.00 0.10 0.08 0.66 0.00
#> TCGA.HC.7745.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.G9.6379.01 5 0.1341 0.8751 0.00 0.00 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.CH.5762.01 5 0.1557 0.8942 0.02 0.00 0.00 0.00 0.92 0.00 0.06 0.00
#> TCGA.EJ.5527.01 7 0.2267 0.7151 0.00 0.00 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.G9.6356.01 8 0.1341 0.6676 0.00 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.G9.6333.01 4 0.0000 0.8656 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5495.01 6 0.3262 0.6453 0.04 0.00 0.02 0.00 0.10 0.82 0.02 0.00
#> TCGA.V1.A8WN.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.HC.A6AS.01 5 0.0808 0.8998 0.00 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.EJ.7328.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.YL.A8SI.01 4 0.5264 0.1504 0.18 0.00 0.00 0.50 0.00 0.30 0.02 0.00
#> TCGA.J4.A67O.01 8 0.0000 0.7123 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.XK.AAIV.01 4 0.3970 0.6313 0.18 0.00 0.00 0.72 0.00 0.08 0.02 0.00
#> TCGA.KK.A8IB.01 2 0.0471 0.9857 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.XK.AAIR.01 6 0.2719 0.7298 0.18 0.00 0.00 0.00 0.00 0.80 0.02 0.00
#> TCGA.EJ.7783.01 7 0.2267 0.7151 0.00 0.00 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.EJ.5502.01 8 0.0941 0.6913 0.02 0.00 0.00 0.00 0.00 0.00 0.02 0.96
#> TCGA.EJ.7785.01 8 0.0471 0.7194 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.4L.AA1F.01 6 0.5577 0.1917 0.26 0.00 0.00 0.32 0.00 0.40 0.02 0.00
#> TCGA.EJ.5516.01 8 0.0941 0.6913 0.02 0.00 0.00 0.00 0.00 0.00 0.02 0.96
#> TCGA.KK.A7B0.01 4 0.1741 0.8386 0.04 0.00 0.00 0.92 0.00 0.02 0.02 0.00
#> TCGA.KK.A8I4.01 7 0.2406 0.7061 0.00 0.00 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.EJ.5512.01 8 0.0471 0.7024 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.2A.A8W3.01 5 0.2071 0.8874 0.04 0.00 0.02 0.00 0.90 0.00 0.04 0.00
#> TCGA.ZG.A9LY.01 5 0.1408 0.8906 0.02 0.00 0.02 0.00 0.94 0.00 0.02 0.00
#> TCGA.EJ.7793.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.HC.8266.01 5 0.1557 0.8942 0.02 0.00 0.00 0.00 0.92 0.00 0.06 0.00
#> TCGA.CH.5792.01 4 0.3618 0.2765 0.00 0.38 0.00 0.60 0.00 0.00 0.02 0.00
#> TCGA.G9.6347.01 3 0.3319 0.7959 0.08 0.02 0.82 0.00 0.00 0.00 0.02 0.06
#> TCGA.EJ.A46I.01 5 0.2348 0.8841 0.02 0.00 0.04 0.00 0.88 0.00 0.06 0.00
#> TCGA.EJ.5508.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.EJ.A7NH.01 3 0.0471 0.7994 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.J9.A52C.01 8 0.3015 0.7626 0.32 0.00 0.00 0.00 0.00 0.00 0.00 0.68
#> TCGA.FC.7708.01 8 0.0808 0.6901 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.J4.A67R.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.EJ.5499.01 6 0.1275 0.7716 0.02 0.00 0.00 0.00 0.00 0.94 0.04 0.00
#> TCGA.CH.5738.01 8 0.0471 0.7194 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.G9.7522.01 8 0.0471 0.7194 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.HC.A6AP.01 4 0.0000 0.8656 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5510.01 6 0.0941 0.7593 0.00 0.00 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.CH.5746.01 8 0.3237 0.7709 0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.ZG.A8QZ.01 8 0.1341 0.6525 0.00 0.00 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.TK.A8OK.01 2 0.0941 0.9784 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.X4.A8KQ.01 3 0.0941 0.7929 0.02 0.00 0.96 0.00 0.02 0.00 0.00 0.00
#> TCGA.HC.7750.01 8 0.0941 0.6913 0.02 0.00 0.00 0.00 0.00 0.00 0.02 0.96
#> TCGA.YL.A9WY.01 2 0.0471 0.9857 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VP.A87E.01 8 0.1804 0.6332 0.08 0.00 0.00 0.00 0.00 0.00 0.02 0.90
#> TCGA.V1.A9ZR.01 2 0.1557 0.9601 0.06 0.92 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EJ.7792.01 3 0.3319 0.7959 0.08 0.02 0.82 0.00 0.00 0.00 0.02 0.06
#> TCGA.ZG.A9L2.01 3 0.2265 0.7945 0.08 0.02 0.88 0.00 0.02 0.00 0.00 0.00
#> TCGA.EJ.5505.01 3 0.3618 0.3694 0.00 0.00 0.60 0.00 0.00 0.00 0.02 0.38
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node05. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["051"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 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 0.976 0.990 0.4903 0.506 0.506
#> 3 3 1.000 0.984 0.993 0.1669 0.920 0.843
#> 4 4 0.696 0.810 0.897 0.2410 0.811 0.580
#> 5 5 0.634 0.645 0.828 0.0633 0.983 0.938
#> 6 6 0.644 0.502 0.765 0.0453 0.885 0.594
#> 7 7 0.668 0.398 0.720 0.0175 0.925 0.684
#> 8 8 0.657 0.427 0.680 0.0176 0.912 0.645
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.YL.A8SB.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.7797.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.5501.01 1 0.000 0.998 1.00 0.00
#> TCGA.G9.6351.01 1 0.000 0.998 1.00 0.00
#> TCGA.KK.A8IM.01 1 0.000 0.998 1.00 0.00
#> TCGA.G9.6348.01 2 0.000 0.975 0.00 1.00
#> TCGA.J4.A67Q.01 1 0.000 0.998 1.00 0.00
#> TCGA.2A.A8VL.01 1 0.000 0.998 1.00 0.00
#> TCGA.G9.6384.01 1 0.000 0.998 1.00 0.00
#> TCGA.V1.A9Z8.01 2 0.000 0.975 0.00 1.00
#> TCGA.J4.A67T.01 1 0.141 0.979 0.98 0.02
#> TCGA.G9.6336.01 2 0.000 0.975 0.00 1.00
#> TCGA.V1.A8MJ.01 1 0.000 0.998 1.00 0.00
#> TCGA.VP.A87C.01 2 0.000 0.975 0.00 1.00
#> TCGA.EJ.5497.01 1 0.000 0.998 1.00 0.00
#> TCGA.V1.A9OY.01 1 0.000 0.998 1.00 0.00
#> TCGA.HC.7747.01 1 0.000 0.998 1.00 0.00
#> TCGA.HC.7745.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.5527.01 2 0.000 0.975 0.00 1.00
#> TCGA.G9.6356.01 2 0.904 0.533 0.32 0.68
#> TCGA.V1.A8WN.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.7328.01 2 0.000 0.975 0.00 1.00
#> TCGA.J4.A67O.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.7783.01 2 0.000 0.975 0.00 1.00
#> TCGA.EJ.5502.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.7785.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.5516.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.5512.01 1 0.000 0.998 1.00 0.00
#> TCGA.EJ.7793.01 1 0.000 0.998 1.00 0.00
#> TCGA.G9.6347.01 2 0.000 0.975 0.00 1.00
#> TCGA.EJ.5508.01 2 0.000 0.975 0.00 1.00
#> TCGA.J9.A52C.01 2 0.000 0.975 0.00 1.00
#> TCGA.FC.7708.01 2 0.000 0.975 0.00 1.00
#> TCGA.J4.A67R.01 2 0.000 0.975 0.00 1.00
#> TCGA.CH.5738.01 1 0.000 0.998 1.00 0.00
#> TCGA.G9.7522.01 1 0.000 0.998 1.00 0.00
#> TCGA.CH.5746.01 1 0.000 0.998 1.00 0.00
#> TCGA.ZG.A8QZ.01 2 0.000 0.975 0.00 1.00
#> TCGA.HC.7750.01 2 0.402 0.900 0.08 0.92
#> TCGA.VP.A87E.01 2 0.000 0.975 0.00 1.00
#> TCGA.EJ.7792.01 1 0.141 0.979 0.98 0.02
#> TCGA.EJ.5505.01 2 0.000 0.975 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.YL.A8SB.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.7797.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.5501.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.G9.6351.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.KK.A8IM.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.G9.6348.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.J4.A67Q.01 1 0.4555 0.754 0.80 0.00 0.2
#> TCGA.2A.A8VL.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.G9.6384.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.V1.A9Z8.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.J4.A67T.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.G9.6336.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.V1.A8MJ.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.VP.A87C.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.EJ.5497.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.V1.A9OY.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.HC.7747.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.HC.7745.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.5527.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.G9.6356.01 2 0.0892 0.971 0.02 0.98 0.0
#> TCGA.V1.A8WN.01 1 0.2537 0.897 0.92 0.08 0.0
#> TCGA.EJ.7328.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.J4.A67O.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.7783.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.EJ.5502.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.7785.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.5516.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.5512.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.EJ.7793.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.G9.6347.01 3 0.0000 1.000 0.00 0.00 1.0
#> TCGA.EJ.5508.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.J9.A52C.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.FC.7708.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.J4.A67R.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.CH.5738.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.G9.7522.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.CH.5746.01 1 0.0000 0.987 1.00 0.00 0.0
#> TCGA.ZG.A8QZ.01 2 0.0000 0.998 0.00 1.00 0.0
#> TCGA.HC.7750.01 3 0.0000 1.000 0.00 0.00 1.0
#> TCGA.VP.A87E.01 3 0.0000 1.000 0.00 0.00 1.0
#> TCGA.EJ.7792.01 3 0.0000 1.000 0.00 0.00 1.0
#> TCGA.EJ.5505.01 2 0.0000 0.998 0.00 1.00 0.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.YL.A8SB.01 1 0.4790 0.358 0.62 0.00 0.00 0.38
#> TCGA.EJ.7797.01 4 0.0707 0.735 0.02 0.00 0.00 0.98
#> TCGA.EJ.5501.01 4 0.4713 0.558 0.36 0.00 0.00 0.64
#> TCGA.G9.6351.01 1 0.0707 0.837 0.98 0.00 0.00 0.02
#> TCGA.KK.A8IM.01 1 0.2921 0.798 0.86 0.00 0.00 0.14
#> TCGA.G9.6348.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.J4.A67Q.01 1 0.7135 0.301 0.56 0.00 0.20 0.24
#> TCGA.2A.A8VL.01 4 0.4907 0.448 0.42 0.00 0.00 0.58
#> TCGA.G9.6384.01 4 0.4277 0.665 0.28 0.00 0.00 0.72
#> TCGA.V1.A9Z8.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.J4.A67T.01 1 0.0707 0.835 0.98 0.00 0.00 0.02
#> TCGA.G9.6336.01 2 0.2345 0.875 0.10 0.90 0.00 0.00
#> TCGA.V1.A8MJ.01 1 0.3198 0.795 0.88 0.00 0.08 0.04
#> TCGA.VP.A87C.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.EJ.5497.01 1 0.1211 0.837 0.96 0.00 0.00 0.04
#> TCGA.V1.A9OY.01 1 0.3400 0.745 0.82 0.00 0.00 0.18
#> TCGA.HC.7747.01 1 0.1637 0.834 0.94 0.00 0.00 0.06
#> TCGA.HC.7745.01 1 0.2345 0.812 0.90 0.00 0.00 0.10
#> TCGA.EJ.5527.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.3801 0.584 0.78 0.22 0.00 0.00
#> TCGA.V1.A8WN.01 1 0.1411 0.834 0.96 0.02 0.00 0.02
#> TCGA.EJ.7328.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.J4.A67O.01 1 0.2921 0.804 0.86 0.00 0.00 0.14
#> TCGA.EJ.7783.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.EJ.5502.01 1 0.1411 0.829 0.96 0.00 0.02 0.02
#> TCGA.EJ.7785.01 1 0.1211 0.838 0.96 0.00 0.00 0.04
#> TCGA.EJ.5516.01 1 0.1637 0.830 0.94 0.00 0.00 0.06
#> TCGA.EJ.5512.01 4 0.0707 0.735 0.02 0.00 0.00 0.98
#> TCGA.EJ.7793.01 4 0.4277 0.730 0.28 0.00 0.00 0.72
#> TCGA.G9.6347.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.EJ.5508.01 2 0.4134 0.667 0.26 0.74 0.00 0.00
#> TCGA.J9.A52C.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.FC.7708.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.J4.A67R.01 2 0.1211 0.932 0.04 0.96 0.00 0.00
#> TCGA.CH.5738.01 4 0.3801 0.737 0.22 0.00 0.00 0.78
#> TCGA.G9.7522.01 4 0.4134 0.743 0.26 0.00 0.00 0.74
#> TCGA.CH.5746.01 4 0.0707 0.735 0.02 0.00 0.00 0.98
#> TCGA.ZG.A8QZ.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.HC.7750.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.VP.A87E.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.EJ.7792.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.EJ.5505.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.YL.A8SB.01 1 0.6794 -0.0287 0.38 0.00 0.00 0.32 0.30
#> TCGA.EJ.7797.01 4 0.0609 0.6261 0.00 0.00 0.00 0.98 0.02
#> TCGA.EJ.5501.01 4 0.5892 0.4108 0.22 0.00 0.00 0.60 0.18
#> TCGA.G9.6351.01 1 0.1648 0.6722 0.94 0.00 0.00 0.02 0.04
#> TCGA.KK.A8IM.01 1 0.5414 0.5552 0.66 0.00 0.00 0.14 0.20
#> TCGA.G9.6348.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67Q.01 5 0.5969 0.0000 0.12 0.00 0.14 0.06 0.68
#> TCGA.2A.A8VL.01 4 0.6674 0.1623 0.28 0.00 0.00 0.44 0.28
#> TCGA.G9.6384.01 4 0.4132 0.5221 0.26 0.00 0.00 0.72 0.02
#> TCGA.V1.A9Z8.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67T.01 1 0.3690 0.6129 0.78 0.00 0.00 0.02 0.20
#> TCGA.G9.6336.01 2 0.3684 0.6390 0.28 0.72 0.00 0.00 0.00
#> TCGA.V1.A8MJ.01 1 0.5525 0.5207 0.70 0.00 0.08 0.04 0.18
#> TCGA.VP.A87C.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5497.01 1 0.1216 0.6706 0.96 0.00 0.00 0.02 0.02
#> TCGA.V1.A9OY.01 1 0.5597 0.4958 0.64 0.00 0.00 0.20 0.16
#> TCGA.HC.7747.01 1 0.2077 0.6754 0.92 0.00 0.00 0.04 0.04
#> TCGA.HC.7745.01 1 0.5263 0.5819 0.66 0.00 0.00 0.10 0.24
#> TCGA.EJ.5527.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.3274 0.4147 0.78 0.22 0.00 0.00 0.00
#> TCGA.V1.A8WN.01 1 0.1216 0.6660 0.96 0.02 0.00 0.00 0.02
#> TCGA.EJ.7328.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67O.01 1 0.5680 0.5019 0.62 0.00 0.00 0.14 0.24
#> TCGA.EJ.7783.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.5502.01 1 0.4106 0.6076 0.80 0.00 0.04 0.02 0.14
#> TCGA.EJ.7785.01 1 0.4075 0.6399 0.78 0.00 0.00 0.06 0.16
#> TCGA.EJ.5516.01 1 0.4872 0.5827 0.72 0.00 0.00 0.12 0.16
#> TCGA.EJ.5512.01 4 0.0609 0.6261 0.00 0.00 0.00 0.98 0.02
#> TCGA.EJ.7793.01 4 0.5680 0.4059 0.14 0.00 0.00 0.62 0.24
#> TCGA.G9.6347.01 3 0.0609 0.9476 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.5508.01 2 0.4287 0.2973 0.46 0.54 0.00 0.00 0.00
#> TCGA.J9.A52C.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.J4.A67R.01 2 0.3274 0.7141 0.22 0.78 0.00 0.00 0.00
#> TCGA.CH.5738.01 4 0.4216 0.5856 0.12 0.00 0.00 0.78 0.10
#> TCGA.G9.7522.01 4 0.5083 0.5458 0.14 0.00 0.00 0.70 0.16
#> TCGA.CH.5746.01 4 0.0000 0.6291 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZG.A8QZ.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
#> TCGA.HC.7750.01 3 0.0609 0.9416 0.00 0.00 0.98 0.00 0.02
#> TCGA.VP.A87E.01 3 0.0609 0.9476 0.00 0.00 0.98 0.00 0.02
#> TCGA.EJ.7792.01 3 0.2020 0.8811 0.00 0.00 0.90 0.00 0.10
#> TCGA.EJ.5505.01 2 0.0000 0.9052 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.YL.A8SB.01 5 0.7484 0.1853 0.28 0.00 0.00 0.14 0.34 0.24
#> TCGA.EJ.7797.01 4 0.0000 0.5873 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EJ.5501.01 4 0.7452 -0.0767 0.26 0.00 0.00 0.38 0.18 0.18
#> TCGA.G9.6351.01 1 0.2941 0.3891 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.KK.A8IM.01 1 0.6015 -0.0346 0.52 0.00 0.00 0.08 0.06 0.34
#> TCGA.G9.6348.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67Q.01 5 0.5111 0.3398 0.02 0.00 0.00 0.10 0.66 0.22
#> TCGA.2A.A8VL.01 6 0.7527 0.0556 0.18 0.00 0.00 0.26 0.20 0.36
#> TCGA.G9.6384.01 4 0.5244 0.2185 0.36 0.00 0.00 0.56 0.06 0.02
#> TCGA.V1.A9Z8.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67T.01 6 0.5285 0.2161 0.42 0.00 0.00 0.00 0.10 0.48
#> TCGA.G9.6336.01 2 0.3647 0.4933 0.36 0.64 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MJ.01 6 0.4731 0.2590 0.40 0.00 0.02 0.02 0.00 0.56
#> TCGA.VP.A87C.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5497.01 1 0.1814 0.5171 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.V1.A9OY.01 1 0.5362 0.3147 0.68 0.00 0.00 0.14 0.12 0.06
#> TCGA.HC.7747.01 1 0.0547 0.5460 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HC.7745.01 1 0.5227 0.2972 0.64 0.00 0.00 0.02 0.24 0.10
#> TCGA.EJ.5527.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.2581 0.4737 0.86 0.12 0.00 0.00 0.00 0.02
#> TCGA.V1.A8WN.01 1 0.1092 0.5438 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.EJ.7328.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67O.01 6 0.5544 0.1728 0.40 0.00 0.00 0.02 0.08 0.50
#> TCGA.EJ.7783.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5502.01 6 0.3797 0.2809 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.EJ.7785.01 1 0.3321 0.4818 0.82 0.00 0.00 0.00 0.10 0.08
#> TCGA.EJ.5516.01 1 0.4328 -0.1989 0.52 0.00 0.00 0.02 0.00 0.46
#> TCGA.EJ.5512.01 4 0.2403 0.5708 0.02 0.00 0.00 0.90 0.04 0.04
#> TCGA.EJ.7793.01 6 0.5734 -0.1816 0.02 0.00 0.00 0.40 0.10 0.48
#> TCGA.G9.6347.01 3 0.1480 0.8283 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.EJ.5508.01 1 0.3578 0.2329 0.66 0.34 0.00 0.00 0.00 0.00
#> TCGA.J9.A52C.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67R.01 2 0.3309 0.6441 0.28 0.72 0.00 0.00 0.00 0.00
#> TCGA.CH.5738.01 4 0.5637 0.4250 0.10 0.00 0.00 0.66 0.10 0.14
#> TCGA.G9.7522.01 4 0.4765 0.3942 0.02 0.00 0.00 0.64 0.04 0.30
#> TCGA.CH.5746.01 4 0.0937 0.5894 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.ZG.A8QZ.01 2 0.0000 0.9291 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7750.01 3 0.1807 0.8329 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.VP.A87E.01 3 0.0000 0.8407 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EJ.7792.01 3 0.5490 0.5702 0.00 0.00 0.56 0.00 0.26 0.18
#> TCGA.EJ.5505.01 2 0.0937 0.8995 0.04 0.96 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.YL.A8SB.01 5 0.623 0.0000 0.26 0.00 0.00 0.18 0.50 0.04 0.02
#> TCGA.EJ.7797.01 4 0.101 0.4920 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.EJ.5501.01 4 0.778 -0.3273 0.24 0.00 0.00 0.34 0.16 0.18 0.08
#> TCGA.G9.6351.01 1 0.324 0.4179 0.78 0.00 0.00 0.00 0.04 0.18 0.00
#> TCGA.KK.A8IM.01 1 0.663 -0.0946 0.42 0.00 0.00 0.12 0.26 0.20 0.00
#> TCGA.G9.6348.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67Q.01 7 0.604 0.0000 0.00 0.00 0.04 0.02 0.24 0.16 0.54
#> TCGA.2A.A8VL.01 6 0.699 -0.1136 0.10 0.00 0.00 0.20 0.30 0.38 0.02
#> TCGA.G9.6384.01 4 0.659 -0.2178 0.22 0.00 0.00 0.44 0.22 0.12 0.00
#> TCGA.V1.A9Z8.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67T.01 1 0.387 0.2048 0.60 0.00 0.00 0.00 0.02 0.38 0.00
#> TCGA.G9.6336.01 1 0.346 0.1534 0.60 0.40 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MJ.01 6 0.715 0.0261 0.38 0.00 0.10 0.04 0.04 0.38 0.06
#> TCGA.VP.A87C.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5497.01 1 0.226 0.4402 0.84 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.V1.A9OY.01 1 0.601 -0.4910 0.42 0.00 0.00 0.18 0.36 0.04 0.00
#> TCGA.HC.7747.01 1 0.242 0.3998 0.88 0.00 0.00 0.02 0.08 0.02 0.00
#> TCGA.HC.7745.01 1 0.591 0.2015 0.56 0.00 0.00 0.02 0.24 0.14 0.04
#> TCGA.EJ.5527.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.136 0.4651 0.94 0.04 0.00 0.00 0.00 0.02 0.00
#> TCGA.V1.A8WN.01 1 0.151 0.4632 0.94 0.02 0.00 0.00 0.02 0.02 0.00
#> TCGA.EJ.7328.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67O.01 6 0.587 0.0806 0.34 0.00 0.00 0.00 0.12 0.48 0.06
#> TCGA.EJ.7783.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5502.01 1 0.483 0.0479 0.52 0.00 0.02 0.00 0.02 0.42 0.02
#> TCGA.EJ.7785.01 1 0.438 0.2538 0.70 0.00 0.00 0.02 0.20 0.08 0.00
#> TCGA.EJ.5516.01 1 0.498 -0.0124 0.50 0.00 0.00 0.04 0.04 0.42 0.00
#> TCGA.EJ.5512.01 4 0.393 0.4208 0.00 0.00 0.00 0.76 0.14 0.02 0.08
#> TCGA.EJ.7793.01 4 0.623 0.1232 0.06 0.00 0.00 0.44 0.20 0.30 0.00
#> TCGA.G9.6347.01 3 0.166 0.7424 0.00 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.EJ.5508.01 1 0.275 0.3767 0.82 0.16 0.00 0.00 0.00 0.02 0.00
#> TCGA.J9.A52C.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67R.01 2 0.341 0.3625 0.38 0.62 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5738.01 4 0.493 0.1794 0.08 0.00 0.00 0.64 0.24 0.04 0.00
#> TCGA.G9.7522.01 4 0.584 0.3529 0.02 0.00 0.00 0.58 0.10 0.24 0.06
#> TCGA.CH.5746.01 4 0.000 0.4923 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZG.A8QZ.01 2 0.000 0.9465 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7750.01 3 0.257 0.7300 0.00 0.00 0.84 0.00 0.00 0.02 0.14
#> TCGA.VP.A87E.01 3 0.000 0.7655 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.7792.01 3 0.464 0.3640 0.00 0.00 0.54 0.00 0.00 0.08 0.38
#> TCGA.EJ.5505.01 2 0.136 0.8958 0.04 0.94 0.00 0.00 0.02 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.YL.A8SB.01 5 0.8201 0.14312 0.24 0.00 0.00 0.16 0.26 0.06 0.14 0.14
#> TCGA.EJ.7797.01 8 0.3198 0.53372 0.00 0.00 0.00 0.00 0.02 0.26 0.00 0.72
#> TCGA.EJ.5501.01 5 0.6805 0.09301 0.12 0.00 0.00 0.00 0.44 0.20 0.06 0.18
#> TCGA.G9.6351.01 1 0.2862 0.52641 0.82 0.00 0.00 0.00 0.08 0.10 0.00 0.00
#> TCGA.KK.A8IM.01 1 0.6413 -0.11888 0.34 0.00 0.00 0.00 0.24 0.34 0.04 0.04
#> TCGA.G9.6348.01 2 0.0471 0.87382 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.J4.A67Q.01 7 0.2350 0.00000 0.04 0.00 0.00 0.00 0.00 0.10 0.86 0.00
#> TCGA.2A.A8VL.01 5 0.6529 0.03968 0.04 0.00 0.00 0.08 0.46 0.30 0.02 0.10
#> TCGA.G9.6384.01 8 0.6726 0.10597 0.24 0.00 0.00 0.04 0.18 0.12 0.00 0.42
#> TCGA.V1.A9Z8.01 2 0.0000 0.88412 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67T.01 1 0.5560 0.39671 0.62 0.02 0.00 0.08 0.04 0.20 0.04 0.00
#> TCGA.G9.6336.01 2 0.3729 0.12909 0.46 0.52 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.V1.A8MJ.01 6 0.7209 0.13030 0.28 0.00 0.04 0.18 0.06 0.38 0.06 0.00
#> TCGA.VP.A87C.01 2 0.1275 0.85131 0.00 0.94 0.00 0.04 0.02 0.00 0.00 0.00
#> TCGA.EJ.5497.01 1 0.2025 0.54266 0.88 0.00 0.00 0.00 0.02 0.10 0.00 0.00
#> TCGA.V1.A9OY.01 1 0.6217 0.14339 0.56 0.00 0.00 0.06 0.20 0.06 0.02 0.10
#> TCGA.HC.7747.01 1 0.2224 0.54878 0.86 0.00 0.00 0.02 0.12 0.00 0.00 0.00
#> TCGA.HC.7745.01 1 0.6886 0.23598 0.50 0.00 0.00 0.12 0.14 0.14 0.08 0.02
#> TCGA.EJ.5527.01 2 0.0000 0.88412 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.2569 0.47677 0.82 0.16 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.V1.A8WN.01 1 0.1804 0.54931 0.90 0.00 0.00 0.02 0.08 0.00 0.00 0.00
#> TCGA.EJ.7328.01 2 0.0000 0.88412 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67O.01 1 0.7358 0.01830 0.40 0.00 0.00 0.16 0.10 0.24 0.04 0.06
#> TCGA.EJ.7783.01 2 0.0000 0.88412 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EJ.5502.01 1 0.5378 0.27438 0.56 0.00 0.02 0.10 0.00 0.28 0.04 0.00
#> TCGA.EJ.7785.01 1 0.2725 0.52705 0.82 0.00 0.00 0.00 0.14 0.04 0.00 0.00
#> TCGA.EJ.5516.01 6 0.4940 -0.01634 0.40 0.00 0.00 0.00 0.10 0.48 0.02 0.00
#> TCGA.EJ.5512.01 8 0.2020 0.36438 0.00 0.00 0.00 0.02 0.06 0.00 0.02 0.90
#> TCGA.EJ.7793.01 6 0.3270 0.17913 0.00 0.00 0.00 0.00 0.02 0.80 0.06 0.12
#> TCGA.G9.6347.01 3 0.0808 0.64633 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.EJ.5508.01 1 0.3746 0.31707 0.64 0.32 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.J9.A52C.01 2 0.0000 0.88412 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FC.7708.01 2 0.0000 0.88412 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J4.A67R.01 2 0.3658 0.30050 0.40 0.58 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CH.5738.01 8 0.6445 0.11486 0.14 0.00 0.00 0.00 0.14 0.26 0.02 0.44
#> TCGA.G9.7522.01 6 0.4478 -0.00464 0.04 0.00 0.00 0.04 0.02 0.68 0.00 0.22
#> TCGA.CH.5746.01 8 0.3594 0.52164 0.00 0.00 0.00 0.00 0.00 0.28 0.04 0.68
#> TCGA.ZG.A8QZ.01 2 0.0000 0.88412 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7750.01 3 0.4862 0.51201 0.00 0.00 0.60 0.16 0.02 0.00 0.22 0.00
#> TCGA.VP.A87E.01 3 0.0941 0.66420 0.00 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.EJ.7792.01 3 0.5123 0.30523 0.00 0.00 0.42 0.36 0.00 0.00 0.22 0.00
#> TCGA.EJ.5505.01 2 0.1341 0.83598 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node051. Child nodes: Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node05121-leaf , Node05122-leaf , Node05123-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0512"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 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 0.736 0.929 0.957 0.3875 0.560 0.560
#> 3 3 1.000 0.998 0.994 0.4334 0.835 0.717
#> 4 4 1.000 0.924 0.994 0.0485 0.978 0.950
#> 5 5 1.000 0.919 0.983 0.2452 0.846 0.632
#> 6 6 0.967 0.739 0.949 0.0330 0.989 0.958
#> 7 7 0.824 0.535 0.914 0.0948 0.934 0.739
#> 8 8 0.868 0.643 0.897 0.0616 0.912 0.529
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] 3
There is also optional best \(k\) = 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.G9.6348.01 2 0.881 0.714 0.3 0.7
#> TCGA.V1.A9Z8.01 2 0.000 0.787 0.0 1.0
#> TCGA.G9.6336.01 1 0.000 1.000 1.0 0.0
#> TCGA.VP.A87C.01 2 0.000 0.787 0.0 1.0
#> TCGA.EJ.5527.01 1 0.000 1.000 1.0 0.0
#> TCGA.G9.6356.01 1 0.000 1.000 1.0 0.0
#> TCGA.EJ.7328.01 1 0.000 1.000 1.0 0.0
#> TCGA.EJ.7783.01 1 0.000 1.000 1.0 0.0
#> TCGA.EJ.5508.01 1 0.000 1.000 1.0 0.0
#> TCGA.J9.A52C.01 1 0.000 1.000 1.0 0.0
#> TCGA.FC.7708.01 1 0.000 1.000 1.0 0.0
#> TCGA.J4.A67R.01 1 0.000 1.000 1.0 0.0
#> TCGA.ZG.A8QZ.01 1 0.000 1.000 1.0 0.0
#> TCGA.EJ.5505.01 2 0.881 0.714 0.3 0.7
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.G9.6348.01 2 0.0892 1.000 0.02 0.98 0.00
#> TCGA.V1.A9Z8.01 3 0.0892 0.987 0.00 0.02 0.98
#> TCGA.G9.6336.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VP.A87C.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.EJ.5527.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EJ.7328.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EJ.7783.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EJ.5508.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.J9.A52C.01 2 0.0892 1.000 0.02 0.98 0.00
#> TCGA.FC.7708.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.J4.A67R.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.ZG.A8QZ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EJ.5505.01 2 0.0892 1.000 0.02 0.98 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.G9.6348.01 2 0.000 1.000 0 1.00 0.00 0.00
#> TCGA.V1.A9Z8.01 3 0.121 0.967 0 0.00 0.96 0.04
#> TCGA.G9.6336.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.VP.A87C.01 3 0.000 0.967 0 0.00 1.00 0.00
#> TCGA.EJ.5527.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.EJ.7328.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.EJ.7783.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.EJ.5508.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.J9.A52C.01 4 0.121 0.000 0 0.04 0.00 0.96
#> TCGA.FC.7708.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.J4.A67R.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.ZG.A8QZ.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.EJ.5505.01 2 0.000 1.000 0 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.G9.6348.01 2 0.0609 0.984 0.00 0.98 0.00 0 0.02
#> TCGA.V1.A9Z8.01 3 0.1410 0.950 0.00 0.00 0.94 0 0.06
#> TCGA.G9.6336.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.VP.A87C.01 3 0.0000 0.950 0.00 0.00 1.00 0 0.00
#> TCGA.EJ.5527.01 5 0.1732 1.000 0.08 0.00 0.00 0 0.92
#> TCGA.G9.6356.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.EJ.7328.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.EJ.7783.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.EJ.5508.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.J9.A52C.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00
#> TCGA.FC.7708.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.J4.A67R.01 1 0.0000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.ZG.A8QZ.01 5 0.1732 1.000 0.08 0.00 0.00 0 0.92
#> TCGA.EJ.5505.01 2 0.0000 0.984 0.00 1.00 0.00 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.G9.6348.01 2 0.2454 0.862 0.00 0.84 0.00 0 0.16 0.00
#> TCGA.V1.A9Z8.01 3 0.2631 0.844 0.00 0.00 0.82 0 0.18 0.00
#> TCGA.G9.6336.01 1 0.0547 0.983 0.98 0.00 0.00 0 0.00 0.02
#> TCGA.VP.A87C.01 3 0.0000 0.844 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EJ.5527.01 5 0.3578 0.000 0.00 0.00 0.00 0 0.66 0.34
#> TCGA.G9.6356.01 1 0.0000 0.993 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EJ.7328.01 1 0.0000 0.993 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EJ.7783.01 1 0.0000 0.993 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EJ.5508.01 1 0.0000 0.993 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.J9.A52C.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.FC.7708.01 1 0.0000 0.993 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.J4.A67R.01 1 0.0547 0.983 0.98 0.00 0.00 0 0.00 0.02
#> TCGA.ZG.A8QZ.01 6 0.0000 0.000 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EJ.5505.01 2 0.0000 0.862 0.00 1.00 0.00 0 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.G9.6348.01 2 0.0000 0.916 0.00 1.0 0.00 0 0.00 0.00 0.00
#> TCGA.V1.A9Z8.01 3 0.2422 0.844 0.00 0.0 0.82 0 0.00 0.00 0.18
#> TCGA.G9.6336.01 1 0.3221 0.390 0.68 0.0 0.00 0 0.00 0.00 0.32
#> TCGA.VP.A87C.01 3 0.0000 0.844 0.00 0.0 1.00 0 0.00 0.00 0.00
#> TCGA.EJ.5527.01 5 0.0000 0.000 0.00 0.0 0.00 0 1.00 0.00 0.00
#> TCGA.G9.6356.01 1 0.0000 0.796 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.EJ.7328.01 1 0.0000 0.796 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.EJ.7783.01 1 0.0000 0.796 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.EJ.5508.01 1 0.0000 0.796 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.J9.A52C.01 4 0.0000 0.000 0.00 0.0 0.00 1 0.00 0.00 0.00
#> TCGA.FC.7708.01 7 0.2945 0.000 0.26 0.0 0.00 0 0.00 0.00 0.74
#> TCGA.J4.A67R.01 1 0.3221 0.390 0.68 0.0 0.00 0 0.00 0.00 0.32
#> TCGA.ZG.A8QZ.01 6 0.0504 0.000 0.00 0.0 0.00 0 0.02 0.98 0.00
#> TCGA.EJ.5505.01 2 0.1928 0.916 0.00 0.9 0.00 0 0.00 0.02 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.G9.6348.01 2 0.2224 0.880 0.00 0.86 0.00 0 0 0 0.02 0.12
#> TCGA.V1.A9Z8.01 3 0.4437 0.652 0.00 0.00 0.62 0 0 0 0.16 0.22
#> TCGA.G9.6336.01 8 0.3142 1.000 0.36 0.00 0.00 0 0 0 0.00 0.64
#> TCGA.VP.A87C.01 3 0.0000 0.652 0.00 0.00 1.00 0 0 0 0.00 0.00
#> TCGA.EJ.5527.01 5 0.0000 0.000 0.00 0.00 0.00 0 1 0 0.00 0.00
#> TCGA.G9.6356.01 1 0.0000 0.990 1.00 0.00 0.00 0 0 0 0.00 0.00
#> TCGA.EJ.7328.01 1 0.0000 0.990 1.00 0.00 0.00 0 0 0 0.00 0.00
#> TCGA.EJ.7783.01 1 0.0471 0.969 0.98 0.00 0.00 0 0 0 0.00 0.02
#> TCGA.EJ.5508.01 1 0.0000 0.990 1.00 0.00 0.00 0 0 0 0.00 0.00
#> TCGA.J9.A52C.01 4 0.0000 0.000 0.00 0.00 0.00 1 0 0 0.00 0.00
#> TCGA.FC.7708.01 7 0.2725 0.000 0.04 0.00 0.00 0 0 0 0.82 0.14
#> TCGA.J4.A67R.01 8 0.3142 1.000 0.36 0.00 0.00 0 0 0 0.00 0.64
#> TCGA.ZG.A8QZ.01 6 0.0000 0.000 0.00 0.00 0.00 0 0 1 0.00 0.00
#> TCGA.EJ.5505.01 2 0.0000 0.880 0.00 1.00 0.00 0 0 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node05. Child nodes: Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241-leaf , Node0242-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442-leaf , Node0443-leaf , Node0511-leaf , Node0512 , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["052"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 20 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 0.4795 0.521 0.521
#> 3 3 1.000 1.000 1.000 0.1316 0.937 0.879
#> 4 4 0.747 0.848 0.908 0.1337 1.000 1.000
#> 5 5 0.742 0.748 0.895 0.0864 0.874 0.724
#> 6 6 0.668 0.566 0.853 0.0932 0.868 0.627
#> 7 7 0.695 0.292 0.715 0.0360 0.789 0.375
#> 8 8 0.679 0.367 0.737 0.0423 0.763 0.274
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.EJ.7330.01 1 0 1 1 0
#> TCGA.V1.A9ZK.01 1 0 1 1 0
#> TCGA.HC.7737.01 1 0 1 1 0
#> TCGA.V1.A9ZG.01 2 0 1 0 1
#> TCGA.EJ.7794.01 1 0 1 1 0
#> TCGA.YL.A9WJ.01 1 0 1 1 0
#> TCGA.G9.6499.01 1 0 1 1 0
#> TCGA.XK.AAJR.01 1 0 1 1 0
#> TCGA.V1.A9OH.01 2 0 1 0 1
#> TCGA.G9.6333.01 1 0 1 1 0
#> TCGA.YL.A8SI.01 1 0 1 1 0
#> TCGA.XK.AAIV.01 2 0 1 0 1
#> TCGA.KK.A8IB.01 1 0 1 1 0
#> TCGA.4L.AA1F.01 2 0 1 0 1
#> TCGA.KK.A7B0.01 1 0 1 1 0
#> TCGA.CH.5792.01 1 0 1 1 0
#> TCGA.HC.A6AP.01 1 0 1 1 0
#> TCGA.TK.A8OK.01 2 0 1 0 1
#> TCGA.YL.A9WY.01 2 0 1 0 1
#> TCGA.V1.A9ZR.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EJ.7330.01 1 0 1 1 0 0
#> TCGA.V1.A9ZK.01 1 0 1 1 0 0
#> TCGA.HC.7737.01 1 0 1 1 0 0
#> TCGA.V1.A9ZG.01 2 0 1 0 1 0
#> TCGA.EJ.7794.01 1 0 1 1 0 0
#> TCGA.YL.A9WJ.01 1 0 1 1 0 0
#> TCGA.G9.6499.01 1 0 1 1 0 0
#> TCGA.XK.AAJR.01 1 0 1 1 0 0
#> TCGA.V1.A9OH.01 2 0 1 0 1 0
#> TCGA.G9.6333.01 1 0 1 1 0 0
#> TCGA.YL.A8SI.01 1 0 1 1 0 0
#> TCGA.XK.AAIV.01 3 0 1 0 0 1
#> TCGA.KK.A8IB.01 1 0 1 1 0 0
#> TCGA.4L.AA1F.01 3 0 1 0 0 1
#> TCGA.KK.A7B0.01 1 0 1 1 0 0
#> TCGA.CH.5792.01 1 0 1 1 0 0
#> TCGA.HC.A6AP.01 1 0 1 1 0 0
#> TCGA.TK.A8OK.01 2 0 1 0 1 0
#> TCGA.YL.A9WY.01 3 0 1 0 0 1
#> TCGA.V1.A9ZR.01 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EJ.7330.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.V1.A9ZK.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.HC.7737.01 1 0.265 0.855 0.88 0.12 0.00 0.00
#> TCGA.V1.A9ZG.01 4 0.000 0.984 0.00 0.00 0.00 1.00
#> TCGA.EJ.7794.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.YL.A9WJ.01 1 0.265 0.855 0.88 0.12 0.00 0.00
#> TCGA.G9.6499.01 1 0.499 0.497 0.52 0.48 0.00 0.00
#> TCGA.XK.AAJR.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.V1.A9OH.01 4 0.000 0.984 0.00 0.00 0.00 1.00
#> TCGA.G9.6333.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.YL.A8SI.01 1 0.265 0.855 0.88 0.12 0.00 0.00
#> TCGA.XK.AAIV.01 3 0.000 0.839 0.00 0.00 1.00 0.00
#> TCGA.KK.A8IB.01 1 0.499 0.497 0.52 0.48 0.00 0.00
#> TCGA.4L.AA1F.01 3 0.498 0.657 0.00 0.46 0.54 0.00
#> TCGA.KK.A7B0.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.CH.5792.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.HC.A6AP.01 1 0.000 0.897 1.00 0.00 0.00 0.00
#> TCGA.TK.A8OK.01 4 0.000 0.984 0.00 0.00 0.00 1.00
#> TCGA.YL.A9WY.01 3 0.000 0.839 0.00 0.00 1.00 0.00
#> TCGA.V1.A9ZR.01 4 0.164 0.950 0.00 0.06 0.00 0.94
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EJ.7330.01 1 0.1648 0.806 0.94 0.02 0.00 0.00 0.04
#> TCGA.V1.A9ZK.01 1 0.0000 0.826 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.7737.01 1 0.3684 0.382 0.72 0.00 0.00 0.00 0.28
#> TCGA.V1.A9ZG.01 4 0.0609 0.905 0.00 0.00 0.00 0.98 0.02
#> TCGA.EJ.7794.01 1 0.0609 0.816 0.98 0.00 0.00 0.00 0.02
#> TCGA.YL.A9WJ.01 1 0.3684 0.382 0.72 0.00 0.00 0.00 0.28
#> TCGA.G9.6499.01 5 0.4060 0.918 0.36 0.00 0.00 0.00 0.64
#> TCGA.XK.AAJR.01 1 0.0000 0.826 1.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9OH.01 4 0.1043 0.907 0.00 0.00 0.00 0.96 0.04
#> TCGA.G9.6333.01 1 0.0609 0.821 0.98 0.00 0.00 0.00 0.02
#> TCGA.YL.A8SI.01 1 0.3424 0.479 0.76 0.00 0.00 0.00 0.24
#> TCGA.XK.AAIV.01 3 0.1043 0.925 0.00 0.04 0.96 0.00 0.00
#> TCGA.KK.A8IB.01 5 0.3895 0.923 0.32 0.00 0.00 0.00 0.68
#> TCGA.4L.AA1F.01 2 0.0609 0.000 0.00 0.98 0.02 0.00 0.00
#> TCGA.KK.A7B0.01 1 0.1648 0.806 0.94 0.02 0.00 0.00 0.04
#> TCGA.CH.5792.01 1 0.0000 0.826 1.00 0.00 0.00 0.00 0.00
#> TCGA.HC.A6AP.01 1 0.1648 0.806 0.94 0.02 0.00 0.00 0.04
#> TCGA.TK.A8OK.01 4 0.0000 0.911 0.00 0.00 0.00 1.00 0.00
#> TCGA.YL.A9WY.01 3 0.1043 0.926 0.00 0.00 0.96 0.00 0.04
#> TCGA.V1.A9ZR.01 4 0.3424 0.777 0.00 0.00 0.00 0.76 0.24
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EJ.7330.01 1 0.0000 0.811 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V1.A9ZK.01 1 0.0547 0.808 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HC.7737.01 5 0.3864 0.188 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.V1.A9ZG.01 4 0.0547 0.774 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.EJ.7794.01 1 0.2793 0.684 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.YL.A9WJ.01 5 0.3864 0.188 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.G9.6499.01 5 0.3258 0.440 0.10 0.02 0.00 0.00 0.84 0.04
#> TCGA.XK.AAJR.01 1 0.2260 0.755 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.V1.A9OH.01 4 0.3198 0.705 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.G9.6333.01 1 0.0000 0.811 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YL.A8SI.01 1 0.3869 -0.408 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.XK.AAIV.01 3 0.0547 0.983 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.KK.A8IB.01 5 0.3007 0.411 0.08 0.02 0.00 0.00 0.86 0.04
#> TCGA.4L.AA1F.01 2 0.0547 0.000 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.KK.A7B0.01 1 0.0000 0.811 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CH.5792.01 1 0.2454 0.738 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.HC.A6AP.01 1 0.0000 0.811 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TK.A8OK.01 4 0.1814 0.821 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.YL.A9WY.01 3 0.0000 0.983 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.V1.A9ZR.01 6 0.1267 0.000 0.00 0.00 0.00 0.06 0.00 0.94
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EJ.7330.01 5 0.3546 -0.346 0.46 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.V1.A9ZK.01 1 0.3413 0.530 0.62 0.00 0.00 0.00 0.38 0.00 0.00
#> TCGA.HC.7737.01 1 0.0504 0.508 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.V1.A9ZG.01 4 0.2945 0.585 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.EJ.7794.01 1 0.2832 0.622 0.76 0.00 0.00 0.00 0.24 0.00 0.00
#> TCGA.YL.A9WJ.01 1 0.0504 0.508 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.G9.6499.01 5 0.5452 -0.136 0.30 0.00 0.00 0.00 0.46 0.00 0.24
#> TCGA.XK.AAJR.01 1 0.3221 0.616 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.V1.A9OH.01 4 0.3517 0.471 0.00 0.00 0.00 0.70 0.00 0.28 0.02
#> TCGA.G9.6333.01 1 0.3525 0.419 0.56 0.00 0.00 0.00 0.44 0.00 0.00
#> TCGA.YL.A8SI.01 1 0.1671 0.510 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.XK.AAIV.01 3 0.0504 0.562 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.KK.A8IB.01 5 0.5560 -0.173 0.28 0.00 0.00 0.00 0.42 0.00 0.30
#> TCGA.4L.AA1F.01 2 0.0000 0.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B0.01 5 0.3546 -0.346 0.46 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.CH.5792.01 1 0.3221 0.616 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.HC.A6AP.01 5 0.3546 -0.346 0.46 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.TK.A8OK.01 4 0.0504 0.680 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.YL.A9WY.01 3 0.3943 0.568 0.00 0.00 0.56 0.00 0.00 0.02 0.42
#> TCGA.V1.A9ZR.01 6 0.0504 0.000 0.00 0.00 0.00 0.02 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.EJ.7330.01 5 0.0808 0.7606 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.V1.A9ZK.01 5 0.2267 0.7416 0.18 0.00 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.HC.7737.01 1 0.2938 0.3697 0.70 0.00 0.00 0.00 0.30 0.00 0.00 0.00
#> TCGA.V1.A9ZG.01 8 0.3193 0.0000 0.00 0.00 0.00 0.38 0.00 0.00 0.00 0.62
#> TCGA.EJ.7794.01 1 0.3329 -0.0764 0.52 0.00 0.00 0.00 0.48 0.00 0.00 0.00
#> TCGA.YL.A9WJ.01 1 0.3291 0.3945 0.70 0.00 0.02 0.00 0.28 0.00 0.00 0.00
#> TCGA.G9.6499.01 1 0.6064 0.0324 0.44 0.00 0.26 0.00 0.04 0.02 0.00 0.24
#> TCGA.XK.AAJR.01 5 0.2756 0.6644 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.V1.A9OH.01 4 0.1947 0.7395 0.00 0.00 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.G9.6333.01 5 0.1563 0.7728 0.10 0.00 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.YL.A8SI.01 1 0.3971 0.1008 0.54 0.00 0.00 0.00 0.42 0.00 0.00 0.04
#> TCGA.XK.AAIV.01 3 0.3198 0.0000 0.00 0.02 0.72 0.00 0.00 0.00 0.26 0.00
#> TCGA.KK.A8IB.01 1 0.4757 -0.0329 0.56 0.00 0.20 0.00 0.00 0.00 0.00 0.24
#> TCGA.4L.AA1F.01 2 0.0000 0.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KK.A7B0.01 5 0.1275 0.7405 0.02 0.00 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.CH.5792.01 5 0.2756 0.6569 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.HC.A6AP.01 5 0.0808 0.7606 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.TK.A8OK.01 4 0.0471 0.7129 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.YL.A9WY.01 7 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.V1.A9ZR.01 6 0.0471 0.0000 0.00 0.00 0.00 0.02 0.00 0.98 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6