Date: 2021-07-22 20:16:37 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 375955 rows and 907 columns.
#> Performed in total 154000 partitions.
#> There are 77 groups under the following parameters:
#> - min_samples: 9
#> - 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, 907 cols
#> |-- 01, 128 cols, 4160 signatures
#> | |-- 011, 40 cols, 26140 signatures
#> | | |-- 0111, 17 cols (b)
#> | | |-- 0112, 14 cols (b)
#> | | |-- 0113, 3 cols (b)
#> | | `-- 0114, 6 cols (b)
#> | |-- 012, 38 cols, 6247 signatures
#> | | |-- 0121, 23 cols, 198 signatures (c)
#> | | |-- 0122, 6 cols (b)
#> | | `-- 0123, 9 cols (b)
#> | |-- 013, 31 cols, 10893 signatures
#> | | |-- 0131, 11 cols (b)
#> | | |-- 0132, 10 cols (b)
#> | | |-- 0133, 2 cols (b)
#> | | `-- 0134, 8 cols (b)
#> | `-- 014, 19 cols, 107 signatures (c)
#> |-- 02, 290 cols, 7180 signatures
#> | |-- 021, 73 cols, 6744 signatures
#> | | |-- 0211, 16 cols (b)
#> | | |-- 0212, 17 cols (b)
#> | | |-- 0213, 26 cols, 2922 signatures
#> | | | |-- 02131, 17 cols (b)
#> | | | `-- 02132, 9 cols (b)
#> | | `-- 0214, 14 cols (b)
#> | |-- 022, 44 cols, 2507 signatures
#> | | |-- 0221, 21 cols, 3223 signatures
#> | | | |-- 02211, 5 cols (b)
#> | | | `-- 02212, 16 cols (b)
#> | | |-- 0222, 15 cols (b)
#> | | `-- 0223, 8 cols (b)
#> | |-- 023, 93 cols, 5315 signatures
#> | | |-- 0231, 23 cols, 9072 signatures
#> | | | |-- 02311, 10 cols (b)
#> | | | |-- 02312, 7 cols (b)
#> | | | |-- 02313, 2 cols (b)
#> | | | `-- 02314, 4 cols (b)
#> | | |-- 0232, 16 cols (b)
#> | | |-- 0233, 17 cols (b)
#> | | |-- 0234, 27 cols, 5955 signatures
#> | | | |-- 02341, 10 cols (b)
#> | | | |-- 02342, 4 cols (b)
#> | | | |-- 02343, 4 cols (b)
#> | | | |-- 02344, 2 cols (b)
#> | | | `-- 02345, 7 cols (b)
#> | | `-- 0235, 10 cols (b)
#> | `-- 024, 80 cols, 2667 signatures
#> | |-- 0241, 32 cols, 20 signatures (c)
#> | `-- 0242, 48 cols, 3829 signatures
#> | |-- 02421, 9 cols (b)
#> | |-- 02422, 18 cols, 146 signatures (c)
#> | `-- 02423, 21 cols, 48 signatures (c)
#> |-- 03, 48 cols, 17308 signatures
#> | |-- 031, 8 cols (b)
#> | `-- 032, 40 cols, 842 signatures (c)
#> |-- 04, 83 cols, 23556 signatures
#> | |-- 041, 34 cols, 1325 signatures
#> | | |-- 0411, 20 cols, 241 signatures (c)
#> | | `-- 0412, 14 cols (b)
#> | |-- 042, 31 cols, 5593 signatures
#> | | |-- 0421, 11 cols (b)
#> | | |-- 0422, 15 cols (b)
#> | | `-- 0423, 5 cols (b)
#> | `-- 043, 18 cols, 1393 signatures
#> | |-- 0431, 12 cols (b)
#> | `-- 0432, 6 cols (b)
#> |-- 05, 89 cols, 3363 signatures
#> | |-- 051, 36 cols, 2908 signatures
#> | | |-- 0511, 11 cols (b)
#> | | |-- 0512, 8 cols (b)
#> | | |-- 0513, 15 cols (b)
#> | | `-- 0514, 2 cols (b)
#> | `-- 052, 53 cols, 9538 signatures
#> | |-- 0521, 17 cols (b)
#> | |-- 0522, 13 cols (b)
#> | |-- 0523, 3 cols (b)
#> | |-- 0524, 6 cols (b)
#> | `-- 0525, 14 cols (b)
#> |-- 06, 131 cols, 1256 signatures
#> | |-- 061, 45 cols, 5122 signatures
#> | | |-- 0611, 14 cols (b)
#> | | |-- 0612, 18 cols, 3090 signatures
#> | | | |-- 06121, 5 cols (b)
#> | | | |-- 06122, 9 cols (b)
#> | | | `-- 06123, 4 cols (b)
#> | | `-- 0613, 13 cols (b)
#> | `-- 062, 86 cols, 241 signatures (c)
#> `-- 07, 138 cols, 2814 signatures
#> |-- 071, 59 cols, 3229 signatures
#> | |-- 0711, 29 cols, 1063 signatures
#> | | |-- 07111, 22 cols, 6049 signatures
#> | | | |-- 071111, 4 cols (b)
#> | | | |-- 071112, 7 cols (b)
#> | | | |-- 071113, 2 cols (b)
#> | | | |-- 071114, 3 cols (b)
#> | | | `-- 071115, 6 cols (b)
#> | | `-- 07112, 7 cols (b)
#> | |-- 0712, 16 cols (b)
#> | `-- 0713, 14 cols (b)
#> |-- 072, 46 cols, 1019 signatures
#> | |-- 0721, 31 cols, 5220 signatures
#> | | |-- 07211, 9 cols (b)
#> | | |-- 07212, 11 cols (b)
#> | | |-- 07213, 8 cols (b)
#> | | `-- 07214, 3 cols (b)
#> | `-- 0722, 15 cols (b)
#> `-- 073, 33 cols, 4655 signatures
#> |-- 0731, 10 cols (b)
#> |-- 0732, 14 cols (b)
#> `-- 0733, 9 cols (b)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375955 907
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "0112" "0113" "0114" "012" "0121" "0122"
#> [11] "0123" "013" "0131" "0132" "0133" "0134" "014" "02" "021" "0211"
#> [21] "0212" "0213" "02131" "02132" "0214" "022" "0221" "02211" "02212" "0222"
#> [31] "0223" "023" "0231" "02311" "02312" "02313" "02314" "0232" "0233" "0234"
#> [41] "02341" "02342" "02343" "02344" "02345" "0235" "024" "0241" "0242" "02421"
#> [51] "02422" "02423" "03" "031" "032" "04" "041" "0411" "0412" "042"
#> [61] "0421" "0422" "0423" "043" "0431" "0432" "05" "051" "0511" "0512"
#> [71] "0513" "0514" "052" "0521" "0522" "0523" "0524" "0525" "06" "061"
#> [81] "0611" "0612" "06121" "06122" "06123" "0613" "062" "07" "071" "0711"
#> [91] "07111" "071111" "071112" "071113" "071114" "071115" "07112" "0712" "0713" "072"
#> [101] "0721" "07211" "07212" "07213" "07214" "0722" "073" "0731" "0732" "0733"
all_leaves(res_rh)
#> [1] "0111" "0112" "0113" "0114" "0121" "0122" "0123" "0131" "0132" "0133"
#> [11] "0134" "014" "0211" "0212" "02131" "02132" "0214" "02211" "02212" "0222"
#> [21] "0223" "02311" "02312" "02313" "02314" "0232" "0233" "02341" "02342" "02343"
#> [31] "02344" "02345" "0235" "0241" "02421" "02422" "02423" "031" "032" "0411"
#> [41] "0412" "0421" "0422" "0423" "0431" "0432" "0511" "0512" "0513" "0514"
#> [51] "0521" "0522" "0523" "0524" "0525" "0611" "06121" "06122" "06123" "0613"
#> [61] "062" "071111" "071112" "071113" "071114" "071115" "07112" "0712" "0713" "07211"
#> [71] "07212" "07213" "07214" "0722" "0731" "0732" "0733"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 7 907 54725 1.46e-01 FALSE
#> 2 01 ATC:skmeans 2 4 128 4160 1.11e-02 FALSE
#> 3 011 ATC:kmeans 3 4 40 26140 6.95e-02 FALSE
#> 4 0111 not applied 4 NA 17 NA NA TRUE
#> 5 0112 not applied 4 NA 14 NA NA TRUE
#> 6 0113 not applied 4 NA 3 NA NA TRUE
#> 7 0114 not applied 4 NA 6 NA NA TRUE
#> 8 012 ATC:skmeans 3 3 38 6247 1.66e-02 FALSE
#> 9 0121 ATC:skmeans 4 2 23 198 5.27e-04 TRUE
#> 10 0122 not applied 4 NA 6 NA NA TRUE
#> 11 0123 not applied 4 NA 9 NA NA TRUE
#> 12 013 ATC:kmeans 3 4 31 10893 2.90e-02 FALSE
#> 13 0131 not applied 4 NA 11 NA NA TRUE
#> 14 0132 not applied 4 NA 10 NA NA TRUE
#> 15 0133 not applied 4 NA 2 NA NA TRUE
#> 16 0134 not applied 4 NA 8 NA NA TRUE
#> 17 014 ATC:kmeans 3 2 19 107 2.85e-04 TRUE
#> 18 02 ATC:kmeans 2 4 290 7180 1.91e-02 FALSE
#> 19 021 ATC:kmeans 3 4 73 6744 1.79e-02 FALSE
#> 20 0211 not applied 4 NA 16 NA NA TRUE
#> 21 0212 not applied 4 NA 17 NA NA TRUE
#> 22 0213 ATC:kmeans 4 2 26 2922 7.77e-03 FALSE
#> 23 02131 not applied 5 NA 17 NA NA TRUE
#> 24 02132 not applied 5 NA 9 NA NA TRUE
#> 25 0214 not applied 4 NA 14 NA NA TRUE
#> 26 022 SD:skmeans 3 3 44 2507 6.67e-03 FALSE
#> 27 0221 ATC:kmeans 4 2 21 3223 8.57e-03 FALSE
#> 28 02211 not applied 5 NA 5 NA NA TRUE
#> 29 02212 not applied 5 NA 16 NA NA TRUE
#> 30 0222 not applied 4 NA 15 NA NA TRUE
#> 31 0223 not applied 4 NA 8 NA NA TRUE
#> 32 023 ATC:skmeans 3 5 93 5315 1.41e-02 FALSE
#> 33 0231 ATC:kmeans 4 4 23 9072 2.41e-02 FALSE
#> 34 02311 not applied 5 NA 10 NA NA TRUE
#> 35 02312 not applied 5 NA 7 NA NA TRUE
#> 36 02313 not applied 5 NA 2 NA NA TRUE
#> 37 02314 not applied 5 NA 4 NA NA TRUE
#> 38 0232 not applied 4 NA 16 NA NA TRUE
#> 39 0233 not applied 4 NA 17 NA NA TRUE
#> 40 0234 ATC:skmeans 4 5 27 5955 1.58e-02 FALSE
#> 41 02341 not applied 5 NA 10 NA NA TRUE
#> 42 02342 not applied 5 NA 4 NA NA TRUE
#> 43 02343 not applied 5 NA 4 NA NA TRUE
#> 44 02344 not applied 5 NA 2 NA NA TRUE
#> 45 02345 not applied 5 NA 7 NA NA TRUE
#> 46 0235 not applied 4 NA 10 NA NA TRUE
#> 47 024 SD:kmeans 3 2 80 2667 7.09e-03 FALSE
#> 48 0241 ATC:skmeans 4 2 32 20 5.32e-05 TRUE
#> 49 0242 ATC:skmeans 4 3 48 3829 1.02e-02 FALSE
#> 50 02421 not applied 5 NA 9 NA NA TRUE
#> 51 02422 ATC:skmeans 5 3 18 146 3.88e-04 TRUE
#> 52 02423 ATC:kmeans 5 2 21 48 1.28e-04 TRUE
#> 53 03 ATC:kmeans 2 2 48 17308 4.60e-02 FALSE
#> 54 031 not applied 3 NA 8 NA NA TRUE
#> 55 032 ATC:skmeans 3 2 40 842 2.24e-03 TRUE
#> 56 04 ATC:kmeans 2 3 83 23556 6.27e-02 FALSE
#> 57 041 ATC:kmeans 3 2 34 1325 3.52e-03 FALSE
#> 58 0411 ATC:skmeans 4 3 20 241 6.41e-04 TRUE
#> 59 0412 not applied 4 NA 14 NA NA TRUE
#> 60 042 ATC:skmeans 3 3 31 5593 1.49e-02 FALSE
#> 61 0421 not applied 4 NA 11 NA NA TRUE
#> 62 0422 not applied 4 NA 15 NA NA TRUE
#> 63 0423 not applied 4 NA 5 NA NA TRUE
#> 64 043 ATC:kmeans 3 2 18 1393 3.71e-03 FALSE
#> 65 0431 not applied 4 NA 12 NA NA TRUE
#> 66 0432 not applied 4 NA 6 NA NA TRUE
#> 67 05 SD:kmeans 2 2 89 3363 8.95e-03 FALSE
#> 68 051 ATC:kmeans 3 4 36 2908 7.73e-03 FALSE
#> 69 0511 not applied 4 NA 11 NA NA TRUE
#> 70 0512 not applied 4 NA 8 NA NA TRUE
#> 71 0513 not applied 4 NA 15 NA NA TRUE
#> 72 0514 not applied 4 NA 2 NA NA TRUE
#> 73 052 ATC:skmeans 3 5 53 9538 2.54e-02 FALSE
#> 74 0521 not applied 4 NA 17 NA NA TRUE
#> 75 0522 not applied 4 NA 13 NA NA TRUE
#> 76 0523 not applied 4 NA 3 NA NA TRUE
#> 77 0524 not applied 4 NA 6 NA NA TRUE
#> 78 0525 not applied 4 NA 14 NA NA TRUE
#> 79 06 ATC:skmeans 2 2 131 1256 3.34e-03 FALSE
#> 80 061 ATC:kmeans 3 3 45 5122 1.36e-02 FALSE
#> 81 0611 not applied 4 NA 14 NA NA TRUE
#> 82 0612 ATC:kmeans 4 3 18 3090 8.22e-03 FALSE
#> 83 06121 not applied 5 NA 5 NA NA TRUE
#> 84 06122 not applied 5 NA 9 NA NA TRUE
#> 85 06123 not applied 5 NA 4 NA NA TRUE
#> 86 0613 not applied 4 NA 13 NA NA TRUE
#> 87 062 ATC:kmeans 3 2 86 241 6.41e-04 TRUE
#> 88 07 SD:skmeans 2 3 138 2814 7.48e-03 FALSE
#> 89 071 ATC:kmeans 3 3 59 3229 8.59e-03 FALSE
#> 90 0711 ATC:kmeans 4 2 29 1063 2.83e-03 FALSE
#> 91 07111 ATC:skmeans 5 5 22 6049 1.61e-02 FALSE
#> 92 071111 not applied 6 NA 4 NA NA TRUE
#> 93 071112 not applied 6 NA 7 NA NA TRUE
#> 94 071113 not applied 6 NA 2 NA NA TRUE
#> 95 071114 not applied 6 NA 3 NA NA TRUE
#> 96 071115 not applied 6 NA 6 NA NA TRUE
#> 97 07112 not applied 5 NA 7 NA NA TRUE
#> 98 0712 not applied 4 NA 16 NA NA TRUE
#> 99 0713 not applied 4 NA 14 NA NA TRUE
#> 100 072 ATC:kmeans 3 2 46 1019 2.71e-03 FALSE
#> 101 0721 ATC:skmeans 4 4 31 5220 1.39e-02 FALSE
#> 102 07211 not applied 5 NA 9 NA NA TRUE
#> 103 07212 not applied 5 NA 11 NA NA TRUE
#> 104 07213 not applied 5 NA 8 NA NA TRUE
#> 105 07214 not applied 5 NA 3 NA NA TRUE
#> 106 0722 not applied 4 NA 15 NA NA TRUE
#> 107 073 SD:skmeans 3 3 33 4655 1.24e-02 FALSE
#> 108 0731 not applied 4 NA 10 NA NA TRUE
#> 109 0732 not applied 4 NA 14 NA NA TRUE
#> 110 0733 not applied 4 NA 9 NA NA TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:skmeans | 8 | 0.94 | 0.86 | 0.93 | 907 | * | |
| Node01 | ATC:skmeans | 4 | 1.00 | 0.96 | 0.98 | 128 | ** | |
| Node011 | ATC:kmeans | 4 | 0.99 | 0.95 | 0.98 | 40 | ** | |
| Node0111-leaf | not applied | ✓ (b) | 17 | |||||
| Node0112-leaf | not applied | ✓ (b) | 14 | |||||
| Node0113-leaf | not applied | ✓ (b) | 3 | |||||
| Node0114-leaf | not applied | ✓ (b) | 6 | |||||
| Node012 | ATC:skmeans | 4 | 0.93 | 0.92 | 0.96 | 38 | * | |
| Node0121-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.95 | 0.98 | 23 | ** |
| Node0122-leaf | not applied | ✓ (b) | 6 | |||||
| Node0123-leaf | not applied | ✓ (b) | 9 | |||||
| Node013 | ATC:kmeans | 4 | 1.00 | 0.97 | 0.98 | 31 | ** | |
| Node0131-leaf | not applied | ✓ (b) | 11 | |||||
| Node0132-leaf | not applied | ✓ (b) | 10 | |||||
| Node0133-leaf | not applied | ✓ (b) | 2 | |||||
| Node0134-leaf | not applied | ✓ (b) | 8 | |||||
| Node014-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 19 | ** |
| Node02 | ATC:kmeans | 4 | 1.00 | 0.96 | 0.96 | 290 | ** | |
| Node021 | ATC:kmeans | 4 | 1.00 | 1.00 | 1.00 | 73 | ** | |
| Node0211-leaf | not applied | ✓ (b) | 16 | |||||
| Node0212-leaf | not applied | ✓ (b) | 17 | |||||
| Node0213 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 26 | ** | |
| Node02131-leaf | not applied | ✓ (b) | 17 | |||||
| Node02132-leaf | not applied | ✓ (b) | 9 | |||||
| Node0214-leaf | not applied | ✓ (b) | 14 | |||||
| Node022 | SD:skmeans | 3 | 0.97 | 0.96 | 0.97 | 44 | ** | |
| Node0221 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 21 | ** | |
| Node02211-leaf | not applied | ✓ (b) | 5 | |||||
| Node02212-leaf | not applied | ✓ (b) | 16 | |||||
| Node0222-leaf | not applied | ✓ (b) | 15 | |||||
| Node0223-leaf | not applied | ✓ (b) | 8 | |||||
| Node023 | ATC:skmeans | 5 | 1.00 | 0.97 | 0.99 | 93 | ** | |
| Node0231 | ATC:kmeans | 5 | 0.92 | 0.96 | 0.94 | 23 | * | |
| Node02311-leaf | not applied | ✓ (b) | 10 | |||||
| Node02312-leaf | not applied | ✓ (b) | 7 | |||||
| Node02313-leaf | not applied | ✓ (b) | 2 | |||||
| Node02314-leaf | not applied | ✓ (b) | 4 | |||||
| Node0232-leaf | not applied | ✓ (b) | 16 | |||||
| Node0233-leaf | not applied | ✓ (b) | 17 | |||||
| Node0234 | ATC:skmeans | 5 | 1.00 | 0.99 | 0.99 | 27 | ** | |
| Node02341-leaf | not applied | ✓ (b) | 10 | |||||
| Node02342-leaf | not applied | ✓ (b) | 4 | |||||
| Node02343-leaf | not applied | ✓ (b) | 4 | |||||
| Node02344-leaf | not applied | ✓ (b) | 2 | |||||
| Node02345-leaf | not applied | ✓ (b) | 7 | |||||
| Node0235-leaf | not applied | ✓ (b) | 10 | |||||
| Node024 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 80 | ** | |
| Node0241-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 32 | ** |
| Node0242 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 48 | ** | |
| Node02421-leaf | not applied | ✓ (b) | 9 | |||||
| Node02422-leaf | ATC:skmeans | ✓ (c) | 2 | 0.63 | 0.95 | 0.97 | 18 | |
| Node02423-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 21 | ** |
| Node03 | ATC:kmeans | 3 | 0.93 | 0.92 | 0.97 | 48 | * | |
| Node031-leaf | not applied | ✓ (b) | 8 | |||||
| Node032-leaf | ATC:skmeans | ✓ (c) | 4 | 0.91 | 0.93 | 0.97 | 40 | * |
| Node04 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.99 | 83 | ** | |
| Node041 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 34 | ** | |
| Node0411-leaf | ATC:skmeans | ✓ (c) | 3 | 0.92 | 0.97 | 0.99 | 20 | * |
| Node0412-leaf | not applied | ✓ (b) | 14 | |||||
| Node042 | ATC:skmeans | 3 | 1.00 | 0.99 | 0.99 | 31 | ** | |
| Node0421-leaf | not applied | ✓ (b) | 11 | |||||
| Node0422-leaf | not applied | ✓ (b) | 15 | |||||
| Node0423-leaf | not applied | ✓ (b) | 5 | |||||
| Node043 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 18 | ** | |
| Node0431-leaf | not applied | ✓ (b) | 12 | |||||
| Node0432-leaf | not applied | ✓ (b) | 6 | |||||
| Node05 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 89 | ** | |
| Node051 | ATC:kmeans | 6 | 0.91 | 0.90 | 0.87 | 36 | * | |
| Node0511-leaf | not applied | ✓ (b) | 11 | |||||
| Node0512-leaf | not applied | ✓ (b) | 8 | |||||
| Node0513-leaf | not applied | ✓ (b) | 15 | |||||
| Node0514-leaf | not applied | ✓ (b) | 2 | |||||
| Node052 | ATC:skmeans | 6 | 1.00 | 0.96 | 0.98 | 53 | ** | |
| Node0521-leaf | not applied | ✓ (b) | 17 | |||||
| Node0522-leaf | not applied | ✓ (b) | 13 | |||||
| Node0523-leaf | not applied | ✓ (b) | 3 | |||||
| Node0524-leaf | not applied | ✓ (b) | 6 | |||||
| Node0525-leaf | not applied | ✓ (b) | 14 | |||||
| Node06 | ATC:skmeans | 2 | 1.00 | 0.97 | 0.99 | 131 | ** | |
| Node061 | ATC:kmeans | 4 | 0.91 | 0.92 | 0.95 | 45 | * | |
| Node0611-leaf | not applied | ✓ (b) | 14 | |||||
| Node0612 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 18 | ** | |
| Node06121-leaf | not applied | ✓ (b) | 5 | |||||
| Node06122-leaf | not applied | ✓ (b) | 9 | |||||
| Node06123-leaf | not applied | ✓ (b) | 4 | |||||
| Node0613-leaf | not applied | ✓ (b) | 13 | |||||
| Node062-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 1.00 | 86 | ** |
| Node07 | SD:skmeans | 5 | 0.95 | 0.93 | 0.96 | 138 | * | |
| Node071 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 59 | ** | |
| Node0711 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 29 | ** | |
| Node07111 | ATC:skmeans | 5 | 1.00 | 1.00 | 1.00 | 22 | ** | |
| Node071111-leaf | not applied | ✓ (b) | 4 | |||||
| Node071112-leaf | not applied | ✓ (b) | 7 | |||||
| Node071113-leaf | not applied | ✓ (b) | 2 | |||||
| Node071114-leaf | not applied | ✓ (b) | 3 | |||||
| Node071115-leaf | not applied | ✓ (b) | 6 | |||||
| Node07112-leaf | not applied | ✓ (b) | 7 | |||||
| Node0712-leaf | not applied | ✓ (b) | 16 | |||||
| Node0713-leaf | not applied | ✓ (b) | 14 | |||||
| Node072 | ATC:kmeans | 2 | 1.00 | 0.98 | 0.99 | 46 | ** | |
| Node0721 | ATC:skmeans | 4 | 0.98 | 0.96 | 0.97 | 31 | ** | |
| Node07211-leaf | not applied | ✓ (b) | 9 | |||||
| Node07212-leaf | not applied | ✓ (b) | 11 | |||||
| Node07213-leaf | not applied | ✓ (b) | 8 | |||||
| Node07214-leaf | not applied | ✓ (b) | 3 | |||||
| Node0722-leaf | not applied | ✓ (b) | 15 | |||||
| Node073 | SD:skmeans | 3 | 1.00 | 0.97 | 0.98 | 33 | ** | |
| Node0731-leaf | not applied | ✓ (b) | 10 | |||||
| Node0732-leaf | not applied | ✓ (b) | 14 | |||||
| Node0733-leaf | not applied | ✓ (b) | 9 |
Stop reason: b) Subgroup had too few columns. c) There were too few signatures.
**: 1-PAC > 0.95, *: 1-PAC > 0.9
The nodes of the hierarchy can be merged by setting the merge_node parameters. Here we
control the hierarchy with the min_n_signatures parameter. The value of min_n_signatures is
from node_info().
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1019))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1063))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1256))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1325))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1393))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2507))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2667))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2814))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2908))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2922))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3090))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3223))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3229))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3363))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3829))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4160))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4655))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5122))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5220))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5315))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5593))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5955))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6049))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6247))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6744))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7180))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9072))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9538))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10893))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17308))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23556))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 26140))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 54725))
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 = 1019))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02423" "0241" "0431" "0411" "0733" "02423"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "0411" "032" "032" "02423" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "062" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "0411" "062"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "062" "0121" "0511" "0412" "0212" "071113"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02422" "0241" "0712" "0732" "062" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "0241" "0511" "0241" "0241"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "062" "0241" "062" "0113" "06121" "0411"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "062" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "0613" "062" "0611" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "0241" "0111" "0212" "062" "062" "0713"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "0431" "0731" "02212" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "062" "062" "062" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "0412" "07211" "0525" "02344" "0223"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07212" "062" "0111" "0211" "0241"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07211" "02341" "0732" "02311" "0241" "071112"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "062" "0513" "02423" "02423" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07212" "032" "0412" "0423" "0732"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "071115" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "0222" "0521" "06121" "0412" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "062" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07213" "031" "0524" "02312" "0241" "0511"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02423" "0513" "062" "02423" "0713" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07212" "02344" "0431" "0114" "0241" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "0713" "032" "06123" "02131" "0731" "062"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "07213" "0212" "014" "02422" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "062" "0432" "0613" "0422" "0422" "0732"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "02212" "0731" "062" "0611" "062"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02422" "0232" "0232" "0521" "062" "0411"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "062" "07112" "02423" "07211"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "0411" "0422" "0222" "0514" "0241"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "071112" "0114" "02421" "0712" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "0613" "07112" "062" "0522" "0241"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "0411" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "062" "0235" "062" "02341" "071115"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "062" "0412" "02422" "0722" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "0241" "0232" "0732" "07112" "0431"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "0511" "02421" "0121" "0521" "062" "0223"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "0511" "0512" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "0512" "0611" "0411" "0421" "0412"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "0411" "0511" "0121" "0522" "06123"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "062" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "0513" "071111" "0412" "07214" "0111" "02423"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "0713" "02345" "0732" "071112" "02131"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "062" "06122" "062"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "02423" "0222" "062" "062"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "0222" "062" "02132"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07112" "07213" "02131" "0212" "02132" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "062" "07213" "0511" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "062" "0722" "0722" "0241" "0232" "0713"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "0613" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "0732" "062" "0214" "02211" "0431" "07211"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "071114" "0713" "02423" "0241" "0422" "0241"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "0411" "0722" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "0732" "0512" "0233" "0411" "0521"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "0223" "02131" "02312" "0613" "0521" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "0522" "0112" "02212"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "0223" "0214" "014" "0241" "0123" "0511"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "062" "0223" "02314" "02422" "0525" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "062" "0132" "02311" "02345" "062" "02421"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "0525" "02345" "0422" "0412" "0233" "02131"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "062" "0241" "0111" "0422" "0122" "062"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "02423" "0512" "062" "0232" "0411" "014"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "0613" "02422" "0521" "0731" "0233" "0131"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "0712" "02211" "0121" "0112" "032" "0111"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "0513" "062" "02211" "0113" "0611" "06122"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "02212" "071112" "0422" "0512" "07213" "0521"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "062" "0235" "0432" "0733" "0134" "0722"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "0241" "062" "062" "0431" "0722"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "0241" "0212" "062" "02211" "0241" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "02212" "0733" "0513" "02422" "02132" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "062" "0121" "0712" "062" "0121" "0712"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "062" "0211" "014" "0513" "0732" "0432"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "02132" "0732" "0233" "0524" "062"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "062" "0241" "0235" "02342" "0733" "0712"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "02422" "0513" "0613" "0412" "0121" "071111"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "0521" "02131" "0712" "0431" "062" "0525"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "0121" "071112" "0722" "0522" "0722" "0432"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "0222" "0121" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "062" "0422" "014" "062" "02314" "02422"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "0131" "06121" "031" "0212" "02343" "062"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "0133" "0525" "0134" "0212" "071115" "07212"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "02132" "0241" "071111" "0523" "0222" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "0112" "0212" "0123" "0431" "0112" "0114"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07112" "06122" "0512" "0712" "0233" "0222"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "0222" "0121" "0232" "0423" "0233" "0731"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "02132" "02341" "0214" "031" "062" "0122"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "02421" "02423" "0235" "0431" "0611" "0122"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "062" "0111" "0421" "07213" "07211" "0412"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "02423" "07212" "0233" "02312" "02212" "0522"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "0713" "0712" "0611" "0114" "0132"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "02423" "02423" "0111" "062"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06122" "071112" "0423" "0523" "062" "014"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "0521" "07211" "032" "0241" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "062" "0222" "0241" "0112" "0241" "071115"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "0611" "0422" "0611" "0722" "07112" "0121"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "0111" "06122" "0131" "0733" "062" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "0524" "02343" "02131" "062" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "0512" "0611"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "0733" "0525" "0235" "02422" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "062" "0722" "0522" "0525" "0431" "02131"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "062" "0232" "032" "0713" "0525" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "0432" "071114" "0513" "07211"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "0712" "02421" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "0733" "02422" "02312" "0222" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02422" "0712" "032" "02422" "0611" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07211" "0214" "02131" "07212" "0722" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "062" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "0732" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "0713" "02212" "06122" "0712"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "0412" "02131" "0412" "06122" "0722" "02421"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "0513" "0514" "02423" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "062" "062" "0713" "0733"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "0222" "0121" "0411" "0411" "02212"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "0611" "0421" "0513" "062" "062" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02131" "014" "02131" "0513" "032" "0432"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "062" "0211" "0131" "0223" "02212" "062"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02423" "0521" "071113" "0134" "0525" "02422"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02421" "0114" "014" "07212" "032" "02422"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "0712" "02422" "0521" "02422" "0513" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "07212" "0232" "0222" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "02212" "0211" "0233" "071115" "0613"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "062" "0731" "0513" "02212" "0513" "02132"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "0222" "07212" "02423" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "0713" "0523" "02211"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "0511" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "0241" "0521" "0134" "02341" "032" "0722"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "0223" "0232" "02132" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02423" "0214" "02421" "0123" "0241" "0241"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "0733" "0134" "062" "062"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "0431" "07213" "0613" "0722" "0411"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07212" "0211" "0412" "0233" "0222" "02212"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "071111" "0411" "032" "0223" "02212" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "02212" "0712" "02423" "0712" "062"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "0513" "0411"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "062" "071114" "032" "062" "0731" "062"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "062" "02131" "0111" "0611"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "0411" "02421" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "0731" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "071115" "062" "0722" "02312" "0613" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "0611" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "0222" "014" "0713" "07112" "0521" "0613"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07212" "0122" "02342" "0732" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07213" "0731" "02311" "0712" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "0613" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "0713" "0131" "0122" "0421" "02212" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "0613" "062" "0131" "02422" "07211"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "0411" "0112" "02311" "0411" "062" "062"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "062" "07214" "0241" "032" "0611" "07214"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "0732" "071112" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "0412" "0431" "031" "0511" "0123" "0241"
#> TCGA.05.4425.01
#> "02212"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1063))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02423" "0241" "0431" "0411" "0733" "02423"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "0411" "032" "032" "02423" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "062" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "0411" "062"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "062" "0121" "0511" "0412" "0212" "071113"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02422" "0241" "0712" "0732" "062" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "0241" "0511" "0241" "0241"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "062" "0241" "062" "0113" "06121" "0411"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "062" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "0613" "062" "0611" "0422"
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#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "0432" "071114" "0513" "072"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "0712" "02421" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "0733" "02422" "02312" "0222" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02422" "0712" "032" "02422" "0611" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "072" "0214" "02131" "072" "072" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "062" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "0732" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "0713" "02212" "06122" "0712"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "0412" "02131" "0412" "06122" "072" "02421"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "0513" "0514" "02423" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "062" "062" "0713" "0733"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "0222" "0121" "0411" "0411" "02212"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "0611" "0421" "0513" "062" "062" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02131" "014" "02131" "0513" "032" "0432"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "062" "0211" "0131" "0223" "02212" "062"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02423" "0521" "071113" "0134" "0525" "02422"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02421" "0114" "014" "072" "032" "02422"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "0712" "02422" "0521" "02422" "0513" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "072" "0232" "0222" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "02212" "0211" "0233" "071115" "0613"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "062" "0731" "0513" "02212" "0513" "02132"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "0222" "072" "02423" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "0713" "0523" "02211"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "0511" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "0241" "0521" "0134" "02341" "032" "072"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "0223" "0232" "02132" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02423" "0214" "02421" "0123" "0241" "0241"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "0733" "0134" "062" "062"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "0431" "072" "0613" "072" "0411"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "072" "0211" "0412" "0233" "0222" "02212"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "071111" "0411" "032" "0223" "02212" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "02212" "0712" "02423" "0712" "062"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "0513" "0411"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "062" "071114" "032" "062" "0731" "062"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "062" "02131" "0111" "0611"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "0411" "02421" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "0731" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "071115" "062" "072" "02312" "0613" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "0611" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "0222" "014" "0713" "07112" "0521" "0613"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "072" "0122" "02342" "0732" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "072" "0731" "02311" "0712" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "0613" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "0713" "0131" "0122" "0421" "02212" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "0613" "062" "0131" "02422" "072"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "0411" "0112" "02311" "0411" "062" "062"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "062" "072" "0241" "032" "0611" "072"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "0732" "071112" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "0412" "0431" "031" "0511" "0123" "0241"
#> TCGA.05.4425.01
#> "02212"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1256))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02423" "0241" "0431" "0411" "0733" "02423"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "0411" "032" "032" "02423" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "062" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "0411" "062"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "062" "0121" "0511" "0412" "0212" "0711"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02422" "0241" "0712" "0732" "062" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "0241" "0511" "0241" "0241"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "062" "0241" "062" "0113" "06121" "0411"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "062" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "0613" "062" "0611" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "0241" "0111" "0212" "062" "062" "0713"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "0431" "0731" "02212" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "062" "062" "062" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "0412" "072" "0525" "02344" "0223"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "072" "062" "0111" "0211" "0241"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "072" "02341" "0732" "02311" "0241" "0711"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "062" "0513" "02423" "02423" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "072" "032" "0412" "0423" "0732"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "0711" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "0222" "0521" "06121" "0412" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "062" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "072" "031" "0524" "02312" "0241" "0511"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02423" "0513" "062" "02423" "0713" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "072" "02344" "0431" "0114" "0241" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "0713" "032" "06123" "02131" "0731" "062"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "072" "0212" "014" "02422" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "062" "0432" "0613" "0422" "0422" "0732"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "02212" "0731" "062" "0611" "062"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02422" "0232" "0232" "0521" "062" "0411"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "062" "0711" "02423" "072"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "0411" "0422" "0222" "0514" "0241"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "0711" "0114" "02421" "0712" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "0613" "0711" "062" "0522" "0241"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "0411" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "062" "0235" "062" "02341" "0711"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "062" "0412" "02422" "072" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "0241" "0232" "0732" "0711" "0431"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "0511" "02421" "0121" "0521" "062" "0223"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "0511" "0512" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "0512" "0611" "0411" "0421" "0412"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "0411" "0511" "0121" "0522" "06123"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "062" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "0513" "0711" "0412" "072" "0111" "02423"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "0713" "02345" "0732" "0711" "02131"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
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#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "0411" "02421" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "0731" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "0711" "062" "072" "02312" "0613" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "0611" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "0222" "014" "0713" "0711" "0521" "0613"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "072" "0122" "02342" "0732" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "072" "0731" "02311" "0712" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "0613" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "0713" "0131" "0122" "0421" "02212" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "0613" "062" "0131" "02422" "072"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "0411" "0112" "02311" "0411" "062" "062"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "062" "072" "0241" "032" "0611" "072"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "0732" "0711" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "0412" "0431" "031" "0511" "0123" "0241"
#> TCGA.05.4425.01
#> "02212"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1325))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02423" "0241" "0431" "0411" "0733" "02423"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "0411" "032" "032" "02423" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "0411" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "0511" "0412" "0212" "0711"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02422" "0241" "0712" "0732" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "0241" "0511" "0241" "0241"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "0241" "06" "0113" "06121" "0411"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "06" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "0241" "0111" "0212" "06" "06" "0713"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "0431" "0731" "02212" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "0412" "072" "0525" "02344" "0223"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "072" "06" "0111" "0211" "0241"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "072" "02341" "0732" "02311" "0241" "0711"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "0513" "02423" "02423" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "072" "032" "0412" "0423" "0732"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "0711" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "0222" "0521" "06121" "0412" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "072" "031" "0524" "02312" "0241" "0511"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02423" "0513" "06" "02423" "0713" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "072" "02344" "0431" "0114" "0241" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "0713" "032" "06123" "02131" "0731" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "072" "0212" "014" "02422" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "0432" "06" "0422" "0422" "0732"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "02212" "0731" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02422" "0232" "0232" "0521" "06" "0411"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "06" "0711" "02423" "072"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "0411" "0422" "0222" "0514" "0241"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "0711" "0114" "02421" "0712" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "0711" "06" "0522" "0241"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "0411" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "0711"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "0412" "02422" "072" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "0241" "0232" "0732" "0711" "0431"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "0511" "02421" "0121" "0521" "06" "0223"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "0511" "0512" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "0512" "06" "0411" "0421" "0412"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "0411" "0511" "0121" "0522" "06123"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "06" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "0513" "0711" "0412" "072" "0111" "02423"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "0713" "02345" "0732" "0711" "02131"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "06" "06122" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "02423" "0222" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "0222" "06" "02132"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "0711" "072" "02131" "0212" "02132" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "06" "072" "0511" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "072" "072" "0241" "0232" "0713"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "0732" "06" "0214" "02211" "0431" "072"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "0711" "0713" "02423" "0241" "0422" "0241"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "0411" "072" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "0732" "0512" "0233" "0411" "0521"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "0223" "02131" "02312" "06" "0521" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "0522" "0112" "02212"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "0223" "0214" "014" "0241" "0123" "0511"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "0223" "02314" "02422" "0525" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "0132" "02311" "02345" "06" "02421"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "0525" "02345" "0422" "0412" "0233" "02131"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "0241" "0111" "0422" "0122" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "02423" "0512" "06" "0232" "0411" "014"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "02422" "0521" "0731" "0233" "0131"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "0712" "02211" "0121" "0112" "032" "0111"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "0513" "06" "02211" "0113" "06" "06122"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "02212" "0711" "0422" "0512" "072" "0521"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "0235" "0432" "0733" "0134" "072"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "0241" "06" "06" "0431" "072"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "0241" "0212" "06" "02211" "0241" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "02212" "0733" "0513" "02422" "02132" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "0121" "0712" "06" "0121" "0712"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "014" "0513" "0732" "0432"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "02132" "0732" "0233" "0524" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "0241" "0235" "02342" "0733" "0712"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "02422" "0513" "06" "0412" "0121" "0711"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "0521" "02131" "0712" "0431" "06" "0525"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "0121" "0711" "072" "0522" "072" "0432"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "0222" "0121" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "014" "06" "02314" "02422"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "0131" "06121" "031" "0212" "02343" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "0133" "0525" "0134" "0212" "0711" "072"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "02132" "0241" "0711" "0523" "0222" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "0112" "0212" "0123" "0431" "0112" "0114"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "0711" "06122" "0512" "0712" "0233" "0222"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "0222" "0121" "0232" "0423" "0233" "0731"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "02132" "02341" "0214" "031" "06" "0122"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "02421" "02423" "0235" "0431" "06" "0122"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "0111" "0421" "072" "072" "0412"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "02423" "072" "0233" "02312" "02212" "0522"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "0713" "0712" "06" "0114" "0132"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "02423" "02423" "0111" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06122" "0711" "0423" "0523" "06" "014"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "0521" "072" "032" "0241" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "0222" "0241" "0112" "0241" "0711"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "072" "0711" "0121"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "0111" "06122" "0131" "0733" "06" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "0524" "02343" "02131" "06" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "0512" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "0733" "0525" "0235" "02422" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "072" "0522" "0525" "0431" "02131"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "0713" "0525" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "0432" "0711" "0513" "072"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "0712" "02421" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "0733" "02422" "02312" "0222" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02422" "0712" "032" "02422" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "072" "0214" "02131" "072" "072" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "06" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "0732" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "0713" "02212" "06122" "0712"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "0412" "02131" "0412" "06122" "072" "02421"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "0513" "0514" "02423" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "06" "06" "0713" "0733"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "0222" "0121" "0411" "0411" "02212"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "0513" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02131" "014" "02131" "0513" "032" "0432"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "0223" "02212" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02423" "0521" "0711" "0134" "0525" "02422"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02421" "0114" "014" "072" "032" "02422"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "0712" "02422" "0521" "02422" "0513" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "072" "0232" "0222" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "02212" "0211" "0233" "0711" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "0731" "0513" "02212" "0513" "02132"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "0222" "072" "02423" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "0713" "0523" "02211"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "0511" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "0241" "0521" "0134" "02341" "032" "072"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "0223" "0232" "02132" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02423" "0214" "02421" "0123" "0241" "0241"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "0733" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "0431" "072" "06" "072" "0411"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "072" "0211" "0412" "0233" "0222" "02212"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "0711" "0411" "032" "0223" "02212" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "02212" "0712" "02423" "0712" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "0513" "0411"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "0711" "032" "06" "0731" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "02131" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "0411" "02421" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "0731" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "0711" "06" "072" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "0222" "014" "0713" "0711" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "072" "0122" "02342" "0732" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "072" "0731" "02311" "0712" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "0713" "0131" "0122" "0421" "02212" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "02422" "072"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "0411" "0112" "02311" "0411" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "072" "0241" "032" "06" "072"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "0732" "0711" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "0412" "0431" "031" "0511" "0123" "0241"
#> TCGA.05.4425.01
#> "02212"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1393))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02423" "0241" "0431" "041" "0733" "02423"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "02423" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "0511" "041" "0212" "0711"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02422" "0241" "0712" "0732" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "0241" "0511" "0241" "0241"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "0241" "06" "0113" "06121" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "06" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "0241" "0111" "0212" "06" "06" "0713"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "0431" "0731" "02212" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "072" "0525" "02344" "0223"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "072" "06" "0111" "0211" "0241"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "072" "02341" "0732" "02311" "0241" "0711"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "0513" "02423" "02423" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "072" "032" "041" "0423" "0732"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "0711" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "0222" "0521" "06121" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
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#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "0513" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02131" "014" "02131" "0513" "032" "0432"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "0223" "02212" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02423" "0521" "0711" "0134" "0525" "02422"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02421" "0114" "014" "072" "032" "02422"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "0712" "02422" "0521" "02422" "0513" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "072" "0232" "0222" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "02212" "0211" "0233" "0711" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "0731" "0513" "02212" "0513" "02132"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "0222" "072" "02423" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "0713" "0523" "02211"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "0511" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "0241" "0521" "0134" "02341" "032" "072"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "0223" "0232" "02132" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02423" "0214" "02421" "0123" "0241" "0241"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "0733" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "0431" "072" "06" "072" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "072" "0211" "041" "0233" "0222" "02212"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "0711" "041" "032" "0223" "02212" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "02212" "0712" "02423" "0712" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "0513" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "0711" "032" "06" "0731" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "02131" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "02421" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "0731" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "0711" "06" "072" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "0222" "014" "0713" "0711" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "072" "0122" "02342" "0732" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "072" "0731" "02311" "0712" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "0713" "0131" "0122" "0421" "02212" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "02422" "072"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "072" "0241" "032" "06" "072"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "0732" "0711" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "0431" "031" "0511" "0123" "0241"
#> TCGA.05.4425.01
#> "02212"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2507))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02423" "0241" "043" "041" "0733" "02423"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "02423" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "0511" "041" "0212" "0711"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02422" "0241" "0712" "0732" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "0241" "0511" "0241" "0241"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "0241" "06" "0113" "06121" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "06" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "0241" "0111" "0212" "06" "06" "0713"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "0731" "02212" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "072" "0525" "02344" "0223"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "072" "06" "0111" "0211" "0241"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "072" "02341" "0732" "02311" "0241" "0711"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "0513" "02423" "02423" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "072" "032" "041" "0423" "0732"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "0711" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "0222" "0521" "06121" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "072" "031" "0524" "02312" "0241" "0511"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02423" "0513" "06" "02423" "0713" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "072" "02344" "043" "0114" "0241" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "0713" "032" "06123" "02131" "0731" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "072" "0212" "014" "02422" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "0732"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "02212" "0731" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02422" "0232" "0232" "0521" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "06" "0711" "02423" "072"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "0222" "0514" "0241"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "0711" "0114" "02421" "0712" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "0711" "06" "0522" "0241"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "0711"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "02422" "072" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "0241" "0232" "0732" "0711" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "0511" "02421" "0121" "0521" "06" "0223"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "0511" "0512" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "0512" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "0511" "0121" "0522" "06123"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "06" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "0513" "0711" "041" "072" "0111" "02423"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "0713" "02345" "0732" "0711" "02131"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "06" "06122" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "02423" "0222" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "0222" "06" "02132"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "0711" "072" "02131" "0212" "02132" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "06" "072" "0511" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "072" "072" "0241" "0232" "0713"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "0732" "06" "0214" "02211" "043" "072"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "0711" "0713" "02423" "0241" "0422" "0241"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "072" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "0732" "0512" "0233" "041" "0521"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "0223" "02131" "02312" "06" "0521" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "0522" "0112" "02212"
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#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "0511" "0123" "0241"
#> TCGA.05.4425.01
#> "02212"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2667))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02423" "0241" "043" "041" "0733" "02423"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "02423" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "0511" "041" "0212" "0711"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02422" "0241" "0712" "0732" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "0241" "0511" "0241" "0241"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "0241" "06" "0113" "06121" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "06" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "0241" "0111" "0212" "06" "06" "0713"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "0731" "022" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "072" "0525" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "072" "06" "0111" "0211" "0241"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "072" "02341" "0732" "02311" "0241" "0711"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "0513" "02423" "02423" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "072" "032" "041" "0423" "0732"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "0711" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "022" "0521" "06121" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "072" "031" "0524" "02312" "0241" "0511"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02423" "0513" "06" "02423" "0713" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "072" "02344" "043" "0114" "0241" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "0713" "032" "06123" "02131" "0731" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "072" "0212" "014" "02422" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "0732"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "0731" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02422" "0232" "0232" "0521" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "06" "0711" "02423" "072"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "022" "0514" "0241"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "0711" "0114" "02421" "0712" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "0711" "06" "0522" "0241"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "0711"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "02422" "072" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "0241" "0232" "0732" "0711" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "0511" "02421" "0121" "0521" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "0511" "0512" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "0512" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "0511" "0121" "0522" "06123"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "06" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "0513" "0711" "041" "072" "0111" "02423"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "0713" "02345" "0732" "0711" "02131"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "06" "06122" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "02423" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "02132"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "0711" "072" "02131" "0212" "02132" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "06" "072" "0511" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "072" "072" "0241" "0232" "0713"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "0732" "06" "0214" "022" "043" "072"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "0711" "0713" "02423" "0241" "0422" "0241"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "072" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "0732" "0512" "0233" "041" "0521"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "02131" "02312" "06" "0521" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "0522" "0112" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "014" "0241" "0123" "0511"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "02314" "02422" "0525" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "0132" "02311" "02345" "06" "02421"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "0525" "02345" "0422" "041" "0233" "02131"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "0241" "0111" "0422" "0122" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "02423" "0512" "06" "0232" "041" "014"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "02422" "0521" "0731" "0233" "0131"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "0712" "022" "0121" "0112" "032" "0111"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "0513" "06" "022" "0113" "06" "06122"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "0711" "0422" "0512" "072" "0521"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "0235" "043" "0733" "0134" "072"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "0241" "06" "06" "043" "072"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "0241" "0212" "06" "022" "0241" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "0733" "0513" "02422" "02132" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "0121" "0712" "06" "0121" "0712"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "014" "0513" "0732" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "02132" "0732" "0233" "0524" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "0241" "0235" "02342" "0733" "0712"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "02422" "0513" "06" "041" "0121" "0711"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "0521" "02131" "0712" "043" "06" "0525"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "0121" "0711" "072" "0522" "072" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "0121" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "014" "06" "02314" "02422"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "0131" "06121" "031" "0212" "02343" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "0133" "0525" "0134" "0212" "0711" "072"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "02132" "0241" "0711" "0523" "022" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "0112" "0212" "0123" "043" "0112" "0114"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "0711" "06122" "0512" "0712" "0233" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "0121" "0232" "0423" "0233" "0731"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "02132" "02341" "0214" "031" "06" "0122"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "02421" "02423" "0235" "043" "06" "0122"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "0111" "0421" "072" "072" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "02423" "072" "0233" "02312" "022" "0522"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "0713" "0712" "06" "0114" "0132"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "02423" "02423" "0111" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06122" "0711" "0423" "0523" "06" "014"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "0521" "072" "032" "0241" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "0241" "0112" "0241" "0711"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "072" "0711" "0121"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "0111" "06122" "0131" "0733" "06" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "0524" "02343" "02131" "06" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "0512" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "0733" "0525" "0235" "02422" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "072" "0522" "0525" "043" "02131"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "0713" "0525" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "043" "0711" "0513" "072"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "0712" "02421" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "0733" "02422" "02312" "022" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02422" "0712" "032" "02422" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "072" "0214" "02131" "072" "072" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "06" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "0732" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "0713" "022" "06122" "0712"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "02131" "041" "06122" "072" "02421"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "0513" "0514" "02423" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "06" "06" "0713" "0733"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "0121" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "0513" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02131" "014" "02131" "0513" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02423" "0521" "0711" "0134" "0525" "02422"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02421" "0114" "014" "072" "032" "02422"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "0712" "02422" "0521" "02422" "0513" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "072" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "0711" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "0731" "0513" "022" "0513" "02132"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "022" "072" "02423" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "0713" "0523" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "0511" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "0241" "0521" "0134" "02341" "032" "072"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "02132" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02423" "0214" "02421" "0123" "0241" "0241"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "0733" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "072" "06" "072" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "072" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "0711" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "0712" "02423" "0712" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "0513" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "0711" "032" "06" "0731" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "02131" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "02421" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "0731" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "0711" "06" "072" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "0713" "0711" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "072" "0122" "02342" "0732" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "072" "0731" "02311" "0712" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "0713" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "02422" "072"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "072" "0241" "032" "06" "072"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "0732" "0711" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "0511" "0123" "0241"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2814))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "0733" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "0732"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "0511" "041" "0212" "0711"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "0712" "0732" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "024" "0511" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06121" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "0713" "0131" "06" "0731" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "0713"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "0731" "022" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "072" "0525" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "072" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "072" "02341" "0732" "02311" "024" "0711"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "0513" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "072" "032" "041" "0423" "0732"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "0711" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "022" "0521" "06121" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "072" "031" "0524" "02312" "024" "0511"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "0513" "06" "024" "0713" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "072" "02344" "043" "0114" "024" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "0713" "032" "06123" "02131" "0731" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "072" "0212" "014" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "0732"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "0731" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "0521" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "06" "0711" "024" "072"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "022" "0514" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "0711" "0114" "024" "0712" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "0711" "06" "0522" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "0711"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "072" "0123" "0121"
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#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "072" "06" "072" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "072" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "0711" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "0712" "024" "0712" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "0513" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "0711" "032" "06" "0731" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "02131" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "0731" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "0711" "06" "072" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "0713" "0711" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "072" "0122" "02342" "0732" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "072" "0731" "02311" "0712" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "0713" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "024" "072"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "072" "024" "032" "06" "072"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "0732" "0711" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "0511" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2908))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "0511" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "024" "0511" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06121" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "07" "0131" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "07" "022" "0511"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "07" "0525" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "0513" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "02131" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "022" "0521" "06121" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "0524" "02312" "024" "0511"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "0513" "06" "024" "07" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "0114" "024" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06123" "02131" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "07" "0212" "014" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "0521" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "022" "0514" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "07" "0114" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "0522" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "0511" "024" "0121" "0521" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "0511" "0512" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "0512" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "0511" "0121" "0522" "06123"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "06" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "0513" "07" "041" "07" "0111" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "07" "02345" "07" "07" "02131"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "06" "06122" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "02132"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "02131" "0212" "02132" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "06" "07" "0511" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "0232" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "0422" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "07" "0512" "0233" "041" "0521"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "02131" "02312" "06" "0521" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "0522" "0112" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "014" "024" "0123" "0511"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "02314" "024" "0525" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "0132" "02311" "02345" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "0525" "02345" "0422" "041" "0233" "02131"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "0111" "0422" "0122" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "0512" "06" "0232" "041" "014"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "0521" "07" "0233" "0131"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "0121" "0112" "032" "0111"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "0513" "06" "022" "0113" "06" "06122"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "0422" "0512" "07" "0521"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "0235" "043" "07" "0134" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "0513" "024" "02132" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "0121" "07" "06" "0121" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "014" "0513" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "02132" "07" "0233" "0524" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "0235" "02342" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "0513" "06" "041" "0121" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "0521" "02131" "07" "043" "06" "0525"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "0121" "07" "07" "0522" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "0121" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "014" "06" "02314" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "0131" "06121" "031" "0212" "02343" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "0133" "0525" "0134" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "02132" "024" "07" "0523" "022" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "0112" "0212" "0123" "043" "0112" "0114"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06122" "0512" "07" "0233" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "0121" "0232" "0423" "0233" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "02132" "02341" "0214" "031" "06" "0122"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "0235" "043" "06" "0122"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "0111" "0421" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "0233" "02312" "022" "0522"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "0114" "0132"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "024" "024" "0111" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06122" "07" "0423" "0523" "06" "014"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "0521" "07" "032" "024" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "0112" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "07" "07" "0121"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "0111" "06122" "0131" "07" "06" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "0524" "02343" "02131" "06" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "0512" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "0525" "0235" "024" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "0522" "0525" "043" "02131"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "07" "0525" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "043" "07" "0513" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "02312" "022" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "02131" "07" "07" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "06" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "07" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "07" "022" "06122" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "02131" "041" "06122" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "0513" "0514" "024" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "0121" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "0513" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02131" "014" "02131" "0513" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "0521" "07" "0134" "0525" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "0114" "014" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "0521" "024" "0513" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "0513" "022" "0513" "02132"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "0523" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "0511" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "0521" "0134" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "02132" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "0123" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "07" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "0513" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "02131" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "02132" "0121" "0512"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "0511" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2922))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02131" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "051" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "024" "051" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06121" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "07" "0131" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "07" "022" "051"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "07" "0525" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "051" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
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#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "0121" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "051" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02131" "014" "02131" "051" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "0521" "07" "0134" "0525" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "0114" "014" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "0521" "024" "051" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "051" "022" "051" "02132"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "0523" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "051" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "0521" "0134" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "02132" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "0123" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "07" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "02131" "0121" "051" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "02131" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "02132" "0121" "051"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "02131"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "051" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3090))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06122" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "051" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "024" "051" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06121" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "07" "0131" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "07" "022" "051"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "07" "0525" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "051" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "022" "0521" "06121" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "0524" "02312" "024" "051"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "051" "06" "024" "07" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "0114" "024" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06123" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "07" "0212" "014" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "0521" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06123" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "022" "051" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "07" "0114" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "0522" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06121" "0211" "06123"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "051" "024" "0121" "0521" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "051" "051" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "051" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "051" "0121" "0522" "06123"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "06" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "051" "07" "041" "07" "0111" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "07" "02345" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "06" "06122" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "06" "07" "051" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "0232" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "0422" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "07" "051" "0233" "041" "0521"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "0213" "02312" "06" "0521" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "0522" "0112" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "014" "024" "0123" "051"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "02314" "024" "0525" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "0132" "02311" "02345" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "0525" "02345" "0422" "041" "0233" "0213"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "0111" "0422" "0122" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "051" "06" "0232" "041" "014"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "0521" "07" "0233" "0131"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "0121" "0112" "032" "0111"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "051" "06" "022" "0113" "06" "06122"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "0422" "051" "07" "0521"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "0235" "043" "07" "0134" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "051" "024" "0213" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "0121" "07" "06" "0121" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "014" "051" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "0213" "07" "0233" "0524" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "0235" "02342" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "051" "06" "041" "0121" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "0521" "0213" "07" "043" "06" "0525"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "0121" "07" "07" "0522" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "0121" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "014" "06" "02314" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "0131" "06121" "031" "0212" "02343" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "0133" "0525" "0134" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "0213" "024" "07" "0523" "022" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "0112" "0212" "0123" "043" "0112" "0114"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06122" "051" "07" "0233" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "0121" "0232" "0423" "0233" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "0213" "02341" "0214" "031" "06" "0122"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "0235" "043" "06" "0122"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "0111" "0421" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "0233" "02312" "022" "0522"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "0114" "0132"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "024" "024" "0111" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06122" "07" "0423" "0523" "06" "014"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "0521" "07" "032" "024" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "0112" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "07" "07" "0121"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "0111" "06122" "0131" "07" "06" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "0524" "02343" "0213" "06" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "051" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "0525" "0235" "024" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "0522" "0525" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "07" "0525" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "043" "07" "051" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "02312" "022" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "06" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "07" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "07" "022" "06122" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06122" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "051" "051" "024" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "0121" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "051" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "014" "0213" "051" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "0521" "07" "0134" "0525" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "0114" "014" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "0521" "024" "051" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "051" "022" "051" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06122" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "0523" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "051" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "0521" "0134" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "0213" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "0123" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "07" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06121" "02313" "0213" "0121" "051" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "0213" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "0121" "051"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "051" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3223))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
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#> "0111" "06" "0131" "07" "06" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "0524" "02343" "0213" "06" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "051" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "0525" "0235" "024" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "0522" "0525" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "07" "0525" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "043" "07" "051" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "02312" "022" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "06" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "07" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "051" "051" "024" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "0121" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "051" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "014" "0213" "051" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "0521" "07" "0134" "0525" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "0114" "014" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "0521" "024" "051" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "051" "022" "051" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "0523" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "051" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "0521" "0134" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "0213" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "0123" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "07" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02313" "0213" "0121" "051" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "0213" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "0121" "051"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "051" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3229))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "051" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "024" "051" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "07" "0131" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "07" "022" "051"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "07" "0525" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "051" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "022" "0521" "06" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "0524" "02312" "024" "051"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "051" "06" "024" "07" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "0114" "024" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "07" "0212" "014" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "0521" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "022" "051" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "07" "0114" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "0522" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "051" "024" "0121" "0521" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "051" "051" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "051" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "051" "0121" "0522" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "06" "0522" "0132" "02341" "014"
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#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "0121" "051"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "051" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3363))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "051" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "0524" "024" "051" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "07" "0131" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "07" "022" "051"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "0521" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "07" "0525" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "051" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "0525" "022" "0521" "06" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "0524"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "0524" "02312" "024" "051"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "051" "06" "024" "07" "0525"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "0114" "024" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "0525" "07" "0212" "014" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "0521" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "022" "051" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "07" "0114" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "0522" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "051" "024" "0121" "0521" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "051" "051" "014" "0522" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "051" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "051" "0121" "0522" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "0522" "06" "0522" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "051" "07" "041" "07" "0111" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "07" "02345" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "06" "07" "051" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "0232" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "0422" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "07" "051" "0233" "041" "0521"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "0213" "02312" "06" "0521" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "0522" "0112" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "014" "024" "0123" "051"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "02314" "024" "0525" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "0132" "02311" "02345" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "0525" "02345" "0422" "041" "0233" "0213"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "0111" "0422" "0122" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "051" "06" "0232" "041" "014"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "0521" "07" "0233" "0131"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "0121" "0112" "032" "0111"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "051" "06" "022" "0113" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "0422" "051" "07" "0521"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "0235" "043" "07" "0134" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "051" "024" "0213" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "0121" "07" "06" "0121" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "014" "051" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "0213" "07" "0233" "0524" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "0235" "02342" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "051" "06" "041" "0121" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "0521" "0213" "07" "043" "06" "0525"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "0121" "07" "07" "0522" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "0121" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "014" "06" "02314" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "0131" "06" "031" "0212" "02343" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "0133" "0525" "0134" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "0213" "024" "07" "0523" "022" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "0112" "0212" "0123" "043" "0112" "0114"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "051" "07" "0233" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "0121" "0232" "0423" "0233" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "0213" "02341" "0214" "031" "06" "0122"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "0235" "043" "06" "0122"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "0111" "0421" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "0233" "02312" "022" "0522"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "0114" "0132"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "024" "024" "0111" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "0423" "0523" "06" "014"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "0521" "07" "032" "024" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "0112" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "07" "07" "0121"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "0111" "06" "0131" "07" "06" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "0524" "02343" "0213" "06" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "051" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "0525" "0235" "024" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "0522" "0525" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "07" "0525" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "043" "07" "051" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "02312" "022" "0212" "0521"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "06" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "0524" "0121" "014" "0214" "07" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "0522" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "051" "051" "024" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "0521" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "0121" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "051" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "014" "0213" "051" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "0521" "07" "0134" "0525" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "0114" "014" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "0521" "024" "051" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "051" "022" "051" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "0523" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "051" "0132" "0421" "0214" "0522" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "0521" "0134" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "0213" "0525"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "0123" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "07" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02313" "0213" "0121" "051" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "0213" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "0525"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "0521"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "0121" "051"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "0521" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "0522" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "0522" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "051" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3829))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "07" "0131" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "07" "05" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "05" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02312" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "0114" "024" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "014" "024" "0423"
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#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "0132" "0421" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "0134" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "0123" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "07" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02313" "0213" "0121" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "0213" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "0121" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "05" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4160))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "0112" "06" "0112" "0123"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "0121" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "0121"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "0113" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "0123" "07" "0131" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "0122" "0112" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "0111" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "0132" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02311" "014"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "0114" "041" "07" "05" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "0111" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "05" "024" "024" "0121"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "0133"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "0132" "0131" "0235" "0112" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02312" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "0114" "024" "0134"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "014" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "0121" "041" "0422" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "0131" "07" "0114" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "05" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "0112" "0422" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "0123" "0121"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "024" "0121" "05" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "014" "05" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "0134" "05" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "05" "0121" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "0132" "02341" "014"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "0111" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "07" "02345" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "0111" "0233" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "0112" "031" "06" "07" "05" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "0232" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "0134" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "0422" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "0232" "0111"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "07" "05" "0233" "041" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "0213" "02312" "06" "05" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "05" "0112" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "014" "024" "0123" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "02314" "024" "05" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "0132" "02311" "02345" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "02345" "0422" "041" "0233" "0213"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "0111" "0422" "0122" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "05" "06" "0232" "041" "014"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "05" "07" "0233" "0131"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "0121" "0112" "032" "0111"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "022" "0113" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "0422" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "0235" "043" "07" "0134" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "05" "024" "0213" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "0121" "07" "06" "0121" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "014" "05" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "0213" "07" "0233" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "0235" "02342" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "05" "06" "041" "0121" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "0213" "07" "043" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "0121" "07" "07" "05" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "0121" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "014" "06" "02314" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "0131" "06" "031" "0212" "02343" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "0133" "05" "0134" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "0213" "024" "07" "05" "022" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "0112" "0212" "0123" "043" "0112" "0114"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "0233" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "0121" "0232" "0423" "0233" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "0213" "02341" "0214" "031" "06" "0122"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "0235" "043" "06" "0122"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "0111" "0421" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "0233" "02312" "022" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "0114" "0132"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "024" "024" "0111" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "0423" "05" "06" "014"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "032" "024" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "0112" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "07" "07" "0121"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "0111" "06" "0131" "07" "06" "0123"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "02343" "0213" "06" "0131" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "0111" "0132" "02341" "02314" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "05" "0235" "024" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "07" "05" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "0121" "043" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "0232" "014" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "02312" "022" "0212" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "0121" "014" "06" "0121" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "0121" "014" "0214" "07" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "014" "05" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "05" "05" "024" "0132"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "0121" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "014" "0213" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "0131" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "05" "07" "0134" "05" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "0114" "014" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "0111" "014" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "0132" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "0112" "06" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "0132" "0421" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "0134" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "014" "0233" "022" "0232" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "0123" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "0112" "07" "0134" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "0113" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "0111"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "0111" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02313" "0213" "0121" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "0111" "06" "0213" "0111" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "0132" "032" "032" "07" "02342" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "0121" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "014" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "0122" "02342" "07" "014" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "0111" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "0121" "0131" "02341" "05" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "0131" "0122" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "0131" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "0112" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "0123"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "0123" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4655))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
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#> "01" "01" "06" "01" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "0214" "07" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "05" "05" "024" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "01" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "01" "0213" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "01" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "05" "07" "01" "05" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "01" "01" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "0421" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "01" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "0233" "022" "0232" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "01" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02313" "0213" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "01" "06" "0213" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "02342" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02342" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02341" "05" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5122))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02311" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "0235" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02312" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "01" "024" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "01" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "0422" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "05" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "0422" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "024" "01" "05" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02341" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "07" "02345" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "0233" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "0232" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "01" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "0422" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "0232" "01"
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#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5220))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02311" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "0235" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02312" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "01" "024" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "01" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "0422" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "05" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "0422" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "024" "01" "05" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02341" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02341" "07" "02345" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "0233" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "0232" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "01" "0212" "02313" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "0422" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "0232" "01"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "0233" "07" "05" "0233" "041" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "0213" "02312" "06" "05" "02314"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "02312" "0212" "05" "01" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "01" "024" "01" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "02314" "024" "05" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "01" "02311" "02345" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "02345" "0422" "041" "0233" "0213"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "01" "0422" "01" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "05" "06" "0232" "041" "01"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "05" "07" "0233" "01"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "01" "01" "032" "01"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "022" "01" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "0422" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "0235" "043" "07" "01" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "05" "024" "0213" "0232"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "01" "07" "06" "01" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "01" "05" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02343" "0213" "07" "0233" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "0235" "02342" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "05" "06" "041" "01" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "0213" "07" "043" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "01" "07" "07" "05" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "01" "032" "0212" "02311" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "01" "06" "02314" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "01" "06" "031" "0212" "02343" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "01" "05" "01" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "0213" "024" "07" "05" "022" "0235"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "01" "0212" "01" "043" "01" "01"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "0233" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "01" "0232" "0423" "0233" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "0213" "02341" "0214" "031" "06" "01"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "0235" "043" "06" "01"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "01" "0421" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "0233" "02312" "022" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "01" "01"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02311" "0212" "024" "024" "01" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "0423" "05" "06" "01"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "032" "024" "02345" "02312"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "01" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "07" "07" "01"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "01" "06" "01" "07" "06" "01"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "02343" "0213" "06" "01" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "01" "01" "02341" "02314" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "05" "0235" "024" "02311"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "0232" "032" "07" "05" "0233"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "01" "043" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "0232" "01" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "02312" "022" "0212" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "0232" "02345"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "0214" "07" "0233"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "0232" "05" "05" "024" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "01" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "01" "0213" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "01" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "05" "07" "01" "05" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "01" "01" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "02341"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "0232" "022" "02345"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "022" "0211" "0233" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "022" "07" "024" "0232"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "0421" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "01" "02341" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "0233" "022" "0232" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "01" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "0233" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02313" "0213" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02311" "01" "06" "0213" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "02342" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02342" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02341" "05" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5315))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02343" "0214" "0235" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02345"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02311" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "02344" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02341" "07" "02311" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "0235"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "0235" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02312" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02344" "043" "01" "024" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "01" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "0232" "0232" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "0422" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "0233" "06" "07" "06" "05" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "0422" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "0235" "06" "02341" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02341" "024" "0232" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "024" "01" "05" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02342" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "0233" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02341" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
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#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02312" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "0233" "02311" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02342" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02311" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02341" "05" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "02311" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "0232" "0421" "0235" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5593))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "023" "0214" "023" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "0422" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "023"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "0422"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "023" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "023" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "023" "07" "023" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "0422" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "0423" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "023"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "023" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "023" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "023" "043" "01" "024" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "01" "024" "0423"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "0422" "0422" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "023" "023" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "0422" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "023" "06" "07" "06" "05" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "0422" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "023" "06" "023" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "023" "024" "023" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "024" "01" "05" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "023" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "0421" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "023" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "023" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "023" "07" "023" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "023" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "0423"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "023" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "01" "0212" "023" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "0422" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "023" "01"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "023" "07" "05" "023" "041" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "0213" "023" "06" "05" "023"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "023" "0212" "05" "01" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "01" "024" "01" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "023" "024" "05" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "01" "023" "023" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "023" "0422" "041" "023" "0213"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "01" "0422" "01" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "05" "06" "023" "041" "01"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "05" "07" "023" "01"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "01" "01" "032" "01"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "022" "01" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "0422" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "023" "043" "07" "01" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "0422" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "05" "024" "0213" "023"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "01" "07" "06" "01" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "01" "05" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "023" "0213" "07" "023" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "023" "023" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "05" "06" "041" "01" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "0213" "07" "043" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "01" "07" "07" "05" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "01" "032" "0212" "023" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "0422" "01" "06" "023" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "01" "06" "031" "0212" "023" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "01" "05" "01" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "0213" "024" "07" "05" "022" "023"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "01" "0212" "01" "043" "01" "01"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "023" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "01" "023" "0423" "023" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "0213" "023" "0214" "031" "06" "01"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "023" "043" "06" "01"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "01" "0421" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "023" "023" "022" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "01" "01"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "023" "0212" "024" "024" "01" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "0423" "05" "06" "01"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "032" "024" "023" "023"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "01" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "0422" "06" "07" "07" "01"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "01" "06" "01" "07" "06" "01"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "023" "0213" "06" "01" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "01" "01" "023" "023" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "05" "023" "024" "023"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "023" "032" "07" "05" "023"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "01" "043" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "023" "01" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "023" "022" "0212" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "0421"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "023" "023"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "0214" "07" "023"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "0422" "023" "05" "05" "024" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "0421" "022" "01" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "0421" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "01" "0213" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "01" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "05" "07" "01" "05" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "01" "01" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "023"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "023" "022" "023"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "022" "0211" "023" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "022" "07" "024" "023"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "0421" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "01" "023" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "023" "022" "023" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "01" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "023" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "023" "0213" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "023" "01" "06" "0213" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "0421" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "023" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "023" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "023" "023" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "023" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "023" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "023" "05" "06" "0421"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "0421" "022" "0421"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "023" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "023" "0421" "023" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5955))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "023" "0214" "023" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "023"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "023" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "023" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "023" "07" "023" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "023"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "023" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "023" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "023" "043" "01" "024" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "01" "024" "042"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "042" "042" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "023" "023" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "042" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "024" "07" "0211"
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#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "023" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "023" "0213" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "023" "01" "06" "0213" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "023" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "023" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "023" "023" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "023" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "023" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "023" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "022" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "023" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "023" "042" "023" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6049))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "023" "0214" "023" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "023"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "023" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "023" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "023" "07" "023" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "023"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "023" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "023" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "023" "043" "01" "024" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "01" "024" "042"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "042" "042" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "023" "023" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "042" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "023" "06" "07" "06" "05" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "042" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "023" "06" "023" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "023" "024" "023" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "024" "01" "05" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "023" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "042" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "023" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "023" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "023" "07" "023" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "023" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "042"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "023" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "01" "0212" "023" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "042" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "023" "01"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "023" "07" "05" "023" "041" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "0213" "023" "06" "05" "023"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "023" "0212" "05" "01" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "01" "024" "01" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "023" "024" "05" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "01" "023" "023" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "023" "042" "041" "023" "0213"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "01" "042" "01" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "05" "06" "023" "041" "01"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "05" "07" "023" "01"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "01" "01" "032" "01"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "022" "01" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "042" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "023" "043" "07" "01" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "042" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "05" "024" "0213" "023"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "01" "07" "06" "01" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "01" "05" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "023" "0213" "07" "023" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "023" "023" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "05" "06" "041" "01" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "0213" "07" "043" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "01" "07" "07" "05" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "01" "032" "0212" "023" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "042" "01" "06" "023" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "01" "06" "031" "0212" "023" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "01" "05" "01" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "0213" "024" "07" "05" "022" "023"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "01" "0212" "01" "043" "01" "01"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "023" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "01" "023" "042" "023" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "0213" "023" "0214" "031" "06" "01"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "023" "043" "06" "01"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "01" "042" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "023" "023" "022" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "01" "01"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "023" "0212" "024" "024" "01" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "042" "05" "06" "01"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "032" "024" "023" "023"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "01" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "042" "06" "07" "07" "01"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "01" "06" "01" "07" "06" "01"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "023" "0213" "06" "01" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "01" "01" "023" "023" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "05" "023" "024" "023"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "023" "032" "07" "05" "023"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "01" "043" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "023" "01" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "023" "022" "0212" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "042"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "023" "023"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "0214" "07" "023"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "042" "023" "05" "05" "024" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "042" "022" "01" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "042" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "01" "0213" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "01" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "05" "07" "01" "05" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "01" "01" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "023"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "023" "022" "023"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "022" "0211" "023" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "022" "07" "024" "023"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "042" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "01" "023" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "023" "022" "023" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "01" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "023" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "023" "0213" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "023" "01" "06" "0213" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "023" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "023" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "023" "023" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "023" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "023" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "023" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "022" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "023" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "023" "042" "023" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6247))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "023" "0214" "023" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "023"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "023" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "023" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "023" "07" "023" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "023"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "023" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "023" "024" "05"
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#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "023"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "023" "022" "023"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "022" "0211" "023" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "022" "07" "024" "023"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "042" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "01" "023" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "023" "022" "023" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "01" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "023" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "023" "0213" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "023" "01" "06" "0213" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "023" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "023" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "023" "023" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "023" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "023" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "023" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "022" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "023" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "023" "042" "023" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6744))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "0211" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "0213" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "023" "0214" "023" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "0212" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "023"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "0212" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "0212" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "023" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "023" "022"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "0211" "024"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "023" "07" "023" "024" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "024" "024" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "0211" "07" "032" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "0211" "0212" "0213" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "022" "05" "06" "041" "023"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "023" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "023" "024" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "024" "05" "06" "024" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "023" "043" "01" "024" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "0213" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "0212" "01" "024" "042"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "042" "042" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "022" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "024" "023" "023" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "0211" "06" "07" "024" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "042" "022" "05" "024"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "024" "07" "0211"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "023" "06" "07" "06" "05" "024"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "042" "041" "06" "0211" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "023" "06" "023" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "024" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "023" "024" "023" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "024" "01" "05" "06" "022"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "023" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "042" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "023" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "023" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "024"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "023" "07" "023" "07" "07" "0213"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "023" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "0214" "024" "022" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "0212" "0214" "0211" "022" "06" "0213"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "0213" "0212" "0213" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "042"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "024" "023" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "0211" "01" "0212" "023" "06" "0211"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "0214" "022" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "024" "024" "042" "024"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "0214" "023" "01"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "023" "07" "05" "023" "041" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "022" "0213" "023" "06" "05" "023"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "0214" "023" "0212" "05" "01" "022"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "022" "0214" "01" "024" "01" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "022" "023" "024" "05" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "01" "023" "023" "06" "024"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "023" "042" "041" "023" "0213"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "024" "01" "042" "01" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "024" "05" "06" "023" "041" "01"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "024" "05" "07" "023" "01"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "022" "01" "01" "032" "01"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "022" "01" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "022" "07" "042" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "023" "043" "07" "01" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "042" "024" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "024" "0212" "06" "022" "024" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "022" "07" "05" "024" "0213" "023"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "01" "07" "06" "01" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "0211" "01" "05" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "023" "0213" "07" "023" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "024" "023" "023" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "024" "05" "06" "041" "01" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "0213" "07" "043" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "01" "07" "07" "05" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "022" "01" "032" "0212" "023" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "042" "01" "06" "023" "024"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "01" "06" "031" "0212" "023" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "01" "05" "01" "0212" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "0213" "024" "07" "05" "022" "023"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "01" "0212" "01" "043" "01" "01"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "023" "022"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "022" "01" "023" "042" "023" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "0213" "023" "0214" "031" "06" "01"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "024" "024" "023" "043" "06" "01"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "01" "042" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "024" "07" "023" "023" "022" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "0214" "07" "07" "06" "01" "01"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "023" "0212" "024" "024" "01" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "042" "05" "06" "01"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "032" "024" "023" "023"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "022" "024" "01" "024" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "042" "06" "07" "07" "01"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "01" "06" "01" "07" "06" "01"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "023" "0213" "06" "01" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "01" "01" "023" "023" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "05" "023" "024" "023"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "043" "0213"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "023" "032" "07" "05" "023"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "0212" "01" "043" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "024" "023" "01" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "024" "023" "022" "0212" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "024" "07" "032" "024" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "0214" "0213" "07" "07" "042"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "023" "023"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "0214" "07" "023"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "022" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "0213" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "042" "023" "05" "05" "024" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "042" "022" "01" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "042" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "0213" "01" "0213" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "0211" "01" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "05" "07" "01" "05" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "01" "01" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "023"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "023" "022" "023"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "022" "0211" "023" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "0213"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "022" "07" "024" "023"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "042" "0214" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "01" "023" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "023" "022" "023" "0213" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "0214" "024" "01" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "0214" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "0211" "041" "023" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "023" "0213" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "023" "01" "06" "0213" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "0211" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "023" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "023" "06" "0211"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "023" "023" "06" "0213" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "023" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "023" "07" "01" "0213"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "023" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "022" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "023" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "023" "042" "023" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7180))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "024" "024" "043" "041" "07" "024"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "024" "021" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "021" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "023" "021" "023" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "021" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "024" "024" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "024" "05" "024" "024"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "024" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "023"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "024" "01" "021" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "021" "043" "07" "022" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "023" "01"
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#> "041" "021" "041" "06" "07" "024"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "042" "023" "05" "05" "024" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "042" "022" "01" "041" "041" "022"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "042" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "021" "01" "021" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "021" "01" "022" "022" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "024" "05" "07" "01" "05" "024"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "024" "01" "01" "07" "032" "024"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "024" "05" "024" "05" "023"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "023" "022" "023"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "022" "021" "023" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "022" "05" "021"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "022" "07" "024" "023"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "022"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "042" "021" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "024" "05" "01" "023" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "023" "022" "023" "021" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "024" "021" "024" "01" "024" "024"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "021" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "021" "041" "023" "022" "022"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "022" "022" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "022" "07" "024" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "023" "021" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "023" "01" "06" "021" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "024" "021" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "023" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "023" "06" "021"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "023" "023" "06" "021" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "022" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "023" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "023" "07" "01" "021"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "023" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "022" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "024" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "023" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "024" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "023" "042" "023" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "024"
#> TCGA.05.4425.01
#> "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9072))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02" "02" "043" "041" "07" "02"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "02" "02" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02" "02" "02" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "02" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02" "02" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "02" "05" "02" "02"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "02" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "02" "01" "02" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "02" "043" "07" "02" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "02" "02"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "02" "02"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02" "07" "02" "02" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "02" "02" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "02" "07" "032" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "02" "02" "02" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "02" "05" "06" "041" "02"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "02" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02" "02" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02" "05" "06" "02" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02" "043" "01" "02" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "02" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "02" "01" "02" "042"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "042" "042" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "02" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02" "02" "02" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "02" "06" "07" "02" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "042" "02" "05" "02"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "02" "07" "02"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "02" "06" "07" "06" "05" "02"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "042" "041" "06" "02" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "02" "06" "02" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "02" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02" "02" "02" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "02" "01" "05" "06" "02"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "042" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "02" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "02"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02" "07" "02" "07" "07" "02"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "02" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "02" "02" "02" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "02" "02" "02" "02" "06" "02"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "02" "02" "02" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "042"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "02" "02" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "02" "01" "02" "02" "06" "02"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "02" "02" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "02" "02" "042" "02"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "02" "02" "01"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "02" "07" "05" "02" "041" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "02" "02" "02" "06" "05" "02"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "02" "02" "02" "05" "01" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "02" "02" "01" "02" "01" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "02" "02" "02" "05" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "01" "02" "02" "06" "02"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "02" "042" "041" "02" "02"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "02" "01" "042" "01" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "02" "05" "06" "02" "041" "01"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "02" "05" "07" "02" "01"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "02" "01" "01" "032" "01"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "02" "01" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "02" "07" "042" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "02" "043" "07" "01" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "042" "02" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "02" "02" "06" "02" "02" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "02" "07" "05" "02" "02" "02"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "01" "07" "06" "01" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "02" "01" "05" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02" "02" "07" "02" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "02" "02" "02" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "02" "05" "06" "041" "01" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "02" "07" "043" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "01" "07" "07" "05" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "02" "01" "032" "02" "02" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "042" "01" "06" "02" "02"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "01" "06" "031" "02" "02" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "01" "05" "01" "02" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "02" "02" "07" "05" "02" "02"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "01" "02" "01" "043" "01" "01"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "02" "02"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "02" "01" "02" "042" "02" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "02" "02" "02" "031" "06" "01"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "02" "02" "02" "043" "06" "01"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "01" "042" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "02" "07" "02" "02" "02" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "02" "07" "07" "06" "01" "01"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02" "02" "02" "02" "01" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "042" "05" "06" "01"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "032" "02" "02" "02"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "02" "02" "01" "02" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "042" "06" "07" "07" "01"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "01" "06" "01" "07" "06" "01"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "02" "02" "06" "01" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "01" "01" "02" "02" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "05" "02" "02" "02"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "043" "02"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "02" "032" "07" "05" "02"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "02" "01" "043" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "02" "02" "01" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "02" "02" "02" "02" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02" "07" "032" "02" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "02" "02" "07" "07" "042"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "02" "02"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "02" "07" "02"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "02" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "02" "041" "06" "07" "02"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "042" "02" "05" "05" "02" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "042" "02" "01" "041" "041" "02"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "042" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02" "01" "02" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "02" "01" "02" "02" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02" "05" "07" "01" "05" "02"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02" "01" "01" "07" "032" "02"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "02" "05" "02" "05" "02"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "02" "02" "02"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "02" "02" "02" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "02" "05" "02"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "02" "07" "02" "02"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "02"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "042" "02" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "02" "05" "01" "02" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "02" "02" "02" "02" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "02" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "02" "041" "02" "02" "02"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "02" "02" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "02" "07" "02" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02" "02" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02" "01" "06" "02" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "02" "02" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "02" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02" "06" "02"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "02" "02" "06" "02" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "02" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02" "07" "01" "02"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "02" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "02" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "02" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "02" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "02" "042" "02" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "02"
#> TCGA.05.4425.01
#> "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9538))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02" "02" "043" "041" "07" "02"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "02" "02" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02" "02" "02" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "02" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02" "02" "07" "07" "06" "01"
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#> "032" "07" "02" "02" "01" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "02" "02" "02" "02" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02" "07" "032" "02" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "02" "02" "07" "07" "042"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "02" "02"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "02" "07" "02"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "02" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "02" "041" "06" "07" "02"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "042" "02" "05" "05" "02" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "042" "02" "01" "041" "041" "02"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "042" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02" "01" "02" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "02" "01" "02" "02" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02" "05" "07" "01" "05" "02"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02" "01" "01" "07" "032" "02"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "02" "05" "02" "05" "02"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "02" "02" "02"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "02" "02" "02" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "02" "05" "02"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "02" "07" "02" "02"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "02"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "042" "02" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "02" "05" "01" "02" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "02" "02" "02" "02" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "02" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "02" "041" "02" "02" "02"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "02" "02" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "02" "07" "02" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02" "02" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02" "01" "06" "02" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "02" "02" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "02" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02" "06" "02"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "02" "02" "06" "02" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "02" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02" "07" "01" "02"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "02" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "02" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "02" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "02" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "02" "042" "02" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "02"
#> TCGA.05.4425.01
#> "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10893))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02" "02" "043" "041" "07" "02"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "02" "02" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02" "02" "02" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "02" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02" "02" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "02" "05" "02" "02"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "02" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "02" "01" "02" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "02" "043" "07" "02" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "02" "02"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "02" "02"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02" "07" "02" "02" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "02" "02" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "02" "07" "032" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "02" "02" "02" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "02" "05" "06" "041" "02"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "02" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02" "02" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02" "05" "06" "02" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02" "043" "01" "02" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "02" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "02" "01" "02" "042"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "042" "042" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "02" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02" "02" "02" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "02" "06" "07" "02" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "042" "02" "05" "02"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "02" "07" "02"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "02" "06" "07" "06" "05" "02"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "042" "041" "06" "02" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "02" "06" "02" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "02" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02" "02" "02" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "02" "01" "05" "06" "02"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "042" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "02" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "02"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02" "07" "02" "07" "07" "02"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "02" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "02" "02" "02" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "02" "02" "02" "02" "06" "02"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "02" "02" "02" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "042"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "02" "02" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "02" "01" "02" "02" "06" "02"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "02" "02" "043" "07"
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#> "07" "07" "02" "042" "02" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "02"
#> TCGA.05.4425.01
#> "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17308))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02" "02" "043" "041" "07" "02"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "032" "032" "02" "02" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "032" "02" "02" "02" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "02" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02" "02" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "02" "05" "02" "02"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "02" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "02" "01" "02" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "02" "043" "07" "02" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "02" "02"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "031" "07" "06" "01" "02" "02"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02" "07" "02" "02" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "02" "02" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "02" "07" "032" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "032" "02" "02" "02" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "02" "05" "06" "041" "02"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "02" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "031" "05" "02" "02" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02" "05" "06" "02" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02" "043" "01" "02" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "032" "06" "02" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "02" "01" "02" "042"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "042" "042" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "032" "02" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02" "02" "02" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "02" "06" "07" "02" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "042" "02" "05" "02"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "02" "07" "02"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "02" "06" "07" "06" "05" "02"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "042" "041" "06" "02" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "032" "06" "02" "06" "02" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "02" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02" "02" "02" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "02" "01" "05" "06" "02"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02" "032"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "042" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "02" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "02"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02" "07" "02" "07" "07" "02"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "02" "031" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "032" "02" "02" "02" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "02" "02" "02" "02" "06" "02"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "02" "02" "02" "032"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "031" "06" "07" "05" "042"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "02" "02" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "02" "01" "02" "02" "06" "02"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "02" "02" "043" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "02" "02" "042" "02"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "041" "07" "032" "02" "02" "01"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "02" "07" "05" "02" "041" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "02" "02" "02" "06" "05" "02"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "02" "02" "02" "05" "01" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "02" "02" "01" "02" "01" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "02" "02" "02" "05" "032"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "01" "02" "02" "06" "02"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "02" "042" "041" "02" "02"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "02" "01" "042" "01" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "02" "05" "06" "02" "041" "01"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "02" "05" "07" "02" "01"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "02" "01" "01" "032" "01"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "02" "01" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "02" "07" "042" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "02" "043" "07" "01" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "042" "02" "06" "06" "043" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "02" "02" "06" "02" "02" "032"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "02" "07" "05" "02" "02" "02"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "01" "07" "06" "01" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "02" "01" "05" "07" "043"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02" "02" "07" "02" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "02" "02" "02" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "02" "05" "06" "041" "01" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "02" "07" "043" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "01" "07" "07" "05" "07" "043"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "02" "01" "032" "02" "02" "032"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "042" "01" "06" "02" "02"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "01" "06" "031" "02" "02" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "01" "05" "01" "02" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "02" "02" "07" "05" "02" "02"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "01" "02" "01" "043" "01" "01"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "02" "02"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "02" "01" "02" "042" "02" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "02" "02" "02" "031" "06" "01"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "02" "02" "02" "043" "06" "01"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "01" "042" "07" "07" "041"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "02" "07" "02" "02" "02" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "02" "07" "07" "06" "01" "01"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02" "02" "02" "02" "01" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "042" "05" "06" "01"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "032" "02" "02" "02"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "02" "02" "01" "02" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "042" "06" "07" "07" "01"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "01" "06" "01" "07" "06" "01"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "02" "02" "06" "01" "032"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "01" "01" "02" "02" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "032" "07" "05" "02" "02" "02"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "043" "02"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "02" "032" "07" "05" "02"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "02" "01" "043" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "032" "07" "02" "02" "01" "032"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "02" "02" "02" "02" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02" "07" "032" "02" "06" "031"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "02" "02" "07" "07" "042"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "02" "02"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "02" "07" "02"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "02" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "041" "02" "041" "06" "07" "02"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "042" "02" "05" "05" "02" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "032" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "042" "02" "01" "041" "041" "02"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "042" "05" "06" "06" "032"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02" "01" "02" "05" "032" "043"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "02" "01" "02" "02" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02" "05" "07" "01" "05" "02"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02" "01" "01" "07" "032" "02"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "02" "05" "02" "05" "02"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "02" "02" "02"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "02" "02" "02" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "02" "05" "02"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "02" "07" "02" "02"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "032" "032" "032" "07" "05" "02"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "042" "02" "05" "032"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "02" "05" "01" "02" "032" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "02" "02" "02" "02" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "02" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "043" "07" "06" "07" "041"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "02" "041" "02" "02" "02"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "041" "032" "02" "02" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "02" "07" "02" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02" "02" "01" "05" "041"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "032" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02" "01" "06" "02" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "032" "041" "02" "02" "042" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "032" "032" "07" "02" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02" "06" "02"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "02" "02" "06" "02" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "02" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02" "07" "01" "032"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02" "07" "01" "02"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "02" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "02" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "02" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "02" "032" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "02" "042" "02" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "031" "05" "01" "02"
#> TCGA.05.4425.01
#> "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23556))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02" "02" "043" "041" "07" "02"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "041" "03" "03" "02" "02" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "03" "02" "02" "02" "041" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "041" "02" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02" "02" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "042" "05" "02" "05" "02" "02"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "02" "06" "01" "06" "041"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "042"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "02" "01" "02" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "02" "043" "07" "02" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "041" "07" "05" "02" "02"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "03" "07" "06" "01" "02" "02"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02" "07" "02" "02" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "042" "06" "05" "02" "02" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "02" "07" "03" "041" "042" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "03" "02" "02" "02" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "02" "05" "06" "041" "02"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "02" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "03" "05" "02" "02" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02" "05" "06" "02" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02" "043" "01" "02" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "03" "06" "02" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "02" "01" "02" "042"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "043" "06" "042" "042" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "03" "02" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02" "02" "02" "05" "06" "041"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "02" "06" "07" "02" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "041" "042" "02" "05" "02"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "02" "07" "02"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "02" "06" "07" "06" "05" "02"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "042" "041" "06" "02" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "03" "06" "02" "06" "02" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "041" "02" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02" "02" "02" "07" "07" "043"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "02" "01" "05" "06" "02"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02" "03"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "041" "042" "041"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "02" "041" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "041" "07" "01" "02"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02" "07" "02" "07" "07" "02"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
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#> "07" "01" "02" "07" "01" "03"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02" "07" "01" "02"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02" "05" "06" "042"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "042" "02" "042"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "02" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "041" "01" "02" "041" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "02" "03" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "02" "042" "02" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "041" "043" "03" "05" "01" "02"
#> TCGA.05.4425.01
#> "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 26140))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02" "02" "04" "04" "07" "02"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "04" "03" "03" "02" "02" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "03" "02" "02" "02" "04" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "04" "02" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02" "02" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "04" "05" "02" "05" "02" "02"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "02" "06" "01" "06" "04"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "04"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "02" "01" "02" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "02" "04" "07" "02" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "04" "07" "05" "02" "02"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "03" "07" "06" "01" "02" "02"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02" "07" "02" "02" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "04" "06" "05" "02" "02" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "02" "07" "03" "04" "04" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "03" "02" "02" "02" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "02" "05" "06" "04" "02"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "02" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "03" "05" "02" "02" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02" "05" "06" "02" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02" "04" "01" "02" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "03" "06" "02" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "02" "01" "02" "04"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "04" "06" "04" "04" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "03" "02" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02" "02" "02" "05" "06" "04"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "02" "06" "07" "02" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "04" "04" "02" "05" "02"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "02" "07" "02"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "02" "06" "07" "06" "05" "02"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "04" "04" "06" "02" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "03" "06" "02" "06" "02" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "04" "02" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02" "02" "02" "07" "07" "04"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
#> "05" "02" "01" "05" "06" "02"
#> TCGA.34.5929.11 TCGA.55.7816.01 TCGA.77.A5GH.01 TCGA.39.5019.11 TCGA.55.7815.01 TCGA.85.A510.01
#> "05" "05" "01" "05" "02" "03"
#> TCGA.52.7622.01 TCGA.50.6593.11 TCGA.77.7337.01 TCGA.37.A5EN.01 TCGA.77.8148.01 TCGA.18.5592.01
#> "01" "05" "06" "04" "04" "04"
#> TCGA.05.5423.01 TCGA.92.7341.01 TCGA.22.4613.11 TCGA.34.A5IX.01 TCGA.56.8623.01 TCGA.63.A5MI.01
#> "02" "04" "05" "01" "05" "06"
#> TCGA.44.2656.11 TCGA.85.A4CL.01 TCGA.44.6778.11 TCGA.34.8454.01 TCGA.55.6985.01 TCGA.77.8146.01
#> "05" "06" "05" "01" "02" "01"
#> TCGA.38.4631.11 TCGA.L9.A5IP.01 TCGA.56.7582.01 TCGA.55.8615.01 TCGA.56.8309.01 TCGA.55.7281.01
#> "05" "07" "04" "07" "01" "02"
#> TCGA.93.7347.01 TCGA.MP.A4TF.01 TCGA.44.6777.01 TCGA.62.A471.01 TCGA.49.4490.01 TCGA.97.8177.01
#> "02" "07" "02" "07" "07" "02"
#> TCGA.63.7021.01 TCGA.99.7458.01 TCGA.85.8352.01 TCGA.85.7698.01 TCGA.77.8139.01 TCGA.39.5019.01
#> "01" "02" "03" "06" "06" "06"
#> TCGA.64.5775.01 TCGA.91.A4BD.01 TCGA.38.6178.01 TCGA.44.A47B.01 TCGA.22.4599.01 TCGA.85.8052.01
#> "03" "02" "02" "02" "06" "06"
#> TCGA.55.6979.01 TCGA.55.7573.01 TCGA.55.8097.01 TCGA.05.5429.01 TCGA.77.7142.01 TCGA.93.A4JP.01
#> "02" "02" "02" "02" "06" "02"
#> TCGA.NC.A5HK.01 TCGA.05.5425.01 TCGA.S2.AA1A.01 TCGA.93.A4JQ.01 TCGA.78.7160.01 TCGA.50.5946.02
#> "07" "07" "02" "02" "02" "03"
#> TCGA.58.8387.01 TCGA.43.7658.01 TCGA.96.A4JK.01 TCGA.50.5066.02 TCGA.33.4579.11 TCGA.43.6143.01
#> "01" "03" "06" "07" "05" "04"
#> TCGA.56.8305.01 TCGA.55.8092.01 TCGA.75.6207.01 TCGA.75.5122.01 TCGA.97.7938.01 TCGA.49.AARE.01
#> "06" "07" "07" "02" "02" "07"
#> TCGA.44.7671.01 TCGA.55.7726.01 TCGA.50.5055.01 TCGA.85.6560.01 TCGA.98.8022.01 TCGA.91.8496.01
#> "02" "01" "02" "02" "06" "02"
#> TCGA.43.5668.01 TCGA.21.5786.01 TCGA.MP.A4T2.01 TCGA.62.A46R.01 TCGA.34.8456.01 TCGA.69.7764.01
#> "07" "06" "02" "02" "04" "07"
#> TCGA.91.6840.01 TCGA.95.7043.01 TCGA.L9.A443.01 TCGA.86.7701.01 TCGA.56.7222.01 TCGA.52.7812.01
#> "07" "07" "02" "02" "04" "02"
#> TCGA.94.8490.01 TCGA.73.4676.01 TCGA.55.8514.01 TCGA.78.7162.01 TCGA.L9.A50W.01 TCGA.39.5028.01
#> "04" "07" "03" "02" "02" "01"
#> TCGA.50.8460.01 TCGA.55.8505.01 TCGA.86.A4P8.01 TCGA.67.6217.01 TCGA.22.5482.01 TCGA.33.4586.11
#> "02" "07" "05" "02" "04" "05"
#> TCGA.78.7535.01 TCGA.93.7348.01 TCGA.86.8671.01 TCGA.21.5782.01 TCGA.39.5039.11 TCGA.50.6592.01
#> "02" "02" "02" "06" "05" "02"
#> TCGA.97.7546.01 TCGA.44.7661.01 TCGA.95.7944.01 TCGA.38.4632.11 TCGA.77.8008.01 TCGA.97.A4M0.01
#> "02" "02" "02" "05" "01" "02"
#> TCGA.50.5933.01 TCGA.86.8280.01 TCGA.22.4609.01 TCGA.78.8660.01 TCGA.43.8115.01 TCGA.44.2655.11
#> "02" "02" "01" "02" "01" "05"
#> TCGA.39.5016.01 TCGA.55.7907.01 TCGA.49.6767.01 TCGA.MP.A4TK.01 TCGA.33.4582.11 TCGA.78.7155.01
#> "06" "02" "02" "02" "05" "03"
#> TCGA.85.A4CN.01 TCGA.56.A5DS.01 TCGA.69.7761.01 TCGA.91.6835.01 TCGA.O2.A52N.01 TCGA.78.7540.01
#> "06" "01" "02" "02" "06" "02"
#> TCGA.50.5939.11 TCGA.95.A4VN.01 TCGA.46.6026.01 TCGA.85.7710.01 TCGA.44.A47F.01 TCGA.55.A48Z.01
#> "05" "02" "04" "04" "02" "02"
#> TCGA.85.8664.01 TCGA.69.7763.01 TCGA.34.5241.01 TCGA.43.A474.01 TCGA.96.A4JL.01 TCGA.NC.A5HO.01
#> "06" "02" "01" "04" "01" "06"
#> TCGA.J2.A4AE.01 TCGA.75.6203.01 TCGA.77.8133.01 TCGA.50.5942.01 TCGA.22.5473.01 TCGA.33.AASI.01
#> "02" "05" "06" "02" "04" "01"
#> TCGA.98.A53B.01 TCGA.50.6590.01 TCGA.18.4721.11 TCGA.78.7148.01 TCGA.80.5608.01 TCGA.43.6647.01
#> "06" "02" "05" "07" "02" "01"
#> TCGA.55.8205.01 TCGA.55.8511.01 TCGA.77.A5GA.01 TCGA.56.6546.01 TCGA.44.7669.01 TCGA.85.7697.01
#> "07" "02" "01" "01" "03" "01"
#> TCGA.50.6594.11 TCGA.56.5898.01 TCGA.99.8025.01 TCGA.77.6842.01 TCGA.34.8455.01 TCGA.43.A56V.01
#> "05" "06" "02" "01" "06" "06"
#> TCGA.55.7283.01 TCGA.91.6830.01 TCGA.77.8154.01 TCGA.49.4488.11 TCGA.MN.A4N4.01 TCGA.22.5477.11
#> "02" "07" "04" "05" "07" "05"
#> TCGA.85.A4QQ.01 TCGA.55.A491.01 TCGA.22.5491.01 TCGA.39.5022.01 TCGA.63.A5MR.01 TCGA.44.8120.01
#> "06" "02" "04" "07" "01" "07"
#> TCGA.77.7139.01 TCGA.MN.A4N5.01 TCGA.37.A5EL.01 TCGA.39.5036.01 TCGA.58.8392.01 TCGA.73.A9RS.01
#> "04" "02" "06" "06" "04" "07"
#> TCGA.69.7978.01 TCGA.55.8299.01 TCGA.22.5479.01 TCGA.44.8117.01 TCGA.MP.A4TD.01 TCGA.49.AAR2.01
#> "02" "02" "06" "02" "02" "03"
#> TCGA.05.4405.01 TCGA.70.6722.01 TCGA.39.5035.11 TCGA.83.5908.01 TCGA.55.6980.01 TCGA.44.6146.01
#> "02" "07" "05" "02" "02" "02"
#> TCGA.58.A46K.01 TCGA.94.A5I6.01 TCGA.69.7979.01 TCGA.56.A4BY.01 TCGA.85.8049.01 TCGA.95.7039.01
#> "06" "01" "07" "06" "01" "07"
#> TCGA.18.3417.01 TCGA.62.8397.01 TCGA.56.8201.01 TCGA.44.6145.11 TCGA.91.6848.01 TCGA.63.7023.01
#> "06" "02" "01" "05" "07" "04"
#> TCGA.97.7552.01 TCGA.50.5936.01 TCGA.33.6738.01 TCGA.91.7771.01 TCGA.18.5595.11 TCGA.56.A4BW.01
#> "02" "02" "07" "02" "05" "06"
#> TCGA.56.8308.01 TCGA.NJ.A4YG.01 TCGA.86.8359.01 TCGA.55.8301.01 TCGA.43.6773.01 TCGA.78.7146.01
#> "06" "02" "02" "02" "07" "07"
#> TCGA.44.3918.01 TCGA.50.5935.11 TCGA.63.7020.01 TCGA.33.AASJ.01 TCGA.85.8353.01 TCGA.49.6743.01
#> "02" "05" "06" "04" "01" "07"
#> TCGA.22.5478.11 TCGA.55.8621.01 TCGA.78.7161.01 TCGA.85.8070.01 TCGA.NC.A5HQ.01 TCGA.49.6745.11
#> "05" "02" "07" "04" "06" "05"
#> TCGA.96.7545.01 TCGA.44.A4SU.01 TCGA.97.7937.01 TCGA.49.AARR.01 TCGA.05.5428.01 TCGA.98.A53A.01
#> "01" "07" "07" "05" "07" "04"
#> TCGA.49.6745.01 TCGA.85.8276.01 TCGA.64.5774.01 TCGA.44.A4SS.01 TCGA.55.8089.01 TCGA.55.8094.01
#> "02" "01" "03" "02" "02" "03"
#> TCGA.LA.A446.01 TCGA.NC.A5HT.01 TCGA.58.8386.01 TCGA.77.A5GF.01 TCGA.NJ.A4YQ.01 TCGA.55.7574.01
#> "06" "04" "01" "06" "02" "02"
#> TCGA.56.7731.01 TCGA.56.8304.01 TCGA.22.5481.01 TCGA.63.A5MN.01 TCGA.50.8459.01 TCGA.NC.A5HR.01
#> "01" "06" "03" "02" "02" "06"
#> TCGA.96.8169.01 TCGA.18.5592.11 TCGA.33.4589.01 TCGA.78.8648.01 TCGA.L9.A8F4.01 TCGA.91.A4BC.01
#> "01" "05" "01" "02" "07" "07"
#> TCGA.NC.A5HJ.01 TCGA.44.2656.01 TCGA.J2.A4AD.01 TCGA.85.A4PA.01 TCGA.86.8673.01 TCGA.73.7499.01
#> "02" "02" "07" "05" "02" "02"
#> TCGA.98.8023.01 TCGA.97.A4LX.01 TCGA.56.8625.01 TCGA.43.6770.01 TCGA.60.2703.01 TCGA.77.A5GB.01
#> "01" "02" "01" "04" "01" "01"
#> TCGA.38.4631.01 TCGA.39.5029.01 TCGA.99.AA5R.01 TCGA.05.4390.01 TCGA.MP.A4T7.01 TCGA.69.7765.01
#> "07" "06" "05" "07" "02" "02"
#> TCGA.95.8494.01 TCGA.90.A4EE.01 TCGA.97.8171.01 TCGA.34.5929.01 TCGA.50.8457.01 TCGA.55.6972.01
#> "02" "01" "02" "04" "02" "07"
#> TCGA.97.A4M5.01 TCGA.53.7626.01 TCGA.44.5645.01 TCGA.22.5483.01 TCGA.56.8629.01 TCGA.63.A5MG.01
#> "02" "02" "02" "03" "06" "01"
#> TCGA.78.7158.01 TCGA.86.8056.01 TCGA.69.7980.01 TCGA.77.7140.01 TCGA.77.7465.01 TCGA.94.8491.01
#> "02" "02" "02" "04" "06" "01"
#> TCGA.43.7657.01 TCGA.85.A4JC.01 TCGA.NC.A5HF.01 TCGA.05.4433.01 TCGA.50.5932.01 TCGA.63.A5MB.01
#> "06" "01" "04" "07" "07" "04"
#> TCGA.97.8175.01 TCGA.50.7109.01 TCGA.86.8668.01 TCGA.MP.A4T4.01 TCGA.44.A47A.01 TCGA.73.4676.11
#> "02" "07" "02" "02" "02" "05"
#> TCGA.NJ.A55O.01 TCGA.55.8508.01 TCGA.71.6725.01 TCGA.33.4579.01 TCGA.77.7138.01 TCGA.68.A59I.01
#> "02" "07" "07" "06" "01" "01"
#> TCGA.93.A4JO.01 TCGA.44.6145.01 TCGA.97.8547.01 TCGA.44.6147.01 TCGA.77.8131.01 TCGA.94.A4VJ.01
#> "02" "02" "02" "02" "01" "06"
#> TCGA.56.A5DR.01 TCGA.86.8075.01 TCGA.34.5927.01 TCGA.60.2697.01 TCGA.85.7844.01 TCGA.68.7756.01
#> "06" "07" "04" "05" "06" "01"
#> TCGA.43.5668.11 TCGA.78.7633.01 TCGA.75.6211.01 TCGA.77.8007.01 TCGA.55.8510.01 TCGA.49.AARO.01
#> "05" "07" "03" "02" "02" "02"
#> TCGA.98.8021.01 TCGA.55.8090.01 TCGA.86.8073.01 TCGA.58.A46J.01 TCGA.91.6828.01 TCGA.49.4514.01
#> "06" "02" "02" "01" "02" "07"
#> TCGA.22.5472.01 TCGA.NC.A5HN.01 TCGA.34.5239.01 TCGA.05.4396.01 TCGA.75.5147.01 TCGA.92.8064.01
#> "06" "04" "06" "07" "07" "01"
#> TCGA.85.A50Z.01 TCGA.77.7463.01 TCGA.55.8204.01 TCGA.86.7711.01 TCGA.44.5643.01 TCGA.O2.A52V.01
#> "01" "06" "01" "07" "06" "01"
#> TCGA.L4.A4E6.01 TCGA.86.8076.01 TCGA.97.A4M6.01 TCGA.33.4586.01 TCGA.85.6175.01 TCGA.75.7031.01
#> "05" "02" "02" "06" "01" "03"
#> TCGA.39.5039.01 TCGA.39.5024.01 TCGA.50.5044.01 TCGA.64.5781.01 TCGA.73.4658.11 TCGA.52.7810.01
#> "01" "01" "02" "02" "05" "06"
#> TCGA.44.8119.01 TCGA.05.5420.01 TCGA.43.3394.11 TCGA.NJ.A4YF.01 TCGA.38.7271.01 TCGA.49.AAR3.01
#> "03" "07" "05" "02" "02" "02"
#> TCGA.90.7767.01 TCGA.78.7154.01 TCGA.39.5016.11 TCGA.90.6837.01 TCGA.77.8150.01 TCGA.MP.A4TJ.01
#> "06" "07" "05" "05" "04" "02"
#> TCGA.33.4582.01 TCGA.69.7760.01 TCGA.55.A4DF.01 TCGA.44.7667.01 TCGA.44.6148.11 TCGA.49.4512.01
#> "06" "02" "03" "07" "05" "02"
#> TCGA.50.5939.01 TCGA.33.A4WN.01 TCGA.18.5595.01 TCGA.O1.A52J.01 TCGA.50.6592.11 TCGA.78.7167.01
#> "02" "01" "04" "07" "05" "07"
#> TCGA.78.8662.01 TCGA.05.4427.01 TCGA.78.7143.01 TCGA.97.A4M3.01 TCGA.NK.A5CT.01 TCGA.78.7220.01
#> "03" "07" "02" "02" "01" "03"
#> TCGA.86.8585.01 TCGA.75.6205.01 TCGA.99.8028.01 TCGA.55.7903.01 TCGA.49.4487.01 TCGA.50.5933.11
#> "07" "02" "02" "02" "02" "05"
#> TCGA.55.A493.01 TCGA.78.7147.01 TCGA.44.5644.01 TCGA.75.5126.01 TCGA.85.8288.01 TCGA.50.6591.01
#> "02" "07" "03" "02" "06" "03"
#> TCGA.55.8085.01 TCGA.55.8206.01 TCGA.97.7553.01 TCGA.MP.A4TE.01 TCGA.78.7542.01 TCGA.79.5596.01
#> "07" "02" "02" "07" "07" "04"
#> TCGA.18.4721.01 TCGA.85.8351.01 TCGA.85.7843.01 TCGA.60.2709.01 TCGA.NJ.A7XG.01 TCGA.55.A48X.01
#> "01" "01" "06" "01" "02" "02"
#> TCGA.98.A53D.01 TCGA.85.8666.01 TCGA.94.7943.01 TCGA.64.5778.01 TCGA.49.AAR9.01 TCGA.50.6594.01
#> "05" "01" "01" "02" "07" "02"
#> TCGA.NK.A5CX.01 TCGA.44.2668.11 TCGA.95.A4VK.01 TCGA.78.7153.01 TCGA.56.7221.01 TCGA.49.4488.01
#> "01" "05" "07" "02" "06" "07"
#> TCGA.63.A5ML.01 TCGA.55.7728.01 TCGA.22.5477.01 TCGA.98.A538.01 TCGA.55.7994.01 TCGA.67.6215.01
#> "04" "02" "04" "06" "07" "02"
#> TCGA.85.8071.01 TCGA.78.7537.01 TCGA.39.5034.11 TCGA.98.A53H.01 TCGA.55.6982.01 TCGA.XC.AA0X.01
#> "04" "02" "05" "05" "02" "01"
#> TCGA.L9.A7SV.01 TCGA.39.5036.11 TCGA.98.A53J.01 TCGA.85.8277.01 TCGA.MP.A5C7.01 TCGA.05.4424.01
#> "03" "05" "06" "06" "07" "07"
#> TCGA.77.8143.01 TCGA.55.7227.01 TCGA.85.6561.01 TCGA.77.6845.01 TCGA.56.7730.01 TCGA.86.A456.01
#> "04" "02" "01" "04" "04" "02"
#> TCGA.39.5035.01 TCGA.56.7579.01 TCGA.22.4599.11 TCGA.58.A46M.01 TCGA.77.7338.01 TCGA.80.5611.01
#> "06" "04" "05" "06" "06" "03"
#> TCGA.44.6774.01 TCGA.85.8582.01 TCGA.49.AAQV.01 TCGA.39.5031.11 TCGA.49.6742.01 TCGA.63.A5MH.01
#> "02" "01" "02" "05" "03" "04"
#> TCGA.51.6867.01 TCGA.73.7498.01 TCGA.34.5234.01 TCGA.38.4632.01 TCGA.69.7974.01 TCGA.63.A5MJ.01
#> "06" "02" "01" "02" "02" "06"
#> TCGA.55.6986.01 TCGA.50.5936.11 TCGA.4B.A93V.01 TCGA.22.4605.01 TCGA.22.5471.11 TCGA.49.6761.01
#> "02" "05" "07" "01" "05" "02"
#> TCGA.MP.A4T6.01 TCGA.56.8624.01 TCGA.94.7033.01 TCGA.86.A4D0.01 TCGA.62.A46O.01 TCGA.44.6779.01
#> "02" "01" "01" "07" "03" "02"
#> TCGA.78.7159.01 TCGA.86.A4P7.01 TCGA.50.5932.11 TCGA.73.4658.01 TCGA.22.5480.11 TCGA.85.A513.01
#> "07" "02" "05" "02" "05" "02"
#> TCGA.60.2704.01 TCGA.63.A5MT.01 TCGA.99.8032.01 TCGA.50.5935.01 TCGA.55.7727.01 TCGA.55.6981.01
#> "01" "01" "07" "02" "02" "02"
#> TCGA.55.7724.01 TCGA.78.8655.01 TCGA.78.7163.01 TCGA.97.7941.01 TCGA.MP.A4TA.01 TCGA.56.7822.01
#> "01" "02" "02" "02" "07" "06"
#> TCGA.56.A62T.01 TCGA.75.5146.01 TCGA.50.5931.11 TCGA.55.7914.01 TCGA.22.4601.11 TCGA.75.7030.01
#> "06" "07" "05" "02" "05" "02"
#> TCGA.85.A4JB.01 TCGA.56.A49D.01 TCGA.62.A472.01 TCGA.64.5779.01 TCGA.05.4417.01 TCGA.67.4679.01
#> "01" "06" "02" "07" "02" "02"
#> TCGA.39.5034.01 TCGA.55.8620.01 TCGA.55.7570.01 TCGA.50.6673.01 TCGA.77.A5FZ.01 TCGA.97.7554.01
#> "03" "03" "03" "07" "05" "02"
#> TCGA.33.4589.11 TCGA.39.5030.01 TCGA.58.8390.01 TCGA.75.7025.01 TCGA.18.3417.11 TCGA.55.5899.01
#> "05" "01" "04" "02" "05" "03"
#> TCGA.95.8039.01 TCGA.44.6144.11 TCGA.43.8118.01 TCGA.50.5941.01 TCGA.62.8399.01 TCGA.95.7562.01
#> "02" "05" "01" "02" "03" "07"
#> TCGA.68.7757.01 TCGA.97.8174.01 TCGA.55.7576.01 TCGA.55.7725.01 TCGA.38.A44F.01 TCGA.39.5029.11
#> "01" "02" "02" "02" "02" "05"
#> TCGA.80.5607.01 TCGA.55.8091.01 TCGA.62.8395.01 TCGA.92.8065.01 TCGA.86.8672.01 TCGA.64.5815.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.75.6212.01 TCGA.52.7811.01 TCGA.50.5930.01 TCGA.77.8136.01 TCGA.22.5474.01 TCGA.68.A59J.01
#> "02" "01" "07" "01" "06" "06"
#> TCGA.33.4587.01 TCGA.39.5027.01 TCGA.55.7284.01 TCGA.22.5492.01 TCGA.91.6829.01 TCGA.22.5485.01
#> "01" "04" "07" "06" "07" "04"
#> TCGA.86.8669.01 TCGA.44.6776.01 TCGA.33.4583.01 TCGA.55.6983.01 TCGA.93.8067.01 TCGA.69.A59K.01
#> "07" "02" "04" "02" "02" "02"
#> TCGA.64.1679.01 TCGA.MF.A522.01 TCGA.91.8499.01 TCGA.95.7567.01 TCGA.49.AARN.01 TCGA.56.8628.01
#> "07" "04" "03" "02" "02" "01"
#> TCGA.21.A5DI.01 TCGA.91.6836.01 TCGA.55.8616.01 TCGA.97.8172.01 TCGA.50.5051.01 TCGA.77.7141.01
#> "01" "02" "07" "02" "07" "06"
#> TCGA.90.7766.01 TCGA.O2.A52Q.01 TCGA.50.5045.01 TCGA.22.5489.01 TCGA.44.6147.11 TCGA.70.6723.01
#> "06" "02" "02" "01" "05" "04"
#> TCGA.NC.A5HD.01 TCGA.64.1681.01 TCGA.78.7150.01 TCGA.NC.A5HM.01 TCGA.86.8674.01 TCGA.46.6025.01
#> "06" "07" "03" "06" "07" "06"
#> TCGA.55.6978.01 TCGA.56.5897.01 TCGA.52.7809.01 TCGA.95.A4VP.01 TCGA.85.8048.01 TCGA.43.8116.01
#> "02" "01" "06" "02" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "03" "04" "02" "02" "04" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "03" "03" "07" "02" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02" "06" "02"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "02" "02" "06" "02" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "02" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02" "07" "01" "03"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02" "07" "01" "02"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02" "05" "06" "04"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "04" "02" "04"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "02" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "04" "01" "02" "04" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "02" "03" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "02" "04" "02" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "04" "04" "03" "05" "01" "02"
#> TCGA.05.4425.01
#> "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 54725))
#> TCGA.44.4112.01 TCGA.NJ.A4YP.01 TCGA.22.4613.01 TCGA.90.7769.01 TCGA.77.A5G1.01 TCGA.86.8278.01
#> "02" "02" "04" "04" "07" "02"
#> TCGA.77.A5G3.01 TCGA.62.A470.01 TCGA.44.6778.01 TCGA.49.AARQ.01 TCGA.97.A4M1.01 TCGA.55.6975.01
#> "04" "03" "03" "02" "02" "07"
#> TCGA.99.8033.01 TCGA.43.7656.01 TCGA.85.8481.01 TCGA.56.A4ZK.01 TCGA.77.8156.01 TCGA.43.A475.01
#> "02" "06" "01" "06" "01" "01"
#> TCGA.69.8255.01 TCGA.69.8453.01 TCGA.97.8552.01 TCGA.53.A4EZ.01 TCGA.58.A46N.01 TCGA.63.A5MW.01
#> "03" "02" "02" "02" "04" "06"
#> TCGA.85.8479.01 TCGA.68.8251.01 TCGA.44.2659.11 TCGA.34.7107.01 TCGA.50.5066.01 TCGA.55.7910.01
#> "06" "01" "05" "04" "02" "07"
#> TCGA.62.A46U.01 TCGA.MP.A4T8.01 TCGA.78.7539.01 TCGA.39.5040.01 TCGA.63.A5M9.01 TCGA.92.8063.01
#> "02" "02" "07" "07" "06" "01"
#> TCGA.56.7823.01 TCGA.43.3920.11 TCGA.MP.A4SY.01 TCGA.44.5645.11 TCGA.93.A4JN.01 TCGA.86.A4JF.01
#> "04" "05" "02" "05" "02" "02"
#> TCGA.37.A5EM.01 TCGA.63.6202.01 TCGA.98.A53I.01 TCGA.44.7660.01 TCGA.98.8020.01 TCGA.58.8391.01
#> "06" "02" "06" "01" "06" "04"
#> TCGA.85.8580.01 TCGA.86.6851.01 TCGA.34.5232.01 TCGA.39.5031.01 TCGA.62.8398.01 TCGA.J2.A4AG.01
#> "01" "07" "01" "06" "07" "02"
#> TCGA.92.7340.01 TCGA.85.8287.01 TCGA.56.8622.01 TCGA.22.5471.01 TCGA.85.7950.01 TCGA.85.A4QR.01
#> "01" "01" "06" "06" "06" "04"
#> TCGA.MP.A4TI.01 TCGA.77.8138.01 TCGA.55.8208.01 TCGA.22.5480.01 TCGA.58.8388.01 TCGA.62.8394.01
#> "02" "01" "02" "06" "06" "07"
#> TCGA.63.7022.01 TCGA.85.8584.01 TCGA.77.8128.01 TCGA.97.8176.01 TCGA.NJ.A4YI.01 TCGA.44.2665.11
#> "01" "02" "04" "07" "02" "05"
#> TCGA.85.7699.01 TCGA.33.AAS8.01 TCGA.50.5931.01 TCGA.22.5473.11 TCGA.49.AAR4.01 TCGA.56.8626.01
#> "06" "06" "06" "05" "02" "01"
#> TCGA.39.5028.11 TCGA.22.4601.01 TCGA.86.8281.01 TCGA.22.5482.11 TCGA.55.6984.01 TCGA.MN.A4N1.01
#> "01" "04" "07" "05" "02" "02"
#> TCGA.91.6847.01 TCGA.86.8358.01 TCGA.77.A5G8.01 TCGA.85.8355.01 TCGA.75.6206.01 TCGA.MP.A4TC.01
#> "03" "07" "06" "01" "02" "02"
#> TCGA.78.7149.01 TCGA.49.6744.01 TCGA.91.6831.01 TCGA.L9.A743.01 TCGA.05.4410.01 TCGA.86.7954.01
#> "07" "02" "07" "02" "02" "07"
#> TCGA.22.4593.01 TCGA.43.5670.01 TCGA.39.5030.11 TCGA.62.A46Y.01 TCGA.50.6597.01 TCGA.NC.A5HE.01
#> "04" "06" "05" "02" "02" "01"
#> TCGA.05.4384.01 TCGA.55.6642.01 TCGA.44.6144.01 TCGA.34.5240.01 TCGA.63.5131.01 TCGA.05.4415.01
#> "02" "07" "03" "04" "04" "07"
#> TCGA.44.A479.01 TCGA.86.7955.01 TCGA.55.8087.01 TCGA.85.A50M.01 TCGA.MP.A4TH.01 TCGA.75.6214.01
#> "07" "03" "02" "02" "02" "01"
#> TCGA.22.5489.11 TCGA.55.8207.01 TCGA.44.2662.11 TCGA.NC.A5HI.01 TCGA.77.8009.01 TCGA.86.6562.01
#> "05" "02" "05" "06" "04" "02"
#> TCGA.43.A56U.01 TCGA.56.8503.01 TCGA.86.8074.01 TCGA.34.5236.01 TCGA.NK.A5D1.01 TCGA.50.5930.11
#> "01" "01" "02" "01" "06" "05"
#> TCGA.33.6737.01 TCGA.56.7223.01 TCGA.22.5474.11 TCGA.39.5011.01 TCGA.MP.A4SW.01 TCGA.22.5492.11
#> "07" "03" "05" "02" "02" "05"
#> TCGA.67.6216.01 TCGA.22.5485.11 TCGA.21.5783.01 TCGA.55.8203.01 TCGA.J2.8194.01 TCGA.33.4583.11
#> "02" "05" "06" "02" "07" "05"
#> TCGA.55.6968.01 TCGA.55.8619.01 TCGA.77.8153.01 TCGA.L3.A4E7.01 TCGA.44.2668.01 TCGA.90.A59Q.01
#> "07" "02" "04" "01" "02" "01"
#> TCGA.55.A57B.01 TCGA.55.8507.01 TCGA.94.7557.01 TCGA.55.6971.01 TCGA.49.AAR0.01 TCGA.85.6798.01
#> "07" "03" "06" "02" "07" "06"
#> TCGA.22.5491.11 TCGA.75.7027.01 TCGA.98.7454.01 TCGA.55.8614.01 TCGA.L9.A444.01 TCGA.56.8083.01
#> "05" "07" "02" "01" "02" "04"
#> TCGA.85.7696.01 TCGA.77.A5G6.01 TCGA.90.A4ED.01 TCGA.56.A4BX.01 TCGA.NC.A5HG.01 TCGA.50.5072.01
#> "06" "04" "06" "04" "04" "07"
#> TCGA.37.5819.01 TCGA.62.A46V.01 TCGA.55.8512.01 TCGA.77.6843.01 TCGA.77.8130.01 TCGA.34.5928.01
#> "03" "02" "07" "06" "06" "06"
#> TCGA.44.A47G.01 TCGA.69.8253.01 TCGA.91.6849.01 TCGA.44.6146.11 TCGA.22.A5C4.01 TCGA.33.A5GW.01
#> "02" "02" "02" "05" "06" "04"
#> TCGA.94.8035.01 TCGA.50.5944.01 TCGA.94.A5I4.01 TCGA.O2.A5IC.01 TCGA.44.2665.01 TCGA.86.8279.01
#> "06" "02" "06" "07" "02" "07"
#> TCGA.85.A53L.01 TCGA.63.5128.01 TCGA.63.A5MU.01 TCGA.62.A46P.01 TCGA.98.A53C.01 TCGA.44.2666.01
#> "01" "04" "04" "02" "05" "02"
#> TCGA.56.A4ZJ.01 TCGA.55.8096.01 TCGA.44.6148.01 TCGA.55.A494.01 TCGA.44.3917.01 TCGA.97.7547.01
#> "01" "07" "01" "02" "07" "02"
#> TCGA.69.8254.01 TCGA.77.8145.01 TCGA.53.7624.01 TCGA.O2.A52W.01 TCGA.43.6771.11 TCGA.75.5125.01
#> "02" "06" "07" "06" "05" "02"
#> TCGA.63.A5MV.01 TCGA.34.5231.01 TCGA.33.AASD.01 TCGA.77.8140.01 TCGA.69.7973.01 TCGA.22.5478.01
#> "01" "04" "04" "06" "02" "06"
#> TCGA.86.8054.01 TCGA.90.7964.01 TCGA.L4.A4E5.01 TCGA.68.8250.01 TCGA.44.6775.01 TCGA.55.7913.01
#> "03" "06" "02" "06" "02" "07"
#> TCGA.56.8504.01 TCGA.NC.A5HP.01 TCGA.55.7911.01 TCGA.33.4566.01 TCGA.58.8393.01 TCGA.63.A5MS.01
#> "06" "04" "02" "07" "01" "01"
#> TCGA.MP.A4T9.01 TCGA.55.6712.01 TCGA.86.7714.01 TCGA.78.8640.01 TCGA.44.7670.01 TCGA.39.5037.01
#> "02" "02" "02" "07" "07" "04"
#> TCGA.39.5011.11 TCGA.95.7948.01 TCGA.63.A5MP.01 TCGA.39.5021.11 TCGA.85.8072.01 TCGA.55.A4DG.01
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#> "06" "07" "03" "06" "07" "06"
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#> "02" "01" "06" "02" "01" "06"
#> TCGA.55.A490.01 TCGA.68.7755.01 TCGA.05.5715.01 TCGA.55.A492.01 TCGA.NC.A5HH.01 TCGA.22.5472.11
#> "03" "04" "02" "02" "04" "05"
#> TCGA.96.8170.01 TCGA.55.6969.01 TCGA.21.5787.01 TCGA.78.7166.01 TCGA.55.A48Y.01 TCGA.44.5643.11
#> "01" "03" "03" "07" "02" "05"
#> TCGA.86.7953.01 TCGA.85.8350.01 TCGA.MP.A4SV.01 TCGA.50.6595.01 TCGA.LA.A7SW.01 TCGA.55.6543.01
#> "07" "06" "07" "02" "06" "02"
#> TCGA.91.8497.01 TCGA.50.5049.01 TCGA.96.7544.01 TCGA.97.A4M2.01 TCGA.NC.A5HL.01 TCGA.55.8513.01
#> "02" "02" "06" "02" "01" "05"
#> TCGA.44.7659.01 TCGA.43.6771.01 TCGA.62.8402.01 TCGA.55.7995.01 TCGA.05.5420.11 TCGA.77.A5G7.01
#> "02" "01" "07" "07" "05" "06"
#> TCGA.NJ.A55R.01 TCGA.35.5375.01 TCGA.97.A4M7.01 TCGA.86.8055.01 TCGA.6A.AB49.01 TCGA.78.7536.01
#> "07" "01" "02" "07" "01" "03"
#> TCGA.33.AASB.01 TCGA.78.7156.01 TCGA.44.7662.01 TCGA.55.8506.01 TCGA.85.A511.01 TCGA.55.6970.01
#> "07" "07" "02" "07" "01" "02"
#> TCGA.NK.A7XE.01 TCGA.56.6545.01 TCGA.50.5068.01 TCGA.33.4566.11 TCGA.56.8307.01 TCGA.NK.A5CR.01
#> "01" "01" "02" "05" "06" "04"
#> TCGA.53.7813.01 TCGA.NJ.A55A.01 TCGA.63.A5MM.01 TCGA.77.6844.01 TCGA.71.8520.01 TCGA.56.8082.01
#> "07" "01" "01" "04" "02" "04"
#> TCGA.39.5037.11 TCGA.98.A539.01 TCGA.O2.A52S.01 TCGA.21.5784.01 TCGA.44.7672.01 TCGA.97.8179.01
#> "05" "06" "06" "01" "02" "07"
#> TCGA.L3.A524.01 TCGA.39.5021.01 TCGA.55.6987.01 TCGA.85.A5B5.01 TCGA.58.A46L.01 TCGA.77.8144.01
#> "04" "01" "02" "04" "06" "06"
#> TCGA.J1.A4AH.01 TCGA.86.7713.01 TCGA.78.7152.01 TCGA.50.5946.01 TCGA.56.7580.01 TCGA.62.A46S.01
#> "06" "07" "02" "03" "06" "07"
#> TCGA.95.7947.01 TCGA.J2.8192.01 TCGA.78.7145.01 TCGA.63.A5MY.01 TCGA.50.6593.01 TCGA.33.AASL.01
#> "07" "07" "02" "04" "02" "01"
#> TCGA.85.A512.01 TCGA.85.8354.01 TCGA.O2.A5IB.01 TCGA.50.6591.11 TCGA.77.7335.01 TCGA.55.8302.01
#> "04" "04" "03" "05" "01" "02"
#> TCGA.05.4425.01
#> "02"
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
#> Error in h(simpleError(msg, call)) :
#> error in evaluating the argument 'object' in selecting a method for function 'draw': no applicable method for 'height' applied to an object of class "list"
Top rows on each node:
top_rows_overlap(res_rh, method = "upset")
#> Error: Only support number of sets <= 31.
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 = 1019),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1019),
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 = 1063),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1063),
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 = 1256),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1256),
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 = 1325),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1325),
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 = 1393),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1393),
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 = 2507),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2507),
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 = 2667),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2667),
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 = 2814),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2814),
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 = 2908),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2908),
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 = 2922),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2922),
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 = 3090),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3090),
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 = 3223),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3223),
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 = 3229),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3229),
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 = 3363),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3363),
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 = 3829),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3829),
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 = 4160),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4160),
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 = 4655),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4655),
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 = 5122),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5122),
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 = 5220),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5220),
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 = 5315),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5315),
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 = 5593),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5593),
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 = 5955),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5955),
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 = 6049),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6049),
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 = 6247),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6247),
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 = 6744),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6744),
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 = 7180),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7180),
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 = 9072),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9072),
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 = 9538),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9538),
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 = 10893),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10893),
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 = 17308),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17308),
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 = 23556),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 23556),
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 = 26140),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 26140),
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 = 54725),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 54725),
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 = 1019))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1063))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1256))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1325))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1393))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2507))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2667))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2814))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2908))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2922))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3090))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3223))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3229))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3363))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3829))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4160))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4655))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5122))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5220))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5315))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5593))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5955))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6049))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6247))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6744))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7180))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9072))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9538))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10893))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 17308))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 23556))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 26140))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 54725))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
#> Error: Only support number of sets <= 31.
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 , Node06 , Node07 .
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 375955 rows and 500 columns, randomly sampled from 907 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 8.
#>
#> Following methods can be applied to this '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 0.991 0.996 0.3599 0.645 0.645
#> 3 3 1.000 0.972 0.989 0.6095 0.765 0.638
#> 4 4 0.948 0.909 0.967 0.1520 0.879 0.725
#> 5 5 0.814 0.854 0.936 0.1195 0.767 0.426
#> 6 6 0.914 0.888 0.940 0.0340 0.894 0.638
#> 7 7 0.986 0.951 0.977 0.0620 0.899 0.610
#> 8 8 0.942 0.864 0.932 0.0117 0.971 0.848
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 3 4 6 7
There is also optional best \(k\) = 2 3 4 6 7 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
get_classes(res, k = 2)
#> class p
#> TCGA.44.4112.01 2 0.000
#> TCGA.NJ.A4YP.01 2 0.000
#> TCGA.22.4613.01 1 0.000
#> TCGA.90.7769.01 1 0.000
#> TCGA.77.A5G1.01 2 0.000
#> TCGA.86.8278.01 2 0.000
#> TCGA.77.A5G3.01 1 0.000
#> TCGA.62.A470.01 2 0.000
#> TCGA.44.6778.01 2 0.000
#> TCGA.49.AARQ.01 2 0.000
#> TCGA.97.A4M1.01 2 0.000
#> TCGA.55.6975.01 2 0.000
#> TCGA.99.8033.01 2 0.000
#> TCGA.43.7656.01 1 0.000
#> TCGA.85.8481.01 2 0.000
#> TCGA.56.A4ZK.01 1 0.000
#> TCGA.77.8156.01 2 0.000
#> TCGA.43.A475.01 2 1.000
#> TCGA.69.8255.01 2 0.000
#> TCGA.69.8453.01 2 0.000
#> TCGA.97.8552.01 2 0.000
#> TCGA.53.A4EZ.01 2 0.000
#> TCGA.58.A46N.01 1 0.000
#> TCGA.63.A5MW.01 1 0.000
#> TCGA.85.8479.01 1 0.000
#> TCGA.68.8251.01 1 0.000
#> TCGA.44.2659.11 2 0.000
#> TCGA.34.7107.01 1 0.000
#> TCGA.50.5066.01 2 0.000
#> TCGA.55.7910.01 2 0.000
#> TCGA.62.A46U.01 2 0.000
#> TCGA.MP.A4T8.01 2 0.000
#> TCGA.78.7539.01 2 0.000
#> TCGA.39.5040.01 2 0.000
#> TCGA.63.A5M9.01 1 0.000
#> TCGA.92.8063.01 1 0.000
#> TCGA.56.7823.01 1 0.000
#> TCGA.43.3920.11 2 0.000
#> TCGA.MP.A4SY.01 2 0.000
#> TCGA.44.5645.11 2 0.000
#> TCGA.93.A4JN.01 2 0.000
#> TCGA.86.A4JF.01 2 0.000
#> TCGA.37.A5EM.01 1 0.000
#> TCGA.63.6202.01 2 0.000
#> TCGA.98.A53I.01 1 0.000
#> TCGA.44.7660.01 1 0.000
#> TCGA.98.8020.01 1 0.000
#> TCGA.58.8391.01 1 0.000
#> TCGA.85.8580.01 2 0.249
#> TCGA.86.6851.01 2 0.000
#> TCGA.34.5232.01 2 0.000
#> TCGA.39.5031.01 1 0.000
#> TCGA.62.8398.01 2 0.000
#> TCGA.J2.A4AG.01 2 0.000
#> TCGA.92.7340.01 1 0.498
#> TCGA.85.8287.01 1 0.000
#> TCGA.56.8622.01 1 0.000
#> TCGA.22.5471.01 1 0.000
#> TCGA.85.7950.01 1 0.000
#> TCGA.85.A4QR.01 1 0.000
#> TCGA.MP.A4TI.01 2 0.000
#> TCGA.77.8138.01 2 0.000
#> TCGA.55.8208.01 2 0.000
#> TCGA.22.5480.01 1 0.000
#> TCGA.58.8388.01 1 0.000
#> TCGA.62.8394.01 2 0.000
#> TCGA.63.7022.01 2 0.000
#> TCGA.85.8584.01 2 0.000
#> TCGA.77.8128.01 1 0.000
#> TCGA.97.8176.01 2 0.000
#> TCGA.NJ.A4YI.01 2 0.000
#> TCGA.44.2665.11 2 0.000
#> TCGA.85.7699.01 1 0.000
#> TCGA.33.AAS8.01 1 0.000
#> TCGA.50.5931.01 1 0.000
#> TCGA.22.5473.11 2 0.000
#> TCGA.49.AAR4.01 2 0.000
#> TCGA.56.8626.01 2 0.498
#> TCGA.39.5028.11 2 0.000
#> TCGA.22.4601.01 1 0.000
#> TCGA.86.8281.01 2 0.000
#> TCGA.22.5482.11 2 0.000
#> TCGA.55.6984.01 2 0.000
#> TCGA.MN.A4N1.01 2 0.000
#> TCGA.91.6847.01 2 0.000
#> TCGA.86.8358.01 2 0.000
#> TCGA.77.A5G8.01 1 0.000
#> TCGA.85.8355.01 2 0.000
#> TCGA.75.6206.01 2 0.000
#> TCGA.MP.A4TC.01 2 0.000
#> TCGA.78.7149.01 2 0.000
#> TCGA.49.6744.01 2 0.000
#> TCGA.91.6831.01 2 0.000
#> TCGA.L9.A743.01 2 0.000
#> TCGA.05.4410.01 2 0.000
#> TCGA.86.7954.01 2 0.000
#> TCGA.22.4593.01 1 0.000
#> TCGA.43.5670.01 1 0.000
#> TCGA.39.5030.11 2 0.000
#> TCGA.62.A46Y.01 2 0.000
#> TCGA.50.6597.01 2 0.000
#> TCGA.NC.A5HE.01 2 0.000
#> TCGA.05.4384.01 2 0.000
#> TCGA.55.6642.01 2 0.000
#> TCGA.44.6144.01 2 0.000
#> TCGA.34.5240.01 1 0.000
#> TCGA.63.5131.01 1 0.000
#> TCGA.05.4415.01 2 0.000
#> TCGA.44.A479.01 2 0.000
#> TCGA.86.7955.01 2 0.000
#> TCGA.55.8087.01 2 0.000
#> TCGA.85.A50M.01 2 0.000
#> TCGA.MP.A4TH.01 2 0.000
#> TCGA.75.6214.01 1 0.249
#> TCGA.22.5489.11 2 0.000
#> TCGA.55.8207.01 2 0.000
#> TCGA.44.2662.11 2 0.000
#> TCGA.NC.A5HI.01 1 0.000
#> TCGA.77.8009.01 1 0.000
#> TCGA.86.6562.01 2 0.000
#> TCGA.43.A56U.01 2 0.000
#> TCGA.56.8503.01 2 0.000
#> TCGA.86.8074.01 2 0.000
#> TCGA.34.5236.01 2 0.249
#> TCGA.NK.A5D1.01 1 0.000
#> TCGA.50.5930.11 2 0.000
#> TCGA.33.6737.01 2 0.000
#> TCGA.56.7223.01 2 0.000
#> TCGA.22.5474.11 2 0.000
#> TCGA.39.5011.01 2 0.000
#> TCGA.MP.A4SW.01 2 0.000
#> TCGA.22.5492.11 2 0.000
#> TCGA.67.6216.01 2 0.000
#> TCGA.22.5485.11 2 0.000
#> TCGA.21.5783.01 1 0.000
#> TCGA.55.8203.01 2 0.000
#> TCGA.J2.8194.01 2 0.000
#> TCGA.33.4583.11 2 0.000
#> TCGA.55.6968.01 2 0.000
#> TCGA.55.8619.01 2 0.000
#> TCGA.77.8153.01 1 0.000
#> TCGA.L3.A4E7.01 1 0.000
#> TCGA.44.2668.01 2 0.000
#> TCGA.90.A59Q.01 2 0.000
#> TCGA.55.A57B.01 2 0.000
#> TCGA.55.8507.01 2 0.000
#> TCGA.94.7557.01 1 0.000
#> TCGA.55.6971.01 2 0.000
#> TCGA.49.AAR0.01 2 0.000
#> TCGA.85.6798.01 1 0.000
#> TCGA.22.5491.11 2 0.000
#> TCGA.75.7027.01 2 0.000
#> TCGA.98.7454.01 2 0.000
#> TCGA.55.8614.01 1 0.000
#> TCGA.L9.A444.01 2 0.000
#> TCGA.56.8083.01 1 0.000
#> TCGA.85.7696.01 1 0.000
#> TCGA.77.A5G6.01 1 0.000
#> TCGA.90.A4ED.01 1 0.000
#> TCGA.56.A4BX.01 1 0.000
#> TCGA.NC.A5HG.01 1 0.000
#> TCGA.50.5072.01 2 0.000
#> TCGA.37.5819.01 2 0.000
#> TCGA.62.A46V.01 2 0.000
#> TCGA.55.8512.01 2 0.000
#> TCGA.77.6843.01 1 0.000
#> TCGA.77.8130.01 1 0.000
#> TCGA.34.5928.01 1 0.000
#> TCGA.44.A47G.01 2 0.000
#> TCGA.69.8253.01 2 0.000
#> TCGA.91.6849.01 2 0.000
#> TCGA.44.6146.11 2 0.000
#> TCGA.22.A5C4.01 1 0.000
#> TCGA.33.A5GW.01 1 0.000
#> TCGA.94.8035.01 1 0.000
#> TCGA.50.5944.01 2 0.000
#> TCGA.94.A5I4.01 1 0.000
#> TCGA.O2.A5IC.01 2 0.000
#> TCGA.44.2665.01 2 0.000
#> TCGA.86.8279.01 2 0.000
#> TCGA.85.A53L.01 1 0.000
#> TCGA.63.5128.01 1 0.000
#> TCGA.63.A5MU.01 1 0.000
#> TCGA.62.A46P.01 2 0.000
#> TCGA.98.A53C.01 2 0.000
#> TCGA.44.2666.01 2 0.000
#> TCGA.56.A4ZJ.01 2 0.000
#> TCGA.55.8096.01 2 0.000
#> TCGA.44.6148.01 2 0.000
#> TCGA.55.A494.01 2 0.000
#> TCGA.44.3917.01 2 0.000
#> TCGA.97.7547.01 2 0.000
#> TCGA.69.8254.01 2 0.000
#> TCGA.77.8145.01 1 0.000
#> TCGA.53.7624.01 2 0.000
#> TCGA.O2.A52W.01 1 0.000
#> TCGA.43.6771.11 2 0.000
#> TCGA.75.5125.01 2 0.000
#> TCGA.63.A5MV.01 1 0.000
#> TCGA.34.5231.01 1 0.000
#> TCGA.33.AASD.01 1 0.000
#> TCGA.77.8140.01 1 0.000
#> TCGA.69.7973.01 2 0.000
#> TCGA.22.5478.01 1 0.000
#> TCGA.86.8054.01 2 0.000
#> TCGA.90.7964.01 1 0.000
#> TCGA.L4.A4E5.01 2 0.000
#> TCGA.68.8250.01 1 0.000
#> TCGA.44.6775.01 2 0.000
#> TCGA.55.7913.01 2 0.000
#> TCGA.56.8504.01 1 0.000
#> TCGA.NC.A5HP.01 1 0.000
#> TCGA.55.7911.01 2 0.000
#> TCGA.33.4566.01 2 0.000
#> TCGA.58.8393.01 2 0.000
#> TCGA.63.A5MS.01 2 0.249
#> TCGA.MP.A4T9.01 2 0.000
#> TCGA.55.6712.01 2 0.000
#> TCGA.86.7714.01 2 0.000
#> TCGA.78.8640.01 2 0.000
#> TCGA.44.7670.01 2 0.000
#> TCGA.39.5037.01 1 0.000
#> TCGA.39.5011.11 2 0.000
#> TCGA.95.7948.01 2 0.000
#> TCGA.63.A5MP.01 2 1.000
#> TCGA.39.5021.11 2 0.000
#> TCGA.85.8072.01 1 0.000
#> TCGA.55.A4DG.01 2 0.000
#> TCGA.34.5929.11 2 0.000
#> TCGA.55.7816.01 2 0.000
#> TCGA.77.A5GH.01 1 0.000
#> TCGA.39.5019.11 2 0.000
#> TCGA.55.7815.01 2 0.000
#> TCGA.85.A510.01 2 0.000
#> TCGA.52.7622.01 1 0.000
#> TCGA.50.6593.11 2 0.000
#> TCGA.77.7337.01 1 0.000
#> TCGA.37.A5EN.01 1 0.000
#> TCGA.77.8148.01 1 0.000
#> TCGA.18.5592.01 1 0.000
#> TCGA.05.5423.01 2 0.000
#> TCGA.92.7341.01 1 0.000
#> TCGA.22.4613.11 2 0.000
#> TCGA.34.A5IX.01 1 0.000
#> TCGA.56.8623.01 2 0.000
#> TCGA.63.A5MI.01 1 0.000
#> TCGA.44.2656.11 2 0.000
#> TCGA.85.A4CL.01 1 0.000
#> TCGA.44.6778.11 2 0.000
#> TCGA.34.8454.01 1 0.000
#> TCGA.55.6985.01 2 0.000
#> TCGA.77.8146.01 1 0.000
#> TCGA.38.4631.11 2 0.000
#> TCGA.L9.A5IP.01 2 0.000
#> TCGA.56.7582.01 1 0.000
#> TCGA.55.8615.01 2 0.000
#> TCGA.56.8309.01 2 0.000
#> TCGA.55.7281.01 2 0.000
#> TCGA.93.7347.01 2 0.000
#> TCGA.MP.A4TF.01 2 0.000
#> TCGA.44.6777.01 2 0.000
#> TCGA.62.A471.01 2 0.000
#> TCGA.49.4490.01 2 0.000
#> TCGA.97.8177.01 2 0.000
#> TCGA.63.7021.01 2 0.751
#> TCGA.99.7458.01 2 0.000
#> TCGA.85.8352.01 2 0.249
#> TCGA.85.7698.01 1 0.000
#> TCGA.77.8139.01 1 0.000
#> TCGA.39.5019.01 1 0.000
#> TCGA.64.5775.01 2 0.000
#> TCGA.91.A4BD.01 2 0.000
#> TCGA.38.6178.01 2 0.000
#> TCGA.44.A47B.01 2 0.000
#> TCGA.22.4599.01 1 0.000
#> TCGA.85.8052.01 1 0.000
#> TCGA.55.6979.01 2 0.000
#> TCGA.55.7573.01 2 0.000
#> TCGA.55.8097.01 2 0.000
#> TCGA.05.5429.01 2 0.000
#> TCGA.77.7142.01 1 0.000
#> TCGA.93.A4JP.01 2 0.000
#> TCGA.NC.A5HK.01 2 0.000
#> TCGA.05.5425.01 2 0.000
#> TCGA.S2.AA1A.01 2 0.000
#> TCGA.93.A4JQ.01 2 0.000
#> TCGA.78.7160.01 2 0.000
#> TCGA.50.5946.02 2 0.000
#> TCGA.58.8387.01 1 0.000
#> TCGA.43.7658.01 2 0.000
#> TCGA.96.A4JK.01 1 0.000
#> TCGA.50.5066.02 2 0.000
#> TCGA.33.4579.11 2 0.000
#> TCGA.43.6143.01 1 0.000
#> TCGA.56.8305.01 1 0.000
#> TCGA.55.8092.01 2 0.000
#> TCGA.75.6207.01 2 0.000
#> TCGA.75.5122.01 2 0.000
#> TCGA.97.7938.01 2 0.000
#> TCGA.49.AARE.01 2 0.000
#> TCGA.44.7671.01 2 0.000
#> TCGA.55.7726.01 1 0.000
#> TCGA.50.5055.01 2 0.000
#> TCGA.85.6560.01 2 0.000
#> TCGA.98.8022.01 1 0.000
#> TCGA.91.8496.01 2 0.000
#> TCGA.43.5668.01 2 0.000
#> TCGA.21.5786.01 1 0.000
#> TCGA.MP.A4T2.01 2 0.000
#> TCGA.62.A46R.01 2 0.000
#> TCGA.34.8456.01 1 0.000
#> TCGA.69.7764.01 2 0.000
#> TCGA.91.6840.01 2 0.000
#> TCGA.95.7043.01 2 0.000
#> TCGA.L9.A443.01 2 0.000
#> TCGA.86.7701.01 2 0.000
#> TCGA.56.7222.01 1 0.000
#> TCGA.52.7812.01 2 0.000
#> TCGA.94.8490.01 1 0.000
#> TCGA.73.4676.01 2 0.000
#> TCGA.55.8514.01 2 0.000
#> TCGA.78.7162.01 2 0.000
#> TCGA.L9.A50W.01 2 0.000
#> TCGA.39.5028.01 1 0.000
#> TCGA.50.8460.01 2 0.000
#> TCGA.55.8505.01 2 0.000
#> TCGA.86.A4P8.01 2 0.000
#> TCGA.67.6217.01 2 0.000
#> TCGA.22.5482.01 1 0.000
#> TCGA.33.4586.11 2 0.000
#> TCGA.78.7535.01 2 0.000
#> TCGA.93.7348.01 2 0.000
#> TCGA.86.8671.01 2 0.000
#> TCGA.21.5782.01 1 0.000
#> TCGA.39.5039.11 2 0.000
#> TCGA.50.6592.01 2 0.000
#> TCGA.97.7546.01 2 0.000
#> TCGA.44.7661.01 2 0.000
#> TCGA.95.7944.01 2 0.000
#> TCGA.38.4632.11 2 0.000
#> TCGA.77.8008.01 2 0.000
#> TCGA.97.A4M0.01 2 0.000
#> TCGA.50.5933.01 2 0.000
#> TCGA.86.8280.01 2 0.000
#> TCGA.22.4609.01 1 0.000
#> TCGA.78.8660.01 2 0.000
#> TCGA.43.8115.01 1 0.000
#> TCGA.44.2655.11 2 0.000
#> TCGA.39.5016.01 1 0.000
#> TCGA.55.7907.01 2 0.000
#> TCGA.49.6767.01 2 0.000
#> TCGA.MP.A4TK.01 2 0.000
#> TCGA.33.4582.11 2 0.000
#> TCGA.78.7155.01 2 0.000
#> TCGA.85.A4CN.01 1 0.000
#> TCGA.56.A5DS.01 2 0.249
#> TCGA.69.7761.01 2 0.000
#> TCGA.91.6835.01 2 0.000
#> TCGA.O2.A52N.01 1 0.000
#> TCGA.78.7540.01 2 0.000
#> TCGA.50.5939.11 2 0.000
#> TCGA.95.A4VN.01 2 0.000
#> TCGA.46.6026.01 1 0.000
#> TCGA.85.7710.01 1 0.000
#> TCGA.44.A47F.01 2 0.000
#> TCGA.55.A48Z.01 2 0.000
#> TCGA.85.8664.01 1 0.000
#> TCGA.69.7763.01 2 0.000
#> TCGA.34.5241.01 1 0.000
#> TCGA.43.A474.01 1 0.000
#> TCGA.96.A4JL.01 2 0.000
#> TCGA.NC.A5HO.01 1 0.000
#> TCGA.J2.A4AE.01 2 0.000
#> TCGA.75.6203.01 2 0.000
#> TCGA.77.8133.01 1 0.000
#> TCGA.50.5942.01 2 0.000
#> TCGA.22.5473.01 1 0.000
#> TCGA.33.AASI.01 2 0.498
#> TCGA.98.A53B.01 1 0.000
#> TCGA.50.6590.01 2 0.000
#> TCGA.18.4721.11 2 0.000
#> TCGA.78.7148.01 2 0.000
#> TCGA.80.5608.01 2 0.000
#> TCGA.43.6647.01 2 0.000
#> TCGA.55.8205.01 2 0.000
#> TCGA.55.8511.01 2 0.000
#> TCGA.77.A5GA.01 1 0.000
#> TCGA.56.6546.01 2 0.000
#> TCGA.44.7669.01 2 0.000
#> TCGA.85.7697.01 1 0.000
#> TCGA.50.6594.11 2 0.000
#> TCGA.56.5898.01 1 0.000
#> TCGA.99.8025.01 2 0.000
#> TCGA.77.6842.01 1 0.000
#> TCGA.34.8455.01 1 0.000
#> TCGA.43.A56V.01 1 0.000
#> TCGA.55.7283.01 2 0.000
#> TCGA.91.6830.01 2 0.000
#> TCGA.77.8154.01 1 0.000
#> TCGA.49.4488.11 2 0.000
#> TCGA.MN.A4N4.01 2 0.000
#> TCGA.22.5477.11 2 0.000
#> TCGA.85.A4QQ.01 1 0.000
#> TCGA.55.A491.01 2 0.000
#> TCGA.22.5491.01 1 0.000
#> TCGA.39.5022.01 2 0.000
#> TCGA.63.A5MR.01 1 0.000
#> TCGA.44.8120.01 2 0.000
#> TCGA.77.7139.01 1 0.000
#> TCGA.MN.A4N5.01 2 0.000
#> TCGA.37.A5EL.01 1 0.000
#> TCGA.39.5036.01 1 0.000
#> TCGA.58.8392.01 1 0.000
#> TCGA.73.A9RS.01 2 0.000
#> TCGA.69.7978.01 2 0.000
#> TCGA.55.8299.01 2 0.000
#> TCGA.22.5479.01 1 0.000
#> TCGA.44.8117.01 2 0.000
#> TCGA.MP.A4TD.01 2 0.000
#> TCGA.49.AAR2.01 2 0.000
#> TCGA.05.4405.01 2 0.000
#> TCGA.70.6722.01 2 0.000
#> TCGA.39.5035.11 2 0.000
#> TCGA.83.5908.01 2 0.000
#> TCGA.55.6980.01 2 0.000
#> TCGA.44.6146.01 2 0.000
#> TCGA.58.A46K.01 1 0.000
#> TCGA.94.A5I6.01 1 0.000
#> TCGA.69.7979.01 2 0.000
#> TCGA.56.A4BY.01 1 0.000
#> TCGA.85.8049.01 1 0.000
#> TCGA.95.7039.01 2 0.000
#> TCGA.18.3417.01 1 0.000
#> TCGA.62.8397.01 2 0.000
#> TCGA.56.8201.01 2 0.000
#> TCGA.44.6145.11 2 0.000
#> TCGA.91.6848.01 2 0.000
#> TCGA.63.7023.01 1 0.000
#> TCGA.97.7552.01 2 0.000
#> TCGA.50.5936.01 2 0.000
#> TCGA.33.6738.01 2 0.000
#> TCGA.91.7771.01 2 0.000
#> TCGA.18.5595.11 2 0.000
#> TCGA.56.A4BW.01 1 0.000
#> TCGA.56.8308.01 1 0.000
#> TCGA.NJ.A4YG.01 2 0.000
#> TCGA.86.8359.01 2 0.000
#> TCGA.55.8301.01 2 0.000
#> TCGA.43.6773.01 2 0.000
#> TCGA.78.7146.01 2 0.000
#> TCGA.44.3918.01 2 0.000
#> TCGA.50.5935.11 2 0.000
#> TCGA.63.7020.01 1 0.000
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get_classes(res, k = 3)
#> class p
#> TCGA.44.4112.01 2 0.000
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#> TCGA.L3.A524.01 1 0.000
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get_classes(res, k = 4)
#> class p
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#> TCGA.55.7910.01 3 1.000
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#> TCGA.MP.A4T8.01 2 0.000
#> TCGA.78.7539.01 2 0.498
#> TCGA.39.5040.01 2 1.000
#> TCGA.63.A5M9.01 4 0.000
#> TCGA.92.8063.01 1 0.000
#> TCGA.56.7823.01 4 0.000
#> TCGA.43.3920.11 2 0.000
#> TCGA.MP.A4SY.01 2 0.000
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get_classes(res, k = 5)
#> class p
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#> TCGA.L3.A524.01 4 0.000
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get_classes(res, k = 6)
#> class p
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#> TCGA.92.8063.01 1 0.000
#> TCGA.56.7823.01 4 0.000
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#> TCGA.MP.A4TC.01 2 1.000
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#> TCGA.43.5670.01 6 0.000
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#> TCGA.62.A46Y.01 2 0.747
#> TCGA.50.6597.01 2 0.000
#> TCGA.NC.A5HE.01 1 1.000
#> TCGA.05.4384.01 2 1.000
#> TCGA.55.6642.01 2 0.000
#> TCGA.44.6144.01 3 0.000
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#> TCGA.05.4415.01 2 0.000
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#> TCGA.05.4425.01 2 1.000
get_classes(res, k = 7)
#> class p
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#> TCGA.39.5040.01 7 1.000
#> TCGA.63.A5M9.01 6 0.751
#> TCGA.92.8063.01 1 0.000
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#> TCGA.86.8074.01 2 0.751
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get_classes(res, k = 8)
#> class p
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#> TCGA.77.6843.01 6 1.000
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#> TCGA.91.6849.01 2 0.000
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#> TCGA.85.8351.01 1 0.249
#> TCGA.85.7843.01 6 0.000
#> TCGA.60.2709.01 1 0.000
#> TCGA.NJ.A7XG.01 2 0.000
#> TCGA.55.A48X.01 2 0.000
#> TCGA.98.A53D.01 5 0.000
#> TCGA.85.8666.01 1 0.000
#> TCGA.94.7943.01 1 1.000
#> TCGA.64.5778.01 2 0.000
#> TCGA.49.AAR9.01 3 0.502
#> TCGA.50.6594.01 2 0.000
#> TCGA.NK.A5CX.01 1 0.000
#> TCGA.44.2668.11 5 0.000
#> TCGA.95.A4VK.01 7 0.000
#> TCGA.78.7153.01 2 0.000
#> TCGA.56.7221.01 6 1.000
#> TCGA.49.4488.01 7 0.751
#> TCGA.63.A5ML.01 4 0.000
#> TCGA.55.7728.01 2 0.000
#> TCGA.22.5477.01 4 0.000
#> TCGA.98.A538.01 6 0.000
#> TCGA.55.7994.01 7 0.000
#> TCGA.67.6215.01 2 0.000
#> TCGA.85.8071.01 4 0.000
#> TCGA.78.7537.01 2 0.000
#> TCGA.39.5034.11 5 0.000
#> TCGA.98.A53H.01 5 0.000
#> TCGA.55.6982.01 2 0.000
#> TCGA.XC.AA0X.01 1 0.000
#> TCGA.L9.A7SV.01 3 0.000
#> TCGA.39.5036.11 5 0.000
#> TCGA.98.A53J.01 6 0.000
#> TCGA.85.8277.01 6 1.000
#> TCGA.MP.A5C7.01 7 0.000
#> TCGA.05.4424.01 7 0.000
#> TCGA.77.8143.01 4 0.000
#> TCGA.55.7227.01 2 0.000
#> TCGA.85.6561.01 1 0.000
#> TCGA.77.6845.01 4 0.000
#> TCGA.56.7730.01 4 0.000
#> TCGA.86.A456.01 2 0.000
#> TCGA.39.5035.01 8 0.000
#> TCGA.56.7579.01 6 0.751
#> TCGA.22.4599.11 5 0.000
#> TCGA.58.A46M.01 6 1.000
#> TCGA.77.7338.01 6 0.000
#> TCGA.80.5611.01 3 0.000
#> TCGA.44.6774.01 7 1.000
#> TCGA.85.8582.01 1 0.000
#> TCGA.49.AAQV.01 2 0.000
#> TCGA.39.5031.11 5 0.000
#> TCGA.49.6742.01 3 0.000
#> TCGA.63.A5MH.01 4 0.000
#> TCGA.51.6867.01 8 0.253
#> TCGA.73.7498.01 2 0.000
#> TCGA.34.5234.01 1 0.000
#> TCGA.38.4632.01 2 0.000
#> TCGA.69.7974.01 2 0.000
#> TCGA.63.A5MJ.01 8 0.253
#> TCGA.55.6986.01 2 0.000
#> TCGA.50.5936.11 5 0.000
#> TCGA.4B.A93V.01 7 0.000
#> TCGA.22.4605.01 1 0.000
#> TCGA.22.5471.11 5 0.000
#> TCGA.49.6761.01 2 0.000
#> TCGA.MP.A4T6.01 2 0.000
#> TCGA.56.8624.01 1 0.000
#> TCGA.94.7033.01 1 0.000
#> TCGA.86.A4D0.01 7 0.000
#> TCGA.62.A46O.01 3 0.000
#> TCGA.44.6779.01 2 0.000
#> TCGA.78.7159.01 7 0.000
#> TCGA.86.A4P7.01 2 0.000
#> TCGA.50.5932.11 5 0.000
#> TCGA.73.4658.01 2 0.000
#> TCGA.22.5480.11 5 0.000
#> TCGA.85.A513.01 2 0.000
#> TCGA.60.2704.01 1 0.000
#> TCGA.63.A5MT.01 1 0.000
#> TCGA.99.8032.01 7 0.000
#> TCGA.50.5935.01 2 0.000
#> TCGA.55.7727.01 2 0.000
#> TCGA.55.6981.01 2 1.000
#> TCGA.55.7724.01 1 0.000
#> TCGA.78.8655.01 2 0.000
#> TCGA.78.7163.01 2 0.000
#> TCGA.97.7941.01 2 0.000
#> TCGA.MP.A4TA.01 7 0.000
#> TCGA.56.7822.01 6 0.000
#> TCGA.56.A62T.01 8 1.000
#> TCGA.75.5146.01 7 0.498
#> TCGA.50.5931.11 5 0.000
#> TCGA.55.7914.01 2 0.000
#> TCGA.22.4601.11 5 0.000
#> TCGA.75.7030.01 2 0.000
#> TCGA.85.A4JB.01 1 0.000
#> TCGA.56.A49D.01 6 0.000
#> TCGA.62.A472.01 2 0.000
#> TCGA.64.5779.01 7 0.000
#> TCGA.05.4417.01 2 0.000
#> TCGA.67.4679.01 2 0.000
#> TCGA.39.5034.01 3 0.000
#> TCGA.55.8620.01 3 0.000
#> TCGA.55.7570.01 3 1.000
#> TCGA.50.6673.01 7 0.000
#> TCGA.77.A5FZ.01 5 0.000
#> TCGA.97.7554.01 2 0.000
#> TCGA.33.4589.11 5 0.000
#> TCGA.39.5030.01 1 0.000
#> TCGA.58.8390.01 4 0.000
#> TCGA.75.7025.01 2 0.000
#> TCGA.18.3417.11 5 0.000
#> TCGA.55.5899.01 3 0.000
#> TCGA.95.8039.01 2 0.000
#> TCGA.44.6144.11 5 0.000
#> TCGA.43.8118.01 1 0.000
#> TCGA.50.5941.01 2 0.000
#> TCGA.62.8399.01 3 0.000
#> TCGA.95.7562.01 7 1.000
#> TCGA.68.7757.01 1 0.000
#> TCGA.97.8174.01 2 0.000
#> TCGA.55.7576.01 2 0.000
#> TCGA.55.7725.01 2 0.000
#> TCGA.38.A44F.01 2 0.000
#> TCGA.39.5029.11 5 0.000
#> TCGA.80.5607.01 2 0.000
#> TCGA.55.8091.01 2 0.000
#> TCGA.62.8395.01 2 0.000
#> TCGA.92.8065.01 1 0.000
#> TCGA.86.8672.01 7 1.000
#> TCGA.64.5815.01 2 0.000
#> TCGA.75.6212.01 2 0.502
#> TCGA.52.7811.01 1 0.000
#> TCGA.50.5930.01 7 0.000
#> TCGA.77.8136.01 1 0.000
#> TCGA.22.5474.01 8 0.000
#> TCGA.68.A59J.01 6 0.000
#> TCGA.33.4587.01 3 1.000
#> TCGA.39.5027.01 4 0.000
#> TCGA.55.7284.01 7 0.000
#> TCGA.22.5492.01 6 0.751
#> TCGA.91.6829.01 7 0.000
#> TCGA.22.5485.01 4 0.000
#> TCGA.86.8669.01 7 0.000
#> TCGA.44.6776.01 7 1.000
#> TCGA.33.4583.01 4 0.000
#> TCGA.55.6983.01 2 0.000
#> TCGA.93.8067.01 2 0.000
#> TCGA.69.A59K.01 2 0.000
#> TCGA.64.1679.01 7 0.000
#> TCGA.MF.A522.01 4 0.000
#> TCGA.91.8499.01 3 0.000
#> TCGA.95.7567.01 2 0.000
#> TCGA.49.AARN.01 2 0.000
#> TCGA.56.8628.01 1 0.000
#> TCGA.21.A5DI.01 1 0.249
#> TCGA.91.6836.01 2 0.000
#> TCGA.55.8616.01 7 0.000
#> TCGA.97.8172.01 2 0.000
#> TCGA.50.5051.01 7 0.000
#> TCGA.77.7141.01 8 0.000
#> TCGA.90.7766.01 6 0.000
#> TCGA.O2.A52Q.01 2 1.000
#> TCGA.50.5045.01 2 0.000
#> TCGA.22.5489.01 1 0.000
#> TCGA.44.6147.11 5 0.000
#> TCGA.70.6723.01 4 0.000
#> TCGA.NC.A5HD.01 8 0.000
#> TCGA.64.1681.01 7 0.000
#> TCGA.78.7150.01 3 0.000
#> TCGA.NC.A5HM.01 6 1.000
#> TCGA.86.8674.01 7 0.000
#> TCGA.46.6025.01 8 1.000
#> TCGA.55.6978.01 2 0.000
#> TCGA.56.5897.01 1 0.000
#> TCGA.52.7809.01 8 0.747
#> TCGA.95.A4VP.01 2 0.000
#> TCGA.85.8048.01 1 0.000
#> TCGA.43.8116.01 6 1.000
#> TCGA.55.A490.01 3 0.000
#> TCGA.68.7755.01 4 0.000
#> TCGA.05.5715.01 2 0.000
#> TCGA.55.A492.01 2 0.000
#> TCGA.NC.A5HH.01 4 0.000
#> TCGA.22.5472.11 5 0.000
#> TCGA.96.8170.01 1 0.000
#> TCGA.55.6969.01 3 1.000
#> TCGA.21.5787.01 3 0.000
#> TCGA.78.7166.01 7 0.000
#> TCGA.55.A48Y.01 2 0.751
#> TCGA.44.5643.11 5 0.000
#> TCGA.86.7953.01 7 1.000
#> TCGA.85.8350.01 6 0.502
#> TCGA.MP.A4SV.01 7 0.000
#> TCGA.50.6595.01 2 0.000
#> TCGA.LA.A7SW.01 8 0.000
#> TCGA.55.6543.01 2 0.000
#> TCGA.91.8497.01 2 0.000
#> TCGA.50.5049.01 7 0.751
#> TCGA.96.7544.01 6 0.000
#> TCGA.97.A4M2.01 2 1.000
#> TCGA.NC.A5HL.01 1 1.000
#> TCGA.55.8513.01 5 1.000
#> TCGA.44.7659.01 2 0.000
#> TCGA.43.6771.01 1 0.000
#> TCGA.62.8402.01 7 0.000
#> TCGA.55.7995.01 7 0.000
#> TCGA.05.5420.11 5 0.000
#> TCGA.77.A5G7.01 6 0.000
#> TCGA.NJ.A55R.01 7 0.000
#> TCGA.35.5375.01 1 0.000
#> TCGA.97.A4M7.01 2 0.000
#> TCGA.86.8055.01 7 0.000
#> TCGA.6A.AB49.01 1 1.000
#> TCGA.78.7536.01 3 0.000
#> TCGA.33.AASB.01 7 0.000
#> TCGA.78.7156.01 7 0.000
#> TCGA.44.7662.01 2 0.000
#> TCGA.55.8506.01 7 1.000
#> TCGA.85.A511.01 1 0.000
#> TCGA.55.6970.01 2 0.000
#> TCGA.NK.A7XE.01 1 0.000
#> TCGA.56.6545.01 1 0.000
#> TCGA.50.5068.01 2 0.000
#> TCGA.33.4566.11 5 0.000
#> TCGA.56.8307.01 8 1.000
#> TCGA.NK.A5CR.01 4 0.000
#> TCGA.53.7813.01 7 0.000
#> TCGA.NJ.A55A.01 1 0.000
#> TCGA.63.A5MM.01 1 0.000
#> TCGA.77.6844.01 4 0.000
#> TCGA.71.8520.01 2 0.000
#> TCGA.56.8082.01 4 0.000
#> TCGA.39.5037.11 5 0.000
#> TCGA.98.A539.01 6 0.751
#> TCGA.O2.A52S.01 4 1.000
#> TCGA.21.5784.01 1 0.000
#> TCGA.44.7672.01 2 0.000
#> TCGA.97.8179.01 7 0.000
#> TCGA.L3.A524.01 4 0.000
#> TCGA.39.5021.01 1 0.000
#> TCGA.55.6987.01 2 1.000
#> TCGA.85.A5B5.01 4 0.000
#> TCGA.58.A46L.01 6 0.000
#> TCGA.77.8144.01 8 1.000
#> TCGA.J1.A4AH.01 6 0.000
#> TCGA.86.7713.01 7 0.000
#> TCGA.78.7152.01 2 0.000
#> TCGA.50.5946.01 3 0.000
#> TCGA.56.7580.01 6 1.000
#> TCGA.62.A46S.01 7 0.000
#> TCGA.95.7947.01 7 0.000
#> TCGA.J2.8192.01 7 0.000
#> TCGA.78.7145.01 2 1.000
#> TCGA.63.A5MY.01 4 0.000
#> TCGA.50.6593.01 2 0.000
#> TCGA.33.AASL.01 1 0.000
#> TCGA.85.A512.01 4 0.000
#> TCGA.85.8354.01 4 0.000
#> TCGA.O2.A5IB.01 3 0.000
#> TCGA.50.6591.11 5 0.000
#> TCGA.77.7335.01 1 0.000
#> TCGA.55.8302.01 2 0.000
#> TCGA.05.4425.01 2 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node041 , Node042 , Node043 , Node051 , Node052 , Node061 , Node062-leaf , Node071 , Node072 , Node073 .
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 128 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.903 0.928 0.971 0.4974 0.504 0.504
#> 3 3 0.958 0.951 0.979 0.3432 0.743 0.531
#> 4 4 0.997 0.961 0.980 0.1049 0.900 0.712
#> 5 5 0.862 0.870 0.932 0.0655 0.952 0.815
#> 6 6 0.818 0.733 0.858 0.0331 0.969 0.858
#> 7 7 0.736 0.568 0.782 0.0191 0.953 0.784
#> 8 8 0.729 0.560 0.787 0.0100 0.965 0.820
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.85.8481.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.8156.01 1 0.000 0.9766 1.00 0.00
#> TCGA.43.A475.01 2 0.000 0.9638 0.00 1.00
#> TCGA.68.8251.01 2 0.000 0.9638 0.00 1.00
#> TCGA.92.8063.01 2 0.000 0.9638 0.00 1.00
#> TCGA.44.7660.01 1 0.000 0.9766 1.00 0.00
#> TCGA.85.8580.01 2 0.000 0.9638 0.00 1.00
#> TCGA.34.5232.01 2 0.000 0.9638 0.00 1.00
#> TCGA.92.7340.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.8287.01 1 0.999 0.0269 0.52 0.48
#> TCGA.77.8138.01 1 0.000 0.9766 1.00 0.00
#> TCGA.63.7022.01 1 0.242 0.9384 0.96 0.04
#> TCGA.56.8626.01 2 0.529 0.8528 0.12 0.88
#> TCGA.39.5028.11 1 0.000 0.9766 1.00 0.00
#> TCGA.85.8355.01 1 0.000 0.9766 1.00 0.00
#> TCGA.NC.A5HE.01 2 0.000 0.9638 0.00 1.00
#> TCGA.75.6214.01 2 0.000 0.9638 0.00 1.00
#> TCGA.43.A56U.01 2 0.000 0.9638 0.00 1.00
#> TCGA.56.8503.01 1 0.000 0.9766 1.00 0.00
#> TCGA.34.5236.01 1 0.000 0.9766 1.00 0.00
#> TCGA.L3.A4E7.01 1 0.000 0.9766 1.00 0.00
#> TCGA.90.A59Q.01 2 0.000 0.9638 0.00 1.00
#> TCGA.55.8614.01 1 0.469 0.8722 0.90 0.10
#> TCGA.85.A53L.01 2 0.000 0.9638 0.00 1.00
#> TCGA.56.A4ZJ.01 1 0.000 0.9766 1.00 0.00
#> TCGA.44.6148.01 1 0.000 0.9766 1.00 0.00
#> TCGA.63.A5MV.01 1 0.000 0.9766 1.00 0.00
#> TCGA.58.8393.01 2 0.000 0.9638 0.00 1.00
#> TCGA.63.A5MS.01 2 0.000 0.9638 0.00 1.00
#> TCGA.63.A5MP.01 2 0.000 0.9638 0.00 1.00
#> TCGA.77.A5GH.01 1 0.722 0.7357 0.80 0.20
#> TCGA.52.7622.01 2 0.000 0.9638 0.00 1.00
#> TCGA.34.A5IX.01 2 0.000 0.9638 0.00 1.00
#> TCGA.34.8454.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.8146.01 1 0.000 0.9766 1.00 0.00
#> TCGA.56.8309.01 1 0.000 0.9766 1.00 0.00
#> TCGA.63.7021.01 1 0.000 0.9766 1.00 0.00
#> TCGA.58.8387.01 1 0.958 0.3648 0.62 0.38
#> TCGA.55.7726.01 2 0.000 0.9638 0.00 1.00
#> TCGA.39.5028.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.8008.01 1 0.000 0.9766 1.00 0.00
#> TCGA.22.4609.01 1 0.000 0.9766 1.00 0.00
#> TCGA.43.8115.01 2 0.000 0.9638 0.00 1.00
#> TCGA.56.A5DS.01 2 0.000 0.9638 0.00 1.00
#> TCGA.34.5241.01 1 0.000 0.9766 1.00 0.00
#> TCGA.96.A4JL.01 2 0.000 0.9638 0.00 1.00
#> TCGA.33.AASI.01 2 0.000 0.9638 0.00 1.00
#> TCGA.43.6647.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.A5GA.01 2 0.000 0.9638 0.00 1.00
#> TCGA.56.6546.01 1 0.000 0.9766 1.00 0.00
#> TCGA.85.7697.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.6842.01 1 0.000 0.9766 1.00 0.00
#> TCGA.63.A5MR.01 2 0.943 0.4619 0.36 0.64
#> TCGA.94.A5I6.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.8049.01 2 0.000 0.9638 0.00 1.00
#> TCGA.56.8201.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.8353.01 2 0.000 0.9638 0.00 1.00
#> TCGA.96.7545.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.8276.01 2 0.000 0.9638 0.00 1.00
#> TCGA.58.8386.01 2 0.971 0.3616 0.40 0.60
#> TCGA.56.7731.01 1 0.000 0.9766 1.00 0.00
#> TCGA.96.8169.01 2 0.000 0.9638 0.00 1.00
#> TCGA.33.4589.01 2 0.000 0.9638 0.00 1.00
#> TCGA.98.8023.01 1 0.000 0.9766 1.00 0.00
#> TCGA.56.8625.01 2 0.000 0.9638 0.00 1.00
#> TCGA.60.2703.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.A5GB.01 1 0.000 0.9766 1.00 0.00
#> TCGA.90.A4EE.01 2 0.000 0.9638 0.00 1.00
#> TCGA.63.A5MG.01 2 0.000 0.9638 0.00 1.00
#> TCGA.94.8491.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.A4JC.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.7138.01 1 0.000 0.9766 1.00 0.00
#> TCGA.68.A59I.01 2 0.000 0.9638 0.00 1.00
#> TCGA.77.8131.01 1 0.000 0.9766 1.00 0.00
#> TCGA.68.7756.01 1 0.000 0.9766 1.00 0.00
#> TCGA.58.A46J.01 1 0.000 0.9766 1.00 0.00
#> TCGA.92.8064.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.A50Z.01 1 0.000 0.9766 1.00 0.00
#> TCGA.55.8204.01 2 0.000 0.9638 0.00 1.00
#> TCGA.O2.A52V.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.6175.01 1 0.000 0.9766 1.00 0.00
#> TCGA.39.5039.01 1 0.000 0.9766 1.00 0.00
#> TCGA.39.5024.01 2 0.000 0.9638 0.00 1.00
#> TCGA.33.A4WN.01 2 0.000 0.9638 0.00 1.00
#> TCGA.NK.A5CT.01 2 0.722 0.7529 0.20 0.80
#> TCGA.18.4721.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.8351.01 2 0.000 0.9638 0.00 1.00
#> TCGA.60.2709.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.8666.01 2 0.000 0.9638 0.00 1.00
#> TCGA.94.7943.01 2 0.469 0.8748 0.10 0.90
#> TCGA.NK.A5CX.01 1 0.000 0.9766 1.00 0.00
#> TCGA.XC.AA0X.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.6561.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.8582.01 2 0.000 0.9638 0.00 1.00
#> TCGA.34.5234.01 1 0.000 0.9766 1.00 0.00
#> TCGA.22.4605.01 2 0.529 0.8525 0.12 0.88
#> TCGA.56.8624.01 1 0.000 0.9766 1.00 0.00
#> TCGA.94.7033.01 1 0.000 0.9766 1.00 0.00
#> TCGA.60.2704.01 1 0.000 0.9766 1.00 0.00
#> TCGA.63.A5MT.01 2 0.000 0.9638 0.00 1.00
#> TCGA.55.7724.01 2 0.000 0.9638 0.00 1.00
#> TCGA.85.A4JB.01 1 0.000 0.9766 1.00 0.00
#> TCGA.39.5030.01 2 0.141 0.9476 0.02 0.98
#> TCGA.43.8118.01 2 0.760 0.7236 0.22 0.78
#> TCGA.68.7757.01 1 0.000 0.9766 1.00 0.00
#> TCGA.92.8065.01 2 0.000 0.9638 0.00 1.00
#> TCGA.52.7811.01 1 0.000 0.9766 1.00 0.00
#> TCGA.77.8136.01 2 0.000 0.9638 0.00 1.00
#> TCGA.33.4587.01 1 0.000 0.9766 1.00 0.00
#> TCGA.56.8628.01 1 0.141 0.9583 0.98 0.02
#> TCGA.21.A5DI.01 1 0.000 0.9766 1.00 0.00
#> TCGA.22.5489.01 2 0.000 0.9638 0.00 1.00
#> TCGA.56.5897.01 1 0.000 0.9766 1.00 0.00
#> TCGA.85.8048.01 1 0.000 0.9766 1.00 0.00
#> TCGA.96.8170.01 2 0.402 0.8942 0.08 0.92
#> TCGA.NC.A5HL.01 2 0.000 0.9638 0.00 1.00
#> TCGA.43.6771.01 2 0.000 0.9638 0.00 1.00
#> TCGA.35.5375.01 2 0.000 0.9638 0.00 1.00
#> TCGA.6A.AB49.01 2 0.990 0.2445 0.44 0.56
#> TCGA.85.A511.01 2 0.990 0.2423 0.44 0.56
#> TCGA.NK.A7XE.01 2 0.000 0.9638 0.00 1.00
#> TCGA.56.6545.01 2 0.000 0.9638 0.00 1.00
#> TCGA.NJ.A55A.01 2 0.000 0.9638 0.00 1.00
#> TCGA.63.A5MM.01 2 0.000 0.9638 0.00 1.00
#> TCGA.21.5784.01 1 0.000 0.9766 1.00 0.00
#> TCGA.39.5021.01 1 0.000 0.9766 1.00 0.00
#> TCGA.33.AASL.01 2 0.000 0.9638 0.00 1.00
#> TCGA.77.7335.01 2 0.000 0.9638 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.85.8481.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.77.8156.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.43.A475.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.68.8251.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.92.8063.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.44.7660.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.85.8580.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.34.5232.01 3 0.207 0.927 0.00 0.06 0.94
#> TCGA.92.7340.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.8287.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.77.8138.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.63.7022.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.56.8626.01 1 0.628 0.148 0.54 0.46 0.00
#> TCGA.39.5028.11 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.85.8355.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.NC.A5HE.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.75.6214.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.43.A56U.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.56.8503.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.34.5236.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.L3.A4E7.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.90.A59Q.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.55.8614.01 1 0.556 0.575 0.70 0.00 0.30
#> TCGA.85.A53L.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.56.A4ZJ.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.44.6148.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.63.A5MV.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.58.8393.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.63.A5MS.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.63.A5MP.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.77.A5GH.01 1 0.604 0.394 0.62 0.00 0.38
#> TCGA.52.7622.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.34.A5IX.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.34.8454.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.77.8146.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.56.8309.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.63.7021.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.58.8387.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.55.7726.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.39.5028.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.77.8008.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.22.4609.01 1 0.334 0.846 0.88 0.00 0.12
#> TCGA.43.8115.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.56.A5DS.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.34.5241.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.96.A4JL.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.33.AASI.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.43.6647.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.77.A5GA.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.56.6546.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.85.7697.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.77.6842.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.63.A5MR.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.94.A5I6.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.8049.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.56.8201.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.8353.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.96.7545.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.8276.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.58.8386.01 3 0.429 0.782 0.18 0.00 0.82
#> TCGA.56.7731.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.96.8169.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.33.4589.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.98.8023.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.56.8625.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.60.2703.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.77.A5GB.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.90.A4EE.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.63.A5MG.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.94.8491.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.A4JC.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.77.7138.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.68.A59I.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.77.8131.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.68.7756.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.58.A46J.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.92.8064.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.A50Z.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.55.8204.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.O2.A52V.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.6175.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.39.5039.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.39.5024.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.33.A4WN.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.NK.A5CT.01 3 0.400 0.810 0.16 0.00 0.84
#> TCGA.18.4721.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.8351.01 3 0.497 0.846 0.06 0.10 0.84
#> TCGA.60.2709.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.8666.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.94.7943.01 2 0.649 0.686 0.20 0.74 0.06
#> TCGA.NK.A5CX.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.XC.AA0X.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.85.6561.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.85.8582.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.34.5234.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.22.4605.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.56.8624.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.94.7033.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.60.2704.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.63.A5MT.01 3 0.482 0.840 0.04 0.12 0.84
#> TCGA.55.7724.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.85.A4JB.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.39.5030.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.43.8118.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.68.7757.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.92.8065.01 2 0.400 0.804 0.00 0.84 0.16
#> TCGA.52.7811.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.77.8136.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.33.4587.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.56.8628.01 1 0.522 0.649 0.74 0.00 0.26
#> TCGA.21.A5DI.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.22.5489.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.56.5897.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.85.8048.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.96.8170.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.NC.A5HL.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.43.6771.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.35.5375.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.6A.AB49.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.85.A511.01 1 0.153 0.929 0.96 0.04 0.00
#> TCGA.NK.A7XE.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.56.6545.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.NJ.A55A.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.63.A5MM.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.21.5784.01 3 0.000 0.980 0.00 0.00 1.00
#> TCGA.39.5021.01 1 0.000 0.966 1.00 0.00 0.00
#> TCGA.33.AASL.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.77.7335.01 2 0.000 0.990 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.85.8481.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.77.8156.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.43.A475.01 2 0.1637 0.928 0.00 0.94 0.06 0.00
#> TCGA.68.8251.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.92.8063.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.44.7660.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.85.8580.01 2 0.1211 0.950 0.00 0.96 0.04 0.00
#> TCGA.34.5232.01 3 0.1211 0.949 0.00 0.04 0.96 0.00
#> TCGA.92.7340.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.8287.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.77.8138.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.63.7022.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.56.8626.01 4 0.5383 0.752 0.16 0.10 0.00 0.74
#> TCGA.39.5028.11 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.85.8355.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HE.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.75.6214.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.43.A56U.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.56.8503.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.34.5236.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.L3.A4E7.01 1 0.3610 0.761 0.80 0.00 0.00 0.20
#> TCGA.90.A59Q.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.55.8614.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.85.A53L.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.56.A4ZJ.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.44.6148.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.63.A5MV.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.58.8393.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.63.A5MS.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.63.A5MP.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.77.A5GH.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.52.7622.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.34.A5IX.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.34.8454.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.77.8146.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.56.8309.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.63.7021.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.58.8387.01 1 0.0707 0.959 0.98 0.02 0.00 0.00
#> TCGA.55.7726.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.39.5028.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.77.8008.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.22.4609.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.43.8115.01 2 0.1211 0.950 0.00 0.96 0.04 0.00
#> TCGA.56.A5DS.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.34.5241.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.96.A4JL.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.33.AASI.01 4 0.4406 0.576 0.00 0.00 0.30 0.70
#> TCGA.43.6647.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.77.A5GA.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.56.6546.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.85.7697.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.77.6842.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.63.A5MR.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.94.A5I6.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.8049.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.56.8201.01 4 0.3400 0.784 0.00 0.18 0.00 0.82
#> TCGA.85.8353.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.96.7545.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.8276.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.58.8386.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.56.7731.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.96.8169.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.33.4589.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.98.8023.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.56.8625.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.60.2703.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.77.A5GB.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.90.A4EE.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.63.A5MG.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.94.8491.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.A4JC.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.77.7138.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.68.A59I.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.77.8131.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.68.7756.01 4 0.0707 0.924 0.02 0.00 0.00 0.98
#> TCGA.58.A46J.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.92.8064.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.A50Z.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.55.8204.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.O2.A52V.01 2 0.1211 0.950 0.00 0.96 0.04 0.00
#> TCGA.85.6175.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.39.5039.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.39.5024.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.33.A4WN.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.NK.A5CT.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.18.4721.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.8351.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.60.2709.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.8666.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.94.7943.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.NK.A5CX.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.XC.AA0X.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.85.6561.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.85.8582.01 4 0.0707 0.922 0.00 0.02 0.00 0.98
#> TCGA.34.5234.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.22.4605.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.56.8624.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.94.7033.01 4 0.2011 0.880 0.08 0.00 0.00 0.92
#> TCGA.60.2704.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.63.A5MT.01 4 0.0000 0.933 0.00 0.00 0.00 1.00
#> TCGA.55.7724.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.85.A4JB.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.39.5030.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.43.8118.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.68.7757.01 4 0.1637 0.899 0.06 0.00 0.00 0.94
#> TCGA.92.8065.01 2 0.3610 0.738 0.00 0.80 0.20 0.00
#> TCGA.52.7811.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.77.8136.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.33.4587.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.56.8628.01 1 0.5883 0.498 0.64 0.00 0.30 0.06
#> TCGA.21.A5DI.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.22.5489.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.56.5897.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.85.8048.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.96.8170.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.NC.A5HL.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.43.6771.01 4 0.4134 0.670 0.00 0.26 0.00 0.74
#> TCGA.35.5375.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.6A.AB49.01 4 0.0707 0.920 0.00 0.00 0.02 0.98
#> TCGA.85.A511.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.NK.A7XE.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.56.6545.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.NJ.A55A.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.63.A5MM.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.21.5784.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.39.5021.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.33.AASL.01 2 0.0000 0.988 0.00 1.00 0.00 0.00
#> TCGA.77.7335.01 2 0.0000 0.988 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.85.8481.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8156.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.A475.01 2 0.3513 0.77039 0.00 0.80 0.18 0.00 0.02
#> TCGA.68.8251.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.92.8063.01 2 0.2012 0.89933 0.06 0.92 0.00 0.00 0.02
#> TCGA.44.7660.01 1 0.2929 0.77126 0.82 0.00 0.00 0.00 0.18
#> TCGA.85.8580.01 2 0.3513 0.77039 0.00 0.80 0.18 0.00 0.02
#> TCGA.34.5232.01 3 0.2020 0.84769 0.00 0.10 0.90 0.00 0.00
#> TCGA.92.7340.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8287.01 1 0.0609 0.89767 0.98 0.00 0.00 0.00 0.02
#> TCGA.77.8138.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.63.7022.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.56.8626.01 4 0.5524 0.53102 0.28 0.06 0.00 0.64 0.02
#> TCGA.39.5028.11 5 0.0609 0.90528 0.02 0.00 0.00 0.00 0.98
#> TCGA.85.8355.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HE.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6214.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.43.A56U.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.56.8503.01 3 0.3895 0.60076 0.00 0.00 0.68 0.00 0.32
#> TCGA.34.5236.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.L3.A4E7.01 5 0.0609 0.90528 0.02 0.00 0.00 0.00 0.98
#> TCGA.90.A59Q.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8614.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.A53L.01 2 0.2331 0.88314 0.08 0.90 0.00 0.00 0.02
#> TCGA.56.A4ZJ.01 3 0.4307 0.16157 0.00 0.00 0.50 0.00 0.50
#> TCGA.44.6148.01 5 0.0609 0.90528 0.02 0.00 0.00 0.00 0.98
#> TCGA.63.A5MV.01 1 0.1410 0.89034 0.94 0.00 0.00 0.00 0.06
#> TCGA.58.8393.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5MS.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5MP.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.A5GH.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.52.7622.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.34.A5IX.01 2 0.2249 0.90186 0.02 0.92 0.00 0.04 0.02
#> TCGA.34.8454.01 3 0.1410 0.92240 0.00 0.00 0.94 0.00 0.06
#> TCGA.77.8146.01 4 0.2020 0.81485 0.00 0.00 0.00 0.90 0.10
#> TCGA.56.8309.01 1 0.2020 0.86314 0.90 0.00 0.00 0.00 0.10
#> TCGA.63.7021.01 1 0.1410 0.89034 0.94 0.00 0.00 0.00 0.06
#> TCGA.58.8387.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7726.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.39.5028.01 1 0.4302 0.00177 0.52 0.00 0.00 0.00 0.48
#> TCGA.77.8008.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.22.4609.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.43.8115.01 2 0.3999 0.69526 0.00 0.74 0.24 0.00 0.02
#> TCGA.56.A5DS.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.34.5241.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.96.A4JL.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.33.AASI.01 4 0.4227 0.26715 0.00 0.00 0.42 0.58 0.00
#> TCGA.43.6647.01 3 0.1732 0.90995 0.00 0.00 0.92 0.00 0.08
#> TCGA.77.A5GA.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.6546.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.7697.01 1 0.3895 0.52269 0.68 0.00 0.00 0.00 0.32
#> TCGA.77.6842.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MR.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.94.A5I6.01 2 0.0609 0.93411 0.00 0.98 0.00 0.00 0.02
#> TCGA.85.8049.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.8201.01 4 0.3684 0.60022 0.00 0.28 0.00 0.72 0.00
#> TCGA.85.8353.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.96.7545.01 2 0.0609 0.93411 0.00 0.98 0.00 0.00 0.02
#> TCGA.85.8276.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.58.8386.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.56.7731.01 3 0.1732 0.90995 0.00 0.00 0.92 0.00 0.08
#> TCGA.96.8169.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.33.4589.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.98.8023.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.8625.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.60.2703.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.77.A5GB.01 5 0.3109 0.83878 0.20 0.00 0.00 0.00 0.80
#> TCGA.90.A4EE.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5MG.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.94.8491.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.A4JC.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.77.7138.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.68.A59I.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.77.8131.01 1 0.2020 0.86314 0.90 0.00 0.00 0.00 0.10
#> TCGA.68.7756.01 4 0.2331 0.81484 0.02 0.00 0.00 0.90 0.08
#> TCGA.58.A46J.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.92.8064.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.A50Z.01 1 0.1043 0.90107 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.8204.01 3 0.0609 0.94033 0.00 0.00 0.98 0.02 0.00
#> TCGA.O2.A52V.01 2 0.4816 0.62544 0.02 0.68 0.28 0.00 0.02
#> TCGA.85.6175.01 3 0.1732 0.90995 0.00 0.00 0.92 0.00 0.08
#> TCGA.39.5039.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.39.5024.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.33.A4WN.01 2 0.1648 0.91319 0.04 0.94 0.00 0.00 0.02
#> TCGA.NK.A5CT.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.18.4721.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8351.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.60.2709.01 2 0.2873 0.84735 0.12 0.86 0.00 0.00 0.02
#> TCGA.85.8666.01 2 0.0609 0.93411 0.00 0.98 0.00 0.00 0.02
#> TCGA.94.7943.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.NK.A5CX.01 4 0.0609 0.86161 0.00 0.00 0.00 0.98 0.02
#> TCGA.XC.AA0X.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.85.6561.01 2 0.1216 0.92498 0.02 0.96 0.00 0.00 0.02
#> TCGA.85.8582.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.34.5234.01 3 0.1410 0.92240 0.00 0.00 0.94 0.00 0.06
#> TCGA.22.4605.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.56.8624.01 5 0.1410 0.93081 0.06 0.00 0.00 0.00 0.94
#> TCGA.94.7033.01 4 0.2873 0.78184 0.02 0.00 0.00 0.86 0.12
#> TCGA.60.2704.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MT.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.7724.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.85.A4JB.01 1 0.0000 0.91294 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5030.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.43.8118.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.68.7757.01 4 0.3319 0.73567 0.02 0.00 0.00 0.82 0.16
#> TCGA.92.8065.01 2 0.3983 0.52053 0.00 0.66 0.34 0.00 0.00
#> TCGA.52.7811.01 5 0.3424 0.77904 0.24 0.00 0.00 0.00 0.76
#> TCGA.77.8136.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.33.4587.01 5 0.0609 0.90528 0.02 0.00 0.00 0.00 0.98
#> TCGA.56.8628.01 1 0.2873 0.78247 0.86 0.00 0.12 0.02 0.00
#> TCGA.21.A5DI.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.22.5489.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.5897.01 5 0.2020 0.95080 0.10 0.00 0.00 0.00 0.90
#> TCGA.85.8048.01 1 0.2020 0.86460 0.90 0.00 0.00 0.00 0.10
#> TCGA.96.8170.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.NC.A5HL.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.43.6771.01 4 0.4262 0.24801 0.00 0.44 0.00 0.56 0.00
#> TCGA.35.5375.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.6A.AB49.01 4 0.0000 0.87036 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.A511.01 1 0.0609 0.89767 0.98 0.00 0.00 0.00 0.02
#> TCGA.NK.A7XE.01 2 0.2873 0.84644 0.12 0.86 0.00 0.00 0.02
#> TCGA.56.6545.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.NJ.A55A.01 3 0.0000 0.95335 0.00 0.00 1.00 0.00 0.00
#> TCGA.63.A5MM.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.21.5784.01 3 0.1732 0.90995 0.00 0.00 0.92 0.00 0.08
#> TCGA.39.5021.01 1 0.0609 0.90780 0.98 0.00 0.00 0.00 0.02
#> TCGA.33.AASL.01 2 0.0000 0.94181 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7335.01 2 0.0000 0.94181 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.85.8481.01 1 0.0937 0.8917 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.77.8156.01 1 0.0547 0.8940 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.43.A475.01 6 0.5837 0.6263 0.00 0.34 0.20 0.00 0.00 0.46
#> TCGA.68.8251.01 2 0.0547 0.8180 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.92.8063.01 2 0.5095 0.3105 0.08 0.50 0.00 0.00 0.00 0.42
#> TCGA.44.7660.01 1 0.3198 0.6739 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.85.8580.01 6 0.5575 0.5916 0.00 0.40 0.14 0.00 0.00 0.46
#> TCGA.34.5232.01 3 0.5618 0.3751 0.00 0.16 0.50 0.00 0.00 0.34
#> TCGA.92.7340.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8287.01 1 0.0937 0.8866 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.77.8138.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.63.7022.01 3 0.0000 0.6347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.8626.01 6 0.6721 -0.2276 0.20 0.06 0.00 0.28 0.00 0.46
#> TCGA.39.5028.11 5 0.0547 0.9374 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.85.8355.01 1 0.0547 0.8940 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.NC.A5HE.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6214.01 3 0.3499 0.7656 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.43.A56U.01 3 0.3499 0.7662 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.56.8503.01 3 0.2793 0.3751 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.34.5236.01 1 0.0937 0.8917 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.L3.A4E7.01 5 0.0547 0.9374 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.90.A59Q.01 3 0.3499 0.7662 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.55.8614.01 4 0.0000 0.8844 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.85.A53L.01 2 0.4632 0.3457 0.04 0.52 0.00 0.00 0.00 0.44
#> TCGA.56.A4ZJ.01 3 0.3706 0.0388 0.00 0.00 0.62 0.00 0.38 0.00
#> TCGA.44.6148.01 5 0.0547 0.9374 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.63.A5MV.01 1 0.1556 0.8706 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.58.8393.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MS.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MP.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5GH.01 4 0.1092 0.8783 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.52.7622.01 3 0.3578 0.7560 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.34.A5IX.01 2 0.5660 0.2870 0.06 0.48 0.00 0.04 0.00 0.42
#> TCGA.34.8454.01 3 0.0000 0.6347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8146.01 4 0.3321 0.8371 0.00 0.00 0.00 0.82 0.10 0.08
#> TCGA.56.8309.01 1 0.1267 0.8824 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.63.7021.01 1 0.1267 0.8827 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.58.8387.01 1 0.0547 0.8940 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.7726.01 3 0.2454 0.7294 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.39.5028.01 1 0.4337 0.1255 0.50 0.00 0.00 0.02 0.48 0.00
#> TCGA.77.8008.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.22.4609.01 4 0.0937 0.8822 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.43.8115.01 6 0.5921 0.5884 0.00 0.30 0.24 0.00 0.00 0.46
#> TCGA.56.A5DS.01 3 0.3409 0.7704 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.34.5241.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.96.A4JL.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASI.01 3 0.5945 0.3497 0.00 0.00 0.42 0.22 0.00 0.36
#> TCGA.43.6647.01 3 0.0000 0.6347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.A5GA.01 2 0.0547 0.8187 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.56.6546.01 1 0.0937 0.8917 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.85.7697.01 1 0.4078 0.5137 0.64 0.00 0.00 0.02 0.34 0.00
#> TCGA.77.6842.01 1 0.0547 0.8940 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.63.A5MR.01 3 0.2454 0.7306 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.94.A5I6.01 2 0.2631 0.7086 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.85.8049.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.8201.01 4 0.4938 0.3461 0.00 0.34 0.00 0.58 0.00 0.08
#> TCGA.85.8353.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.96.7545.01 2 0.2260 0.7384 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.85.8276.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.58.8386.01 4 0.0000 0.8844 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.56.7731.01 3 0.0000 0.6347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.96.8169.01 3 0.3578 0.7560 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.33.4589.01 3 0.3578 0.7562 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.98.8023.01 1 0.0000 0.8923 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8625.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.60.2703.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.77.A5GB.01 5 0.2474 0.8461 0.08 0.00 0.00 0.04 0.88 0.00
#> TCGA.90.A4EE.01 2 0.0547 0.8180 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.63.A5MG.01 2 0.1865 0.7670 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.94.8491.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JC.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.77.7138.01 5 0.0547 0.9374 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.68.A59I.01 3 0.3409 0.7704 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.77.8131.01 1 0.1807 0.8851 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.68.7756.01 4 0.2094 0.8640 0.00 0.00 0.00 0.90 0.08 0.02
#> TCGA.58.A46J.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.92.8064.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A50Z.01 1 0.2725 0.8625 0.88 0.00 0.00 0.02 0.04 0.06
#> TCGA.55.8204.01 3 0.3499 0.7639 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.O2.A52V.01 6 0.5938 0.5378 0.00 0.28 0.26 0.00 0.00 0.46
#> TCGA.85.6175.01 3 0.0937 0.5939 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.39.5039.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.39.5024.01 3 0.3647 0.7381 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.33.A4WN.01 2 0.2981 0.7038 0.02 0.82 0.00 0.00 0.00 0.16
#> TCGA.NK.A5CT.01 4 0.0000 0.8844 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.18.4721.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8351.01 4 0.1267 0.8761 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.60.2709.01 2 0.5628 0.2982 0.24 0.54 0.00 0.00 0.00 0.22
#> TCGA.85.8666.01 2 0.2631 0.7046 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.94.7943.01 4 0.3578 0.6446 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.NK.A5CX.01 4 0.1092 0.8832 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.XC.AA0X.01 3 0.3499 0.7662 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.85.6561.01 2 0.3523 0.6677 0.04 0.78 0.00 0.00 0.00 0.18
#> TCGA.85.8582.01 4 0.1092 0.8733 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.34.5234.01 3 0.0000 0.6347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.4605.01 3 0.3578 0.7560 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.56.8624.01 5 0.0547 0.9374 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.94.7033.01 4 0.2260 0.8296 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.60.2704.01 1 0.2190 0.8704 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.63.A5MT.01 4 0.0547 0.8805 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.55.7724.01 3 0.3409 0.7704 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.85.A4JB.01 1 0.0937 0.8917 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.39.5030.01 3 0.3499 0.7662 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.43.8118.01 3 0.3409 0.7535 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.68.7757.01 4 0.2981 0.7998 0.02 0.00 0.00 0.82 0.16 0.00
#> TCGA.92.8065.01 2 0.5747 -0.4331 0.00 0.50 0.20 0.00 0.00 0.30
#> TCGA.52.7811.01 5 0.3828 0.0679 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.77.8136.01 3 0.3578 0.7560 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.33.4587.01 5 0.2981 0.7911 0.02 0.00 0.16 0.00 0.82 0.00
#> TCGA.56.8628.01 1 0.5018 0.6237 0.72 0.00 0.08 0.10 0.00 0.10
#> TCGA.21.A5DI.01 5 0.1092 0.9186 0.02 0.00 0.00 0.02 0.96 0.00
#> TCGA.22.5489.01 2 0.1267 0.7975 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.56.5897.01 5 0.0000 0.9407 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.8048.01 1 0.1814 0.8570 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.96.8170.01 3 0.2631 0.7383 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.NC.A5HL.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.6771.01 2 0.4873 0.1067 0.00 0.52 0.00 0.42 0.00 0.06
#> TCGA.35.5375.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.6A.AB49.01 4 0.2790 0.8358 0.00 0.00 0.02 0.84 0.00 0.14
#> TCGA.85.A511.01 1 0.1267 0.8687 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.NK.A7XE.01 2 0.5110 0.2820 0.08 0.48 0.00 0.00 0.00 0.44
#> TCGA.56.6545.01 3 0.3309 0.7694 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.NJ.A55A.01 3 0.3409 0.7704 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.63.A5MM.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.21.5784.01 3 0.0000 0.6347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.39.5021.01 1 0.0547 0.8940 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.33.AASL.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7335.01 2 0.0000 0.8281 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.85.8481.01 1 0.1363 0.80124 0.94 0.00 0.00 0.00 0.04 0.02 0.00
#> TCGA.77.8156.01 1 0.1718 0.80239 0.92 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.43.A475.01 3 0.6690 0.04726 0.02 0.24 0.46 0.00 0.00 0.20 0.08
#> TCGA.68.8251.01 2 0.1928 0.74924 0.00 0.90 0.00 0.00 0.00 0.08 0.02
#> TCGA.92.8063.01 6 0.4015 0.79534 0.06 0.26 0.00 0.00 0.00 0.68 0.00
#> TCGA.44.7660.01 1 0.4212 0.53392 0.62 0.00 0.00 0.02 0.34 0.00 0.02
#> TCGA.85.8580.01 3 0.6700 0.05022 0.02 0.22 0.46 0.00 0.00 0.22 0.08
#> TCGA.34.5232.01 3 0.3199 0.45828 0.00 0.14 0.80 0.00 0.00 0.00 0.06
#> TCGA.92.7340.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8287.01 1 0.3386 0.65928 0.78 0.00 0.00 0.02 0.00 0.18 0.02
#> TCGA.77.8138.01 5 0.0504 0.87855 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.63.7022.01 3 0.3525 -0.38344 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.56.8626.01 6 0.6577 0.58451 0.14 0.10 0.00 0.16 0.02 0.56 0.02
#> TCGA.39.5028.11 5 0.0504 0.86679 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.85.8355.01 1 0.1363 0.80478 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.NC.A5HE.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6214.01 3 0.1664 0.58880 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.43.A56U.01 3 0.0000 0.60817 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.8503.01 7 0.5016 0.71670 0.00 0.00 0.42 0.00 0.12 0.00 0.46
#> TCGA.34.5236.01 1 0.1718 0.80239 0.92 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.L3.A4E7.01 5 0.1006 0.85329 0.00 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.90.A59Q.01 3 0.0504 0.60761 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.8614.01 4 0.0504 0.77799 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.85.A53L.01 6 0.4447 0.76840 0.02 0.28 0.00 0.02 0.00 0.66 0.02
#> TCGA.56.A4ZJ.01 7 0.5421 0.75899 0.00 0.00 0.32 0.00 0.22 0.00 0.46
#> TCGA.44.6148.01 5 0.0504 0.86679 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.63.A5MV.01 1 0.3052 0.74525 0.78 0.00 0.00 0.02 0.20 0.00 0.00
#> TCGA.58.8393.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MS.01 2 0.1886 0.70474 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.63.A5MP.01 2 0.1718 0.75802 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.77.A5GH.01 4 0.0504 0.77894 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.52.7622.01 3 0.1363 0.59877 0.02 0.00 0.94 0.00 0.00 0.00 0.04
#> TCGA.34.A5IX.01 6 0.4938 0.68911 0.00 0.32 0.00 0.08 0.00 0.58 0.02
#> TCGA.34.8454.01 3 0.3546 -0.42655 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.77.8146.01 4 0.5128 0.61133 0.00 0.00 0.00 0.62 0.24 0.04 0.10
#> TCGA.56.8309.01 1 0.2906 0.76115 0.80 0.00 0.00 0.02 0.18 0.00 0.00
#> TCGA.63.7021.01 1 0.3244 0.74310 0.78 0.00 0.00 0.04 0.18 0.00 0.00
#> TCGA.58.8387.01 1 0.1363 0.76350 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.55.7726.01 3 0.2569 0.49087 0.00 0.00 0.84 0.00 0.00 0.02 0.14
#> TCGA.39.5028.01 5 0.4875 -0.11796 0.44 0.00 0.00 0.10 0.46 0.00 0.00
#> TCGA.77.8008.01 5 0.1433 0.84872 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.22.4609.01 4 0.1433 0.77785 0.00 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.43.8115.01 3 0.6428 0.20267 0.02 0.18 0.52 0.00 0.00 0.20 0.08
#> TCGA.56.A5DS.01 3 0.0863 0.59857 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.34.5241.01 5 0.0504 0.87855 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.96.A4JL.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASI.01 3 0.4737 0.29761 0.00 0.00 0.68 0.20 0.00 0.06 0.06
#> TCGA.43.6647.01 3 0.3546 -0.42655 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.77.A5GA.01 2 0.2722 0.67425 0.00 0.84 0.00 0.00 0.00 0.12 0.04
#> TCGA.56.6546.01 1 0.1860 0.79959 0.92 0.00 0.00 0.00 0.04 0.02 0.02
#> TCGA.85.7697.01 1 0.4848 0.25560 0.50 0.00 0.00 0.10 0.40 0.00 0.00
#> TCGA.77.6842.01 1 0.0863 0.80474 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.63.A5MR.01 3 0.2572 0.40539 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.94.A5I6.01 2 0.3558 -0.25259 0.00 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.85.8049.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8201.01 4 0.4954 0.14832 0.00 0.40 0.00 0.52 0.00 0.04 0.04
#> TCGA.85.8353.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.96.7545.01 2 0.3943 -0.07329 0.00 0.56 0.00 0.00 0.00 0.42 0.02
#> TCGA.85.8276.01 2 0.0863 0.77946 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.58.8386.01 4 0.0000 0.77840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.7731.01 3 0.3546 -0.42655 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.96.8169.01 3 0.1006 0.60667 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.33.4589.01 3 0.1664 0.58321 0.00 0.02 0.92 0.00 0.00 0.00 0.06
#> TCGA.98.8023.01 1 0.1363 0.79170 0.94 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.56.8625.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.60.2703.01 5 0.0863 0.87852 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.77.A5GB.01 5 0.3835 0.67823 0.16 0.00 0.00 0.10 0.74 0.00 0.00
#> TCGA.90.A4EE.01 2 0.1718 0.75743 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.63.A5MG.01 2 0.2159 0.70871 0.00 0.90 0.00 0.06 0.00 0.02 0.02
#> TCGA.94.8491.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JC.01 5 0.0863 0.87852 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.77.7138.01 5 0.0504 0.86679 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.68.A59I.01 3 0.0504 0.60608 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.77.8131.01 1 0.2572 0.75176 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.68.7756.01 4 0.3386 0.71749 0.02 0.00 0.00 0.78 0.18 0.02 0.00
#> TCGA.58.A46J.01 5 0.0863 0.87852 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.92.8064.01 2 0.0504 0.78524 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.85.A50Z.01 1 0.5453 0.65147 0.64 0.00 0.00 0.14 0.16 0.02 0.04
#> TCGA.55.8204.01 3 0.2355 0.57969 0.00 0.02 0.90 0.02 0.00 0.02 0.04
#> TCGA.O2.A52V.01 3 0.6277 0.24519 0.02 0.14 0.54 0.00 0.00 0.22 0.08
#> TCGA.85.6175.01 3 0.4408 -0.47195 0.00 0.00 0.52 0.02 0.00 0.02 0.44
#> TCGA.39.5039.01 5 0.0863 0.87852 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.39.5024.01 3 0.2213 0.57542 0.02 0.00 0.90 0.00 0.00 0.04 0.04
#> TCGA.33.A4WN.01 2 0.4990 -0.27384 0.04 0.48 0.00 0.00 0.00 0.44 0.04
#> TCGA.NK.A5CT.01 4 0.1166 0.77584 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.18.4721.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8351.01 4 0.2769 0.75359 0.02 0.00 0.00 0.86 0.00 0.08 0.04
#> TCGA.60.2709.01 6 0.5806 0.63492 0.30 0.22 0.00 0.00 0.00 0.46 0.02
#> TCGA.85.8666.01 2 0.3459 0.05491 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.94.7943.01 4 0.5868 0.28231 0.02 0.04 0.00 0.52 0.00 0.32 0.10
#> TCGA.NK.A5CX.01 4 0.1664 0.77571 0.02 0.00 0.00 0.92 0.06 0.00 0.00
#> TCGA.XC.AA0X.01 3 0.0863 0.60127 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.85.6561.01 2 0.4977 -0.25502 0.04 0.50 0.00 0.00 0.00 0.42 0.04
#> TCGA.85.8582.01 4 0.1505 0.76545 0.00 0.02 0.00 0.94 0.00 0.02 0.02
#> TCGA.34.5234.01 3 0.3546 -0.42655 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.22.4605.01 3 0.1363 0.59877 0.02 0.00 0.94 0.00 0.00 0.00 0.04
#> TCGA.56.8624.01 5 0.0504 0.86679 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.94.7033.01 4 0.3186 0.66848 0.02 0.00 0.00 0.76 0.22 0.00 0.00
#> TCGA.60.2704.01 1 0.5138 0.68830 0.66 0.00 0.00 0.10 0.16 0.08 0.00
#> TCGA.63.A5MT.01 4 0.1166 0.77606 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.55.7724.01 3 0.0000 0.60817 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JB.01 1 0.1860 0.79959 0.92 0.00 0.00 0.00 0.04 0.02 0.02
#> TCGA.39.5030.01 3 0.0504 0.60761 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.43.8118.01 3 0.3055 0.51369 0.02 0.00 0.82 0.00 0.00 0.02 0.14
#> TCGA.68.7757.01 4 0.2945 0.63433 0.00 0.00 0.00 0.74 0.26 0.00 0.00
#> TCGA.92.8065.01 2 0.4710 -0.00446 0.00 0.48 0.46 0.00 0.00 0.02 0.04
#> TCGA.52.7811.01 5 0.3459 0.19313 0.40 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.77.8136.01 3 0.1006 0.60667 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.33.4587.01 5 0.3911 0.59998 0.06 0.00 0.00 0.00 0.70 0.00 0.24
#> TCGA.56.8628.01 1 0.6433 0.45825 0.56 0.00 0.16 0.18 0.02 0.02 0.06
#> TCGA.21.A5DI.01 5 0.0504 0.87855 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.22.5489.01 2 0.2259 0.65405 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.56.5897.01 5 0.0863 0.87852 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.85.8048.01 1 0.2945 0.68869 0.74 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.96.8170.01 3 0.2422 0.44690 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.NC.A5HL.01 2 0.0504 0.78524 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.43.6771.01 2 0.4317 0.18252 0.00 0.58 0.00 0.38 0.00 0.02 0.02
#> TCGA.35.5375.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.6A.AB49.01 4 0.5875 0.48361 0.02 0.00 0.00 0.44 0.00 0.24 0.30
#> TCGA.85.A511.01 1 0.2708 0.61772 0.78 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.NK.A7XE.01 6 0.4015 0.79534 0.06 0.26 0.00 0.00 0.00 0.68 0.00
#> TCGA.56.6545.01 3 0.2163 0.57023 0.00 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.NJ.A55A.01 3 0.2159 0.58373 0.00 0.02 0.90 0.00 0.00 0.02 0.06
#> TCGA.63.A5MM.01 2 0.0504 0.77927 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.21.5784.01 3 0.3546 -0.42655 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.39.5021.01 1 0.1718 0.80239 0.92 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.33.AASL.01 2 0.0000 0.79320 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7335.01 2 0.0000 0.79320 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.85.8481.01 1 0.0941 0.7897 0.96 0.00 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.77.8156.01 1 0.1887 0.7710 0.90 0.00 0.00 0.00 0.00 0.00 0.04 0.06
#> TCGA.43.A475.01 3 0.5584 0.2760 0.00 0.16 0.54 0.00 0.00 0.22 0.08 0.00
#> TCGA.68.8251.01 2 0.1741 0.7897 0.00 0.92 0.00 0.02 0.00 0.04 0.00 0.02
#> TCGA.92.8063.01 6 0.3770 0.5484 0.04 0.12 0.00 0.00 0.02 0.78 0.04 0.00
#> TCGA.44.7660.01 1 0.4530 0.5475 0.66 0.00 0.00 0.06 0.24 0.00 0.02 0.02
#> TCGA.85.8580.01 3 0.5604 0.2695 0.00 0.18 0.54 0.00 0.00 0.20 0.08 0.00
#> TCGA.34.5232.01 3 0.2350 0.5635 0.00 0.10 0.86 0.00 0.00 0.00 0.04 0.00
#> TCGA.92.7340.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8287.01 1 0.3580 0.7030 0.80 0.00 0.00 0.02 0.00 0.10 0.04 0.04
#> TCGA.77.8138.01 5 0.1947 0.8338 0.14 0.00 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.63.7022.01 3 0.3333 -0.8767 0.00 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.56.8626.01 6 0.5923 0.1614 0.06 0.00 0.00 0.12 0.04 0.62 0.12 0.04
#> TCGA.39.5028.11 5 0.0471 0.7751 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.85.8355.01 1 0.0471 0.7863 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.NC.A5HE.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6214.01 3 0.3262 0.5633 0.00 0.00 0.82 0.02 0.00 0.02 0.04 0.10
#> TCGA.43.A56U.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8503.01 7 0.4391 0.8040 0.00 0.00 0.42 0.00 0.08 0.00 0.50 0.00
#> TCGA.34.5236.01 1 0.2947 0.7540 0.84 0.00 0.00 0.00 0.00 0.04 0.06 0.06
#> TCGA.L3.A4E7.01 5 0.0941 0.7766 0.02 0.00 0.00 0.02 0.96 0.00 0.00 0.00
#> TCGA.90.A59Q.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8614.01 4 0.2532 0.5602 0.02 0.00 0.00 0.88 0.00 0.02 0.04 0.04
#> TCGA.85.A53L.01 6 0.4294 0.5255 0.04 0.10 0.00 0.02 0.00 0.76 0.06 0.02
#> TCGA.56.A4ZJ.01 7 0.4841 0.6769 0.00 0.00 0.34 0.00 0.16 0.00 0.50 0.00
#> TCGA.44.6148.01 5 0.0471 0.7751 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.63.A5MV.01 1 0.2591 0.7650 0.86 0.00 0.00 0.04 0.08 0.00 0.00 0.02
#> TCGA.58.8393.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MS.01 2 0.2534 0.5719 0.00 0.78 0.00 0.00 0.00 0.22 0.00 0.00
#> TCGA.63.A5MP.01 2 0.1557 0.7913 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.77.A5GH.01 4 0.2807 0.5545 0.02 0.00 0.00 0.86 0.00 0.02 0.06 0.04
#> TCGA.52.7622.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.A5IX.01 6 0.6538 0.4479 0.04 0.16 0.00 0.08 0.02 0.56 0.12 0.02
#> TCGA.34.8454.01 7 0.3333 0.8470 0.00 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.77.8146.01 4 0.6228 0.2204 0.00 0.00 0.00 0.52 0.18 0.06 0.06 0.18
#> TCGA.56.8309.01 1 0.2484 0.7577 0.86 0.00 0.00 0.02 0.10 0.00 0.00 0.02
#> TCGA.63.7021.01 1 0.3314 0.7343 0.80 0.00 0.00 0.08 0.10 0.00 0.00 0.02
#> TCGA.58.8387.01 1 0.1741 0.7618 0.92 0.00 0.00 0.00 0.00 0.02 0.04 0.02
#> TCGA.55.7726.01 3 0.2856 0.2342 0.00 0.00 0.78 0.02 0.00 0.00 0.20 0.00
#> TCGA.39.5028.01 1 0.5877 0.1672 0.46 0.00 0.00 0.16 0.32 0.04 0.02 0.00
#> TCGA.77.8008.01 5 0.2406 0.8089 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.22.4609.01 4 0.1557 0.5600 0.00 0.00 0.00 0.92 0.06 0.00 0.00 0.02
#> TCGA.43.8115.01 3 0.5254 0.3514 0.00 0.14 0.60 0.00 0.00 0.18 0.08 0.00
#> TCGA.56.A5DS.01 3 0.0941 0.6270 0.00 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.34.5241.01 5 0.2025 0.8250 0.10 0.00 0.00 0.00 0.88 0.00 0.00 0.02
#> TCGA.96.A4JL.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASI.01 3 0.4533 0.3551 0.00 0.00 0.68 0.20 0.00 0.02 0.02 0.08
#> TCGA.43.6647.01 3 0.3333 -0.8767 0.00 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.77.A5GA.01 2 0.1765 0.7230 0.00 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.56.6546.01 1 0.1741 0.7827 0.92 0.00 0.00 0.00 0.00 0.04 0.02 0.02
#> TCGA.85.7697.01 1 0.5400 0.4310 0.56 0.00 0.00 0.18 0.22 0.00 0.02 0.02
#> TCGA.77.6842.01 1 0.2482 0.7774 0.88 0.00 0.00 0.00 0.02 0.02 0.06 0.02
#> TCGA.63.A5MR.01 3 0.3083 -0.3709 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.94.A5I6.01 6 0.3729 0.3380 0.00 0.46 0.00 0.00 0.02 0.52 0.00 0.00
#> TCGA.85.8049.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8201.01 4 0.5566 0.0689 0.00 0.36 0.00 0.48 0.00 0.10 0.04 0.02
#> TCGA.85.8353.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.96.7545.01 2 0.3299 -0.1392 0.00 0.56 0.00 0.00 0.00 0.44 0.00 0.00
#> TCGA.85.8276.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.58.8386.01 4 0.2071 0.5478 0.00 0.00 0.00 0.90 0.00 0.02 0.04 0.04
#> TCGA.56.7731.01 3 0.3333 -0.8767 0.00 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.96.8169.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.4589.01 3 0.1874 0.6280 0.00 0.02 0.92 0.02 0.00 0.02 0.02 0.00
#> TCGA.98.8023.01 1 0.1275 0.7808 0.94 0.00 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.56.8625.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.60.2703.01 5 0.2569 0.8281 0.16 0.00 0.00 0.00 0.82 0.00 0.00 0.02
#> TCGA.77.A5GB.01 5 0.5264 0.4303 0.30 0.00 0.00 0.18 0.50 0.00 0.00 0.02
#> TCGA.90.A4EE.01 2 0.1557 0.7909 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.63.A5MG.01 2 0.2204 0.7583 0.00 0.90 0.00 0.02 0.00 0.04 0.02 0.02
#> TCGA.94.8491.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JC.01 5 0.2404 0.8336 0.14 0.00 0.00 0.00 0.84 0.00 0.00 0.02
#> TCGA.77.7138.01 5 0.1408 0.7776 0.02 0.00 0.00 0.02 0.94 0.00 0.00 0.02
#> TCGA.68.A59I.01 3 0.0471 0.6353 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.77.8131.01 1 0.2025 0.7712 0.88 0.00 0.00 0.00 0.10 0.00 0.02 0.00
#> TCGA.68.7756.01 4 0.4389 0.4540 0.08 0.00 0.00 0.74 0.10 0.00 0.04 0.04
#> TCGA.58.A46J.01 5 0.3021 0.8206 0.16 0.00 0.00 0.02 0.80 0.00 0.00 0.02
#> TCGA.92.8064.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A50Z.01 1 0.5111 0.6959 0.70 0.00 0.00 0.08 0.08 0.04 0.08 0.02
#> TCGA.55.8204.01 3 0.2591 0.5666 0.00 0.02 0.86 0.08 0.00 0.04 0.00 0.00
#> TCGA.O2.A52V.01 3 0.5363 0.3366 0.00 0.14 0.58 0.00 0.00 0.20 0.08 0.00
#> TCGA.85.6175.01 7 0.4004 0.8278 0.00 0.00 0.46 0.04 0.00 0.00 0.50 0.00
#> TCGA.39.5039.01 5 0.2114 0.8320 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.39.5024.01 3 0.1804 0.6065 0.00 0.00 0.90 0.00 0.00 0.02 0.08 0.00
#> TCGA.33.A4WN.01 2 0.4137 -0.3124 0.02 0.50 0.00 0.00 0.00 0.46 0.00 0.02
#> TCGA.NK.A5CT.01 4 0.4528 0.4294 0.00 0.00 0.00 0.68 0.00 0.04 0.14 0.14
#> TCGA.18.4721.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8351.01 4 0.3660 0.3622 0.00 0.00 0.00 0.70 0.00 0.00 0.06 0.24
#> TCGA.60.2709.01 6 0.6205 0.4633 0.24 0.22 0.00 0.00 0.00 0.46 0.04 0.04
#> TCGA.85.8666.01 6 0.3333 0.2278 0.00 0.50 0.00 0.00 0.00 0.50 0.00 0.00
#> TCGA.94.7943.01 4 0.6969 -0.1149 0.02 0.00 0.00 0.38 0.02 0.28 0.14 0.16
#> TCGA.NK.A5CX.01 4 0.1607 0.5605 0.04 0.00 0.00 0.92 0.04 0.00 0.00 0.00
#> TCGA.XC.AA0X.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.6561.01 6 0.4586 0.4560 0.06 0.40 0.00 0.00 0.00 0.52 0.00 0.02
#> TCGA.85.8582.01 4 0.4446 0.4412 0.00 0.08 0.00 0.74 0.00 0.04 0.06 0.08
#> TCGA.34.5234.01 7 0.3333 0.8470 0.00 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.22.4605.01 3 0.0471 0.6343 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.56.8624.01 5 0.0471 0.7751 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.94.7033.01 4 0.5024 0.3528 0.10 0.00 0.00 0.64 0.20 0.00 0.02 0.04
#> TCGA.60.2704.01 1 0.4461 0.7016 0.72 0.00 0.00 0.14 0.06 0.06 0.00 0.02
#> TCGA.63.A5MT.01 4 0.3894 0.4852 0.00 0.00 0.00 0.76 0.00 0.06 0.10 0.08
#> TCGA.55.7724.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JB.01 1 0.1741 0.7780 0.92 0.00 0.00 0.00 0.00 0.02 0.04 0.02
#> TCGA.39.5030.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.8118.01 3 0.2534 0.3968 0.00 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.68.7757.01 4 0.3735 0.4249 0.04 0.00 0.00 0.72 0.22 0.00 0.02 0.00
#> TCGA.92.8065.01 2 0.6424 -0.1034 0.00 0.38 0.38 0.06 0.00 0.14 0.02 0.02
#> TCGA.52.7811.01 5 0.4516 0.3151 0.42 0.00 0.00 0.02 0.52 0.02 0.02 0.00
#> TCGA.77.8136.01 3 0.0000 0.6475 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.4587.01 5 0.4747 0.4875 0.16 0.00 0.00 0.00 0.54 0.00 0.30 0.00
#> TCGA.56.8628.01 1 0.6048 0.4204 0.56 0.00 0.20 0.14 0.02 0.00 0.04 0.04
#> TCGA.21.A5DI.01 5 0.3909 0.7410 0.18 0.00 0.00 0.12 0.70 0.00 0.00 0.00
#> TCGA.22.5489.01 2 0.2404 0.6898 0.00 0.84 0.00 0.00 0.00 0.14 0.00 0.02
#> TCGA.56.5897.01 5 0.2114 0.8320 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.85.8048.01 1 0.3178 0.7199 0.80 0.00 0.00 0.04 0.14 0.00 0.00 0.02
#> TCGA.96.8170.01 3 0.2267 0.3490 0.00 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.NC.A5HL.01 2 0.0471 0.8264 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.43.6771.01 2 0.5639 0.0764 0.00 0.50 0.00 0.32 0.00 0.12 0.04 0.02
#> TCGA.35.5375.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.6A.AB49.01 8 0.3615 0.0000 0.00 0.00 0.00 0.20 0.02 0.00 0.04 0.74
#> TCGA.85.A511.01 1 0.3036 0.6546 0.78 0.00 0.00 0.00 0.00 0.18 0.04 0.00
#> TCGA.NK.A7XE.01 6 0.3454 0.5619 0.04 0.12 0.00 0.00 0.02 0.80 0.02 0.00
#> TCGA.56.6545.01 3 0.1887 0.6254 0.00 0.00 0.90 0.04 0.00 0.00 0.06 0.00
#> TCGA.NJ.A55A.01 3 0.1408 0.6182 0.00 0.00 0.94 0.02 0.00 0.02 0.02 0.00
#> TCGA.63.A5MM.01 2 0.0808 0.8070 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.21.5784.01 7 0.3333 0.8470 0.00 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.39.5021.01 1 0.2591 0.7788 0.86 0.00 0.00 0.00 0.02 0.00 0.04 0.08
#> TCGA.33.AASL.01 2 0.0000 0.8392 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7335.01 2 0.0000 0.8392 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: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["011"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 40 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.704 0.957 0.961 0.3603 0.591 0.591
#> 3 3 0.690 0.768 0.900 0.5529 0.603 0.435
#> 4 4 0.987 0.955 0.979 0.2262 0.741 0.478
#> 5 5 0.878 0.829 0.916 0.1258 0.823 0.498
#> 6 6 0.807 0.797 0.862 0.0623 0.909 0.620
#> 7 7 0.848 0.707 0.837 0.0363 0.936 0.671
#> 8 8 0.844 0.713 0.779 0.0274 0.926 0.564
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.85.8481.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.8156.01 2 0.827 0.832 0.26 0.74
#> TCGA.44.7660.01 2 0.000 0.835 0.00 1.00
#> TCGA.85.8287.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.8138.01 1 0.000 1.000 1.00 0.00
#> TCGA.39.5028.11 1 0.000 1.000 1.00 0.00
#> TCGA.85.8355.01 1 0.000 1.000 1.00 0.00
#> TCGA.34.5236.01 1 0.000 1.000 1.00 0.00
#> TCGA.L3.A4E7.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.6148.01 1 0.000 1.000 1.00 0.00
#> TCGA.63.A5MV.01 2 0.827 0.832 0.26 0.74
#> TCGA.56.8309.01 1 0.000 1.000 1.00 0.00
#> TCGA.63.7021.01 1 0.000 1.000 1.00 0.00
#> TCGA.58.8387.01 2 0.827 0.832 0.26 0.74
#> TCGA.39.5028.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.8008.01 1 0.000 1.000 1.00 0.00
#> TCGA.34.5241.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.6546.01 2 0.000 0.835 0.00 1.00
#> TCGA.85.7697.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.6842.01 2 0.000 0.835 0.00 1.00
#> TCGA.98.8023.01 1 0.000 1.000 1.00 0.00
#> TCGA.60.2703.01 2 0.827 0.832 0.26 0.74
#> TCGA.77.A5GB.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.A4JC.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.7138.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.8131.01 1 0.000 1.000 1.00 0.00
#> TCGA.58.A46J.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.A50Z.01 1 0.000 1.000 1.00 0.00
#> TCGA.39.5039.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.8624.01 1 0.000 1.000 1.00 0.00
#> TCGA.60.2704.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.A4JB.01 2 0.680 0.871 0.18 0.82
#> TCGA.52.7811.01 2 0.680 0.871 0.18 0.82
#> TCGA.33.4587.01 2 0.000 0.835 0.00 1.00
#> TCGA.56.8628.01 1 0.000 1.000 1.00 0.00
#> TCGA.21.A5DI.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.5897.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.8048.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.A511.01 1 0.000 1.000 1.00 0.00
#> TCGA.39.5021.01 2 0.680 0.871 0.18 0.82
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.85.8481.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.77.8156.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.44.7660.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.85.8287.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.77.8138.01 1 0.6302 0.4049 0.52 0.48 0.00
#> TCGA.39.5028.11 1 0.0000 0.7086 1.00 0.00 0.00
#> TCGA.85.8355.01 1 0.6244 0.4653 0.56 0.44 0.00
#> TCGA.34.5236.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.L3.A4E7.01 1 0.0000 0.7086 1.00 0.00 0.00
#> TCGA.44.6148.01 1 0.0000 0.7086 1.00 0.00 0.00
#> TCGA.63.A5MV.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.56.8309.01 1 0.0892 0.7134 0.98 0.02 0.00
#> TCGA.63.7021.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.58.8387.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.39.5028.01 1 0.6244 0.4653 0.56 0.44 0.00
#> TCGA.77.8008.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.34.5241.01 1 0.6302 0.4049 0.52 0.48 0.00
#> TCGA.56.6546.01 2 0.6302 -0.0616 0.00 0.52 0.48
#> TCGA.85.7697.01 1 0.6302 0.4049 0.52 0.48 0.00
#> TCGA.77.6842.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.98.8023.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.60.2703.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.77.A5GB.01 1 0.0000 0.7086 1.00 0.00 0.00
#> TCGA.85.A4JC.01 1 0.0892 0.7134 0.98 0.02 0.00
#> TCGA.77.7138.01 1 0.0000 0.7086 1.00 0.00 0.00
#> TCGA.77.8131.01 1 0.0892 0.7134 0.98 0.02 0.00
#> TCGA.58.A46J.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.85.A50Z.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.39.5039.01 2 0.2066 0.8852 0.06 0.94 0.00
#> TCGA.56.8624.01 1 0.0000 0.7086 1.00 0.00 0.00
#> TCGA.60.2704.01 1 0.0892 0.7134 0.98 0.02 0.00
#> TCGA.85.A4JB.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.52.7811.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.33.4587.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.56.8628.01 2 0.0000 0.9561 0.00 1.00 0.00
#> TCGA.21.A5DI.01 2 0.2959 0.8262 0.10 0.90 0.00
#> TCGA.56.5897.01 1 0.6302 0.4049 0.52 0.48 0.00
#> TCGA.85.8048.01 1 0.0000 0.7086 1.00 0.00 0.00
#> TCGA.85.A511.01 1 0.6302 0.4049 0.52 0.48 0.00
#> TCGA.39.5021.01 2 0.0000 0.9561 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.85.8481.01 2 0.164 0.926 0.06 0.94 0 0.00
#> TCGA.77.8156.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.44.7660.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.85.8287.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.77.8138.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.39.5028.11 4 0.000 1.000 0.00 0.00 0 1.00
#> TCGA.85.8355.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.34.5236.01 2 0.121 0.941 0.04 0.96 0 0.00
#> TCGA.L3.A4E7.01 4 0.000 1.000 0.00 0.00 0 1.00
#> TCGA.44.6148.01 4 0.000 1.000 0.00 0.00 0 1.00
#> TCGA.63.A5MV.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.56.8309.01 1 0.121 0.950 0.96 0.00 0 0.04
#> TCGA.63.7021.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.58.8387.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.39.5028.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.77.8008.01 2 0.164 0.926 0.06 0.94 0 0.00
#> TCGA.34.5241.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.56.6546.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.85.7697.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.77.6842.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.98.8023.01 2 0.380 0.703 0.22 0.78 0 0.00
#> TCGA.60.2703.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.77.A5GB.01 4 0.000 1.000 0.00 0.00 0 1.00
#> TCGA.85.A4JC.01 1 0.121 0.950 0.96 0.00 0 0.04
#> TCGA.77.7138.01 4 0.000 1.000 0.00 0.00 0 1.00
#> TCGA.77.8131.01 1 0.121 0.950 0.96 0.00 0 0.04
#> TCGA.58.A46J.01 2 0.121 0.941 0.04 0.96 0 0.00
#> TCGA.85.A50Z.01 1 0.164 0.912 0.94 0.06 0 0.00
#> TCGA.39.5039.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.56.8624.01 4 0.000 1.000 0.00 0.00 0 1.00
#> TCGA.60.2704.01 1 0.121 0.950 0.96 0.00 0 0.04
#> TCGA.85.A4JB.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.52.7811.01 2 0.000 0.959 0.00 1.00 0 0.00
#> TCGA.33.4587.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.56.8628.01 1 0.317 0.781 0.84 0.16 0 0.00
#> TCGA.21.A5DI.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.56.5897.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.85.8048.01 1 0.121 0.950 0.96 0.00 0 0.04
#> TCGA.85.A511.01 1 0.000 0.968 1.00 0.00 0 0.00
#> TCGA.39.5021.01 2 0.000 0.959 0.00 1.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.85.8481.01 5 0.1216 0.831 0.02 0.02 0 0.00 0.96
#> TCGA.77.8156.01 2 0.3796 0.763 0.00 0.70 0 0.00 0.30
#> TCGA.44.7660.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.85.8287.01 5 0.3684 0.377 0.00 0.28 0 0.00 0.72
#> TCGA.77.8138.01 1 0.4287 -0.015 0.54 0.00 0 0.00 0.46
#> TCGA.39.5028.11 4 0.0000 0.969 0.00 0.00 0 1.00 0.00
#> TCGA.85.8355.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.34.5236.01 5 0.1043 0.813 0.00 0.04 0 0.00 0.96
#> TCGA.L3.A4E7.01 4 0.1648 0.969 0.00 0.02 0 0.94 0.04
#> TCGA.44.6148.01 4 0.1648 0.969 0.00 0.02 0 0.94 0.04
#> TCGA.63.A5MV.01 2 0.3895 0.746 0.00 0.68 0 0.00 0.32
#> TCGA.56.8309.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.63.7021.01 5 0.1410 0.829 0.06 0.00 0 0.00 0.94
#> TCGA.58.8387.01 2 0.3895 0.746 0.00 0.68 0 0.00 0.32
#> TCGA.39.5028.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.77.8008.01 5 0.1216 0.831 0.02 0.02 0 0.00 0.96
#> TCGA.34.5241.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.56.6546.01 2 0.0609 0.775 0.00 0.98 0 0.00 0.02
#> TCGA.85.7697.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.77.6842.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.98.8023.01 5 0.1043 0.836 0.04 0.00 0 0.00 0.96
#> TCGA.60.2703.01 2 0.3796 0.763 0.00 0.70 0 0.00 0.30
#> TCGA.77.A5GB.01 4 0.1648 0.969 0.00 0.02 0 0.94 0.04
#> TCGA.85.A4JC.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.77.7138.01 4 0.0000 0.969 0.00 0.00 0 1.00 0.00
#> TCGA.77.8131.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.58.A46J.01 5 0.1043 0.813 0.00 0.04 0 0.00 0.96
#> TCGA.85.A50Z.01 5 0.1410 0.829 0.06 0.00 0 0.00 0.94
#> TCGA.39.5039.01 5 0.4060 0.445 0.36 0.00 0 0.00 0.64
#> TCGA.56.8624.01 4 0.0000 0.969 0.00 0.00 0 1.00 0.00
#> TCGA.60.2704.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.85.A4JB.01 2 0.0609 0.775 0.00 0.98 0 0.00 0.02
#> TCGA.52.7811.01 2 0.0609 0.775 0.00 0.98 0 0.00 0.02
#> TCGA.33.4587.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.56.8628.01 5 0.1043 0.836 0.04 0.00 0 0.00 0.96
#> TCGA.21.A5DI.01 5 0.4060 0.445 0.36 0.00 0 0.00 0.64
#> TCGA.56.5897.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.85.8048.01 1 0.1043 0.901 0.96 0.00 0 0.00 0.04
#> TCGA.85.A511.01 1 0.0000 0.944 1.00 0.00 0 0.00 0.00
#> TCGA.39.5021.01 2 0.0609 0.775 0.00 0.98 0 0.00 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.85.8481.01 5 0.1814 0.793 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.77.8156.01 2 0.4632 0.443 0.00 0.52 0.00 0.00 0.04 0.44
#> TCGA.44.7660.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8287.01 2 0.4552 0.579 0.00 0.64 0.00 0.00 0.30 0.06
#> TCGA.77.8138.01 5 0.4328 0.596 0.10 0.18 0.00 0.00 0.72 0.00
#> TCGA.39.5028.11 4 0.0000 0.928 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.85.8355.01 1 0.3787 0.820 0.78 0.12 0.00 0.00 0.10 0.00
#> TCGA.34.5236.01 5 0.1814 0.793 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.L3.A4E7.01 4 0.2260 0.928 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.44.6148.01 4 0.2260 0.928 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.63.A5MV.01 2 0.4631 0.565 0.00 0.62 0.00 0.00 0.06 0.32
#> TCGA.56.8309.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.7021.01 5 0.0547 0.798 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.58.8387.01 2 0.4834 0.604 0.00 0.64 0.00 0.00 0.10 0.26
#> TCGA.39.5028.01 1 0.3985 0.810 0.76 0.14 0.00 0.00 0.10 0.00
#> TCGA.77.8008.01 5 0.1814 0.793 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.34.5241.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.6546.01 6 0.0000 0.973 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.85.7697.01 1 0.3985 0.810 0.76 0.14 0.00 0.00 0.10 0.00
#> TCGA.77.6842.01 3 0.0937 0.974 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.98.8023.01 2 0.3828 0.365 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.60.2703.01 2 0.4632 0.443 0.00 0.52 0.00 0.00 0.04 0.44
#> TCGA.77.A5GB.01 4 0.2260 0.928 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.85.A4JC.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7138.01 4 0.0000 0.928 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.77.8131.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.58.A46J.01 2 0.3869 0.228 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.85.A50Z.01 5 0.0937 0.807 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.39.5039.01 5 0.2190 0.754 0.04 0.06 0.00 0.00 0.90 0.00
#> TCGA.56.8624.01 4 0.0000 0.928 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.60.2704.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JB.01 6 0.1267 0.916 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.52.7811.01 6 0.0000 0.973 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.33.4587.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.8628.01 5 0.2048 0.780 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.21.A5DI.01 5 0.3679 0.663 0.04 0.20 0.00 0.00 0.76 0.00
#> TCGA.56.5897.01 1 0.4328 0.777 0.72 0.18 0.00 0.00 0.10 0.00
#> TCGA.85.8048.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A511.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5021.01 6 0.0000 0.973 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.85.8481.01 5 0.0504 0.700 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.77.8156.01 2 0.4475 0.802 0.00 0.72 0.00 0.00 0.04 0.10 0.14
#> TCGA.44.7660.01 3 0.0000 0.993 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8287.01 2 0.2081 0.671 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.77.8138.01 7 0.3755 0.366 0.02 0.00 0.00 0.00 0.34 0.00 0.64
#> TCGA.39.5028.11 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8355.01 1 0.4127 0.416 0.60 0.00 0.00 0.00 0.00 0.04 0.36
#> TCGA.34.5236.01 5 0.0504 0.700 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.L3.A4E7.01 4 0.3914 0.883 0.00 0.06 0.00 0.78 0.00 0.06 0.10
#> TCGA.44.6148.01 4 0.3940 0.882 0.00 0.06 0.00 0.78 0.00 0.08 0.08
#> TCGA.63.A5MV.01 2 0.4295 0.812 0.00 0.74 0.00 0.00 0.06 0.06 0.14
#> TCGA.56.8309.01 1 0.0000 0.822 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.7021.01 5 0.2832 0.610 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.58.8387.01 2 0.1166 0.752 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.39.5028.01 1 0.4127 0.419 0.60 0.00 0.00 0.00 0.00 0.04 0.36
#> TCGA.77.8008.01 5 0.0504 0.700 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.34.5241.01 1 0.1006 0.812 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.56.6546.01 6 0.1886 0.970 0.00 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.85.7697.01 1 0.4127 0.419 0.60 0.00 0.00 0.00 0.00 0.04 0.36
#> TCGA.77.6842.01 3 0.0504 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.98.8023.01 5 0.5332 0.335 0.00 0.38 0.00 0.00 0.44 0.00 0.18
#> TCGA.60.2703.01 2 0.4475 0.802 0.00 0.72 0.00 0.00 0.04 0.10 0.14
#> TCGA.77.A5GB.01 4 0.3914 0.883 0.00 0.06 0.00 0.78 0.00 0.06 0.10
#> TCGA.85.A4JC.01 1 0.0000 0.822 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7138.01 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8131.01 1 0.0000 0.822 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.58.A46J.01 5 0.4266 0.189 0.00 0.44 0.00 0.00 0.52 0.00 0.04
#> TCGA.85.A50Z.01 5 0.1166 0.681 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.39.5039.01 5 0.3358 0.381 0.00 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.56.8624.01 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.60.2704.01 1 0.0000 0.822 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JB.01 6 0.3086 0.935 0.00 0.16 0.00 0.00 0.00 0.80 0.04
#> TCGA.52.7811.01 6 0.2081 0.968 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.33.4587.01 3 0.0000 0.993 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.8628.01 5 0.3052 0.639 0.00 0.02 0.00 0.00 0.78 0.00 0.20
#> TCGA.21.A5DI.01 7 0.3221 0.351 0.00 0.00 0.00 0.00 0.32 0.00 0.68
#> TCGA.56.5897.01 7 0.3985 -0.316 0.46 0.00 0.00 0.00 0.00 0.02 0.52
#> TCGA.85.8048.01 1 0.0000 0.822 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A511.01 1 0.1006 0.812 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.39.5021.01 6 0.1886 0.970 0.00 0.12 0.00 0.00 0.00 0.88 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.85.8481.01 5 0.0471 0.7337 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.77.8156.01 2 0.4733 0.6570 0.00 0.62 0.00 0.00 0.00 0.06 0.06 0.26
#> TCGA.44.7660.01 3 0.0000 0.9932 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8287.01 2 0.0000 0.6744 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8138.01 7 0.4813 0.5374 0.00 0.00 0.00 0.00 0.14 0.00 0.44 0.42
#> TCGA.39.5028.11 4 0.3728 0.8309 0.00 0.00 0.00 0.68 0.00 0.02 0.28 0.02
#> TCGA.85.8355.01 8 0.4137 0.7580 0.46 0.00 0.00 0.00 0.02 0.00 0.02 0.50
#> TCGA.34.5236.01 5 0.0471 0.7337 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.L3.A4E7.01 4 0.0000 0.8237 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6148.01 4 0.0808 0.8211 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.63.A5MV.01 2 0.3845 0.6674 0.00 0.66 0.00 0.00 0.00 0.00 0.06 0.28
#> TCGA.56.8309.01 1 0.0000 0.9007 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.7021.01 5 0.3272 0.1763 0.00 0.00 0.00 0.00 0.58 0.00 0.42 0.00
#> TCGA.58.8387.01 2 0.0471 0.6747 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.39.5028.01 8 0.3318 0.8056 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.77.8008.01 5 0.0471 0.7337 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.34.5241.01 1 0.1275 0.8720 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.56.6546.01 6 0.0471 0.9412 0.00 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.85.7697.01 8 0.3318 0.8056 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.77.6842.01 3 0.0471 0.9863 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.98.8023.01 2 0.4482 0.2998 0.00 0.60 0.00 0.00 0.14 0.00 0.26 0.00
#> TCGA.60.2703.01 2 0.4733 0.6570 0.00 0.62 0.00 0.00 0.00 0.06 0.06 0.26
#> TCGA.77.A5GB.01 4 0.0000 0.8237 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4JC.01 1 0.0000 0.9007 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7138.01 4 0.3728 0.8309 0.00 0.00 0.00 0.68 0.00 0.02 0.28 0.02
#> TCGA.77.8131.01 1 0.2114 0.6047 0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.58.A46J.01 2 0.4412 0.3611 0.00 0.60 0.00 0.00 0.28 0.00 0.12 0.00
#> TCGA.85.A50Z.01 5 0.0000 0.7198 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.39.5039.01 7 0.3729 -0.0997 0.00 0.00 0.00 0.00 0.46 0.00 0.52 0.02
#> TCGA.56.8624.01 4 0.3728 0.8309 0.00 0.00 0.00 0.68 0.00 0.02 0.28 0.02
#> TCGA.60.2704.01 1 0.0471 0.8960 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.85.A4JB.01 6 0.3421 0.8558 0.00 0.08 0.00 0.00 0.00 0.80 0.04 0.08
#> TCGA.52.7811.01 6 0.1275 0.9337 0.00 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.33.4587.01 3 0.0000 0.9932 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8628.01 5 0.3737 -0.0378 0.00 0.02 0.00 0.00 0.50 0.00 0.48 0.00
#> TCGA.21.A5DI.01 7 0.4380 0.6033 0.00 0.00 0.00 0.00 0.10 0.00 0.58 0.32
#> TCGA.56.5897.01 8 0.4730 0.5624 0.26 0.00 0.00 0.00 0.00 0.00 0.18 0.56
#> TCGA.85.8048.01 1 0.0000 0.9007 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A511.01 1 0.2348 0.8066 0.88 0.00 0.00 0.00 0.02 0.00 0.04 0.06
#> TCGA.39.5021.01 6 0.0471 0.9412 0.00 0.02 0.00 0.00 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.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 38 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.892 0.938 0.970 0.3089 0.727 0.727
#> 3 3 1.000 0.998 0.999 0.8416 0.706 0.595
#> 4 4 0.932 0.920 0.964 0.3175 0.784 0.519
#> 5 5 0.779 0.803 0.902 0.0293 0.983 0.932
#> 6 6 0.687 0.690 0.835 0.0350 0.993 0.970
#> 7 7 0.708 0.561 0.805 0.0213 0.969 0.863
#> 8 8 0.702 0.501 0.765 0.0186 0.962 0.819
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] 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.43.A475.01 1 0.141 0.953 0.98 0.02
#> TCGA.68.8251.01 1 0.000 0.962 1.00 0.00
#> TCGA.92.8063.01 1 0.000 0.962 1.00 0.00
#> TCGA.85.8580.01 1 0.141 0.953 0.98 0.02
#> TCGA.92.7340.01 2 0.000 1.000 0.00 1.00
#> TCGA.NC.A5HE.01 1 0.000 0.962 1.00 0.00
#> TCGA.85.A53L.01 1 0.000 0.962 1.00 0.00
#> TCGA.58.8393.01 1 0.141 0.953 0.98 0.02
#> TCGA.63.A5MS.01 1 0.000 0.962 1.00 0.00
#> TCGA.63.A5MP.01 1 0.000 0.962 1.00 0.00
#> TCGA.34.A5IX.01 1 0.000 0.962 1.00 0.00
#> TCGA.43.8115.01 1 0.141 0.953 0.98 0.02
#> TCGA.96.A4JL.01 2 0.000 1.000 0.00 1.00
#> TCGA.77.A5GA.01 1 0.000 0.962 1.00 0.00
#> TCGA.94.A5I6.01 1 0.000 0.962 1.00 0.00
#> TCGA.85.8049.01 1 0.000 0.962 1.00 0.00
#> TCGA.85.8353.01 1 0.000 0.962 1.00 0.00
#> TCGA.96.7545.01 1 0.000 0.962 1.00 0.00
#> TCGA.85.8276.01 1 0.795 0.709 0.76 0.24
#> TCGA.56.8625.01 1 0.141 0.953 0.98 0.02
#> TCGA.90.A4EE.01 1 0.000 0.962 1.00 0.00
#> TCGA.63.A5MG.01 2 0.000 1.000 0.00 1.00
#> TCGA.94.8491.01 2 0.000 1.000 0.00 1.00
#> TCGA.92.8064.01 1 0.680 0.788 0.82 0.18
#> TCGA.O2.A52V.01 1 0.141 0.953 0.98 0.02
#> TCGA.33.A4WN.01 1 0.000 0.962 1.00 0.00
#> TCGA.18.4721.01 1 0.000 0.962 1.00 0.00
#> TCGA.60.2709.01 1 0.000 0.962 1.00 0.00
#> TCGA.85.8666.01 1 0.000 0.962 1.00 0.00
#> TCGA.85.6561.01 1 0.000 0.962 1.00 0.00
#> TCGA.92.8065.01 1 0.904 0.587 0.68 0.32
#> TCGA.22.5489.01 1 0.000 0.962 1.00 0.00
#> TCGA.NC.A5HL.01 1 0.000 0.962 1.00 0.00
#> TCGA.35.5375.01 2 0.000 1.000 0.00 1.00
#> TCGA.NK.A7XE.01 1 0.000 0.962 1.00 0.00
#> TCGA.63.A5MM.01 2 0.000 1.000 0.00 1.00
#> TCGA.33.AASL.01 1 0.000 0.962 1.00 0.00
#> TCGA.77.7335.01 1 0.855 0.658 0.72 0.28
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.43.A475.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.68.8251.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.92.8063.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.85.8580.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.92.7340.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.NC.A5HE.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.85.A53L.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.58.8393.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.63.A5MS.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.63.A5MP.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.34.A5IX.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.43.8115.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.96.A4JL.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.77.A5GA.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.94.A5I6.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.85.8049.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.85.8353.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.96.7545.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.85.8276.01 1 0.153 0.958 0.96 0.04 0
#> TCGA.56.8625.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.90.A4EE.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.63.A5MG.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.94.8491.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.92.8064.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.O2.A52V.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.33.A4WN.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.18.4721.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.60.2709.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.85.8666.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.85.6561.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.92.8065.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.22.5489.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.NC.A5HL.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.35.5375.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.NK.A7XE.01 1 0.000 0.998 1.00 0.00 0
#> TCGA.63.A5MM.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.33.AASL.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.77.7335.01 3 0.000 1.000 0.00 0.00 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.43.A475.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.68.8251.01 1 0.4855 0.329 0.60 0 0.00 0.40
#> TCGA.92.8063.01 4 0.0000 0.963 0.00 0 0.00 1.00
#> TCGA.85.8580.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.92.7340.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.NC.A5HE.01 1 0.3610 0.731 0.80 0 0.00 0.20
#> TCGA.85.A53L.01 4 0.1637 0.948 0.06 0 0.00 0.94
#> TCGA.58.8393.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.63.A5MS.01 1 0.2011 0.856 0.92 0 0.00 0.08
#> TCGA.63.A5MP.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.34.A5IX.01 4 0.0000 0.963 0.00 0 0.00 1.00
#> TCGA.43.8115.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.96.A4JL.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.77.A5GA.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.94.A5I6.01 4 0.0000 0.963 0.00 0 0.00 1.00
#> TCGA.85.8049.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.85.8353.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.96.7545.01 4 0.1211 0.956 0.04 0 0.00 0.96
#> TCGA.85.8276.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.56.8625.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.90.A4EE.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.63.A5MG.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.94.8491.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.92.8064.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.O2.A52V.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.33.A4WN.01 1 0.0000 0.903 1.00 0 0.00 0.00
#> TCGA.18.4721.01 1 0.0707 0.894 0.98 0 0.00 0.02
#> TCGA.60.2709.01 4 0.0000 0.963 0.00 0 0.00 1.00
#> TCGA.85.8666.01 4 0.1637 0.948 0.06 0 0.00 0.94
#> TCGA.85.6561.01 4 0.1637 0.947 0.06 0 0.00 0.94
#> TCGA.92.8065.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.22.5489.01 4 0.0000 0.963 0.00 0 0.00 1.00
#> TCGA.NC.A5HL.01 4 0.2647 0.884 0.12 0 0.00 0.88
#> TCGA.35.5375.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.NK.A7XE.01 4 0.0000 0.963 0.00 0 0.00 1.00
#> TCGA.63.A5MM.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.33.AASL.01 3 0.0000 1.000 0.00 0 1.00 0.00
#> TCGA.77.7335.01 1 0.4624 0.455 0.66 0 0.34 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.43.A475.01 3 0.0000 0.968 0.00 0.00 1.00 0.00 0.00
#> TCGA.68.8251.01 1 0.3983 0.370 0.66 0.00 0.00 0.34 0.00
#> TCGA.92.8063.01 4 0.0000 0.910 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.8580.01 3 0.0000 0.968 0.00 0.00 1.00 0.00 0.00
#> TCGA.92.7340.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HE.01 1 0.4588 0.551 0.72 0.00 0.00 0.22 0.06
#> TCGA.85.A53L.01 4 0.3274 0.772 0.22 0.00 0.00 0.78 0.00
#> TCGA.58.8393.01 3 0.0609 0.965 0.00 0.00 0.98 0.00 0.02
#> TCGA.63.A5MS.01 1 0.1732 0.740 0.92 0.00 0.00 0.08 0.00
#> TCGA.63.A5MP.01 1 0.0609 0.775 0.98 0.00 0.00 0.00 0.02
#> TCGA.34.A5IX.01 4 0.0000 0.910 0.00 0.00 0.00 1.00 0.00
#> TCGA.43.8115.01 3 0.0000 0.968 0.00 0.00 1.00 0.00 0.00
#> TCGA.96.A4JL.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.A5GA.01 1 0.0000 0.778 1.00 0.00 0.00 0.00 0.00
#> TCGA.94.A5I6.01 4 0.0000 0.910 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.8049.01 1 0.2873 0.741 0.86 0.00 0.00 0.02 0.12
#> TCGA.85.8353.01 1 0.1410 0.771 0.94 0.00 0.00 0.00 0.06
#> TCGA.96.7545.01 4 0.2020 0.887 0.10 0.00 0.00 0.90 0.00
#> TCGA.85.8276.01 1 0.1410 0.758 0.94 0.00 0.00 0.00 0.06
#> TCGA.56.8625.01 3 0.0609 0.965 0.00 0.00 0.98 0.00 0.02
#> TCGA.90.A4EE.01 1 0.4456 0.445 0.66 0.00 0.00 0.02 0.32
#> TCGA.63.A5MG.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.94.8491.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.92.8064.01 1 0.2929 0.698 0.82 0.00 0.00 0.00 0.18
#> TCGA.O2.A52V.01 3 0.0000 0.968 0.00 0.00 1.00 0.00 0.00
#> TCGA.33.A4WN.01 1 0.0000 0.778 1.00 0.00 0.00 0.00 0.00
#> TCGA.18.4721.01 1 0.3291 0.724 0.84 0.00 0.00 0.04 0.12
#> TCGA.60.2709.01 4 0.1043 0.906 0.04 0.00 0.00 0.96 0.00
#> TCGA.85.8666.01 4 0.2331 0.891 0.08 0.00 0.00 0.90 0.02
#> TCGA.85.6561.01 4 0.2280 0.878 0.12 0.00 0.00 0.88 0.00
#> TCGA.92.8065.01 3 0.2280 0.843 0.00 0.00 0.88 0.00 0.12
#> TCGA.22.5489.01 4 0.0000 0.910 0.00 0.00 0.00 1.00 0.00
#> TCGA.NC.A5HL.01 4 0.4254 0.722 0.22 0.00 0.00 0.74 0.04
#> TCGA.35.5375.01 2 0.4262 0.551 0.00 0.56 0.00 0.00 0.44
#> TCGA.NK.A7XE.01 4 0.0000 0.910 0.00 0.00 0.00 1.00 0.00
#> TCGA.63.A5MM.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.33.AASL.01 3 0.0609 0.965 0.00 0.00 0.98 0.00 0.02
#> TCGA.77.7335.01 5 0.6794 0.000 0.30 0.00 0.32 0.00 0.38
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.43.A475.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.68.8251.01 1 0.5208 0.379 0.62 0.00 0.00 0.28 0.08 0.02
#> TCGA.92.8063.01 4 0.2474 0.741 0.00 0.00 0.00 0.88 0.04 0.08
#> TCGA.85.8580.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.92.7340.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HE.01 1 0.6424 0.384 0.50 0.00 0.00 0.24 0.22 0.04
#> TCGA.85.A53L.01 4 0.4637 0.498 0.36 0.00 0.00 0.60 0.02 0.02
#> TCGA.58.8393.01 3 0.0937 0.936 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.63.A5MS.01 1 0.2629 0.601 0.88 0.00 0.00 0.08 0.02 0.02
#> TCGA.63.A5MP.01 1 0.2631 0.627 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.34.A5IX.01 4 0.2350 0.759 0.02 0.00 0.00 0.88 0.00 0.10
#> TCGA.43.8115.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.96.A4JL.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5GA.01 1 0.0000 0.640 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.A5I6.01 4 0.1865 0.753 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.85.8049.01 1 0.4105 0.589 0.72 0.00 0.00 0.02 0.24 0.02
#> TCGA.85.8353.01 1 0.3156 0.617 0.80 0.00 0.00 0.00 0.18 0.02
#> TCGA.96.7545.01 4 0.5236 0.673 0.22 0.00 0.00 0.66 0.08 0.04
#> TCGA.85.8276.01 1 0.3351 0.515 0.80 0.00 0.00 0.00 0.16 0.04
#> TCGA.56.8625.01 3 0.0547 0.945 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.90.A4EE.01 1 0.5347 0.350 0.50 0.00 0.00 0.02 0.42 0.06
#> TCGA.63.A5MG.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.94.8491.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.92.8064.01 1 0.3647 0.480 0.64 0.00 0.00 0.00 0.36 0.00
#> TCGA.O2.A52V.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.33.A4WN.01 1 0.1635 0.630 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.18.4721.01 1 0.5663 0.483 0.58 0.00 0.00 0.06 0.30 0.06
#> TCGA.60.2709.01 4 0.1814 0.770 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.85.8666.01 4 0.3821 0.691 0.22 0.00 0.00 0.74 0.04 0.00
#> TCGA.85.6561.01 4 0.3309 0.666 0.28 0.00 0.00 0.72 0.00 0.00
#> TCGA.92.8065.01 3 0.3315 0.677 0.00 0.00 0.78 0.00 0.20 0.02
#> TCGA.22.5489.01 4 0.1092 0.761 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.NC.A5HL.01 4 0.5813 0.549 0.20 0.00 0.00 0.62 0.12 0.06
#> TCGA.35.5375.01 6 0.3198 0.000 0.00 0.26 0.00 0.00 0.00 0.74
#> TCGA.NK.A7XE.01 4 0.1807 0.749 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.63.A5MM.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASL.01 3 0.0547 0.945 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.77.7335.01 5 0.6113 0.000 0.22 0.00 0.18 0.00 0.56 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.43.A475.01 3 0.000 0.9245 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.68.8251.01 1 0.450 0.2379 0.66 0.00 0.00 0.18 0.00 0.00 0.16
#> TCGA.92.8063.01 4 0.166 0.7098 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.85.8580.01 3 0.000 0.9245 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.92.7340.01 2 0.000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HE.01 1 0.704 -0.0372 0.46 0.00 0.00 0.22 0.14 0.04 0.14
#> TCGA.85.A53L.01 4 0.387 0.5048 0.38 0.00 0.00 0.60 0.00 0.00 0.02
#> TCGA.58.8393.01 3 0.202 0.8980 0.00 0.00 0.90 0.00 0.06 0.00 0.04
#> TCGA.63.A5MS.01 1 0.193 0.4847 0.90 0.00 0.00 0.08 0.00 0.00 0.02
#> TCGA.63.A5MP.01 1 0.300 0.4639 0.84 0.00 0.00 0.02 0.10 0.00 0.04
#> TCGA.34.A5IX.01 4 0.189 0.6764 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.43.8115.01 3 0.000 0.9245 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.96.A4JL.01 2 0.000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5GA.01 1 0.172 0.5137 0.92 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.94.A5I6.01 4 0.000 0.7247 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8049.01 1 0.481 0.1851 0.64 0.00 0.00 0.02 0.24 0.00 0.10
#> TCGA.85.8353.01 1 0.238 0.4699 0.86 0.00 0.00 0.00 0.12 0.00 0.02
#> TCGA.96.7545.01 4 0.352 0.6762 0.22 0.00 0.00 0.74 0.00 0.00 0.04
#> TCGA.85.8276.01 1 0.496 0.1294 0.64 0.00 0.00 0.00 0.18 0.02 0.16
#> TCGA.56.8625.01 3 0.172 0.9098 0.00 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.90.A4EE.01 7 0.626 0.0000 0.34 0.00 0.00 0.04 0.28 0.00 0.34
#> TCGA.63.A5MG.01 2 0.117 0.9282 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.94.8491.01 2 0.000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.92.8064.01 5 0.585 -0.3494 0.40 0.00 0.00 0.02 0.44 0.02 0.12
#> TCGA.O2.A52V.01 3 0.000 0.9245 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.A4WN.01 1 0.166 0.5113 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.18.4721.01 1 0.586 0.0590 0.58 0.00 0.00 0.02 0.18 0.04 0.18
#> TCGA.60.2709.01 4 0.208 0.7179 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.85.8666.01 4 0.562 0.4750 0.30 0.00 0.00 0.54 0.06 0.00 0.10
#> TCGA.85.6561.01 4 0.448 0.6259 0.26 0.00 0.00 0.66 0.02 0.00 0.06
#> TCGA.92.8065.01 3 0.391 0.6750 0.00 0.00 0.70 0.00 0.24 0.00 0.06
#> TCGA.22.5489.01 4 0.117 0.7228 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.NC.A5HL.01 4 0.597 0.1401 0.28 0.00 0.00 0.40 0.02 0.00 0.30
#> TCGA.35.5375.01 6 0.143 0.0000 0.00 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.NK.A7XE.01 4 0.117 0.7095 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.63.A5MM.01 2 0.000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASL.01 3 0.221 0.9015 0.00 0.00 0.90 0.00 0.04 0.02 0.04
#> TCGA.77.7335.01 5 0.309 0.0420 0.04 0.00 0.16 0.00 0.80 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.43.A475.01 3 0.000 0.8953 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.68.8251.01 1 0.576 0.1976 0.58 0.00 0.00 0.18 0.00 0.04 0.14 0.06
#> TCGA.92.8063.01 4 0.156 0.6765 0.00 0.00 0.00 0.92 0.06 0.00 0.00 0.02
#> TCGA.85.8580.01 3 0.000 0.8953 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.92.7340.01 2 0.000 0.9774 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HE.01 1 0.657 -0.1399 0.38 0.00 0.00 0.28 0.02 0.00 0.10 0.22
#> TCGA.85.A53L.01 4 0.513 0.3839 0.34 0.00 0.00 0.52 0.00 0.00 0.04 0.10
#> TCGA.58.8393.01 3 0.282 0.8148 0.00 0.00 0.82 0.00 0.12 0.00 0.06 0.00
#> TCGA.63.A5MS.01 1 0.213 0.3908 0.88 0.00 0.00 0.08 0.00 0.00 0.00 0.04
#> TCGA.63.A5MP.01 1 0.478 0.1778 0.66 0.00 0.00 0.02 0.00 0.02 0.18 0.12
#> TCGA.34.A5IX.01 4 0.286 0.6595 0.00 0.00 0.00 0.84 0.06 0.02 0.00 0.08
#> TCGA.43.8115.01 3 0.000 0.8953 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.96.A4JL.01 2 0.000 0.9774 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5GA.01 1 0.241 0.3591 0.86 0.00 0.00 0.00 0.00 0.00 0.08 0.06
#> TCGA.94.A5I6.01 4 0.000 0.6990 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8049.01 1 0.465 0.0304 0.66 0.00 0.00 0.04 0.00 0.00 0.12 0.18
#> TCGA.85.8353.01 1 0.268 0.2866 0.84 0.00 0.00 0.02 0.00 0.00 0.12 0.02
#> TCGA.96.7545.01 4 0.511 0.5363 0.24 0.00 0.00 0.58 0.00 0.00 0.04 0.14
#> TCGA.85.8276.01 1 0.476 0.0883 0.64 0.00 0.00 0.00 0.04 0.00 0.12 0.20
#> TCGA.56.8625.01 3 0.241 0.8505 0.00 0.00 0.86 0.00 0.08 0.00 0.06 0.00
#> TCGA.90.A4EE.01 7 0.437 0.0000 0.26 0.00 0.00 0.02 0.04 0.00 0.66 0.02
#> TCGA.63.A5MG.01 2 0.174 0.9058 0.02 0.92 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.94.8491.01 2 0.000 0.9774 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.92.8064.01 1 0.551 -0.0245 0.56 0.00 0.00 0.02 0.02 0.02 0.28 0.10
#> TCGA.O2.A52V.01 3 0.000 0.8953 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.A4WN.01 1 0.161 0.3946 0.92 0.00 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.18.4721.01 8 0.495 0.0000 0.42 0.00 0.00 0.02 0.00 0.00 0.10 0.46
#> TCGA.60.2709.01 4 0.265 0.6904 0.08 0.00 0.00 0.84 0.00 0.00 0.00 0.08
#> TCGA.85.8666.01 4 0.548 0.5027 0.18 0.00 0.00 0.58 0.02 0.00 0.04 0.18
#> TCGA.85.6561.01 4 0.490 0.4612 0.28 0.00 0.00 0.52 0.00 0.00 0.00 0.20
#> TCGA.92.8065.01 5 0.324 0.1224 0.00 0.00 0.40 0.00 0.60 0.00 0.00 0.00
#> TCGA.22.5489.01 4 0.267 0.6978 0.02 0.00 0.00 0.88 0.02 0.02 0.02 0.04
#> TCGA.NC.A5HL.01 4 0.616 0.2646 0.12 0.00 0.00 0.44 0.04 0.00 0.06 0.34
#> TCGA.35.5375.01 6 0.109 0.0000 0.00 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.NK.A7XE.01 4 0.189 0.6855 0.00 0.00 0.00 0.90 0.06 0.00 0.00 0.04
#> TCGA.63.A5MM.01 2 0.000 0.9774 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASL.01 3 0.262 0.8382 0.00 0.00 0.84 0.00 0.10 0.00 0.06 0.00
#> TCGA.77.7335.01 5 0.749 0.0103 0.10 0.00 0.16 0.00 0.38 0.02 0.22 0.12
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["013"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.754 0.824 0.930 0.4863 0.488 0.488
#> 3 3 0.719 0.853 0.941 0.2032 0.652 0.458
#> 4 4 1.000 0.969 0.985 0.2289 0.828 0.617
#> 5 5 0.732 0.586 0.803 0.0622 0.912 0.713
#> 6 6 0.714 0.696 0.835 0.0553 0.888 0.594
#> 7 7 0.717 0.471 0.803 0.0308 0.959 0.802
#> 8 8 0.739 0.601 0.808 0.0314 0.959 0.787
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.34.5232.01 1 0.000 0.974 1.00 0.00
#> TCGA.63.7022.01 1 0.000 0.974 1.00 0.00
#> TCGA.75.6214.01 2 0.000 0.843 0.00 1.00
#> TCGA.43.A56U.01 2 0.995 0.303 0.46 0.54
#> TCGA.56.8503.01 1 0.000 0.974 1.00 0.00
#> TCGA.90.A59Q.01 2 0.000 0.843 0.00 1.00
#> TCGA.56.A4ZJ.01 1 0.000 0.974 1.00 0.00
#> TCGA.52.7622.01 2 0.000 0.843 0.00 1.00
#> TCGA.34.8454.01 2 0.990 0.346 0.44 0.56
#> TCGA.55.7726.01 2 0.000 0.843 0.00 1.00
#> TCGA.56.A5DS.01 1 0.000 0.974 1.00 0.00
#> TCGA.43.6647.01 1 0.000 0.974 1.00 0.00
#> TCGA.63.A5MR.01 2 0.000 0.843 0.00 1.00
#> TCGA.56.7731.01 1 0.000 0.974 1.00 0.00
#> TCGA.96.8169.01 2 0.000 0.843 0.00 1.00
#> TCGA.33.4589.01 2 0.000 0.843 0.00 1.00
#> TCGA.68.A59I.01 1 0.000 0.974 1.00 0.00
#> TCGA.55.8204.01 1 0.000 0.974 1.00 0.00
#> TCGA.85.6175.01 1 0.000 0.974 1.00 0.00
#> TCGA.39.5024.01 1 0.925 0.322 0.66 0.34
#> TCGA.XC.AA0X.01 2 0.999 0.246 0.48 0.52
#> TCGA.34.5234.01 1 0.000 0.974 1.00 0.00
#> TCGA.22.4605.01 2 0.000 0.843 0.00 1.00
#> TCGA.55.7724.01 1 0.000 0.974 1.00 0.00
#> TCGA.39.5030.01 2 0.995 0.303 0.46 0.54
#> TCGA.43.8118.01 2 0.000 0.843 0.00 1.00
#> TCGA.77.8136.01 2 0.000 0.843 0.00 1.00
#> TCGA.96.8170.01 1 0.000 0.974 1.00 0.00
#> TCGA.56.6545.01 1 0.000 0.974 1.00 0.00
#> TCGA.NJ.A55A.01 1 0.000 0.974 1.00 0.00
#> TCGA.21.5784.01 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.34.5232.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.63.7022.01 2 0.369 0.794 0.14 0.86 0.00
#> TCGA.75.6214.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.43.A56U.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.56.8503.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.90.A59Q.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.56.A4ZJ.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.52.7622.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.34.8454.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.55.7726.01 2 0.630 0.065 0.00 0.52 0.48
#> TCGA.56.A5DS.01 2 0.369 0.794 0.14 0.86 0.00
#> TCGA.43.6647.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.63.A5MR.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.56.7731.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.96.8169.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.33.4589.01 2 0.630 0.065 0.00 0.52 0.48
#> TCGA.68.A59I.01 2 0.369 0.794 0.14 0.86 0.00
#> TCGA.55.8204.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.85.6175.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.39.5024.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.XC.AA0X.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.34.5234.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.22.4605.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.55.7724.01 2 0.571 0.563 0.32 0.68 0.00
#> TCGA.39.5030.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.43.8118.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.77.8136.01 2 0.000 0.871 0.00 1.00 0.00
#> TCGA.96.8170.01 2 0.369 0.794 0.14 0.86 0.00
#> TCGA.56.6545.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.NJ.A55A.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.21.5784.01 1 0.000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.34.5232.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.63.7022.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.75.6214.01 3 0.0000 0.934 0.00 0.00 1.00 0.00
#> TCGA.43.A56U.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.56.8503.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.90.A59Q.01 4 0.0707 0.967 0.00 0.02 0.00 0.98
#> TCGA.56.A4ZJ.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.52.7622.01 4 0.0707 0.967 0.00 0.02 0.00 0.98
#> TCGA.34.8454.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.7726.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.56.A5DS.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.43.6647.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.63.A5MR.01 4 0.0707 0.967 0.00 0.02 0.00 0.98
#> TCGA.56.7731.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.96.8169.01 3 0.2011 0.932 0.00 0.00 0.92 0.08
#> TCGA.33.4589.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.68.A59I.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.8204.01 1 0.3172 0.770 0.84 0.16 0.00 0.00
#> TCGA.85.6175.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.39.5024.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.XC.AA0X.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.34.5234.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.22.4605.01 4 0.0707 0.967 0.00 0.02 0.00 0.98
#> TCGA.55.7724.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.39.5030.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.43.8118.01 4 0.2011 0.919 0.00 0.08 0.00 0.92
#> TCGA.77.8136.01 4 0.2011 0.919 0.00 0.08 0.00 0.92
#> TCGA.96.8170.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.56.6545.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55A.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.21.5784.01 1 0.0000 0.979 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.34.5232.01 1 0.000 0.9128 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.7022.01 2 0.000 0.6958 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6214.01 5 0.000 0.0000 0.00 0.00 0.00 0.00 1.00
#> TCGA.43.A56U.01 2 0.380 0.6713 0.00 0.70 0.00 0.30 0.00
#> TCGA.56.8503.01 1 0.000 0.9128 1.00 0.00 0.00 0.00 0.00
#> TCGA.90.A59Q.01 4 0.429 0.3767 0.00 0.00 0.46 0.54 0.00
#> TCGA.56.A4ZJ.01 1 0.000 0.9128 1.00 0.00 0.00 0.00 0.00
#> TCGA.52.7622.01 3 0.429 -0.3130 0.00 0.00 0.54 0.46 0.00
#> TCGA.34.8454.01 2 0.389 0.6612 0.00 0.68 0.00 0.32 0.00
#> TCGA.55.7726.01 3 0.000 0.5114 0.00 0.00 1.00 0.00 0.00
#> TCGA.56.A5DS.01 2 0.000 0.6958 0.00 1.00 0.00 0.00 0.00
#> TCGA.43.6647.01 1 0.368 0.7558 0.72 0.00 0.00 0.28 0.00
#> TCGA.63.A5MR.01 4 0.398 0.6877 0.00 0.00 0.34 0.66 0.00
#> TCGA.56.7731.01 1 0.104 0.9081 0.96 0.00 0.00 0.04 0.00
#> TCGA.96.8169.01 3 0.368 0.0635 0.00 0.00 0.72 0.00 0.28
#> TCGA.33.4589.01 3 0.000 0.5114 0.00 0.00 1.00 0.00 0.00
#> TCGA.68.A59I.01 2 0.000 0.6958 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8204.01 2 0.679 -0.2903 0.36 0.36 0.00 0.28 0.00
#> TCGA.85.6175.01 1 0.202 0.8911 0.90 0.00 0.00 0.10 0.00
#> TCGA.39.5024.01 2 0.380 0.6713 0.00 0.70 0.00 0.30 0.00
#> TCGA.XC.AA0X.01 2 0.380 0.6713 0.00 0.70 0.00 0.30 0.00
#> TCGA.34.5234.01 1 0.368 0.7558 0.72 0.00 0.00 0.28 0.00
#> TCGA.22.4605.01 3 0.429 -0.3130 0.00 0.00 0.54 0.46 0.00
#> TCGA.55.7724.01 2 0.293 0.5348 0.00 0.82 0.00 0.18 0.00
#> TCGA.39.5030.01 2 0.380 0.6713 0.00 0.70 0.00 0.30 0.00
#> TCGA.43.8118.01 4 0.488 0.7457 0.00 0.08 0.22 0.70 0.00
#> TCGA.77.8136.01 4 0.488 0.7457 0.00 0.08 0.22 0.70 0.00
#> TCGA.96.8170.01 2 0.000 0.6958 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.6545.01 1 0.202 0.8911 0.90 0.00 0.00 0.10 0.00
#> TCGA.NJ.A55A.01 1 0.000 0.9128 1.00 0.00 0.00 0.00 0.00
#> TCGA.21.5784.01 1 0.000 0.9128 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.34.5232.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.7022.01 2 0.3460 0.783 0.00 0.76 0.02 0.00 0.00 0.22
#> TCGA.75.6214.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.43.A56U.01 2 0.0000 0.822 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.8503.01 1 0.1267 0.826 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.90.A59Q.01 4 0.1480 0.784 0.00 0.04 0.02 0.94 0.00 0.00
#> TCGA.56.A4ZJ.01 1 0.1267 0.826 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.52.7622.01 4 0.0000 0.762 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.34.8454.01 2 0.2474 0.758 0.00 0.88 0.08 0.00 0.00 0.04
#> TCGA.55.7726.01 3 0.3851 0.741 0.00 0.00 0.54 0.46 0.00 0.00
#> TCGA.56.A5DS.01 2 0.3460 0.783 0.00 0.76 0.02 0.00 0.00 0.22
#> TCGA.43.6647.01 6 0.4834 0.555 0.26 0.00 0.10 0.00 0.00 0.64
#> TCGA.63.A5MR.01 4 0.2048 0.798 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.56.7731.01 1 0.2350 0.791 0.88 0.00 0.10 0.00 0.00 0.02
#> TCGA.96.8169.01 3 0.6046 0.384 0.00 0.00 0.52 0.18 0.28 0.02
#> TCGA.33.4589.01 3 0.3851 0.741 0.00 0.00 0.54 0.46 0.00 0.00
#> TCGA.68.A59I.01 2 0.3460 0.783 0.00 0.76 0.02 0.00 0.00 0.22
#> TCGA.55.8204.01 6 0.2728 0.551 0.10 0.04 0.00 0.00 0.00 0.86
#> TCGA.85.6175.01 1 0.4810 0.595 0.66 0.00 0.22 0.00 0.00 0.12
#> TCGA.39.5024.01 2 0.2094 0.778 0.00 0.90 0.02 0.00 0.00 0.08
#> TCGA.XC.AA0X.01 2 0.0000 0.822 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.34.5234.01 6 0.4834 0.555 0.26 0.00 0.10 0.00 0.00 0.64
#> TCGA.22.4605.01 4 0.0000 0.762 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7724.01 6 0.3711 0.269 0.00 0.26 0.02 0.00 0.00 0.72
#> TCGA.39.5030.01 2 0.0547 0.814 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.43.8118.01 4 0.2941 0.737 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.77.8136.01 4 0.3460 0.728 0.00 0.22 0.00 0.76 0.00 0.02
#> TCGA.96.8170.01 2 0.4172 0.746 0.00 0.68 0.04 0.00 0.00 0.28
#> TCGA.56.6545.01 1 0.4929 0.556 0.62 0.00 0.28 0.00 0.00 0.10
#> TCGA.NJ.A55A.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.21.5784.01 1 0.0000 0.846 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.34.5232.01 1 0.000 0.7597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.7022.01 2 0.000 0.4143 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6214.01 5 0.000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.43.A56U.01 2 0.424 0.0855 0.00 0.72 0.00 0.18 0.00 0.02 0.08
#> TCGA.56.8503.01 1 0.251 0.7217 0.88 0.00 0.02 0.00 0.00 0.06 0.04
#> TCGA.90.A59Q.01 4 0.265 0.8225 0.00 0.00 0.10 0.86 0.00 0.02 0.02
#> TCGA.56.A4ZJ.01 1 0.251 0.7217 0.88 0.00 0.02 0.00 0.00 0.06 0.04
#> TCGA.52.7622.01 4 0.242 0.7870 0.00 0.00 0.18 0.82 0.00 0.00 0.00
#> TCGA.34.8454.01 2 0.696 -0.2347 0.00 0.44 0.04 0.12 0.00 0.12 0.28
#> TCGA.55.7726.01 3 0.166 0.9090 0.00 0.00 0.92 0.06 0.00 0.00 0.02
#> TCGA.56.A5DS.01 2 0.000 0.4143 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.6647.01 6 0.331 0.5916 0.24 0.00 0.00 0.00 0.00 0.74 0.02
#> TCGA.63.A5MR.01 4 0.101 0.8352 0.00 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.56.7731.01 1 0.291 0.6283 0.80 0.00 0.00 0.00 0.00 0.18 0.02
#> TCGA.96.8169.01 3 0.228 0.8357 0.00 0.00 0.88 0.00 0.08 0.04 0.00
#> TCGA.33.4589.01 3 0.117 0.9120 0.00 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.68.A59I.01 2 0.000 0.4143 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8204.01 6 0.346 0.2772 0.00 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.85.6175.01 1 0.501 0.3290 0.56 0.00 0.00 0.00 0.00 0.28 0.16
#> TCGA.39.5024.01 7 0.534 0.0000 0.00 0.40 0.00 0.18 0.00 0.00 0.42
#> TCGA.XC.AA0X.01 2 0.445 0.0428 0.00 0.70 0.00 0.18 0.00 0.02 0.10
#> TCGA.34.5234.01 6 0.305 0.5781 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.22.4605.01 4 0.242 0.7870 0.00 0.00 0.18 0.82 0.00 0.00 0.00
#> TCGA.55.7724.01 2 0.350 -0.1237 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.39.5030.01 2 0.464 -0.0191 0.00 0.68 0.00 0.18 0.00 0.02 0.12
#> TCGA.43.8118.01 4 0.136 0.7960 0.00 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.77.8136.01 4 0.208 0.7251 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.96.8170.01 2 0.314 -0.1368 0.00 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.56.6545.01 1 0.549 0.1947 0.44 0.00 0.00 0.00 0.00 0.24 0.32
#> TCGA.NJ.A55A.01 1 0.000 0.7597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.21.5784.01 1 0.000 0.7597 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.34.5232.01 1 0.0000 0.7662 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.7022.01 2 0.4482 0.4251 0.00 0.60 0.00 0.00 0.00 0.14 0.26 0.00
#> TCGA.75.6214.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.43.A56U.01 2 0.0000 0.5174 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8503.01 1 0.2650 0.6824 0.76 0.00 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.90.A59Q.01 4 0.3452 0.8182 0.00 0.04 0.06 0.82 0.00 0.00 0.04 0.04
#> TCGA.56.A4ZJ.01 1 0.2650 0.6824 0.76 0.00 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.52.7622.01 4 0.1341 0.8508 0.00 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.34.8454.01 2 0.4174 0.0846 0.00 0.54 0.00 0.00 0.00 0.00 0.06 0.40
#> TCGA.55.7726.01 3 0.1607 0.9050 0.00 0.00 0.92 0.04 0.00 0.00 0.00 0.04
#> TCGA.56.A5DS.01 2 0.4482 0.4251 0.00 0.60 0.00 0.00 0.00 0.14 0.26 0.00
#> TCGA.43.6647.01 6 0.2725 0.5547 0.14 0.00 0.00 0.00 0.00 0.82 0.00 0.04
#> TCGA.63.A5MR.01 4 0.1607 0.8531 0.00 0.04 0.00 0.92 0.00 0.00 0.04 0.00
#> TCGA.56.7731.01 1 0.3293 0.6335 0.74 0.00 0.00 0.00 0.00 0.22 0.00 0.04
#> TCGA.96.8169.01 3 0.2532 0.8598 0.00 0.00 0.88 0.00 0.04 0.04 0.02 0.02
#> TCGA.33.4589.01 3 0.0808 0.9161 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.68.A59I.01 2 0.4482 0.4251 0.00 0.60 0.00 0.00 0.00 0.14 0.26 0.00
#> TCGA.55.8204.01 6 0.2725 0.5310 0.00 0.04 0.00 0.00 0.00 0.82 0.14 0.00
#> TCGA.85.6175.01 1 0.4646 0.5715 0.66 0.00 0.00 0.04 0.00 0.18 0.00 0.12
#> TCGA.39.5024.01 7 0.3618 0.4941 0.00 0.38 0.00 0.00 0.00 0.00 0.60 0.02
#> TCGA.XC.AA0X.01 2 0.0000 0.5174 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5234.01 6 0.3615 0.5046 0.20 0.00 0.00 0.02 0.00 0.74 0.00 0.04
#> TCGA.22.4605.01 4 0.1341 0.8508 0.00 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.55.7724.01 6 0.4332 0.3080 0.00 0.16 0.00 0.00 0.00 0.64 0.20 0.00
#> TCGA.39.5030.01 2 0.0471 0.4958 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.43.8118.01 4 0.2591 0.8255 0.00 0.08 0.00 0.86 0.00 0.00 0.04 0.02
#> TCGA.77.8136.01 4 0.3843 0.6836 0.00 0.24 0.00 0.70 0.00 0.00 0.04 0.02
#> TCGA.96.8170.01 7 0.3299 0.4941 0.00 0.18 0.00 0.00 0.00 0.06 0.76 0.00
#> TCGA.56.6545.01 1 0.6228 0.4126 0.50 0.00 0.04 0.00 0.00 0.14 0.08 0.24
#> TCGA.NJ.A55A.01 1 0.0941 0.7635 0.96 0.00 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.21.5784.01 1 0.0000 0.7662 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node041 , Node042 , Node043 , Node051 , Node052 , Node061 , Node062-leaf , Node071 , Node072 , Node073 .
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 290 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 0.985 0.994 0.4947 0.506 0.506
#> 3 3 1.000 0.969 0.987 0.3319 0.687 0.460
#> 4 4 0.998 0.961 0.965 0.1143 0.757 0.426
#> 5 5 0.820 0.711 0.795 0.0732 0.920 0.707
#> 6 6 0.830 0.833 0.893 0.0452 0.906 0.604
#> 7 7 0.798 0.698 0.807 0.0259 0.962 0.793
#> 8 8 0.809 0.651 0.793 0.0199 0.978 0.864
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.44.4112.01 2 0.000 0.995 0.00 1.00
#> TCGA.NJ.A4YP.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8278.01 2 0.000 0.995 0.00 1.00
#> TCGA.49.AARQ.01 2 0.000 0.995 0.00 1.00
#> TCGA.97.A4M1.01 1 0.000 0.993 1.00 0.00
#> TCGA.99.8033.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.8453.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.8552.01 1 0.000 0.993 1.00 0.00
#> TCGA.53.A4EZ.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5066.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.A46U.01 2 0.000 0.995 0.00 1.00
#> TCGA.MP.A4T8.01 2 0.000 0.995 0.00 1.00
#> TCGA.MP.A4SY.01 2 0.000 0.995 0.00 1.00
#> TCGA.93.A4JN.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.A4JF.01 2 0.000 0.995 0.00 1.00
#> TCGA.63.6202.01 2 0.000 0.995 0.00 1.00
#> TCGA.J2.A4AG.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TI.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8208.01 1 0.000 0.993 1.00 0.00
#> TCGA.85.8584.01 1 0.000 0.993 1.00 0.00
#> TCGA.NJ.A4YI.01 2 0.000 0.995 0.00 1.00
#> TCGA.49.AAR4.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6984.01 1 0.000 0.993 1.00 0.00
#> TCGA.MN.A4N1.01 2 0.000 0.995 0.00 1.00
#> TCGA.75.6206.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TC.01 2 0.141 0.975 0.02 0.98
#> TCGA.49.6744.01 1 0.000 0.993 1.00 0.00
#> TCGA.L9.A743.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.4410.01 2 0.000 0.995 0.00 1.00
#> TCGA.62.A46Y.01 2 0.000 0.995 0.00 1.00
#> TCGA.50.6597.01 2 0.000 0.995 0.00 1.00
#> TCGA.05.4384.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8087.01 1 0.000 0.993 1.00 0.00
#> TCGA.85.A50M.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TH.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8207.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.6562.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8074.01 1 0.000 0.993 1.00 0.00
#> TCGA.39.5011.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4SW.01 2 0.000 0.995 0.00 1.00
#> TCGA.67.6216.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8203.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8619.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.2668.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.6971.01 1 0.000 0.993 1.00 0.00
#> TCGA.98.7454.01 1 0.000 0.993 1.00 0.00
#> TCGA.L9.A444.01 2 0.000 0.995 0.00 1.00
#> TCGA.62.A46V.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.A47G.01 2 0.141 0.975 0.02 0.98
#> TCGA.69.8253.01 1 0.000 0.993 1.00 0.00
#> TCGA.91.6849.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5944.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.2665.01 2 0.000 0.995 0.00 1.00
#> TCGA.62.A46P.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.2666.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.A494.01 2 0.000 0.995 0.00 1.00
#> TCGA.97.7547.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.8254.01 1 0.000 0.993 1.00 0.00
#> TCGA.75.5125.01 2 0.000 0.995 0.00 1.00
#> TCGA.69.7973.01 1 0.000 0.993 1.00 0.00
#> TCGA.L4.A4E5.01 1 0.584 0.835 0.86 0.14
#> TCGA.44.6775.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7911.01 2 0.000 0.995 0.00 1.00
#> TCGA.MP.A4T9.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6712.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.7714.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.7948.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.A4DG.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.7815.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.5423.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6985.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7281.01 2 0.000 0.995 0.00 1.00
#> TCGA.93.7347.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.6777.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.8177.01 1 0.000 0.993 1.00 0.00
#> TCGA.99.7458.01 1 0.827 0.650 0.74 0.26
#> TCGA.91.A4BD.01 1 0.000 0.993 1.00 0.00
#> TCGA.38.6178.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.A47B.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.6979.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7573.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8097.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.5429.01 2 0.000 0.995 0.00 1.00
#> TCGA.93.A4JP.01 1 0.000 0.993 1.00 0.00
#> TCGA.S2.AA1A.01 1 0.000 0.993 1.00 0.00
#> TCGA.93.A4JQ.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7160.01 1 0.000 0.993 1.00 0.00
#> TCGA.75.5122.01 2 0.000 0.995 0.00 1.00
#> TCGA.97.7938.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.7671.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5055.01 1 0.000 0.993 1.00 0.00
#> TCGA.85.6560.01 1 0.000 0.993 1.00 0.00
#> TCGA.91.8496.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4T2.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.A46R.01 2 0.000 0.995 0.00 1.00
#> TCGA.L9.A443.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.7701.01 2 0.000 0.995 0.00 1.00
#> TCGA.52.7812.01 2 0.000 0.995 0.00 1.00
#> TCGA.78.7162.01 1 0.000 0.993 1.00 0.00
#> TCGA.L9.A50W.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.8460.01 1 0.000 0.993 1.00 0.00
#> TCGA.67.6217.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7535.01 2 0.000 0.995 0.00 1.00
#> TCGA.93.7348.01 1 0.000 0.993 1.00 0.00
#> TCGA.86.8671.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6592.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.7546.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.7661.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.7944.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4M0.01 2 0.000 0.995 0.00 1.00
#> TCGA.50.5933.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8280.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.8660.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.7907.01 2 0.000 0.995 0.00 1.00
#> TCGA.49.6767.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TK.01 2 0.000 0.995 0.00 1.00
#> TCGA.69.7761.01 1 0.000 0.993 1.00 0.00
#> TCGA.91.6835.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7540.01 2 0.000 0.995 0.00 1.00
#> TCGA.95.A4VN.01 1 0.971 0.335 0.60 0.40
#> TCGA.44.A47F.01 2 0.904 0.528 0.32 0.68
#> TCGA.55.A48Z.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.7763.01 2 0.000 0.995 0.00 1.00
#> TCGA.J2.A4AE.01 2 0.000 0.995 0.00 1.00
#> TCGA.50.5942.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6590.01 2 0.000 0.995 0.00 1.00
#> TCGA.80.5608.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8511.01 2 0.000 0.995 0.00 1.00
#> TCGA.99.8025.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.7283.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.A491.01 1 0.242 0.953 0.96 0.04
#> TCGA.MN.A4N5.01 2 0.000 0.995 0.00 1.00
#> TCGA.69.7978.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8299.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.8117.01 2 0.000 0.995 0.00 1.00
#> TCGA.MP.A4TD.01 2 0.000 0.995 0.00 1.00
#> TCGA.05.4405.01 2 0.000 0.995 0.00 1.00
#> TCGA.83.5908.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.6980.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.6146.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.8397.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.7552.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5936.01 1 0.000 0.993 1.00 0.00
#> TCGA.91.7771.01 2 0.402 0.911 0.08 0.92
#> TCGA.NJ.A4YG.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8359.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8301.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.3918.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8621.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.6745.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.A4SS.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8089.01 1 0.000 0.993 1.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7574.01 2 0.242 0.955 0.04 0.96
#> TCGA.63.A5MN.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.8459.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.8648.01 1 0.000 0.993 1.00 0.00
#> TCGA.NC.A5HJ.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.2656.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8673.01 2 0.000 0.995 0.00 1.00
#> TCGA.73.7499.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4LX.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4T7.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.7765.01 2 0.000 0.995 0.00 1.00
#> TCGA.95.8494.01 2 0.000 0.995 0.00 1.00
#> TCGA.97.8171.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.8457.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4M5.01 1 0.000 0.993 1.00 0.00
#> TCGA.53.7626.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.5645.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7158.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8056.01 2 0.000 0.995 0.00 1.00
#> TCGA.69.7980.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.8175.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8668.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4T4.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.A47A.01 2 0.000 0.995 0.00 1.00
#> TCGA.NJ.A55O.01 1 0.000 0.993 1.00 0.00
#> TCGA.93.A4JO.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.6145.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.8547.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.6147.01 2 0.000 0.995 0.00 1.00
#> TCGA.77.8007.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8510.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.AARO.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8090.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8073.01 2 0.000 0.995 0.00 1.00
#> TCGA.91.6828.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8076.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4M6.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5044.01 1 0.000 0.993 1.00 0.00
#> TCGA.64.5781.01 1 0.000 0.993 1.00 0.00
#> TCGA.NJ.A4YF.01 1 0.000 0.993 1.00 0.00
#> TCGA.38.7271.01 2 0.000 0.995 0.00 1.00
#> TCGA.49.AAR3.01 1 0.000 0.993 1.00 0.00
#> TCGA.MP.A4TJ.01 1 0.000 0.993 1.00 0.00
#> TCGA.69.7760.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.4512.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5939.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7143.01 2 0.000 0.995 0.00 1.00
#> TCGA.97.A4M3.01 1 0.000 0.993 1.00 0.00
#> TCGA.75.6205.01 2 0.000 0.995 0.00 1.00
#> TCGA.99.8028.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7903.01 2 0.000 0.995 0.00 1.00
#> TCGA.49.4487.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A493.01 2 0.000 0.995 0.00 1.00
#> TCGA.75.5126.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8206.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.7553.01 1 0.000 0.993 1.00 0.00
#> TCGA.NJ.A7XG.01 2 0.722 0.749 0.20 0.80
#> TCGA.55.A48X.01 1 0.827 0.650 0.74 0.26
#> TCGA.64.5778.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6594.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7153.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.7728.01 1 0.000 0.993 1.00 0.00
#> TCGA.67.6215.01 2 0.000 0.995 0.00 1.00
#> TCGA.78.7537.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6982.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.7227.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.A456.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.6774.01 1 0.000 0.993 1.00 0.00
#> TCGA.49.AAQV.01 1 0.000 0.993 1.00 0.00
#> TCGA.73.7498.01 1 0.000 0.993 1.00 0.00
#> TCGA.38.4632.01 2 0.000 0.995 0.00 1.00
#> TCGA.69.7974.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.6986.01 2 0.000 0.995 0.00 1.00
#> TCGA.49.6761.01 2 0.000 0.995 0.00 1.00
#> TCGA.MP.A4T6.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.6779.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.A4P7.01 2 0.000 0.995 0.00 1.00
#> TCGA.73.4658.01 2 0.000 0.995 0.00 1.00
#> TCGA.85.A513.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5935.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7727.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.6981.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.8655.01 2 0.000 0.995 0.00 1.00
#> TCGA.78.7163.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.7941.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7914.01 2 0.000 0.995 0.00 1.00
#> TCGA.75.7030.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.A472.01 2 0.000 0.995 0.00 1.00
#> TCGA.05.4417.01 2 0.000 0.995 0.00 1.00
#> TCGA.67.4679.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.7554.01 2 0.000 0.995 0.00 1.00
#> TCGA.75.7025.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.8039.01 2 0.000 0.995 0.00 1.00
#> TCGA.50.5941.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.8174.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.7576.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.7725.01 1 0.000 0.993 1.00 0.00
#> TCGA.38.A44F.01 1 0.000 0.993 1.00 0.00
#> TCGA.80.5607.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.8091.01 1 0.000 0.993 1.00 0.00
#> TCGA.62.8395.01 2 0.000 0.995 0.00 1.00
#> TCGA.86.8672.01 2 0.000 0.995 0.00 1.00
#> TCGA.64.5815.01 2 0.000 0.995 0.00 1.00
#> TCGA.75.6212.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.6776.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6983.01 1 0.000 0.993 1.00 0.00
#> TCGA.93.8067.01 2 0.000 0.995 0.00 1.00
#> TCGA.69.A59K.01 2 0.000 0.995 0.00 1.00
#> TCGA.95.7567.01 2 0.000 0.995 0.00 1.00
#> TCGA.49.AARN.01 2 0.000 0.995 0.00 1.00
#> TCGA.91.6836.01 2 0.000 0.995 0.00 1.00
#> TCGA.97.8172.01 2 0.000 0.995 0.00 1.00
#> TCGA.O2.A52Q.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5045.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6978.01 1 0.000 0.993 1.00 0.00
#> TCGA.95.A4VP.01 1 0.000 0.993 1.00 0.00
#> TCGA.05.5715.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.A492.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.A48Y.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6595.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6543.01 1 0.000 0.993 1.00 0.00
#> TCGA.91.8497.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5049.01 1 0.000 0.993 1.00 0.00
#> TCGA.97.A4M2.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.7659.01 2 0.000 0.995 0.00 1.00
#> TCGA.97.A4M7.01 1 0.000 0.993 1.00 0.00
#> TCGA.44.7662.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.6970.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.5068.01 1 0.000 0.993 1.00 0.00
#> TCGA.71.8520.01 2 0.000 0.995 0.00 1.00
#> TCGA.44.7672.01 2 0.000 0.995 0.00 1.00
#> TCGA.55.6987.01 1 0.000 0.993 1.00 0.00
#> TCGA.78.7152.01 2 0.000 0.995 0.00 1.00
#> TCGA.78.7145.01 1 0.000 0.993 1.00 0.00
#> TCGA.50.6593.01 1 0.000 0.993 1.00 0.00
#> TCGA.55.8302.01 2 0.000 0.995 0.00 1.00
#> TCGA.05.4425.01 2 0.000 0.995 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.4112.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.NJ.A4YP.01 3 0.4291 0.785 0.00 0.18 0.82
#> TCGA.86.8278.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.49.AARQ.01 2 0.1529 0.958 0.00 0.96 0.04
#> TCGA.97.A4M1.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.99.8033.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.69.8453.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.8552.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.53.A4EZ.01 1 0.2959 0.881 0.90 0.00 0.10
#> TCGA.50.5066.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.62.A46U.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.MP.A4T8.01 3 0.3686 0.838 0.00 0.14 0.86
#> TCGA.MP.A4SY.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.93.A4JN.01 3 0.4555 0.757 0.00 0.20 0.80
#> TCGA.86.A4JF.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.63.6202.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.J2.A4AG.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.MP.A4TI.01 3 0.4002 0.812 0.00 0.16 0.84
#> TCGA.55.8208.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.85.8584.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.NJ.A4YI.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.49.AAR4.01 3 0.2537 0.901 0.08 0.00 0.92
#> TCGA.55.6984.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.MN.A4N1.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.75.6206.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.MP.A4TC.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.49.6744.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.L9.A743.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.05.4410.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.62.A46Y.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.50.6597.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.05.4384.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.85.A50M.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.MP.A4TH.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.8207.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.6562.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.86.8074.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.39.5011.01 1 0.5706 0.548 0.68 0.00 0.32
#> TCGA.MP.A4SW.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.67.6216.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.8203.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.8619.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.2668.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.6971.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.98.7454.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.L9.A444.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.44.A47G.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.69.8253.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.91.6849.01 1 0.5948 0.460 0.64 0.00 0.36
#> TCGA.50.5944.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.2665.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.62.A46P.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.44.2666.01 2 0.2537 0.913 0.00 0.92 0.08
#> TCGA.55.A494.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.7547.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.69.8254.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.75.5125.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.69.7973.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.L4.A4E5.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.44.6775.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.7911.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.MP.A4T9.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.6712.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.86.7714.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.95.7948.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.A4DG.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.7815.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.05.5423.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.6985.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.7281.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.93.7347.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.6777.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.8177.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.99.7458.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.91.A4BD.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.38.6178.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.44.A47B.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.6979.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.7573.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.8097.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.05.5429.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.93.A4JP.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.75.5122.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.7938.01 1 0.0892 0.964 0.98 0.00 0.02
#> TCGA.44.7671.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.5055.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.85.6560.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.91.8496.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.62.A46R.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.L9.A443.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.86.7701.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.52.7812.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.78.7162.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.L9.A50W.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.50.8460.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.67.6217.01 1 0.0892 0.964 0.98 0.00 0.02
#> TCGA.78.7535.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.93.7348.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.86.8671.01 1 0.0892 0.964 0.98 0.00 0.02
#> TCGA.50.6592.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.7546.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.7661.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.95.7944.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.50.5933.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.8280.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.78.8660.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.7907.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.49.6767.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.MP.A4TK.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.69.7761.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.91.6835.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.78.7540.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.95.A4VN.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.44.A47F.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.A48Z.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.69.7763.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.J2.A4AE.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.50.5942.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.6590.01 3 0.5560 0.584 0.00 0.30 0.70
#> TCGA.80.5608.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.8511.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.A491.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.MN.A4N5.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.69.7978.01 3 0.6126 0.351 0.00 0.40 0.60
#> TCGA.55.8299.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.8117.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.MP.A4TD.01 2 0.2066 0.936 0.00 0.94 0.06
#> TCGA.05.4405.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.83.5908.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.6980.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.6146.01 1 0.0892 0.964 0.98 0.00 0.02
#> TCGA.62.8397.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.97.7552.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.50.5936.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.91.7771.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.NJ.A4YG.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.86.8359.01 1 0.0892 0.963 0.98 0.00 0.02
#> TCGA.55.8301.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.44.3918.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.8621.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.44.A4SS.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.8089.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.NJ.A4YQ.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.7574.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.63.A5MN.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.8459.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.78.8648.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.NC.A5HJ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.2656.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.8673.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.73.7499.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.A4LX.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.MP.A4T7.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.69.7765.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.95.8494.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.97.8171.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.8457.01 1 0.6126 0.360 0.60 0.00 0.40
#> TCGA.97.A4M5.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.53.7626.01 3 0.1529 0.945 0.04 0.00 0.96
#> TCGA.44.5645.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.78.7158.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.8056.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.69.7980.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.8175.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.8668.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.MP.A4T4.01 1 0.0892 0.964 0.98 0.00 0.02
#> TCGA.44.A47A.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.NJ.A55O.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.93.A4JO.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.44.6145.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.97.8547.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.44.6147.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.77.8007.01 3 0.2959 0.885 0.00 0.10 0.90
#> TCGA.55.8510.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.49.AARO.01 1 0.2066 0.924 0.94 0.00 0.06
#> TCGA.55.8090.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.8073.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.91.6828.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.8076.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.5044.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.64.5781.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.NJ.A4YF.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.38.7271.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.49.AAR3.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.MP.A4TJ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.69.7760.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.49.4512.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.5939.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.78.7143.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.A4M3.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.75.6205.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.99.8028.01 1 0.0892 0.964 0.98 0.00 0.02
#> TCGA.55.7903.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.49.4487.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.A493.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.75.5126.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.8206.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.97.7553.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.NJ.A7XG.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.A48X.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.64.5778.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.6594.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.78.7153.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.7728.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.67.6215.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.78.7537.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.6982.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.7227.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.A456.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.44.6774.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.49.AAQV.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.73.7498.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.38.4632.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.69.7974.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.6986.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.49.6761.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.MP.A4T6.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.44.6779.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.86.A4P7.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.73.4658.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.85.A513.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.5935.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.7727.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.6981.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.78.8655.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.78.7163.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.97.7941.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.7914.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.75.7030.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.62.A472.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.05.4417.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.67.4679.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.7554.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.75.7025.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.95.8039.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.50.5941.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.97.8174.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.7576.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.7725.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.38.A44F.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.80.5607.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.55.8091.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.62.8395.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.86.8672.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.64.5815.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.75.6212.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.6776.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.6983.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.93.8067.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.69.A59K.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.49.AARN.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.91.6836.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.97.8172.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.O2.A52Q.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.50.5045.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.6978.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.95.A4VP.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.05.5715.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.A492.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.A48Y.01 1 0.6280 0.179 0.54 0.00 0.46
#> TCGA.50.6595.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.55.6543.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.91.8497.01 1 0.2066 0.924 0.94 0.00 0.06
#> TCGA.50.5049.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.97.A4M2.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.44.7659.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.97.A4M7.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.44.7662.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.6970.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.5068.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.71.8520.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.44.7672.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.6987.01 1 0.0892 0.964 0.98 0.00 0.02
#> TCGA.78.7152.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.78.7145.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.50.6593.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.55.8302.01 3 0.0000 0.985 0.00 0.00 1.00
#> TCGA.05.4425.01 2 0.0000 0.997 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.44.4112.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.NJ.A4YP.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.86.8278.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.49.AARQ.01 4 0.121 0.937 0.00 0.04 0.00 0.96
#> TCGA.97.A4M1.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.99.8033.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.69.8453.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.97.8552.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.53.A4EZ.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.5066.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.62.A46U.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.MP.A4T8.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.MP.A4SY.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.93.A4JN.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.86.A4JF.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.63.6202.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.J2.A4AG.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TI.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.8208.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.85.8584.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YI.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.49.AAR4.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.55.6984.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.MN.A4N1.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.75.6206.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 4 0.340 0.850 0.00 0.00 0.18 0.82
#> TCGA.49.6744.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.L9.A743.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.05.4410.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.62.A46Y.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.50.6597.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.05.4384.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.8087.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.85.A50M.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TH.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.8207.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.86.6562.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.86.8074.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.39.5011.01 3 0.121 0.942 0.04 0.00 0.96 0.00
#> TCGA.MP.A4SW.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.67.6216.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.55.8203.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.8619.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.44.2668.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.6971.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.98.7454.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.L9.A444.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.62.A46V.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.44.A47G.01 4 0.265 0.920 0.00 0.00 0.12 0.88
#> TCGA.69.8253.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.91.6849.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.5944.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.44.2665.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.62.A46P.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.44.2666.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.55.A494.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.97.7547.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.69.8254.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.75.5125.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.69.7973.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.L4.A4E5.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.44.6775.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.55.7911.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.MP.A4T9.01 3 0.413 0.708 0.26 0.00 0.74 0.00
#> TCGA.55.6712.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.86.7714.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.95.7948.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.55.A4DG.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.7815.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.05.5423.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.55.6985.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.55.7281.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.93.7347.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.44.6777.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.97.8177.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.99.7458.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.91.A4BD.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.38.6178.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.44.A47B.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.6979.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.7573.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.8097.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.05.5429.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.93.A4JP.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.78.7160.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.75.5122.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.97.7938.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.44.7671.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.85.6560.01 3 0.121 0.940 0.00 0.00 0.96 0.04
#> TCGA.91.8496.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.62.A46R.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.L9.A443.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.86.7701.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.52.7812.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.78.7162.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.50.8460.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.67.6217.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.78.7535.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.93.7348.01 1 0.121 0.952 0.96 0.00 0.04 0.00
#> TCGA.86.8671.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.6592.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.97.7546.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.44.7661.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.95.7944.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.50.5933.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.86.8280.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.78.8660.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.55.7907.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.49.6767.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TK.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.69.7761.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.91.6835.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.78.7540.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.95.A4VN.01 3 0.361 0.714 0.00 0.00 0.80 0.20
#> TCGA.44.A47F.01 3 0.292 0.857 0.00 0.00 0.86 0.14
#> TCGA.55.A48Z.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.69.7763.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.J2.A4AE.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.50.5942.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.6590.01 4 0.241 0.948 0.00 0.04 0.04 0.92
#> TCGA.80.5608.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.55.8511.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.99.8025.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.7283.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.A491.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.MN.A4N5.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.69.7978.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.8299.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.44.8117.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TD.01 4 0.234 0.941 0.00 0.06 0.02 0.92
#> TCGA.05.4405.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.83.5908.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.55.6980.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.44.6146.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.62.8397.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.97.7552.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.50.5936.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.91.7771.01 3 0.398 0.712 0.00 0.00 0.76 0.24
#> TCGA.NJ.A4YG.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.86.8359.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.55.8301.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.44.3918.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.55.8621.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.49.6745.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.44.A4SS.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.8089.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.NJ.A4YQ.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.55.7574.01 4 0.234 0.939 0.00 0.00 0.10 0.90
#> TCGA.63.A5MN.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.50.8459.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.78.8648.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HJ.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.44.2656.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.86.8673.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.73.7499.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.97.A4LX.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T7.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.69.7765.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.95.8494.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.97.8171.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.8457.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.97.A4M5.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.53.7626.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.44.5645.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.78.7158.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.86.8056.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.69.7980.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.97.8175.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.86.8668.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.MP.A4T4.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.44.A47A.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.44.6145.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.97.8547.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.44.6147.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.77.8007.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.8510.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.49.AARO.01 3 0.164 0.937 0.06 0.00 0.94 0.00
#> TCGA.55.8090.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.86.8073.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.91.6828.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.86.8076.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.97.A4M6.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.50.5044.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.64.5781.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.NJ.A4YF.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.38.7271.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.49.AAR3.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TJ.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.69.7760.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.49.4512.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.5939.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.78.7143.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.97.A4M3.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.75.6205.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.99.8028.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.55.7903.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.49.4487.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.A493.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.75.5126.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.8206.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.97.7553.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.NJ.A7XG.01 3 0.234 0.899 0.00 0.00 0.90 0.10
#> TCGA.55.A48X.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.64.5778.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.50.6594.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.78.7153.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.7728.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.67.6215.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.78.7537.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.55.6982.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.7227.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.86.A456.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.44.6774.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.49.AAQV.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.73.7498.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.38.4632.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.69.7974.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.6986.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.49.6761.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.MP.A4T6.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.44.6779.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.86.A4P7.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.73.4658.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.85.A513.01 3 0.265 0.894 0.12 0.00 0.88 0.00
#> TCGA.50.5935.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.55.7727.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.6981.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.78.8655.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.78.7163.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.97.7941.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.55.7914.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.75.7030.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.62.A472.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.05.4417.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.67.4679.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.97.7554.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.75.7025.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.95.8039.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.50.5941.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.97.8174.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.55.7576.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.7725.01 3 0.121 0.943 0.00 0.00 0.96 0.04
#> TCGA.38.A44F.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.80.5607.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.55.8091.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.62.8395.01 4 0.462 0.557 0.00 0.34 0.00 0.66
#> TCGA.86.8672.01 4 0.201 0.932 0.00 0.08 0.00 0.92
#> TCGA.64.5815.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.75.6212.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.44.6776.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.6983.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.93.8067.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.95.7567.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.91.6836.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.97.8172.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.O2.A52Q.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.50.5045.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.6978.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.95.A4VP.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.05.5715.01 4 0.121 0.948 0.00 0.00 0.04 0.96
#> TCGA.55.A492.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 3 0.164 0.937 0.06 0.00 0.94 0.00
#> TCGA.50.6595.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.55.6543.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.5049.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.97.A4M2.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.97.A4M7.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.44.7662.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.55.6970.01 1 0.000 0.999 1.00 0.00 0.00 0.00
#> TCGA.50.5068.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.71.8520.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.44.7672.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.55.6987.01 3 0.164 0.937 0.06 0.00 0.94 0.00
#> TCGA.78.7152.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.78.7145.01 3 0.201 0.929 0.08 0.00 0.92 0.00
#> TCGA.50.6593.01 3 0.000 0.951 0.00 0.00 1.00 0.00
#> TCGA.55.8302.01 4 0.201 0.953 0.00 0.00 0.08 0.92
#> TCGA.05.4425.01 2 0.000 1.000 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.4112.01 4 0.0609 0.8848 0.00 0.00 0.00 0.98 0.02
#> TCGA.NJ.A4YP.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8278.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.49.AARQ.01 4 0.3424 0.7395 0.00 0.00 0.00 0.76 0.24
#> TCGA.97.A4M1.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.8033.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.8453.01 3 0.4182 0.2118 0.00 0.00 0.60 0.00 0.40
#> TCGA.97.8552.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.53.A4EZ.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5066.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46U.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.MP.A4T8.01 4 0.2280 0.8659 0.00 0.00 0.00 0.88 0.12
#> TCGA.MP.A4SY.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.93.A4JN.01 4 0.2020 0.8692 0.00 0.00 0.00 0.90 0.10
#> TCGA.86.A4JF.01 4 0.1410 0.8753 0.00 0.00 0.00 0.94 0.06
#> TCGA.63.6202.01 4 0.1043 0.8801 0.00 0.00 0.00 0.96 0.04
#> TCGA.J2.A4AG.01 3 0.3983 0.3719 0.00 0.00 0.66 0.00 0.34
#> TCGA.MP.A4TI.01 4 0.0609 0.8804 0.00 0.00 0.00 0.98 0.02
#> TCGA.55.8208.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8584.01 1 0.0609 0.9248 0.98 0.00 0.02 0.00 0.00
#> TCGA.NJ.A4YI.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AAR4.01 3 0.3983 0.3633 0.00 0.00 0.66 0.00 0.34
#> TCGA.55.6984.01 3 0.4182 0.2118 0.00 0.00 0.60 0.00 0.40
#> TCGA.MN.A4N1.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 5 0.5048 0.3880 0.00 0.00 0.04 0.38 0.58
#> TCGA.49.6744.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.L9.A743.01 3 0.4307 -0.0545 0.00 0.00 0.50 0.00 0.50
#> TCGA.05.4410.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.62.A46Y.01 4 0.2516 0.8584 0.00 0.00 0.00 0.86 0.14
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#> TCGA.67.6216.01 5 0.2929 0.4160 0.00 0.00 0.00 0.18 0.82
#> TCGA.55.8203.01 4 0.1732 0.8642 0.00 0.00 0.00 0.92 0.08
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#> TCGA.44.2668.01 5 0.4227 0.3094 0.00 0.00 0.00 0.42 0.58
#> TCGA.55.6971.01 1 0.4060 0.5963 0.64 0.00 0.36 0.00 0.00
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#> TCGA.75.5125.01 4 0.1732 0.8666 0.00 0.00 0.00 0.92 0.08
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#> TCGA.86.7714.01 5 0.3796 0.3830 0.00 0.00 0.30 0.00 0.70
#> TCGA.95.7948.01 5 0.3895 0.0662 0.00 0.00 0.00 0.32 0.68
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#> TCGA.55.7815.01 5 0.4287 0.1614 0.00 0.00 0.46 0.00 0.54
#> TCGA.05.5423.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6985.01 3 0.4126 0.2347 0.00 0.00 0.62 0.00 0.38
#> TCGA.55.7281.01 4 0.1410 0.8745 0.00 0.00 0.00 0.94 0.06
#> TCGA.93.7347.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6777.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.97.8177.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.7458.01 5 0.4227 0.2508 0.00 0.00 0.42 0.00 0.58
#> TCGA.91.A4BD.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 4 0.3424 0.7882 0.00 0.00 0.00 0.76 0.24
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#> TCGA.55.7573.01 1 0.1410 0.9019 0.94 0.00 0.06 0.00 0.00
#> TCGA.55.8097.01 1 0.4060 0.5962 0.64 0.00 0.36 0.00 0.00
#> TCGA.05.5429.01 2 0.1732 0.9304 0.00 0.92 0.00 0.08 0.00
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#> TCGA.93.A4JQ.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.5122.01 5 0.4227 0.3094 0.00 0.00 0.00 0.42 0.58
#> TCGA.97.7938.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7671.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 1 0.4060 0.5963 0.64 0.00 0.36 0.00 0.00
#> TCGA.85.6560.01 5 0.4262 0.1548 0.00 0.00 0.44 0.00 0.56
#> TCGA.91.8496.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46R.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A443.01 4 0.4262 0.5421 0.00 0.00 0.00 0.56 0.44
#> TCGA.86.7701.01 4 0.1410 0.8745 0.00 0.00 0.00 0.94 0.06
#> TCGA.52.7812.01 4 0.3109 0.8221 0.00 0.00 0.00 0.80 0.20
#> TCGA.78.7162.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 5 0.4060 0.2935 0.00 0.00 0.36 0.00 0.64
#> TCGA.50.8460.01 3 0.1732 0.6991 0.00 0.00 0.92 0.00 0.08
#> TCGA.67.6217.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7535.01 2 0.1732 0.9304 0.00 0.92 0.00 0.08 0.00
#> TCGA.93.7348.01 3 0.4182 0.0201 0.40 0.00 0.60 0.00 0.00
#> TCGA.86.8671.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6592.01 5 0.4287 0.1614 0.00 0.00 0.46 0.00 0.54
#> TCGA.97.7546.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 3 0.4227 0.1922 0.00 0.00 0.58 0.00 0.42
#> TCGA.95.7944.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5933.01 2 0.1732 0.9304 0.00 0.92 0.00 0.08 0.00
#> TCGA.86.8280.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 4 0.0609 0.8781 0.00 0.02 0.00 0.98 0.00
#> TCGA.55.7907.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.6767.01 5 0.4307 0.0269 0.00 0.00 0.50 0.00 0.50
#> TCGA.MP.A4TK.01 5 0.4227 0.3094 0.00 0.00 0.00 0.42 0.58
#> TCGA.69.7761.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.91.6835.01 3 0.1410 0.7133 0.00 0.00 0.94 0.00 0.06
#> TCGA.78.7540.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.95.A4VN.01 5 0.5888 0.4863 0.00 0.00 0.14 0.28 0.58
#> TCGA.44.A47F.01 5 0.2020 0.5032 0.00 0.00 0.10 0.00 0.90
#> TCGA.55.A48Z.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7763.01 4 0.2020 0.8540 0.00 0.00 0.00 0.90 0.10
#> TCGA.J2.A4AE.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.50.5942.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6590.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.80.5608.01 5 0.2732 0.4993 0.00 0.00 0.16 0.00 0.84
#> TCGA.55.8511.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A491.01 5 0.2929 0.4560 0.00 0.00 0.18 0.00 0.82
#> TCGA.MN.A4N5.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.69.7978.01 4 0.0609 0.8804 0.00 0.00 0.00 0.98 0.02
#> TCGA.55.8299.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.8117.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.05.4405.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.83.5908.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.6980.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6146.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.62.8397.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7552.01 3 0.3895 0.4025 0.00 0.00 0.68 0.00 0.32
#> TCGA.50.5936.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.7771.01 5 0.2012 0.5118 0.00 0.00 0.06 0.02 0.92
#> TCGA.NJ.A4YG.01 4 0.2020 0.8540 0.00 0.00 0.00 0.90 0.10
#> TCGA.86.8359.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8301.01 5 0.4302 0.0976 0.00 0.00 0.48 0.00 0.52
#> TCGA.44.3918.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8621.01 1 0.2020 0.8742 0.90 0.00 0.10 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A4SS.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 5 0.4302 0.0976 0.00 0.00 0.48 0.00 0.52
#> TCGA.NJ.A4YQ.01 5 0.4227 0.2508 0.00 0.00 0.42 0.00 0.58
#> TCGA.55.7574.01 5 0.4726 0.3521 0.00 0.00 0.02 0.40 0.58
#> TCGA.63.A5MN.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.78.8648.01 1 0.1043 0.9137 0.96 0.00 0.04 0.00 0.00
#> TCGA.NC.A5HJ.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2656.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8673.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.7499.01 3 0.2020 0.6935 0.00 0.00 0.90 0.00 0.10
#> TCGA.97.A4LX.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T7.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7765.01 2 0.1043 0.9616 0.00 0.96 0.00 0.04 0.00
#> TCGA.95.8494.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.8171.01 3 0.1648 0.6928 0.02 0.00 0.94 0.00 0.04
#> TCGA.50.8457.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.A4M5.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.53.7626.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.5645.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.86.8056.01 4 0.2280 0.8568 0.00 0.00 0.00 0.88 0.12
#> TCGA.69.7980.01 5 0.3796 0.3867 0.00 0.00 0.30 0.00 0.70
#> TCGA.97.8175.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8668.01 3 0.1410 0.7133 0.00 0.00 0.94 0.00 0.06
#> TCGA.MP.A4T4.01 3 0.0609 0.7366 0.00 0.00 0.98 0.00 0.02
#> TCGA.44.A47A.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.44.6145.01 1 0.3109 0.7909 0.80 0.00 0.20 0.00 0.00
#> TCGA.97.8547.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.44.6147.01 5 0.3424 0.4865 0.00 0.00 0.00 0.24 0.76
#> TCGA.77.8007.01 4 0.0609 0.8804 0.00 0.00 0.00 0.98 0.02
#> TCGA.55.8510.01 3 0.0609 0.7315 0.02 0.00 0.98 0.00 0.00
#> TCGA.49.AARO.01 3 0.1410 0.7112 0.00 0.00 0.94 0.00 0.06
#> TCGA.55.8090.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.2020 0.8540 0.00 0.00 0.00 0.90 0.10
#> TCGA.91.6828.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8076.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.A4M6.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5044.01 5 0.4287 0.1614 0.00 0.00 0.46 0.00 0.54
#> TCGA.64.5781.01 5 0.4302 0.0976 0.00 0.00 0.48 0.00 0.52
#> TCGA.NJ.A4YF.01 5 0.3983 0.3267 0.00 0.00 0.34 0.00 0.66
#> TCGA.38.7271.01 5 0.4227 0.3094 0.00 0.00 0.00 0.42 0.58
#> TCGA.49.AAR3.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.MP.A4TJ.01 1 0.2732 0.8267 0.84 0.00 0.16 0.00 0.00
#> TCGA.69.7760.01 5 0.4262 0.1204 0.00 0.00 0.44 0.00 0.56
#> TCGA.49.4512.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5939.01 1 0.1410 0.9019 0.94 0.00 0.06 0.00 0.00
#> TCGA.78.7143.01 4 0.4302 0.4736 0.00 0.00 0.00 0.52 0.48
#> TCGA.97.A4M3.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.75.6205.01 4 0.2516 0.8192 0.00 0.00 0.00 0.86 0.14
#> TCGA.99.8028.01 3 0.0609 0.7366 0.00 0.00 0.98 0.00 0.02
#> TCGA.55.7903.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
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#> TCGA.75.5126.01 5 0.4227 0.3094 0.00 0.00 0.00 0.42 0.58
#> TCGA.55.8206.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
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#> TCGA.55.A48X.01 5 0.2280 0.5081 0.00 0.00 0.12 0.00 0.88
#> TCGA.64.5778.01 1 0.4060 0.5963 0.64 0.00 0.36 0.00 0.00
#> TCGA.50.6594.01 3 0.2929 0.6012 0.00 0.00 0.82 0.00 0.18
#> TCGA.78.7153.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7728.01 1 0.3796 0.6800 0.70 0.00 0.30 0.00 0.00
#> TCGA.67.6215.01 4 0.3983 0.6798 0.00 0.00 0.00 0.66 0.34
#> TCGA.78.7537.01 5 0.4060 0.3027 0.00 0.00 0.36 0.00 0.64
#> TCGA.55.6982.01 4 0.1043 0.8809 0.00 0.00 0.00 0.96 0.04
#> TCGA.55.7227.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.A456.01 2 0.1043 0.9616 0.00 0.96 0.00 0.04 0.00
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#> TCGA.73.7498.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.38.4632.01 2 0.1732 0.9304 0.00 0.92 0.00 0.08 0.00
#> TCGA.69.7974.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6986.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.49.6761.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4T6.01 4 0.4227 0.5641 0.00 0.00 0.00 0.58 0.42
#> TCGA.44.6779.01 4 0.4287 0.0716 0.00 0.00 0.00 0.54 0.46
#> TCGA.86.A4P7.01 4 0.2929 0.7709 0.00 0.00 0.00 0.82 0.18
#> TCGA.73.4658.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.A513.01 3 0.0609 0.7315 0.02 0.00 0.98 0.00 0.00
#> TCGA.50.5935.01 5 0.3424 0.4395 0.00 0.00 0.24 0.00 0.76
#> TCGA.55.7727.01 2 0.1043 0.9616 0.00 0.96 0.00 0.04 0.00
#> TCGA.55.6981.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.78.8655.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7163.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7941.01 3 0.1732 0.7064 0.00 0.00 0.92 0.00 0.08
#> TCGA.55.7914.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.7030.01 1 0.1410 0.9019 0.94 0.00 0.06 0.00 0.00
#> TCGA.62.A472.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.4417.01 5 0.1732 0.5129 0.00 0.00 0.00 0.08 0.92
#> TCGA.67.4679.01 3 0.4126 0.2456 0.00 0.00 0.62 0.00 0.38
#> TCGA.97.7554.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.7025.01 1 0.3895 0.6541 0.68 0.00 0.32 0.00 0.00
#> TCGA.95.8039.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5941.01 3 0.4182 0.2118 0.00 0.00 0.60 0.00 0.40
#> TCGA.97.8174.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7576.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7725.01 3 0.1732 0.7057 0.00 0.00 0.92 0.00 0.08
#> TCGA.38.A44F.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.80.5607.01 4 0.1732 0.8689 0.00 0.00 0.00 0.92 0.08
#> TCGA.55.8091.01 1 0.3895 0.6541 0.68 0.00 0.32 0.00 0.00
#> TCGA.62.8395.01 4 0.4170 0.7417 0.00 0.14 0.00 0.78 0.08
#> TCGA.86.8672.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00
#> TCGA.64.5815.01 4 0.0609 0.8804 0.00 0.00 0.00 0.98 0.02
#> TCGA.75.6212.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6776.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6983.01 3 0.4182 0.1908 0.00 0.00 0.60 0.00 0.40
#> TCGA.93.8067.01 2 0.0609 0.9740 0.00 0.98 0.00 0.02 0.00
#> TCGA.69.A59K.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.1732 0.9304 0.00 0.92 0.00 0.08 0.00
#> TCGA.91.6836.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.8172.01 4 0.4126 0.6287 0.00 0.00 0.00 0.62 0.38
#> TCGA.O2.A52Q.01 5 0.4302 0.0976 0.00 0.00 0.48 0.00 0.52
#> TCGA.50.5045.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 5 0.4227 0.2508 0.00 0.00 0.42 0.00 0.58
#> TCGA.95.A4VP.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5715.01 4 0.4227 0.5641 0.00 0.00 0.00 0.58 0.42
#> TCGA.55.A492.01 1 0.4287 0.3993 0.54 0.00 0.46 0.00 0.00
#> TCGA.55.A48Y.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6595.01 3 0.0609 0.7315 0.02 0.00 0.98 0.00 0.00
#> TCGA.55.6543.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5049.01 3 0.0609 0.7315 0.02 0.00 0.98 0.00 0.00
#> TCGA.97.A4M2.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.1732 0.9304 0.00 0.92 0.00 0.08 0.00
#> TCGA.97.A4M7.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.44.7662.01 5 0.4287 0.1614 0.00 0.00 0.46 0.00 0.54
#> TCGA.55.6970.01 1 0.0000 0.9354 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 5 0.4227 0.2508 0.00 0.00 0.42 0.00 0.58
#> TCGA.71.8520.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7672.01 4 0.1410 0.8753 0.00 0.00 0.00 0.94 0.06
#> TCGA.55.6987.01 3 0.1410 0.7112 0.00 0.00 0.94 0.00 0.06
#> TCGA.78.7152.01 4 0.1043 0.8809 0.00 0.00 0.00 0.96 0.04
#> TCGA.78.7145.01 3 0.0000 0.7425 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6593.01 3 0.4302 0.0187 0.00 0.00 0.52 0.00 0.48
#> TCGA.55.8302.01 4 0.1732 0.8666 0.00 0.00 0.00 0.92 0.08
#> TCGA.05.4425.01 2 0.0000 0.9856 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.4112.01 4 0.0547 0.851 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.NJ.A4YP.01 4 0.0547 0.851 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.86.8278.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.49.AARQ.01 4 0.3706 0.469 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.97.A4M1.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8033.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.8453.01 5 0.3711 0.802 0.00 0.00 0.26 0.00 0.72 0.02
#> TCGA.97.8552.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.A4EZ.01 3 0.1807 0.817 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.50.5066.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46U.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.MP.A4T8.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.MP.A4SY.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.93.A4JN.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.86.A4JF.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.63.6202.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.J2.A4AG.01 5 0.4360 0.766 0.00 0.00 0.26 0.00 0.68 0.06
#> TCGA.MP.A4TI.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.55.8208.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8584.01 1 0.1807 0.911 0.92 0.00 0.06 0.00 0.00 0.02
#> TCGA.NJ.A4YI.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR4.01 5 0.4067 0.771 0.00 0.00 0.26 0.00 0.70 0.04
#> TCGA.55.6984.01 5 0.3592 0.815 0.00 0.00 0.24 0.00 0.74 0.02
#> TCGA.MN.A4N1.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 5 0.1556 0.736 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.49.6744.01 3 0.0937 0.843 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.L9.A743.01 5 0.2631 0.835 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.05.4410.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.62.A46Y.01 4 0.4536 0.767 0.00 0.00 0.00 0.70 0.12 0.18
#> TCGA.50.6597.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.05.4384.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8087.01 3 0.3916 0.598 0.30 0.00 0.68 0.00 0.00 0.02
#> TCGA.85.A50M.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TH.01 1 0.1807 0.911 0.92 0.00 0.06 0.00 0.00 0.02
#> TCGA.55.8207.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.6562.01 5 0.4144 0.657 0.00 0.00 0.36 0.00 0.62 0.02
#> TCGA.86.8074.01 3 0.2474 0.792 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.39.5011.01 3 0.1865 0.827 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.MP.A4SW.01 5 0.2454 0.664 0.00 0.00 0.00 0.16 0.84 0.00
#> TCGA.67.6216.01 6 0.1267 0.802 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.55.8203.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.55.8619.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.44.2668.01 5 0.2260 0.687 0.00 0.00 0.00 0.14 0.86 0.00
#> TCGA.55.6971.01 3 0.4172 0.618 0.28 0.00 0.68 0.00 0.00 0.04
#> TCGA.98.7454.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A444.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.62.A46V.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 5 0.1556 0.736 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.69.8253.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.91.6849.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.5944.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2665.01 6 0.4265 0.397 0.00 0.00 0.00 0.30 0.04 0.66
#> TCGA.62.A46P.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2666.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.55.A494.01 6 0.2474 0.787 0.00 0.00 0.00 0.08 0.04 0.88
#> TCGA.97.7547.01 3 0.3916 0.598 0.30 0.00 0.68 0.00 0.00 0.02
#> TCGA.69.8254.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.75.5125.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.69.7973.01 3 0.3819 0.629 0.28 0.00 0.70 0.00 0.00 0.02
#> TCGA.L4.A4E5.01 6 0.4310 0.369 0.00 0.00 0.02 0.00 0.44 0.54
#> TCGA.44.6775.01 5 0.2790 0.830 0.00 0.00 0.14 0.00 0.84 0.02
#> TCGA.55.7911.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T9.01 3 0.1480 0.841 0.02 0.00 0.94 0.00 0.00 0.04
#> TCGA.55.6712.01 5 0.3076 0.564 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.86.7714.01 6 0.3679 0.772 0.00 0.00 0.04 0.00 0.20 0.76
#> TCGA.95.7948.01 6 0.1267 0.787 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.55.A4DG.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 5 0.2790 0.830 0.00 0.00 0.14 0.00 0.84 0.02
#> TCGA.05.5423.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.6985.01 5 0.3711 0.802 0.00 0.00 0.26 0.00 0.72 0.02
#> TCGA.55.7281.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.93.7347.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.44.6777.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.97.8177.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.7458.01 5 0.1807 0.793 0.00 0.00 0.06 0.00 0.92 0.02
#> TCGA.91.A4BD.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.6178.01 6 0.4246 0.117 0.00 0.00 0.00 0.40 0.02 0.58
#> TCGA.44.A47B.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7573.01 1 0.1807 0.911 0.92 0.00 0.06 0.00 0.00 0.02
#> TCGA.55.8097.01 3 0.3711 0.648 0.26 0.00 0.72 0.00 0.00 0.02
#> TCGA.05.5429.01 2 0.2454 0.840 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.93.A4JP.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JQ.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5122.01 5 0.2048 0.705 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.97.7938.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.44.7671.01 1 0.0547 0.959 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.50.5055.01 3 0.4265 0.586 0.30 0.00 0.66 0.00 0.00 0.04
#> TCGA.85.6560.01 5 0.3156 0.836 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.91.8496.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.A46R.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A443.01 6 0.1556 0.774 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.86.7701.01 4 0.2048 0.839 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.52.7812.01 4 0.5012 0.625 0.00 0.00 0.00 0.60 0.10 0.30
#> TCGA.78.7162.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 6 0.3787 0.770 0.00 0.00 0.10 0.00 0.12 0.78
#> TCGA.50.8460.01 3 0.2094 0.777 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.67.6217.01 3 0.0000 0.848 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7535.01 2 0.2454 0.840 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.93.7348.01 3 0.2581 0.779 0.12 0.00 0.86 0.00 0.00 0.02
#> TCGA.86.8671.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.50.6592.01 5 0.3156 0.836 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.97.7546.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 5 0.4121 0.801 0.00 0.00 0.22 0.00 0.72 0.06
#> TCGA.95.7944.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 2 0.2260 0.861 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.86.8280.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.8660.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7907.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6767.01 5 0.2981 0.797 0.00 0.00 0.16 0.00 0.82 0.02
#> TCGA.MP.A4TK.01 5 0.2260 0.687 0.00 0.00 0.00 0.14 0.86 0.00
#> TCGA.69.7761.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.91.6835.01 3 0.1807 0.795 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.78.7540.01 4 0.2454 0.778 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.95.A4VN.01 5 0.1556 0.736 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.44.A47F.01 6 0.2581 0.813 0.00 0.00 0.02 0.00 0.12 0.86
#> TCGA.55.A48Z.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7763.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.J2.A4AE.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.50.5942.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.6590.01 4 0.1556 0.846 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.80.5608.01 6 0.3460 0.759 0.00 0.00 0.02 0.00 0.22 0.76
#> TCGA.55.8511.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A491.01 6 0.2981 0.806 0.00 0.00 0.02 0.00 0.16 0.82
#> TCGA.MN.A4N5.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.69.7978.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.55.8299.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8117.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 4 0.0937 0.851 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.05.4405.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.83.5908.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6980.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6146.01 3 0.0000 0.848 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.8397.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7552.01 5 0.4360 0.766 0.00 0.00 0.26 0.00 0.68 0.06
#> TCGA.50.5936.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.7771.01 6 0.2981 0.806 0.00 0.00 0.02 0.00 0.16 0.82
#> TCGA.NJ.A4YG.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.86.8359.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.8301.01 5 0.3156 0.836 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.44.3918.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8621.01 1 0.2956 0.826 0.84 0.00 0.12 0.00 0.00 0.04
#> TCGA.49.6745.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A4SS.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 5 0.3156 0.836 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.NJ.A4YQ.01 5 0.1267 0.788 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.55.7574.01 5 0.1556 0.736 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.63.A5MN.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.78.8648.01 1 0.2190 0.895 0.90 0.00 0.06 0.00 0.00 0.04
#> TCGA.NC.A5HJ.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2656.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8673.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 3 0.3045 0.771 0.00 0.00 0.84 0.00 0.10 0.06
#> TCGA.97.A4LX.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T7.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.69.7765.01 2 0.0937 0.943 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.95.8494.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.8171.01 3 0.1807 0.817 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.50.8457.01 3 0.0000 0.848 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.A4M5.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.7626.01 3 0.2190 0.815 0.00 0.00 0.90 0.00 0.06 0.04
#> TCGA.44.5645.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.86.8056.01 4 0.3660 0.816 0.00 0.00 0.00 0.78 0.16 0.06
#> TCGA.69.7980.01 6 0.3679 0.772 0.00 0.00 0.04 0.00 0.20 0.76
#> TCGA.97.8175.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8668.01 3 0.1480 0.814 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.MP.A4T4.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.44.A47A.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.44.6145.01 1 0.4265 0.490 0.66 0.00 0.30 0.00 0.00 0.04
#> TCGA.97.8547.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.44.6147.01 5 0.1556 0.734 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.77.8007.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.55.8510.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.49.AARO.01 3 0.4646 -0.297 0.00 0.00 0.50 0.00 0.46 0.04
#> TCGA.55.8090.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.91.6828.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8076.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.97.A4M6.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5044.01 5 0.2790 0.830 0.00 0.00 0.14 0.00 0.84 0.02
#> TCGA.64.5781.01 5 0.3156 0.836 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.NJ.A4YF.01 6 0.3523 0.779 0.00 0.00 0.04 0.00 0.18 0.78
#> TCGA.38.7271.01 5 0.2260 0.687 0.00 0.00 0.00 0.14 0.86 0.00
#> TCGA.49.AAR3.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.MP.A4TJ.01 1 0.3950 0.626 0.72 0.00 0.24 0.00 0.00 0.04
#> TCGA.69.7760.01 6 0.3787 0.757 0.00 0.00 0.12 0.00 0.10 0.78
#> TCGA.49.4512.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.5939.01 1 0.2474 0.875 0.88 0.00 0.08 0.00 0.00 0.04
#> TCGA.78.7143.01 6 0.1556 0.774 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.97.A4M3.01 3 0.1092 0.840 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.75.6205.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.99.8028.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.55.7903.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.75.5126.01 5 0.2048 0.705 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.55.8206.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7553.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A7XG.01 6 0.2581 0.813 0.00 0.00 0.02 0.00 0.12 0.86
#> TCGA.55.A48X.01 5 0.2981 0.655 0.00 0.00 0.02 0.00 0.82 0.16
#> TCGA.64.5778.01 3 0.4067 0.644 0.26 0.00 0.70 0.00 0.00 0.04
#> TCGA.50.6594.01 3 0.4608 0.555 0.00 0.00 0.68 0.00 0.10 0.22
#> TCGA.78.7153.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7728.01 3 0.4265 0.586 0.30 0.00 0.66 0.00 0.00 0.04
#> TCGA.67.6215.01 6 0.3499 0.406 0.00 0.00 0.00 0.32 0.00 0.68
#> TCGA.78.7537.01 6 0.4377 0.741 0.00 0.00 0.12 0.00 0.16 0.72
#> TCGA.55.6982.01 4 0.2048 0.839 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.55.7227.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.A456.01 2 0.0937 0.943 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.44.6774.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAQV.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.7498.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4632.01 2 0.2454 0.840 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.69.7974.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6986.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.49.6761.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T6.01 6 0.1556 0.774 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.44.6779.01 5 0.2941 0.589 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.86.A4P7.01 4 0.3409 0.662 0.00 0.00 0.00 0.70 0.30 0.00
#> TCGA.73.4658.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.85.A513.01 3 0.1480 0.841 0.02 0.00 0.94 0.00 0.00 0.04
#> TCGA.50.5935.01 6 0.3351 0.801 0.00 0.00 0.04 0.00 0.16 0.80
#> TCGA.55.7727.01 2 0.2260 0.861 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.55.6981.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.78.8655.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7163.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7941.01 3 0.3045 0.771 0.00 0.00 0.84 0.00 0.10 0.06
#> TCGA.55.7914.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.7030.01 1 0.2190 0.895 0.90 0.00 0.06 0.00 0.00 0.04
#> TCGA.62.A472.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4417.01 6 0.3156 0.795 0.00 0.00 0.02 0.00 0.18 0.80
#> TCGA.67.4679.01 5 0.5289 0.625 0.00 0.00 0.28 0.00 0.58 0.14
#> TCGA.97.7554.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.7025.01 3 0.3819 0.629 0.28 0.00 0.70 0.00 0.00 0.02
#> TCGA.95.8039.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5941.01 5 0.3460 0.822 0.00 0.00 0.22 0.00 0.76 0.02
#> TCGA.97.8174.01 3 0.0547 0.847 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.7576.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 3 0.2794 0.785 0.00 0.00 0.86 0.00 0.08 0.06
#> TCGA.38.A44F.01 1 0.1480 0.929 0.94 0.00 0.04 0.00 0.00 0.02
#> TCGA.80.5607.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.55.8091.01 3 0.3819 0.629 0.28 0.00 0.70 0.00 0.00 0.02
#> TCGA.62.8395.01 4 0.2631 0.765 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.86.8672.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.64.5815.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.75.6212.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6776.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6983.01 5 0.3592 0.815 0.00 0.00 0.24 0.00 0.74 0.02
#> TCGA.93.8067.01 2 0.1556 0.913 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.69.A59K.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.2260 0.861 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.91.6836.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.8172.01 6 0.2941 0.606 0.00 0.00 0.00 0.22 0.00 0.78
#> TCGA.O2.A52Q.01 5 0.3156 0.829 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.50.5045.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 5 0.1267 0.788 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5715.01 6 0.1556 0.774 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.55.A492.01 3 0.3315 0.704 0.20 0.00 0.78 0.00 0.00 0.02
#> TCGA.55.A48Y.01 3 0.2794 0.781 0.00 0.00 0.86 0.00 0.08 0.06
#> TCGA.50.6595.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.55.6543.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0000 0.848 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5049.01 3 0.1480 0.838 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.97.A4M2.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7659.01 2 0.2454 0.840 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.97.A4M7.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.44.7662.01 5 0.1556 0.799 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.55.6970.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 5 0.1267 0.788 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.71.8520.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7672.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.55.6987.01 5 0.4651 0.329 0.00 0.00 0.48 0.00 0.48 0.04
#> TCGA.78.7152.01 4 0.2048 0.839 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.78.7145.01 3 0.0000 0.848 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6593.01 5 0.3315 0.832 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.55.8302.01 4 0.2454 0.826 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.05.4425.01 2 0.0000 0.969 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.44.4112.01 4 0.1433 0.6929 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.NJ.A4YP.01 4 0.1886 0.6701 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.86.8278.01 7 0.3139 0.6926 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.49.AARQ.01 7 0.3835 0.6640 0.00 0.00 0.00 0.16 0.00 0.10 0.74
#> TCGA.97.A4M1.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.99.8033.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.69.8453.01 5 0.4569 0.6363 0.00 0.00 0.28 0.00 0.64 0.06 0.02
#> TCGA.97.8552.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.53.A4EZ.01 3 0.3795 0.5940 0.00 0.00 0.72 0.00 0.00 0.22 0.06
#> TCGA.50.5066.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.62.A46U.01 7 0.3517 0.6663 0.00 0.00 0.02 0.28 0.00 0.00 0.70
#> TCGA.MP.A4T8.01 7 0.3221 0.6725 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.MP.A4SY.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.93.A4JN.01 7 0.2832 0.6899 0.00 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.86.A4JF.01 4 0.0863 0.7260 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.63.6202.01 4 0.0863 0.7260 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.J2.A4AG.01 5 0.3517 0.6847 0.00 0.00 0.28 0.00 0.70 0.00 0.02
#> TCGA.MP.A4TI.01 4 0.0863 0.7260 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.55.8208.01 1 0.1433 0.9077 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.85.8584.01 1 0.2512 0.8169 0.86 0.00 0.10 0.00 0.00 0.00 0.04
#> TCGA.NJ.A4YI.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR4.01 5 0.3637 0.7076 0.00 0.00 0.24 0.00 0.72 0.00 0.04
#> TCGA.55.6984.01 5 0.4569 0.6363 0.00 0.00 0.28 0.00 0.64 0.06 0.02
#> TCGA.MN.A4N1.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0863 0.9120 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.MP.A4TC.01 5 0.3221 0.5159 0.00 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.49.6744.01 3 0.1006 0.7555 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.L9.A743.01 5 0.2081 0.7655 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.05.4410.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.62.A46Y.01 4 0.3968 -0.2575 0.00 0.00 0.00 0.54 0.02 0.00 0.44
#> TCGA.50.6597.01 7 0.3139 0.6926 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.05.4384.01 1 0.0504 0.9115 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.8087.01 3 0.4708 0.5816 0.26 0.00 0.64 0.00 0.00 0.02 0.08
#> TCGA.85.A50M.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.MP.A4TH.01 1 0.3086 0.7427 0.80 0.00 0.16 0.00 0.00 0.00 0.04
#> TCGA.55.8207.01 2 0.0504 0.9027 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.86.6562.01 5 0.4778 0.5498 0.00 0.00 0.34 0.00 0.58 0.06 0.02
#> TCGA.86.8074.01 3 0.4779 0.5666 0.00 0.00 0.68 0.00 0.10 0.18 0.04
#> TCGA.39.5011.01 3 0.3841 0.4180 0.00 0.00 0.68 0.00 0.28 0.00 0.04
#> TCGA.MP.A4SW.01 5 0.3546 0.2132 0.00 0.00 0.00 0.46 0.54 0.00 0.00
#> TCGA.67.6216.01 6 0.3307 0.5505 0.00 0.00 0.00 0.00 0.02 0.74 0.24
#> TCGA.55.8203.01 4 0.1363 0.7131 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.55.8619.01 3 0.1363 0.7503 0.00 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.44.2668.01 5 0.3413 0.4119 0.00 0.00 0.00 0.38 0.62 0.00 0.00
#> TCGA.55.6971.01 3 0.4108 0.5783 0.28 0.00 0.66 0.00 0.00 0.00 0.06
#> TCGA.98.7454.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.L9.A444.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.62.A46V.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 5 0.3221 0.5159 0.00 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.69.8253.01 3 0.2016 0.7484 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.91.6849.01 3 0.2829 0.7279 0.00 0.00 0.84 0.00 0.00 0.08 0.08
#> TCGA.50.5944.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.44.2665.01 7 0.5341 0.4537 0.00 0.00 0.00 0.24 0.00 0.26 0.50
#> TCGA.62.A46P.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2666.01 7 0.3139 0.6926 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.55.A494.01 6 0.2906 0.5996 0.00 0.00 0.00 0.02 0.00 0.80 0.18
#> TCGA.97.7547.01 3 0.4708 0.5816 0.26 0.00 0.64 0.00 0.00 0.02 0.08
#> TCGA.69.8254.01 5 0.2569 0.7619 0.00 0.00 0.14 0.00 0.84 0.00 0.02
#> TCGA.75.5125.01 4 0.1433 0.7082 0.00 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.69.7973.01 3 0.4708 0.5816 0.26 0.00 0.64 0.00 0.00 0.02 0.08
#> TCGA.L4.A4E5.01 6 0.2081 0.6808 0.00 0.00 0.00 0.00 0.14 0.86 0.00
#> TCGA.44.6775.01 5 0.1886 0.7662 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.55.7911.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.MP.A4T9.01 3 0.1860 0.7525 0.02 0.00 0.92 0.00 0.02 0.00 0.04
#> TCGA.55.6712.01 4 0.3294 0.3697 0.00 0.00 0.00 0.66 0.34 0.00 0.00
#> TCGA.86.7714.01 6 0.0504 0.7533 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.95.7948.01 6 0.3606 0.4510 0.00 0.00 0.00 0.00 0.02 0.68 0.30
#> TCGA.55.A4DG.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 5 0.1671 0.7618 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.05.5423.01 3 0.2016 0.7484 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.55.6985.01 5 0.5165 0.5829 0.00 0.00 0.28 0.00 0.58 0.12 0.02
#> TCGA.55.7281.01 4 0.1363 0.7199 0.00 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.93.7347.01 3 0.1363 0.7505 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.44.6777.01 5 0.3052 0.7438 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.97.8177.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.99.7458.01 5 0.2912 0.6978 0.00 0.00 0.04 0.14 0.82 0.00 0.00
#> TCGA.91.A4BD.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.38.6178.01 7 0.5341 0.4629 0.00 0.00 0.00 0.26 0.00 0.24 0.50
#> TCGA.44.A47B.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.7573.01 1 0.3086 0.7427 0.80 0.00 0.16 0.00 0.00 0.00 0.04
#> TCGA.55.8097.01 3 0.4708 0.5816 0.26 0.00 0.64 0.00 0.00 0.02 0.08
#> TCGA.05.5429.01 2 0.5336 0.3255 0.00 0.50 0.02 0.06 0.02 0.00 0.40
#> TCGA.93.A4JP.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.S2.AA1A.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.93.A4JQ.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.78.7160.01 1 0.1433 0.9077 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.75.5122.01 5 0.3358 0.4516 0.00 0.00 0.00 0.36 0.64 0.00 0.00
#> TCGA.97.7938.01 3 0.2278 0.7467 0.00 0.00 0.88 0.00 0.00 0.04 0.08
#> TCGA.44.7671.01 1 0.1006 0.8977 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.50.5055.01 3 0.4070 0.4933 0.34 0.00 0.62 0.00 0.00 0.00 0.04
#> TCGA.85.6560.01 5 0.0863 0.7366 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.91.8496.01 1 0.1166 0.9114 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.MP.A4T2.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.62.A46R.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A443.01 7 0.4505 0.1984 0.00 0.00 0.00 0.06 0.00 0.44 0.50
#> TCGA.86.7701.01 4 0.0863 0.7094 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.52.7812.01 7 0.4505 0.3740 0.00 0.00 0.00 0.44 0.00 0.06 0.50
#> TCGA.78.7162.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.L9.A50W.01 6 0.0000 0.7479 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.8460.01 3 0.3991 0.5118 0.00 0.00 0.72 0.00 0.22 0.04 0.02
#> TCGA.67.6217.01 3 0.1006 0.7523 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.78.7535.01 2 0.5249 0.5373 0.00 0.60 0.02 0.08 0.02 0.00 0.28
#> TCGA.93.7348.01 3 0.3927 0.6758 0.14 0.00 0.76 0.00 0.00 0.02 0.08
#> TCGA.86.8671.01 3 0.1718 0.7432 0.00 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.50.6592.01 5 0.2081 0.7646 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.97.7546.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.44.7661.01 5 0.3307 0.7214 0.00 0.00 0.24 0.00 0.74 0.00 0.02
#> TCGA.95.7944.01 1 0.1433 0.9077 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.97.A4M0.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5933.01 2 0.5166 0.5622 0.00 0.62 0.02 0.08 0.02 0.00 0.26
#> TCGA.86.8280.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.78.8660.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.55.7907.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6767.01 5 0.3667 0.6387 0.00 0.00 0.06 0.00 0.74 0.20 0.00
#> TCGA.MP.A4TK.01 5 0.3413 0.4119 0.00 0.00 0.00 0.38 0.62 0.00 0.00
#> TCGA.69.7761.01 5 0.2906 0.7527 0.00 0.00 0.18 0.00 0.80 0.00 0.02
#> TCGA.91.6835.01 3 0.3965 0.6133 0.00 0.00 0.76 0.00 0.12 0.10 0.02
#> TCGA.78.7540.01 7 0.3984 0.6393 0.00 0.00 0.02 0.28 0.02 0.00 0.68
#> TCGA.95.A4VN.01 5 0.2945 0.5862 0.00 0.00 0.00 0.26 0.74 0.00 0.00
#> TCGA.44.A47F.01 6 0.1664 0.7419 0.00 0.00 0.00 0.00 0.02 0.92 0.06
#> TCGA.55.A48Z.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.69.7763.01 4 0.1166 0.7206 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.J2.A4AE.01 7 0.3139 0.6926 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.50.5942.01 3 0.2016 0.7484 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.50.6590.01 4 0.0504 0.7123 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.80.5608.01 6 0.1363 0.7493 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.55.8511.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8025.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A491.01 6 0.1363 0.7493 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.MN.A4N5.01 7 0.3139 0.6926 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.69.7978.01 4 0.0863 0.7260 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.55.8299.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.8117.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 4 0.1433 0.6813 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.05.4405.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.83.5908.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.55.6980.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.44.6146.01 3 0.1664 0.7552 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.62.8397.01 1 0.0863 0.9088 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.97.7552.01 5 0.4003 0.6148 0.00 0.00 0.32 0.00 0.64 0.00 0.04
#> TCGA.50.5936.01 1 0.0000 0.9099 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.7771.01 6 0.1363 0.7493 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.NJ.A4YG.01 4 0.1671 0.6934 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.86.8359.01 3 0.3058 0.7158 0.00 0.00 0.82 0.00 0.00 0.10 0.08
#> TCGA.55.8301.01 5 0.2081 0.7646 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.44.3918.01 4 0.3887 0.5024 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.55.8621.01 1 0.3637 0.6124 0.72 0.00 0.24 0.00 0.00 0.00 0.04
#> TCGA.49.6745.01 2 0.2706 0.8544 0.00 0.88 0.02 0.04 0.02 0.00 0.04
#> TCGA.44.A4SS.01 1 0.1166 0.9109 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.55.8089.01 5 0.2081 0.7646 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.NJ.A4YQ.01 5 0.2016 0.7404 0.00 0.00 0.04 0.06 0.90 0.00 0.00
#> TCGA.55.7574.01 5 0.3221 0.5159 0.00 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.63.A5MN.01 1 0.1166 0.9109 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.50.8459.01 5 0.3052 0.7438 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.78.8648.01 1 0.2722 0.7986 0.84 0.00 0.12 0.00 0.00 0.00 0.04
#> TCGA.NC.A5HJ.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.44.2656.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.86.8673.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 6 0.4461 0.1855 0.00 0.00 0.40 0.00 0.00 0.54 0.06
#> TCGA.97.A4LX.01 1 0.0504 0.9115 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.MP.A4T7.01 3 0.2016 0.7484 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.69.7765.01 2 0.3000 0.8404 0.00 0.86 0.02 0.04 0.02 0.00 0.06
#> TCGA.95.8494.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8171.01 3 0.3795 0.5893 0.00 0.00 0.72 0.00 0.00 0.22 0.06
#> TCGA.50.8457.01 3 0.1006 0.7523 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.97.A4M5.01 1 0.1166 0.9116 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.53.7626.01 3 0.3519 0.5401 0.00 0.00 0.74 0.00 0.22 0.00 0.04
#> TCGA.44.5645.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.78.7158.01 7 0.3139 0.6926 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.86.8056.01 4 0.3199 0.5802 0.00 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.69.7980.01 6 0.0504 0.7533 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.97.8175.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.86.8668.01 3 0.3566 0.6097 0.00 0.00 0.78 0.00 0.16 0.04 0.02
#> TCGA.MP.A4T4.01 3 0.3086 0.6312 0.00 0.00 0.80 0.00 0.16 0.00 0.04
#> TCGA.44.A47A.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.93.A4JO.01 5 0.3186 0.7340 0.00 0.00 0.22 0.00 0.76 0.00 0.02
#> TCGA.44.6145.01 1 0.4214 0.1910 0.56 0.00 0.40 0.00 0.00 0.00 0.04
#> TCGA.97.8547.01 7 0.3517 0.6663 0.00 0.00 0.02 0.28 0.00 0.00 0.70
#> TCGA.44.6147.01 5 0.3358 0.4542 0.00 0.00 0.00 0.36 0.64 0.00 0.00
#> TCGA.77.8007.01 4 0.0863 0.7260 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.55.8510.01 3 0.1006 0.7555 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.49.AARO.01 5 0.4266 0.3496 0.00 0.00 0.44 0.00 0.52 0.00 0.04
#> TCGA.55.8090.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8073.01 4 0.1166 0.7206 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.91.6828.01 4 0.3887 0.4997 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.86.8076.01 3 0.1006 0.7555 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.97.A4M6.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.50.5044.01 5 0.2016 0.7485 0.00 0.00 0.06 0.04 0.90 0.00 0.00
#> TCGA.64.5781.01 5 0.2081 0.7646 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.NJ.A4YF.01 6 0.1006 0.7493 0.00 0.00 0.02 0.00 0.02 0.96 0.00
#> TCGA.38.7271.01 5 0.3413 0.4119 0.00 0.00 0.00 0.38 0.62 0.00 0.00
#> TCGA.49.AAR3.01 5 0.3186 0.7340 0.00 0.00 0.22 0.00 0.76 0.00 0.02
#> TCGA.MP.A4TJ.01 1 0.4175 0.2595 0.58 0.00 0.38 0.00 0.00 0.00 0.04
#> TCGA.69.7760.01 6 0.0000 0.7479 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.49.4512.01 3 0.2016 0.7484 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.50.5939.01 1 0.3244 0.7182 0.78 0.00 0.18 0.00 0.00 0.00 0.04
#> TCGA.78.7143.01 6 0.3994 -0.0793 0.00 0.00 0.00 0.02 0.00 0.50 0.48
#> TCGA.97.A4M3.01 3 0.3199 0.6832 0.00 0.00 0.80 0.00 0.00 0.14 0.06
#> TCGA.75.6205.01 4 0.2259 0.6350 0.00 0.00 0.00 0.84 0.16 0.00 0.00
#> TCGA.99.8028.01 3 0.3637 0.5046 0.00 0.00 0.72 0.00 0.24 0.00 0.04
#> TCGA.55.7903.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.1006 0.8977 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.55.A493.01 4 0.1671 0.6934 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.75.5126.01 5 0.3358 0.4516 0.00 0.00 0.00 0.36 0.64 0.00 0.00
#> TCGA.55.8206.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.97.7553.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.NJ.A7XG.01 6 0.1664 0.7373 0.00 0.00 0.00 0.00 0.02 0.92 0.06
#> TCGA.55.A48X.01 5 0.3221 0.4576 0.00 0.00 0.00 0.00 0.68 0.32 0.00
#> TCGA.64.5778.01 3 0.4538 0.5688 0.28 0.00 0.62 0.00 0.00 0.00 0.10
#> TCGA.50.6594.01 6 0.4328 0.3225 0.00 0.00 0.34 0.00 0.00 0.60 0.06
#> TCGA.78.7153.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7728.01 3 0.4487 0.5245 0.32 0.00 0.60 0.00 0.00 0.00 0.08
#> TCGA.67.6215.01 7 0.5173 0.3928 0.00 0.00 0.00 0.16 0.00 0.34 0.50
#> TCGA.78.7537.01 6 0.1505 0.7404 0.00 0.00 0.02 0.00 0.02 0.94 0.02
#> TCGA.55.6982.01 4 0.1363 0.7199 0.00 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.55.7227.01 2 0.1860 0.8763 0.00 0.92 0.00 0.02 0.02 0.00 0.04
#> TCGA.86.A456.01 2 0.3000 0.8404 0.00 0.86 0.02 0.04 0.02 0.00 0.06
#> TCGA.44.6774.01 1 0.0504 0.9115 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.49.AAQV.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.73.7498.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.38.4632.01 2 0.5362 0.5279 0.00 0.60 0.02 0.10 0.02 0.00 0.26
#> TCGA.69.7974.01 2 0.2706 0.8544 0.00 0.88 0.02 0.04 0.02 0.00 0.04
#> TCGA.55.6986.01 7 0.3139 0.6926 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.49.6761.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.MP.A4T6.01 7 0.4505 0.1984 0.00 0.00 0.00 0.06 0.00 0.44 0.50
#> TCGA.44.6779.01 4 0.3496 0.1546 0.00 0.00 0.00 0.58 0.42 0.00 0.00
#> TCGA.86.A4P7.01 4 0.3047 0.4993 0.00 0.00 0.00 0.72 0.28 0.00 0.00
#> TCGA.73.4658.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.85.A513.01 3 0.1860 0.7525 0.02 0.00 0.92 0.00 0.02 0.00 0.04
#> TCGA.50.5935.01 6 0.0504 0.7533 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.55.7727.01 2 0.4447 0.6183 0.00 0.66 0.02 0.02 0.02 0.00 0.28
#> TCGA.55.6981.01 5 0.3186 0.7340 0.00 0.00 0.22 0.00 0.76 0.00 0.02
#> TCGA.78.8655.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7163.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.97.7941.01 6 0.4461 0.1855 0.00 0.00 0.40 0.00 0.00 0.54 0.06
#> TCGA.55.7914.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7030.01 1 0.2722 0.7937 0.84 0.00 0.12 0.00 0.00 0.00 0.04
#> TCGA.62.A472.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4417.01 6 0.1860 0.7379 0.00 0.00 0.00 0.02 0.02 0.92 0.04
#> TCGA.67.4679.01 6 0.5709 0.0513 0.00 0.00 0.18 0.00 0.34 0.46 0.02
#> TCGA.97.7554.01 2 0.1505 0.8862 0.00 0.94 0.00 0.02 0.02 0.00 0.02
#> TCGA.75.7025.01 3 0.4708 0.5816 0.26 0.00 0.64 0.00 0.00 0.02 0.08
#> TCGA.95.8039.01 4 0.3887 0.5076 0.00 0.00 0.02 0.70 0.02 0.00 0.26
#> TCGA.50.5941.01 5 0.3517 0.6818 0.00 0.00 0.28 0.00 0.70 0.00 0.02
#> TCGA.97.8174.01 3 0.2016 0.7484 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.55.7576.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 6 0.4487 0.1234 0.00 0.00 0.42 0.00 0.00 0.52 0.06
#> TCGA.38.A44F.01 1 0.2016 0.8551 0.90 0.00 0.06 0.00 0.00 0.00 0.04
#> TCGA.80.5607.01 7 0.3047 0.6854 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.55.8091.01 3 0.4708 0.5816 0.26 0.00 0.64 0.00 0.00 0.02 0.08
#> TCGA.62.8395.01 7 0.3047 0.6854 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.86.8672.01 4 0.3055 0.6102 0.00 0.00 0.02 0.82 0.02 0.00 0.14
#> TCGA.64.5815.01 4 0.0863 0.7260 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.75.6212.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.44.6776.01 1 0.1671 0.9050 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.55.6983.01 5 0.4708 0.6544 0.00 0.00 0.26 0.00 0.64 0.08 0.02
#> TCGA.93.8067.01 2 0.2911 0.8382 0.00 0.86 0.02 0.02 0.02 0.00 0.08
#> TCGA.69.A59K.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7567.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.5249 0.5373 0.00 0.60 0.02 0.08 0.02 0.00 0.28
#> TCGA.91.6836.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8172.01 7 0.4692 0.2531 0.00 0.00 0.00 0.08 0.00 0.42 0.50
#> TCGA.O2.A52Q.01 5 0.2376 0.7632 0.00 0.00 0.12 0.00 0.86 0.02 0.00
#> TCGA.50.5045.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.6978.01 5 0.2016 0.7404 0.00 0.00 0.04 0.06 0.90 0.00 0.00
#> TCGA.95.A4VP.01 1 0.1006 0.8977 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.05.5715.01 7 0.4505 0.1984 0.00 0.00 0.00 0.06 0.00 0.44 0.50
#> TCGA.55.A492.01 3 0.4610 0.5942 0.24 0.00 0.66 0.00 0.00 0.02 0.08
#> TCGA.55.A48Y.01 3 0.3841 0.4206 0.00 0.00 0.68 0.00 0.28 0.00 0.04
#> TCGA.50.6595.01 3 0.1860 0.7514 0.02 0.00 0.92 0.00 0.04 0.00 0.02
#> TCGA.55.6543.01 1 0.0863 0.9120 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.91.8497.01 3 0.1006 0.7523 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.50.5049.01 3 0.2213 0.7481 0.02 0.00 0.90 0.00 0.04 0.00 0.04
#> TCGA.97.A4M2.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.7659.01 2 0.5249 0.5373 0.00 0.60 0.02 0.08 0.02 0.00 0.28
#> TCGA.97.A4M7.01 5 0.3052 0.7438 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.44.7662.01 5 0.2016 0.7404 0.00 0.00 0.04 0.06 0.90 0.00 0.00
#> TCGA.55.6970.01 1 0.0504 0.9068 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.50.5068.01 5 0.2016 0.7404 0.00 0.00 0.04 0.06 0.90 0.00 0.00
#> TCGA.71.8520.01 2 0.0000 0.9133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7672.01 4 0.1166 0.7206 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.55.6987.01 3 0.4278 -0.2047 0.00 0.00 0.50 0.00 0.46 0.00 0.04
#> TCGA.78.7152.01 4 0.1363 0.7131 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.78.7145.01 3 0.2016 0.7484 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.50.6593.01 5 0.3052 0.7438 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.55.8302.01 4 0.1433 0.7082 0.00 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.05.4425.01 2 0.0000 0.9133 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.44.4112.01 4 0.1557 0.6947 0.00 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.NJ.A4YP.01 4 0.2547 0.6567 0.00 0.00 0.00 0.84 0.00 0.00 0.12 0.04
#> TCGA.86.8278.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.49.AARQ.01 8 0.1557 0.5922 0.00 0.00 0.00 0.00 0.00 0.06 0.02 0.92
#> TCGA.97.A4M1.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.99.8033.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.69.8453.01 5 0.4280 0.6270 0.00 0.00 0.06 0.00 0.72 0.10 0.12 0.00
#> TCGA.97.8552.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.53.A4EZ.01 3 0.3586 0.6179 0.00 0.00 0.78 0.00 0.04 0.12 0.06 0.00
#> TCGA.50.5066.01 1 0.1563 0.8553 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.62.A46U.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.MP.A4T8.01 8 0.3970 0.6906 0.00 0.00 0.00 0.22 0.00 0.00 0.10 0.68
#> TCGA.MP.A4SY.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.93.A4JN.01 8 0.2888 0.7125 0.00 0.00 0.00 0.16 0.00 0.00 0.04 0.80
#> TCGA.86.A4JF.01 4 0.0000 0.6912 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.6202.01 4 0.1091 0.7008 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.J2.A4AG.01 5 0.3404 0.5953 0.00 0.00 0.04 0.00 0.72 0.00 0.24 0.00
#> TCGA.MP.A4TI.01 4 0.1341 0.7006 0.00 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.8208.01 1 0.1275 0.8678 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.85.8584.01 1 0.4849 0.4159 0.54 0.00 0.24 0.00 0.00 0.00 0.22 0.00
#> TCGA.NJ.A4YI.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAR4.01 5 0.3404 0.5953 0.00 0.00 0.04 0.00 0.72 0.00 0.24 0.00
#> TCGA.55.6984.01 5 0.4280 0.6270 0.00 0.00 0.06 0.00 0.72 0.10 0.12 0.00
#> TCGA.MN.A4N1.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0471 0.8642 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.MP.A4TC.01 5 0.3272 0.3281 0.00 0.00 0.00 0.42 0.58 0.00 0.00 0.00
#> TCGA.49.6744.01 3 0.3504 0.6992 0.00 0.00 0.70 0.00 0.04 0.00 0.26 0.00
#> TCGA.L9.A743.01 5 0.0000 0.7151 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.4410.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.62.A46Y.01 8 0.3737 0.3449 0.00 0.00 0.00 0.48 0.00 0.00 0.02 0.50
#> TCGA.50.6597.01 8 0.3528 0.7155 0.00 0.00 0.00 0.18 0.00 0.00 0.08 0.74
#> TCGA.05.4384.01 1 0.1091 0.8644 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.55.8087.01 3 0.2224 0.6627 0.12 0.00 0.86 0.00 0.00 0.00 0.00 0.02
#> TCGA.85.A50M.01 1 0.2484 0.8429 0.86 0.00 0.02 0.00 0.00 0.00 0.10 0.02
#> TCGA.MP.A4TH.01 1 0.4921 0.3687 0.52 0.00 0.26 0.00 0.00 0.00 0.22 0.00
#> TCGA.55.8207.01 2 0.1607 0.8483 0.00 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.86.6562.01 5 0.5052 0.5185 0.00 0.00 0.10 0.00 0.62 0.08 0.20 0.00
#> TCGA.86.8074.01 3 0.6030 0.3695 0.00 0.00 0.48 0.00 0.22 0.16 0.14 0.00
#> TCGA.39.5011.01 5 0.4952 0.2185 0.00 0.00 0.20 0.00 0.50 0.00 0.30 0.00
#> TCGA.MP.A4SW.01 4 0.3729 -0.0770 0.00 0.00 0.00 0.52 0.46 0.00 0.02 0.00
#> TCGA.67.6216.01 6 0.2650 0.6728 0.00 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.55.8203.01 4 0.0941 0.6800 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.55.8619.01 3 0.4370 0.6372 0.00 0.00 0.52 0.00 0.08 0.00 0.40 0.00
#> TCGA.44.2668.01 5 0.3318 0.2512 0.00 0.00 0.00 0.46 0.54 0.00 0.00 0.00
#> TCGA.55.6971.01 3 0.4482 0.6058 0.14 0.00 0.60 0.00 0.00 0.00 0.26 0.00
#> TCGA.98.7454.01 1 0.1765 0.8489 0.88 0.00 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.L9.A444.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.62.A46V.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 5 0.3299 0.2951 0.00 0.00 0.00 0.44 0.56 0.00 0.00 0.00
#> TCGA.69.8253.01 3 0.0808 0.7066 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.91.6849.01 3 0.3837 0.6461 0.00 0.00 0.76 0.00 0.04 0.10 0.10 0.00
#> TCGA.50.5944.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.44.2665.01 8 0.4404 0.4792 0.00 0.00 0.00 0.22 0.00 0.10 0.02 0.66
#> TCGA.62.A46P.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2666.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.55.A494.01 6 0.3404 0.6653 0.00 0.00 0.00 0.00 0.00 0.72 0.04 0.24
#> TCGA.97.7547.01 3 0.2224 0.6627 0.12 0.00 0.86 0.00 0.00 0.00 0.00 0.02
#> TCGA.69.8254.01 5 0.1557 0.7037 0.00 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.75.5125.01 4 0.0471 0.6839 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.69.7973.01 3 0.2224 0.6627 0.12 0.00 0.86 0.00 0.00 0.00 0.00 0.02
#> TCGA.L4.A4E5.01 6 0.2719 0.6393 0.00 0.00 0.00 0.00 0.18 0.80 0.00 0.02
#> TCGA.44.6775.01 5 0.0471 0.7154 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.55.7911.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.MP.A4T9.01 3 0.3862 0.6698 0.00 0.00 0.60 0.00 0.04 0.00 0.36 0.00
#> TCGA.55.6712.01 4 0.3449 0.3169 0.00 0.00 0.00 0.66 0.32 0.00 0.02 0.00
#> TCGA.86.7714.01 6 0.0941 0.7346 0.00 0.00 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.95.7948.01 6 0.3142 0.5343 0.00 0.00 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.55.A4DG.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 5 0.0000 0.7151 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.5423.01 3 0.2591 0.6891 0.00 0.00 0.86 0.00 0.04 0.02 0.08 0.00
#> TCGA.55.6985.01 5 0.4664 0.5952 0.00 0.00 0.08 0.00 0.68 0.10 0.14 0.00
#> TCGA.55.7281.01 4 0.0471 0.6839 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.93.7347.01 3 0.3594 0.6941 0.00 0.00 0.68 0.00 0.04 0.00 0.28 0.00
#> TCGA.44.6777.01 5 0.1341 0.7169 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.97.8177.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.99.7458.01 5 0.2719 0.6273 0.00 0.00 0.00 0.18 0.80 0.00 0.02 0.00
#> TCGA.91.A4BD.01 1 0.2484 0.8429 0.86 0.00 0.02 0.00 0.00 0.00 0.10 0.02
#> TCGA.38.6178.01 8 0.4672 0.5101 0.00 0.00 0.00 0.24 0.00 0.12 0.02 0.62
#> TCGA.44.A47B.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 1 0.2025 0.8509 0.88 0.00 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.55.7573.01 1 0.4921 0.3687 0.52 0.00 0.26 0.00 0.00 0.00 0.22 0.00
#> TCGA.55.8097.01 3 0.2224 0.6627 0.12 0.00 0.86 0.00 0.00 0.00 0.00 0.02
#> TCGA.05.5429.01 2 0.5590 0.2643 0.00 0.40 0.02 0.00 0.00 0.00 0.28 0.30
#> TCGA.93.A4JP.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.S2.AA1A.01 1 0.2484 0.8429 0.86 0.00 0.02 0.00 0.00 0.00 0.10 0.02
#> TCGA.93.A4JQ.01 1 0.1947 0.8387 0.86 0.00 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.78.7160.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.75.5122.01 5 0.3299 0.2951 0.00 0.00 0.00 0.44 0.56 0.00 0.00 0.00
#> TCGA.97.7938.01 3 0.3128 0.6799 0.00 0.00 0.82 0.00 0.04 0.04 0.10 0.00
#> TCGA.44.7671.01 1 0.3078 0.8154 0.82 0.00 0.06 0.00 0.00 0.00 0.10 0.02
#> TCGA.50.5055.01 3 0.4686 0.5778 0.16 0.00 0.56 0.00 0.00 0.00 0.28 0.00
#> TCGA.85.6560.01 5 0.2348 0.6778 0.00 0.00 0.02 0.00 0.88 0.04 0.06 0.00
#> TCGA.91.8496.01 1 0.1275 0.8604 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.MP.A4T2.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.62.A46R.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A443.01 8 0.2938 0.2878 0.00 0.00 0.00 0.00 0.00 0.30 0.00 0.70
#> TCGA.86.7701.01 4 0.1275 0.6797 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.52.7812.01 8 0.4284 0.4395 0.00 0.00 0.00 0.36 0.00 0.04 0.02 0.58
#> TCGA.78.7162.01 1 0.2484 0.8429 0.86 0.00 0.02 0.00 0.00 0.00 0.10 0.02
#> TCGA.L9.A50W.01 6 0.1275 0.7296 0.00 0.00 0.04 0.00 0.00 0.94 0.02 0.00
#> TCGA.50.8460.01 5 0.6073 0.0221 0.00 0.00 0.30 0.00 0.40 0.08 0.22 0.00
#> TCGA.67.6217.01 3 0.4041 0.6827 0.00 0.00 0.70 0.00 0.04 0.04 0.22 0.00
#> TCGA.78.7535.01 2 0.4996 0.4539 0.00 0.48 0.00 0.00 0.00 0.00 0.32 0.20
#> TCGA.93.7348.01 3 0.1741 0.7005 0.04 0.00 0.92 0.00 0.02 0.00 0.00 0.02
#> TCGA.86.8671.01 3 0.4318 0.6562 0.00 0.00 0.60 0.00 0.10 0.00 0.30 0.00
#> TCGA.50.6592.01 5 0.0941 0.7121 0.00 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.97.7546.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.44.7661.01 5 0.1765 0.7049 0.00 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.95.7944.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.97.A4M0.01 2 0.0808 0.8623 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.50.5933.01 2 0.5405 0.4246 0.00 0.46 0.00 0.06 0.00 0.00 0.38 0.10
#> TCGA.86.8280.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.78.8660.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.55.7907.01 2 0.0808 0.8623 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.49.6767.01 5 0.2224 0.6790 0.00 0.00 0.00 0.00 0.86 0.12 0.02 0.00
#> TCGA.MP.A4TK.01 5 0.3729 0.2170 0.00 0.00 0.00 0.46 0.52 0.00 0.02 0.00
#> TCGA.69.7761.01 5 0.1341 0.7171 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.91.6835.01 3 0.6452 0.2170 0.00 0.00 0.36 0.00 0.28 0.18 0.18 0.00
#> TCGA.78.7540.01 8 0.4467 0.6771 0.00 0.00 0.02 0.20 0.00 0.00 0.12 0.66
#> TCGA.95.A4VN.01 5 0.3083 0.4472 0.00 0.00 0.00 0.34 0.66 0.00 0.00 0.00
#> TCGA.44.A47F.01 6 0.2534 0.6953 0.00 0.00 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.55.A48Z.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.69.7763.01 4 0.0471 0.6839 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.J2.A4AE.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.50.5942.01 3 0.2071 0.6867 0.00 0.00 0.90 0.00 0.04 0.02 0.04 0.00
#> TCGA.50.6590.01 4 0.1804 0.6975 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.80.5608.01 6 0.2348 0.7292 0.00 0.00 0.00 0.00 0.02 0.88 0.04 0.06
#> TCGA.55.8511.01 2 0.1765 0.8334 0.00 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.99.8025.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7283.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A491.01 6 0.2114 0.7246 0.00 0.00 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.MN.A4N5.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.69.7978.01 4 0.1341 0.7006 0.00 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.8299.01 1 0.1563 0.8553 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.44.8117.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 4 0.1887 0.6907 0.00 0.00 0.00 0.90 0.00 0.00 0.06 0.04
#> TCGA.05.4405.01 2 0.0808 0.8623 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.83.5908.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.55.6980.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.44.6146.01 3 0.4041 0.6731 0.00 0.00 0.70 0.00 0.04 0.04 0.22 0.00
#> TCGA.62.8397.01 1 0.0941 0.8616 0.96 0.00 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.97.7552.01 5 0.3757 0.5658 0.00 0.00 0.06 0.00 0.68 0.00 0.26 0.00
#> TCGA.50.5936.01 1 0.0808 0.8666 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.91.7771.01 6 0.1765 0.7350 0.00 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.NJ.A4YG.01 4 0.0471 0.6839 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.86.8359.01 3 0.3320 0.6739 0.00 0.00 0.80 0.00 0.04 0.04 0.12 0.00
#> TCGA.55.8301.01 5 0.0000 0.7151 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.3918.01 4 0.4669 0.4214 0.00 0.00 0.00 0.58 0.00 0.00 0.22 0.20
#> TCGA.55.8621.01 1 0.5203 0.1057 0.42 0.00 0.30 0.00 0.00 0.00 0.28 0.00
#> TCGA.49.6745.01 2 0.2650 0.7720 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.44.A4SS.01 1 0.1557 0.8667 0.92 0.00 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.55.8089.01 5 0.0000 0.7151 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 5 0.0808 0.7016 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.55.7574.01 5 0.3299 0.2951 0.00 0.00 0.00 0.44 0.56 0.00 0.00 0.00
#> TCGA.63.A5MN.01 1 0.2025 0.8589 0.88 0.00 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.50.8459.01 5 0.1563 0.7129 0.00 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.78.8648.01 1 0.4897 0.4060 0.52 0.00 0.20 0.00 0.00 0.00 0.28 0.00
#> TCGA.NC.A5HJ.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.44.2656.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.86.8673.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.7499.01 6 0.4800 0.2699 0.00 0.00 0.36 0.00 0.04 0.54 0.06 0.00
#> TCGA.97.A4LX.01 1 0.1341 0.8604 0.92 0.00 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.MP.A4T7.01 3 0.0808 0.7066 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.69.7765.01 2 0.2650 0.7720 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.95.8494.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8171.01 3 0.2914 0.6523 0.00 0.00 0.84 0.00 0.04 0.08 0.04 0.00
#> TCGA.50.8457.01 3 0.4147 0.6723 0.00 0.00 0.68 0.00 0.04 0.04 0.24 0.00
#> TCGA.97.A4M5.01 1 0.0471 0.8642 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.53.7626.01 5 0.5838 -0.0547 0.00 0.00 0.28 0.00 0.38 0.04 0.30 0.00
#> TCGA.44.5645.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.78.7158.01 8 0.3528 0.7155 0.00 0.00 0.00 0.18 0.00 0.00 0.08 0.74
#> TCGA.86.8056.01 4 0.3021 0.4645 0.00 0.00 0.00 0.80 0.02 0.00 0.02 0.16
#> TCGA.69.7980.01 6 0.0808 0.7410 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.97.8175.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.86.8668.01 3 0.6106 0.1300 0.00 0.00 0.36 0.00 0.34 0.08 0.22 0.00
#> TCGA.MP.A4T4.01 3 0.5203 0.3791 0.00 0.00 0.42 0.00 0.28 0.00 0.30 0.00
#> TCGA.44.A47A.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.93.A4JO.01 5 0.1341 0.7155 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.44.6145.01 3 0.5165 0.3531 0.28 0.00 0.44 0.00 0.00 0.00 0.28 0.00
#> TCGA.97.8547.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.44.6147.01 5 0.3714 0.2649 0.00 0.00 0.00 0.44 0.54 0.00 0.02 0.00
#> TCGA.77.8007.01 4 0.1341 0.7006 0.00 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.8510.01 3 0.3943 0.6598 0.00 0.00 0.56 0.00 0.04 0.00 0.40 0.00
#> TCGA.49.AARO.01 5 0.4480 0.4069 0.00 0.00 0.12 0.00 0.58 0.00 0.30 0.00
#> TCGA.55.8090.01 2 0.0808 0.8623 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.86.8073.01 4 0.0471 0.6839 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.91.6828.01 4 0.4480 0.4879 0.00 0.00 0.00 0.58 0.00 0.00 0.30 0.12
#> TCGA.86.8076.01 3 0.3504 0.6992 0.00 0.00 0.70 0.00 0.04 0.00 0.26 0.00
#> TCGA.97.A4M6.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.50.5044.01 5 0.0471 0.7099 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.64.5781.01 5 0.0000 0.7151 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 6 0.1275 0.7296 0.00 0.00 0.04 0.00 0.00 0.94 0.02 0.00
#> TCGA.38.7271.01 5 0.3318 0.2512 0.00 0.00 0.00 0.46 0.54 0.00 0.00 0.00
#> TCGA.49.AAR3.01 5 0.1341 0.7155 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.MP.A4TJ.01 3 0.5102 0.3405 0.30 0.00 0.46 0.00 0.00 0.00 0.24 0.00
#> TCGA.69.7760.01 6 0.1804 0.7397 0.00 0.00 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.49.4512.01 3 0.0808 0.7066 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.50.5939.01 1 0.4929 0.3748 0.52 0.00 0.24 0.00 0.00 0.00 0.24 0.00
#> TCGA.78.7143.01 8 0.3083 0.1975 0.00 0.00 0.00 0.00 0.00 0.34 0.00 0.66
#> TCGA.97.A4M3.01 3 0.2399 0.6782 0.00 0.00 0.88 0.00 0.04 0.04 0.04 0.00
#> TCGA.75.6205.01 4 0.1765 0.6024 0.00 0.00 0.00 0.88 0.12 0.00 0.00 0.00
#> TCGA.99.8028.01 5 0.5102 0.1112 0.00 0.00 0.24 0.00 0.46 0.00 0.30 0.00
#> TCGA.55.7903.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 1 0.3434 0.7549 0.76 0.00 0.10 0.00 0.00 0.00 0.14 0.00
#> TCGA.55.A493.01 4 0.1091 0.7008 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.75.5126.01 5 0.3299 0.2951 0.00 0.00 0.00 0.44 0.56 0.00 0.00 0.00
#> TCGA.55.8206.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.97.7553.01 1 0.1765 0.8489 0.88 0.00 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.NJ.A7XG.01 6 0.2406 0.7061 0.00 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.55.A48X.01 5 0.3291 0.4535 0.00 0.00 0.00 0.00 0.70 0.28 0.02 0.00
#> TCGA.64.5778.01 3 0.4073 0.6305 0.10 0.00 0.66 0.00 0.00 0.00 0.24 0.00
#> TCGA.50.6594.01 6 0.3170 0.6229 0.00 0.00 0.20 0.00 0.00 0.76 0.04 0.00
#> TCGA.78.7153.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7728.01 3 0.4730 0.5726 0.18 0.00 0.56 0.00 0.00 0.00 0.26 0.00
#> TCGA.67.6215.01 8 0.3178 0.5211 0.00 0.00 0.00 0.04 0.00 0.14 0.02 0.80
#> TCGA.78.7537.01 6 0.1607 0.7209 0.00 0.00 0.04 0.00 0.00 0.92 0.04 0.00
#> TCGA.55.6982.01 4 0.0941 0.6966 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.55.7227.01 2 0.2650 0.7720 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.86.A456.01 2 0.2650 0.7720 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.44.6774.01 1 0.0471 0.8668 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.49.AAQV.01 1 0.1765 0.8489 0.88 0.00 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.73.7498.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.38.4632.01 2 0.5405 0.4246 0.00 0.46 0.00 0.06 0.00 0.00 0.38 0.10
#> TCGA.69.7974.01 2 0.2650 0.7720 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.55.6986.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.49.6761.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.MP.A4T6.01 8 0.2650 0.3894 0.00 0.00 0.00 0.00 0.00 0.24 0.00 0.76
#> TCGA.44.6779.01 4 0.3570 0.2199 0.00 0.00 0.00 0.62 0.36 0.00 0.02 0.00
#> TCGA.86.A4P7.01 4 0.2981 0.4920 0.00 0.00 0.00 0.76 0.22 0.00 0.02 0.00
#> TCGA.73.4658.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.85.A513.01 3 0.3862 0.6698 0.00 0.00 0.60 0.00 0.04 0.00 0.36 0.00
#> TCGA.50.5935.01 6 0.1563 0.7388 0.00 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.55.7727.01 2 0.4677 0.5392 0.00 0.54 0.00 0.00 0.00 0.00 0.32 0.14
#> TCGA.55.6981.01 5 0.1563 0.7129 0.00 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.78.8655.01 2 0.0471 0.8658 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.78.7163.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.97.7941.01 6 0.4556 0.2475 0.00 0.00 0.38 0.00 0.02 0.54 0.06 0.00
#> TCGA.55.7914.01 2 0.0808 0.8623 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.75.7030.01 1 0.4849 0.4217 0.54 0.00 0.22 0.00 0.00 0.00 0.24 0.00
#> TCGA.62.A472.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4417.01 6 0.2856 0.7031 0.00 0.00 0.00 0.00 0.00 0.78 0.02 0.20
#> TCGA.67.4679.01 6 0.5618 0.2185 0.00 0.00 0.10 0.00 0.30 0.50 0.10 0.00
#> TCGA.97.7554.01 2 0.2406 0.7939 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.75.7025.01 3 0.2224 0.6627 0.12 0.00 0.86 0.00 0.00 0.00 0.00 0.02
#> TCGA.95.8039.01 4 0.4588 0.4766 0.00 0.00 0.00 0.54 0.00 0.00 0.34 0.12
#> TCGA.50.5941.01 5 0.3178 0.6725 0.00 0.00 0.02 0.00 0.80 0.04 0.14 0.00
#> TCGA.97.8174.01 3 0.0808 0.7066 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.55.7576.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 6 0.4399 0.1698 0.00 0.00 0.44 0.00 0.02 0.50 0.04 0.00
#> TCGA.38.A44F.01 1 0.4144 0.6349 0.66 0.00 0.12 0.00 0.00 0.00 0.22 0.00
#> TCGA.80.5607.01 8 0.3729 0.7120 0.00 0.00 0.00 0.18 0.00 0.00 0.10 0.72
#> TCGA.55.8091.01 3 0.3503 0.6299 0.12 0.00 0.78 0.00 0.00 0.00 0.08 0.02
#> TCGA.62.8395.01 8 0.3856 0.7058 0.00 0.00 0.00 0.20 0.00 0.00 0.10 0.70
#> TCGA.86.8672.01 4 0.4412 0.5130 0.00 0.00 0.00 0.60 0.00 0.00 0.28 0.12
#> TCGA.64.5815.01 4 0.1091 0.7008 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.75.6212.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.44.6776.01 1 0.1275 0.8599 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.55.6983.01 5 0.3710 0.6543 0.00 0.00 0.02 0.00 0.76 0.10 0.12 0.00
#> TCGA.93.8067.01 2 0.4059 0.6618 0.00 0.64 0.00 0.00 0.00 0.00 0.28 0.08
#> TCGA.69.A59K.01 2 0.0808 0.8623 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.95.7567.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARN.01 2 0.4759 0.4899 0.00 0.50 0.00 0.00 0.00 0.00 0.36 0.14
#> TCGA.91.6836.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.8172.01 8 0.3873 0.4453 0.00 0.00 0.00 0.06 0.00 0.20 0.02 0.72
#> TCGA.O2.A52Q.01 5 0.0808 0.7070 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.50.5045.01 1 0.1563 0.8553 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.55.6978.01 5 0.0808 0.7016 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.2591 0.8415 0.86 0.00 0.04 0.00 0.00 0.00 0.08 0.02
#> TCGA.05.5715.01 8 0.2650 0.3894 0.00 0.00 0.00 0.00 0.00 0.24 0.00 0.76
#> TCGA.55.A492.01 3 0.1804 0.6836 0.08 0.00 0.90 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.A48Y.01 5 0.5463 0.1092 0.00 0.00 0.26 0.00 0.46 0.02 0.26 0.00
#> TCGA.50.6595.01 3 0.4370 0.6372 0.00 0.00 0.52 0.00 0.08 0.00 0.40 0.00
#> TCGA.55.6543.01 1 0.0471 0.8642 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.91.8497.01 3 0.4041 0.6827 0.00 0.00 0.70 0.00 0.04 0.04 0.22 0.00
#> TCGA.50.5049.01 3 0.4370 0.6372 0.00 0.00 0.52 0.00 0.08 0.00 0.40 0.00
#> TCGA.97.A4M2.01 1 0.1563 0.8553 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.44.7659.01 2 0.4996 0.4539 0.00 0.48 0.00 0.00 0.00 0.00 0.32 0.20
#> TCGA.97.A4M7.01 5 0.1563 0.7129 0.00 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.44.7662.01 5 0.0808 0.7016 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.55.6970.01 1 0.2484 0.8429 0.86 0.00 0.02 0.00 0.00 0.00 0.10 0.02
#> TCGA.50.5068.01 5 0.0808 0.7016 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.71.8520.01 2 0.0000 0.8685 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7672.01 4 0.0000 0.6912 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6987.01 5 0.4747 0.3195 0.00 0.00 0.16 0.00 0.54 0.00 0.30 0.00
#> TCGA.78.7152.01 4 0.0941 0.6853 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.78.7145.01 3 0.2132 0.6992 0.00 0.00 0.88 0.00 0.04 0.00 0.08 0.00
#> TCGA.50.6593.01 5 0.1341 0.7169 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.55.8302.01 4 0.0000 0.6912 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4425.01 2 0.0000 0.8685 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 73 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 0.999 0.999 0.4863 0.514 0.514
#> 3 3 0.843 0.861 0.945 0.3735 0.731 0.514
#> 4 4 1.000 0.999 0.999 0.1150 0.803 0.493
#> 5 5 0.779 0.818 0.888 0.0762 0.899 0.633
#> 6 6 0.811 0.738 0.835 0.0336 0.960 0.814
#> 7 7 0.806 0.652 0.807 0.0213 0.970 0.853
#> 8 8 0.807 0.624 0.745 0.0171 0.937 0.670
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.97.A4M1.01 1 0.000 1.000 1.00 0.00
#> TCGA.99.8033.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.8552.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5066.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.8208.01 2 0.000 0.999 0.00 1.00
#> TCGA.85.8584.01 2 0.000 0.999 0.00 1.00
#> TCGA.75.6206.01 1 0.000 1.000 1.00 0.00
#> TCGA.05.4384.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8087.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.A50M.01 2 0.000 0.999 0.00 1.00
#> TCGA.MP.A4TH.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.6971.01 2 0.000 0.999 0.00 1.00
#> TCGA.98.7454.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.5944.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.7547.01 1 0.000 1.000 1.00 0.00
#> TCGA.69.7973.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8177.01 2 0.000 0.999 0.00 1.00
#> TCGA.91.A4BD.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6979.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.7573.01 2 0.242 0.958 0.04 0.96
#> TCGA.55.8097.01 1 0.000 1.000 1.00 0.00
#> TCGA.93.A4JP.01 2 0.000 0.999 0.00 1.00
#> TCGA.S2.AA1A.01 2 0.000 0.999 0.00 1.00
#> TCGA.93.A4JQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.78.7160.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.7671.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5055.01 2 0.000 0.999 0.00 1.00
#> TCGA.91.8496.01 1 0.000 1.000 1.00 0.00
#> TCGA.MP.A4T2.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.7162.01 1 0.000 1.000 1.00 0.00
#> TCGA.93.7348.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.7546.01 1 0.000 1.000 1.00 0.00
#> TCGA.95.7944.01 2 0.000 0.999 0.00 1.00
#> TCGA.86.8280.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.A48Z.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.8299.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.6980.01 2 0.000 0.999 0.00 1.00
#> TCGA.62.8397.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5936.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.8621.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.A4SS.01 2 0.000 0.999 0.00 1.00
#> TCGA.63.A5MN.01 2 0.000 0.999 0.00 1.00
#> TCGA.78.8648.01 2 0.000 0.999 0.00 1.00
#> TCGA.NC.A5HJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.A4LX.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.A4M5.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.5645.01 1 0.000 1.000 1.00 0.00
#> TCGA.NJ.A55O.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.6145.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.A4M6.01 2 0.000 0.999 0.00 1.00
#> TCGA.MP.A4TJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.5939.01 2 0.000 0.999 0.00 1.00
#> TCGA.49.4487.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.8206.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.7553.01 2 0.000 0.999 0.00 1.00
#> TCGA.64.5778.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7728.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.6774.01 2 0.000 0.999 0.00 1.00
#> TCGA.49.AAQV.01 2 0.000 0.999 0.00 1.00
#> TCGA.73.7498.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.7163.01 1 0.000 1.000 1.00 0.00
#> TCGA.75.7030.01 2 0.000 0.999 0.00 1.00
#> TCGA.75.7025.01 1 0.000 1.000 1.00 0.00
#> TCGA.38.A44F.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.8091.01 1 0.000 1.000 1.00 0.00
#> TCGA.75.6212.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.6776.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5045.01 2 0.000 0.999 0.00 1.00
#> TCGA.95.A4VP.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.A492.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6543.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.A4M2.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.6970.01 2 0.000 0.999 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.97.A4M1.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.99.8033.01 2 0.631 0.1268 0.00 0.50 0.50
#> TCGA.97.8552.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.50.5066.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.55.8208.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.85.8584.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.75.6206.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.05.4384.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.55.8087.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.85.A50M.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.MP.A4TH.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.6971.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.98.7454.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.50.5944.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.97.7547.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.69.7973.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.97.8177.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.91.A4BD.01 1 0.628 0.2554 0.54 0.00 0.46
#> TCGA.55.6979.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.55.7573.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.8097.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.93.A4JP.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.S2.AA1A.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.93.A4JQ.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.78.7160.01 3 0.628 -0.0492 0.00 0.46 0.54
#> TCGA.44.7671.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.50.5055.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.91.8496.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.MP.A4T2.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.78.7162.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.93.7348.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.97.7546.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.95.7944.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.86.8280.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.A48Z.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.8299.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.55.6980.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.62.8397.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.50.5936.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.8621.01 2 0.540 0.6672 0.00 0.72 0.28
#> TCGA.44.A4SS.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.63.A5MN.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.78.8648.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.NC.A5HJ.01 3 0.556 0.4793 0.00 0.30 0.70
#> TCGA.97.A4LX.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.97.A4M5.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.44.5645.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.NJ.A55O.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.44.6145.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.97.A4M6.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.MP.A4TJ.01 2 0.540 0.6672 0.00 0.72 0.28
#> TCGA.50.5939.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.49.4487.01 2 0.000 0.9061 0.00 1.00 0.00
#> TCGA.55.8206.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.97.7553.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.64.5778.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.7728.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.44.6774.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.49.AAQV.01 2 0.540 0.6672 0.00 0.72 0.28
#> TCGA.73.7498.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.78.7163.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.75.7030.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.75.7025.01 1 0.628 0.2554 0.54 0.00 0.46
#> TCGA.38.A44F.01 2 0.540 0.6672 0.00 0.72 0.28
#> TCGA.55.8091.01 1 0.628 0.2554 0.54 0.00 0.46
#> TCGA.75.6212.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.44.6776.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.50.5045.01 2 0.540 0.6672 0.00 0.72 0.28
#> TCGA.95.A4VP.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.A492.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.55.6543.01 1 0.000 0.9351 1.00 0.00 0.00
#> TCGA.97.A4M2.01 3 0.000 0.9641 0.00 0.00 1.00
#> TCGA.55.6970.01 3 0.000 0.9641 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.97.A4M1.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.99.8033.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.97.8552.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.50.5066.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.55.8208.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.85.8584.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.75.6206.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.05.4384.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.85.A50M.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.MP.A4TH.01 3 0.0707 0.980 0 0 0.98 0.02
#> TCGA.55.6971.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.98.7454.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.50.5944.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.97.7547.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.69.7973.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.97.8177.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.91.A4BD.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.55.6979.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.55.7573.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.55.8097.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.93.A4JP.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.S2.AA1A.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.93.A4JQ.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.78.7160.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.44.7671.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.50.5055.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.91.8496.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.MP.A4T2.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.78.7162.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.93.7348.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.97.7546.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.95.7944.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.86.8280.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.55.A48Z.01 3 0.0707 0.980 0 0 0.98 0.02
#> TCGA.55.8299.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.55.6980.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.62.8397.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.50.5936.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.55.8621.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.44.A4SS.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.63.A5MN.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.78.8648.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.NC.A5HJ.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.97.A4LX.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.97.A4M5.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.44.5645.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.NJ.A55O.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.44.6145.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.97.A4M6.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.MP.A4TJ.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.50.5939.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.49.4487.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.55.8206.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.97.7553.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.64.5778.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.55.7728.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.44.6774.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.49.AAQV.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.73.7498.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.78.7163.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.75.7030.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.75.7025.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.38.A44F.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.55.8091.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.75.6212.01 4 0.0000 1.000 0 0 0.00 1.00
#> TCGA.44.6776.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.50.5045.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.95.A4VP.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.55.A492.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.55.6543.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.97.A4M2.01 3 0.0000 0.998 0 0 1.00 0.00
#> TCGA.55.6970.01 3 0.0000 0.998 0 0 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.97.A4M1.01 1 0.4216 0.8618 0.78 0.00 0.10 0.12 0.00
#> TCGA.99.8033.01 5 0.2516 0.7455 0.00 0.00 0.14 0.00 0.86
#> TCGA.97.8552.01 4 0.2020 0.8636 0.00 0.00 0.10 0.90 0.00
#> TCGA.50.5066.01 2 0.2929 0.8806 0.00 0.82 0.00 0.00 0.18
#> TCGA.55.8208.01 2 0.2929 0.8806 0.00 0.82 0.00 0.00 0.18
#> TCGA.85.8584.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4384.01 1 0.4216 0.8618 0.78 0.00 0.10 0.12 0.00
#> TCGA.55.8087.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A50M.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TH.01 3 0.2020 0.7381 0.00 0.00 0.90 0.10 0.00
#> TCGA.55.6971.01 3 0.4060 0.6124 0.00 0.00 0.64 0.00 0.36
#> TCGA.98.7454.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5944.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.4216 0.8618 0.78 0.00 0.10 0.12 0.00
#> TCGA.69.7973.01 1 0.3037 0.9014 0.86 0.00 0.10 0.04 0.00
#> TCGA.97.8177.01 3 0.2280 0.8003 0.00 0.00 0.88 0.00 0.12
#> TCGA.91.A4BD.01 4 0.1043 0.9374 0.00 0.00 0.04 0.96 0.00
#> TCGA.55.6979.01 5 0.4227 -0.0772 0.00 0.42 0.00 0.00 0.58
#> TCGA.55.7573.01 3 0.3561 0.5322 0.00 0.00 0.74 0.26 0.00
#> TCGA.55.8097.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JP.01 3 0.2020 0.8029 0.00 0.00 0.90 0.00 0.10
#> TCGA.S2.AA1A.01 3 0.4182 0.5446 0.00 0.00 0.60 0.00 0.40
#> TCGA.93.A4JQ.01 2 0.2929 0.8806 0.00 0.82 0.00 0.00 0.18
#> TCGA.78.7160.01 5 0.2732 0.7422 0.00 0.00 0.16 0.00 0.84
#> TCGA.44.7671.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 2 0.2516 0.8953 0.00 0.86 0.00 0.00 0.14
#> TCGA.91.8496.01 1 0.4216 0.8618 0.78 0.00 0.10 0.12 0.00
#> TCGA.MP.A4T2.01 4 0.0000 0.9305 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.7162.01 4 0.2020 0.9169 0.00 0.00 0.10 0.90 0.00
#> TCGA.93.7348.01 3 0.3983 0.6380 0.00 0.00 0.66 0.00 0.34
#> TCGA.97.7546.01 4 0.0000 0.9305 0.00 0.00 0.00 1.00 0.00
#> TCGA.95.7944.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8280.01 4 0.2020 0.9169 0.00 0.00 0.10 0.90 0.00
#> TCGA.55.A48Z.01 3 0.2331 0.7546 0.00 0.00 0.90 0.08 0.02
#> TCGA.55.8299.01 2 0.2929 0.8806 0.00 0.82 0.00 0.00 0.18
#> TCGA.55.6980.01 3 0.4182 0.5446 0.00 0.00 0.60 0.00 0.40
#> TCGA.62.8397.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5936.01 3 0.2732 0.7939 0.00 0.00 0.84 0.00 0.16
#> TCGA.55.8621.01 5 0.0609 0.8082 0.00 0.00 0.02 0.00 0.98
#> TCGA.44.A4SS.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5MN.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.8648.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HJ.01 5 0.2929 0.7210 0.00 0.00 0.18 0.00 0.82
#> TCGA.97.A4LX.01 2 0.2516 0.8953 0.00 0.86 0.00 0.00 0.14
#> TCGA.97.A4M5.01 3 0.2020 0.8029 0.00 0.00 0.90 0.00 0.10
#> TCGA.44.5645.01 4 0.0000 0.9305 0.00 0.00 0.00 1.00 0.00
#> TCGA.NJ.A55O.01 3 0.3796 0.4552 0.00 0.00 0.70 0.30 0.00
#> TCGA.44.6145.01 2 0.2929 0.8806 0.00 0.82 0.00 0.00 0.18
#> TCGA.97.A4M6.01 3 0.2020 0.8029 0.00 0.00 0.90 0.00 0.10
#> TCGA.MP.A4TJ.01 5 0.0609 0.8082 0.00 0.00 0.02 0.00 0.98
#> TCGA.50.5939.01 2 0.0000 0.9136 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.4487.01 5 0.2516 0.6623 0.00 0.14 0.00 0.00 0.86
#> TCGA.55.8206.01 4 0.2020 0.8636 0.00 0.00 0.10 0.90 0.00
#> TCGA.97.7553.01 3 0.3109 0.7650 0.00 0.00 0.80 0.00 0.20
#> TCGA.64.5778.01 4 0.2020 0.9169 0.00 0.00 0.10 0.90 0.00
#> TCGA.55.7728.01 5 0.2929 0.6969 0.00 0.00 0.18 0.00 0.82
#> TCGA.44.6774.01 3 0.3109 0.7650 0.00 0.00 0.80 0.00 0.20
#> TCGA.49.AAQV.01 5 0.0609 0.8082 0.00 0.00 0.02 0.00 0.98
#> TCGA.73.7498.01 1 0.3037 0.9014 0.86 0.00 0.10 0.04 0.00
#> TCGA.78.7163.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.7030.01 3 0.4126 0.5811 0.00 0.00 0.62 0.00 0.38
#> TCGA.75.7025.01 4 0.1043 0.9374 0.00 0.00 0.04 0.96 0.00
#> TCGA.38.A44F.01 5 0.0609 0.8082 0.00 0.00 0.02 0.00 0.98
#> TCGA.55.8091.01 4 0.1043 0.9374 0.00 0.00 0.04 0.96 0.00
#> TCGA.75.6212.01 4 0.2020 0.9169 0.00 0.00 0.10 0.90 0.00
#> TCGA.44.6776.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5045.01 5 0.0609 0.8082 0.00 0.00 0.02 0.00 0.98
#> TCGA.95.A4VP.01 3 0.2020 0.8029 0.00 0.00 0.90 0.00 0.10
#> TCGA.55.A492.01 1 0.0000 0.9262 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6543.01 1 0.3037 0.9014 0.86 0.00 0.10 0.04 0.00
#> TCGA.97.A4M2.01 5 0.3109 0.6894 0.00 0.00 0.20 0.00 0.80
#> TCGA.55.6970.01 3 0.2280 0.7965 0.00 0.00 0.88 0.00 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.97.A4M1.01 1 0.5195 0.715 0.54 0.00 0.36 0.10 0.00 0.00
#> TCGA.99.8033.01 5 0.0937 0.780 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.97.8552.01 4 0.3309 0.639 0.00 0.00 0.28 0.72 0.00 0.00
#> TCGA.50.5066.01 2 0.4348 0.826 0.00 0.64 0.32 0.00 0.04 0.00
#> TCGA.55.8208.01 2 0.4348 0.826 0.00 0.64 0.32 0.00 0.04 0.00
#> TCGA.85.8584.01 2 0.0000 0.796 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4384.01 1 0.5195 0.715 0.54 0.00 0.36 0.10 0.00 0.00
#> TCGA.55.8087.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A50M.01 2 0.0547 0.794 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.MP.A4TH.01 6 0.0547 0.803 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.55.6971.01 6 0.3797 0.161 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.98.7454.01 2 0.0000 0.796 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5944.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.5195 0.715 0.54 0.00 0.36 0.10 0.00 0.00
#> TCGA.69.7973.01 1 0.4758 0.737 0.58 0.00 0.36 0.06 0.00 0.00
#> TCGA.97.8177.01 6 0.1556 0.784 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.91.A4BD.01 4 0.1267 0.891 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.55.6979.01 2 0.6103 0.481 0.00 0.38 0.32 0.00 0.30 0.00
#> TCGA.55.7573.01 6 0.2094 0.765 0.00 0.00 0.02 0.08 0.00 0.90
#> TCGA.55.8097.01 1 0.0937 0.805 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.93.A4JP.01 6 0.1807 0.804 0.00 0.00 0.06 0.00 0.02 0.92
#> TCGA.S2.AA1A.01 5 0.3851 0.163 0.00 0.00 0.00 0.00 0.54 0.46
#> TCGA.93.A4JQ.01 2 0.4348 0.826 0.00 0.64 0.32 0.00 0.04 0.00
#> TCGA.78.7160.01 5 0.0937 0.780 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.44.7671.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5055.01 2 0.4172 0.834 0.00 0.68 0.28 0.00 0.04 0.00
#> TCGA.91.8496.01 1 0.5195 0.715 0.54 0.00 0.36 0.10 0.00 0.00
#> TCGA.MP.A4T2.01 4 0.0547 0.874 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.78.7162.01 4 0.2350 0.868 0.00 0.00 0.02 0.88 0.00 0.10
#> TCGA.93.7348.01 6 0.3797 0.161 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.97.7546.01 4 0.0000 0.880 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.7944.01 2 0.0000 0.796 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8280.01 4 0.1814 0.879 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.55.A48Z.01 6 0.1807 0.797 0.00 0.00 0.06 0.02 0.00 0.92
#> TCGA.55.8299.01 2 0.4348 0.826 0.00 0.64 0.32 0.00 0.04 0.00
#> TCGA.55.6980.01 5 0.3851 0.163 0.00 0.00 0.00 0.00 0.54 0.46
#> TCGA.62.8397.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5936.01 6 0.5438 0.529 0.00 0.00 0.28 0.00 0.16 0.56
#> TCGA.55.8621.01 5 0.0937 0.785 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.44.A4SS.01 2 0.0000 0.796 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MN.01 2 0.2941 0.833 0.00 0.78 0.22 0.00 0.00 0.00
#> TCGA.78.8648.01 2 0.2941 0.833 0.00 0.78 0.22 0.00 0.00 0.00
#> TCGA.NC.A5HJ.01 5 0.0937 0.780 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.97.A4LX.01 2 0.4172 0.834 0.00 0.68 0.28 0.00 0.04 0.00
#> TCGA.97.A4M5.01 6 0.1807 0.804 0.00 0.00 0.06 0.00 0.02 0.92
#> TCGA.44.5645.01 4 0.0000 0.880 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.NJ.A55O.01 6 0.4247 0.542 0.00 0.00 0.06 0.24 0.00 0.70
#> TCGA.44.6145.01 2 0.4348 0.826 0.00 0.64 0.32 0.00 0.04 0.00
#> TCGA.97.A4M6.01 6 0.0547 0.806 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.MP.A4TJ.01 5 0.1814 0.771 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.50.5939.01 2 0.0000 0.796 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4487.01 5 0.4348 0.454 0.00 0.04 0.32 0.00 0.64 0.00
#> TCGA.55.8206.01 4 0.3647 0.532 0.00 0.00 0.36 0.64 0.00 0.00
#> TCGA.97.7553.01 6 0.2048 0.756 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.64.5778.01 4 0.1814 0.879 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.55.7728.01 5 0.3351 0.702 0.00 0.00 0.16 0.00 0.80 0.04
#> TCGA.44.6774.01 6 0.2048 0.756 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.49.AAQV.01 5 0.1814 0.771 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.73.7498.01 1 0.4758 0.737 0.58 0.00 0.36 0.06 0.00 0.00
#> TCGA.78.7163.01 1 0.0937 0.805 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.75.7030.01 5 0.5398 0.407 0.00 0.00 0.18 0.00 0.58 0.24
#> TCGA.75.7025.01 4 0.1267 0.891 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.38.A44F.01 5 0.0937 0.785 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.55.8091.01 4 0.1556 0.889 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.75.6212.01 4 0.1814 0.879 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.44.6776.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5045.01 5 0.1814 0.771 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.95.A4VP.01 6 0.0547 0.806 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.55.A492.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6543.01 1 0.4758 0.737 0.58 0.00 0.36 0.06 0.00 0.00
#> TCGA.97.A4M2.01 5 0.1814 0.760 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.55.6970.01 6 0.3829 0.725 0.00 0.00 0.18 0.00 0.06 0.76
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.97.A4M1.01 1 0.5802 0.6379 0.46 0.00 0.08 0.08 0.00 0.00 0.38
#> TCGA.99.8033.01 5 0.0000 0.8170 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.8552.01 3 0.4418 0.5450 0.00 0.00 0.62 0.08 0.00 0.00 0.30
#> TCGA.50.5066.01 2 0.0863 0.7384 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.55.8208.01 2 0.0863 0.7384 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.85.8584.01 2 0.3546 0.6536 0.00 0.54 0.00 0.46 0.00 0.00 0.00
#> TCGA.75.6206.01 1 0.0863 0.7314 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.05.4384.01 1 0.5802 0.6379 0.46 0.00 0.08 0.08 0.00 0.00 0.38
#> TCGA.55.8087.01 1 0.0863 0.7314 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.85.A50M.01 2 0.4461 0.6479 0.00 0.54 0.00 0.40 0.00 0.00 0.06
#> TCGA.MP.A4TH.01 6 0.0000 0.6645 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.6971.01 6 0.3661 0.4867 0.00 0.00 0.00 0.02 0.22 0.74 0.02
#> TCGA.98.7454.01 2 0.3546 0.6536 0.00 0.54 0.00 0.46 0.00 0.00 0.00
#> TCGA.50.5944.01 1 0.0000 0.7346 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.7547.01 1 0.4710 0.6547 0.46 0.00 0.08 0.00 0.00 0.00 0.46
#> TCGA.69.7973.01 1 0.3985 0.6858 0.52 0.00 0.02 0.00 0.00 0.00 0.46
#> TCGA.97.8177.01 6 0.1006 0.6591 0.00 0.00 0.00 0.02 0.02 0.96 0.00
#> TCGA.91.A4BD.01 3 0.0504 0.8464 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.6979.01 2 0.3459 0.0630 0.00 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.55.7573.01 6 0.3061 0.5659 0.00 0.00 0.08 0.06 0.00 0.84 0.02
#> TCGA.55.8097.01 1 0.2259 0.7382 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.93.A4JP.01 6 0.2512 0.5959 0.00 0.00 0.00 0.10 0.00 0.86 0.04
#> TCGA.S2.AA1A.01 6 0.4070 0.3394 0.00 0.00 0.00 0.02 0.30 0.66 0.02
#> TCGA.93.A4JQ.01 2 0.0863 0.7384 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.78.7160.01 5 0.0000 0.8170 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7671.01 1 0.0863 0.7314 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.50.5055.01 2 0.0863 0.7518 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.91.8496.01 1 0.5802 0.6379 0.46 0.00 0.08 0.08 0.00 0.00 0.38
#> TCGA.MP.A4T2.01 3 0.1433 0.8266 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.78.7162.01 3 0.2278 0.8059 0.00 0.00 0.88 0.04 0.00 0.08 0.00
#> TCGA.93.7348.01 6 0.3530 0.5123 0.00 0.00 0.00 0.02 0.20 0.76 0.02
#> TCGA.97.7546.01 3 0.1433 0.8201 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.95.7944.01 2 0.3546 0.6536 0.00 0.54 0.00 0.46 0.00 0.00 0.00
#> TCGA.86.8280.01 3 0.1433 0.8302 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.55.A48Z.01 6 0.2512 0.5959 0.00 0.00 0.00 0.10 0.00 0.86 0.04
#> TCGA.55.8299.01 2 0.0863 0.7384 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.55.6980.01 6 0.3984 0.3795 0.00 0.00 0.00 0.02 0.28 0.68 0.02
#> TCGA.62.8397.01 1 0.0863 0.7325 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.50.5936.01 7 0.5798 0.4143 0.00 0.00 0.00 0.20 0.02 0.34 0.44
#> TCGA.55.8621.01 5 0.0000 0.8170 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A4SS.01 2 0.3546 0.6536 0.00 0.54 0.00 0.46 0.00 0.00 0.00
#> TCGA.63.A5MN.01 2 0.1671 0.7482 0.00 0.90 0.00 0.10 0.00 0.00 0.00
#> TCGA.78.8648.01 2 0.1671 0.7482 0.00 0.90 0.00 0.10 0.00 0.00 0.00
#> TCGA.NC.A5HJ.01 5 0.1718 0.7532 0.00 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.97.A4LX.01 2 0.0863 0.7518 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.97.A4M5.01 6 0.2512 0.5959 0.00 0.00 0.00 0.10 0.00 0.86 0.04
#> TCGA.44.5645.01 3 0.1433 0.8201 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.NJ.A55O.01 6 0.5429 0.0871 0.00 0.00 0.32 0.10 0.00 0.54 0.04
#> TCGA.44.6145.01 2 0.0863 0.7384 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.97.A4M6.01 6 0.0000 0.6645 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TJ.01 5 0.1671 0.7944 0.00 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.50.5939.01 2 0.3546 0.6536 0.00 0.54 0.00 0.46 0.00 0.00 0.00
#> TCGA.49.4487.01 5 0.3221 0.5296 0.00 0.32 0.00 0.00 0.68 0.00 0.00
#> TCGA.55.8206.01 3 0.4638 0.4371 0.00 0.00 0.54 0.08 0.00 0.00 0.38
#> TCGA.97.7553.01 6 0.2421 0.6268 0.00 0.00 0.00 0.02 0.08 0.88 0.02
#> TCGA.64.5778.01 3 0.1928 0.8264 0.00 0.00 0.90 0.02 0.00 0.08 0.00
#> TCGA.55.7728.01 5 0.5483 -0.0738 0.00 0.00 0.00 0.14 0.50 0.02 0.34
#> TCGA.44.6774.01 6 0.2654 0.6143 0.00 0.00 0.00 0.02 0.10 0.86 0.02
#> TCGA.49.AAQV.01 5 0.1671 0.7944 0.00 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.73.7498.01 1 0.3943 0.6943 0.56 0.00 0.02 0.00 0.00 0.00 0.42
#> TCGA.78.7163.01 1 0.2259 0.7382 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.75.7030.01 7 0.6891 0.4609 0.00 0.00 0.00 0.14 0.28 0.24 0.34
#> TCGA.75.7025.01 3 0.0504 0.8464 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.38.A44F.01 5 0.0000 0.8170 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8091.01 3 0.1664 0.8361 0.00 0.00 0.92 0.06 0.00 0.02 0.00
#> TCGA.75.6212.01 3 0.1433 0.8302 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.44.6776.01 1 0.0863 0.7314 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.50.5045.01 5 0.1671 0.7944 0.00 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.95.A4VP.01 6 0.0000 0.6645 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.A492.01 1 0.0000 0.7346 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6543.01 1 0.3943 0.6943 0.56 0.00 0.02 0.00 0.00 0.00 0.42
#> TCGA.97.A4M2.01 5 0.2864 0.6538 0.00 0.00 0.00 0.02 0.84 0.12 0.02
#> TCGA.55.6970.01 6 0.5092 -0.0404 0.00 0.00 0.00 0.22 0.00 0.56 0.22
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.97.A4M1.01 1 0.1557 0.694 0.92 0.00 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.99.8033.01 5 0.0471 0.750 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.97.8552.01 3 0.4471 0.360 0.34 0.00 0.58 0.06 0.00 0.00 0.02 0.00
#> TCGA.50.5066.01 2 0.0000 0.709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8208.01 2 0.0000 0.709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8584.01 4 0.3329 0.977 0.00 0.48 0.00 0.52 0.00 0.00 0.00 0.00
#> TCGA.75.6206.01 8 0.3449 0.984 0.32 0.00 0.00 0.00 0.00 0.00 0.02 0.66
#> TCGA.05.4384.01 1 0.2020 0.685 0.90 0.00 0.02 0.06 0.00 0.00 0.02 0.00
#> TCGA.55.8087.01 8 0.3449 0.984 0.32 0.00 0.00 0.00 0.00 0.00 0.02 0.66
#> TCGA.85.A50M.01 2 0.5782 -0.632 0.00 0.50 0.00 0.26 0.00 0.00 0.10 0.14
#> TCGA.MP.A4TH.01 6 0.0471 0.619 0.00 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.55.6971.01 6 0.4061 0.567 0.00 0.00 0.00 0.12 0.14 0.72 0.00 0.02
#> TCGA.98.7454.01 4 0.3737 0.973 0.00 0.48 0.00 0.50 0.00 0.00 0.00 0.02
#> TCGA.50.5944.01 8 0.3015 0.979 0.32 0.00 0.00 0.00 0.00 0.00 0.00 0.68
#> TCGA.97.7547.01 1 0.0000 0.698 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7973.01 1 0.1557 0.668 0.92 0.00 0.00 0.02 0.00 0.00 0.06 0.00
#> TCGA.97.8177.01 6 0.2020 0.638 0.00 0.00 0.00 0.06 0.02 0.90 0.00 0.02
#> TCGA.91.A4BD.01 3 0.0000 0.874 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6979.01 2 0.3237 0.101 0.00 0.60 0.00 0.00 0.40 0.00 0.00 0.00
#> TCGA.55.7573.01 6 0.3503 0.441 0.00 0.00 0.08 0.12 0.00 0.78 0.00 0.02
#> TCGA.55.8097.01 1 0.3329 -0.603 0.52 0.00 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.93.A4JP.01 6 0.3227 0.417 0.00 0.00 0.00 0.08 0.00 0.78 0.14 0.00
#> TCGA.S2.AA1A.01 6 0.4939 0.454 0.00 0.00 0.00 0.16 0.18 0.62 0.00 0.04
#> TCGA.93.A4JQ.01 2 0.0000 0.709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 5 0.0000 0.750 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7671.01 8 0.3449 0.984 0.32 0.00 0.00 0.00 0.00 0.00 0.02 0.66
#> TCGA.50.5055.01 2 0.1557 0.663 0.00 0.92 0.00 0.06 0.00 0.00 0.00 0.02
#> TCGA.91.8496.01 1 0.1557 0.694 0.92 0.00 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.MP.A4T2.01 3 0.2348 0.841 0.00 0.00 0.88 0.06 0.00 0.00 0.04 0.02
#> TCGA.78.7162.01 3 0.2591 0.823 0.00 0.00 0.86 0.08 0.00 0.04 0.00 0.02
#> TCGA.93.7348.01 6 0.4061 0.567 0.00 0.00 0.00 0.12 0.14 0.72 0.00 0.02
#> TCGA.97.7546.01 3 0.1557 0.847 0.00 0.00 0.92 0.06 0.00 0.00 0.02 0.00
#> TCGA.95.7944.01 4 0.3329 0.977 0.00 0.48 0.00 0.52 0.00 0.00 0.00 0.00
#> TCGA.86.8280.01 3 0.1741 0.863 0.00 0.00 0.92 0.04 0.00 0.02 0.00 0.02
#> TCGA.55.A48Z.01 6 0.3263 0.424 0.00 0.00 0.00 0.10 0.00 0.78 0.12 0.00
#> TCGA.55.8299.01 2 0.0000 0.709 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6980.01 6 0.4345 0.525 0.00 0.00 0.00 0.12 0.18 0.68 0.00 0.02
#> TCGA.62.8397.01 8 0.3449 0.964 0.32 0.00 0.00 0.02 0.00 0.00 0.00 0.66
#> TCGA.50.5936.01 7 0.2981 0.730 0.00 0.00 0.00 0.00 0.02 0.22 0.76 0.00
#> TCGA.55.8621.01 5 0.0808 0.749 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.44.A4SS.01 4 0.3737 0.973 0.00 0.48 0.00 0.50 0.00 0.00 0.00 0.02
#> TCGA.63.A5MN.01 2 0.2350 0.567 0.00 0.86 0.00 0.10 0.00 0.00 0.00 0.04
#> TCGA.78.8648.01 2 0.2350 0.567 0.00 0.86 0.00 0.10 0.00 0.00 0.00 0.04
#> TCGA.NC.A5HJ.01 5 0.2818 0.687 0.00 0.00 0.00 0.12 0.82 0.00 0.00 0.06
#> TCGA.97.A4LX.01 2 0.1557 0.663 0.00 0.92 0.00 0.06 0.00 0.00 0.00 0.02
#> TCGA.97.A4M5.01 6 0.3227 0.417 0.00 0.00 0.00 0.08 0.00 0.78 0.14 0.00
#> TCGA.44.5645.01 3 0.1557 0.847 0.00 0.00 0.92 0.06 0.00 0.00 0.02 0.00
#> TCGA.NJ.A55O.01 6 0.6043 -0.164 0.00 0.00 0.32 0.12 0.00 0.46 0.08 0.02
#> TCGA.44.6145.01 2 0.1275 0.662 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.97.A4M6.01 6 0.0000 0.626 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4TJ.01 5 0.2025 0.728 0.00 0.10 0.00 0.02 0.88 0.00 0.00 0.00
#> TCGA.50.5939.01 4 0.3737 0.962 0.00 0.48 0.00 0.50 0.00 0.00 0.00 0.02
#> TCGA.49.4487.01 5 0.3658 0.342 0.00 0.40 0.00 0.02 0.58 0.00 0.00 0.00
#> TCGA.55.8206.01 1 0.4471 0.143 0.58 0.00 0.34 0.06 0.00 0.00 0.02 0.00
#> TCGA.97.7553.01 6 0.2484 0.632 0.00 0.00 0.00 0.10 0.02 0.86 0.00 0.02
#> TCGA.64.5778.01 3 0.2807 0.845 0.00 0.00 0.86 0.06 0.00 0.02 0.02 0.04
#> TCGA.55.7728.01 5 0.5314 0.369 0.00 0.00 0.00 0.16 0.54 0.00 0.26 0.04
#> TCGA.44.6774.01 6 0.3078 0.620 0.00 0.00 0.00 0.10 0.06 0.82 0.00 0.02
#> TCGA.49.AAQV.01 5 0.2025 0.728 0.00 0.10 0.00 0.02 0.88 0.00 0.00 0.00
#> TCGA.73.7498.01 1 0.0000 0.698 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7163.01 1 0.3329 -0.603 0.52 0.00 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.75.7030.01 5 0.7098 -0.229 0.00 0.00 0.00 0.16 0.30 0.24 0.26 0.04
#> TCGA.75.7025.01 3 0.0000 0.874 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.A44F.01 5 0.0808 0.749 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.8091.01 3 0.1275 0.864 0.00 0.00 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.75.6212.01 3 0.1741 0.863 0.00 0.00 0.92 0.04 0.00 0.02 0.00 0.02
#> TCGA.44.6776.01 8 0.3449 0.984 0.32 0.00 0.00 0.00 0.00 0.00 0.02 0.66
#> TCGA.50.5045.01 5 0.2025 0.728 0.00 0.10 0.00 0.02 0.88 0.00 0.00 0.00
#> TCGA.95.A4VP.01 6 0.0000 0.626 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.A492.01 8 0.3015 0.979 0.32 0.00 0.00 0.00 0.00 0.00 0.00 0.68
#> TCGA.55.6543.01 1 0.0000 0.698 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M2.01 5 0.4204 0.579 0.00 0.00 0.00 0.12 0.72 0.12 0.00 0.04
#> TCGA.55.6970.01 7 0.4100 0.681 0.00 0.00 0.00 0.06 0.00 0.36 0.58 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: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0213"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 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 0.4713 0.529 0.529
#> 3 3 0.736 0.931 0.908 0.2998 0.815 0.651
#> 4 4 0.587 0.645 0.735 0.1292 0.815 0.545
#> 5 5 0.710 0.657 0.812 0.1092 0.938 0.783
#> 6 6 0.804 0.725 0.800 0.0612 0.902 0.614
#> 7 7 0.815 0.699 0.815 0.0224 0.994 0.968
#> 8 8 0.793 0.534 0.781 0.0260 0.966 0.823
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.99.8033.01 1 0 1 1 0
#> TCGA.MP.A4TH.01 1 0 1 1 0
#> TCGA.55.6971.01 1 0 1 1 0
#> TCGA.97.8177.01 1 0 1 1 0
#> TCGA.93.A4JP.01 2 0 1 0 1
#> TCGA.S2.AA1A.01 1 0 1 1 0
#> TCGA.78.7160.01 2 0 1 0 1
#> TCGA.93.7348.01 1 0 1 1 0
#> TCGA.55.A48Z.01 1 0 1 1 0
#> TCGA.55.6980.01 2 0 1 0 1
#> TCGA.50.5936.01 2 0 1 0 1
#> TCGA.55.8621.01 1 0 1 1 0
#> TCGA.NC.A5HJ.01 2 0 1 0 1
#> TCGA.97.A4M5.01 2 0 1 0 1
#> TCGA.97.A4M6.01 1 0 1 1 0
#> TCGA.MP.A4TJ.01 1 0 1 1 0
#> TCGA.97.7553.01 1 0 1 1 0
#> TCGA.55.7728.01 1 0 1 1 0
#> TCGA.44.6774.01 1 0 1 1 0
#> TCGA.49.AAQV.01 1 0 1 1 0
#> TCGA.75.7030.01 2 0 1 0 1
#> TCGA.38.A44F.01 2 0 1 0 1
#> TCGA.50.5045.01 1 0 1 1 0
#> TCGA.95.A4VP.01 1 0 1 1 0
#> TCGA.97.A4M2.01 2 0 1 0 1
#> TCGA.55.6970.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.99.8033.01 1 0.0892 0.926 0.98 0.0 0.02
#> TCGA.MP.A4TH.01 3 0.5560 1.000 0.30 0.0 0.70
#> TCGA.55.6971.01 3 0.5560 1.000 0.30 0.0 0.70
#> TCGA.97.8177.01 1 0.0892 0.926 0.98 0.0 0.02
#> TCGA.93.A4JP.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.S2.AA1A.01 1 0.0000 0.924 1.00 0.0 0.00
#> TCGA.78.7160.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.93.7348.01 1 0.3686 0.821 0.86 0.0 0.14
#> TCGA.55.A48Z.01 1 0.0892 0.926 0.98 0.0 0.02
#> TCGA.55.6980.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.50.5936.01 2 0.5560 0.734 0.00 0.7 0.30
#> TCGA.55.8621.01 1 0.2959 0.872 0.90 0.0 0.10
#> TCGA.NC.A5HJ.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.97.A4M5.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.97.A4M6.01 1 0.2959 0.872 0.90 0.0 0.10
#> TCGA.MP.A4TJ.01 1 0.4291 0.751 0.82 0.0 0.18
#> TCGA.97.7553.01 1 0.0000 0.924 1.00 0.0 0.00
#> TCGA.55.7728.01 3 0.5560 1.000 0.30 0.0 0.70
#> TCGA.44.6774.01 3 0.5560 1.000 0.30 0.0 0.70
#> TCGA.49.AAQV.01 1 0.0000 0.924 1.00 0.0 0.00
#> TCGA.75.7030.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.38.A44F.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.50.5045.01 1 0.0000 0.924 1.00 0.0 0.00
#> TCGA.95.A4VP.01 1 0.0000 0.924 1.00 0.0 0.00
#> TCGA.97.A4M2.01 2 0.0000 0.971 0.00 1.0 0.00
#> TCGA.55.6970.01 3 0.5560 1.000 0.30 0.0 0.70
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.99.8033.01 1 0.549 0.753 0.58 0.00 0.40 0.02
#> TCGA.MP.A4TH.01 3 0.499 0.592 0.00 0.00 0.52 0.48
#> TCGA.55.6971.01 3 0.499 0.592 0.00 0.00 0.52 0.48
#> TCGA.97.8177.01 1 0.491 0.734 0.58 0.00 0.42 0.00
#> TCGA.93.A4JP.01 2 0.380 0.716 0.22 0.78 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.380 0.874 0.78 0.00 0.22 0.00
#> TCGA.78.7160.01 2 0.000 0.716 0.00 1.00 0.00 0.00
#> TCGA.93.7348.01 3 0.317 0.385 0.16 0.00 0.84 0.00
#> TCGA.55.A48Z.01 1 0.553 0.741 0.56 0.00 0.42 0.02
#> TCGA.55.6980.01 2 0.000 0.716 0.00 1.00 0.00 0.00
#> TCGA.50.5936.01 4 0.500 0.000 0.00 0.50 0.00 0.50
#> TCGA.55.8621.01 3 0.340 0.345 0.18 0.00 0.82 0.00
#> TCGA.NC.A5HJ.01 2 0.380 0.716 0.22 0.78 0.00 0.00
#> TCGA.97.A4M5.01 2 0.380 0.716 0.22 0.78 0.00 0.00
#> TCGA.97.A4M6.01 3 0.317 0.363 0.16 0.00 0.84 0.00
#> TCGA.MP.A4TJ.01 3 0.292 0.407 0.14 0.00 0.86 0.00
#> TCGA.97.7553.01 1 0.380 0.874 0.78 0.00 0.22 0.00
#> TCGA.55.7728.01 3 0.380 0.566 0.00 0.00 0.78 0.22
#> TCGA.44.6774.01 3 0.499 0.592 0.00 0.00 0.52 0.48
#> TCGA.49.AAQV.01 1 0.380 0.874 0.78 0.00 0.22 0.00
#> TCGA.75.7030.01 2 0.000 0.716 0.00 1.00 0.00 0.00
#> TCGA.38.A44F.01 2 0.000 0.716 0.00 1.00 0.00 0.00
#> TCGA.50.5045.01 1 0.380 0.874 0.78 0.00 0.22 0.00
#> TCGA.95.A4VP.01 1 0.380 0.874 0.78 0.00 0.22 0.00
#> TCGA.97.A4M2.01 2 0.380 0.716 0.22 0.78 0.00 0.00
#> TCGA.55.6970.01 3 0.499 0.592 0.00 0.00 0.52 0.48
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.99.8033.01 1 0.644 0.3964 0.50 0.00 0.00 0.28 0.22
#> TCGA.MP.A4TH.01 3 0.104 0.8289 0.04 0.00 0.96 0.00 0.00
#> TCGA.55.6971.01 3 0.104 0.8289 0.04 0.00 0.96 0.00 0.00
#> TCGA.97.8177.01 1 0.430 -0.0552 0.52 0.00 0.00 0.00 0.48
#> TCGA.93.A4JP.01 2 0.327 0.7407 0.00 0.78 0.00 0.00 0.22
#> TCGA.S2.AA1A.01 1 0.000 0.7574 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 2 0.104 0.7205 0.00 0.96 0.04 0.00 0.00
#> TCGA.93.7348.01 5 0.487 0.9272 0.16 0.00 0.12 0.00 0.72
#> TCGA.55.A48Z.01 1 0.644 0.3964 0.50 0.00 0.00 0.28 0.22
#> TCGA.55.6980.01 2 0.104 0.7205 0.00 0.96 0.04 0.00 0.00
#> TCGA.50.5936.01 4 0.413 0.0000 0.00 0.38 0.00 0.62 0.00
#> TCGA.55.8621.01 5 0.539 0.9311 0.18 0.00 0.10 0.02 0.70
#> TCGA.NC.A5HJ.01 2 0.327 0.7407 0.00 0.78 0.00 0.00 0.22
#> TCGA.97.A4M5.01 2 0.327 0.7407 0.00 0.78 0.00 0.00 0.22
#> TCGA.97.A4M6.01 5 0.539 0.9311 0.18 0.00 0.10 0.02 0.70
#> TCGA.MP.A4TJ.01 5 0.541 0.8463 0.14 0.00 0.20 0.00 0.66
#> TCGA.97.7553.01 1 0.000 0.7574 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7728.01 3 0.518 -0.2046 0.04 0.00 0.48 0.00 0.48
#> TCGA.44.6774.01 3 0.104 0.8289 0.04 0.00 0.96 0.00 0.00
#> TCGA.49.AAQV.01 1 0.000 0.7574 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.7030.01 2 0.104 0.7205 0.00 0.96 0.00 0.00 0.04
#> TCGA.38.A44F.01 2 0.104 0.7205 0.00 0.96 0.00 0.00 0.04
#> TCGA.50.5045.01 1 0.000 0.7574 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.000 0.7574 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M2.01 2 0.327 0.7407 0.00 0.78 0.00 0.00 0.22
#> TCGA.55.6970.01 3 0.275 0.7863 0.04 0.00 0.88 0.08 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.99.8033.01 4 0.6525 0.389 0.30 0.00 0.00 0.46 0.20 0.04
#> TCGA.MP.A4TH.01 3 0.0000 0.938 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6971.01 3 0.0547 0.942 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.97.8177.01 5 0.3916 0.328 0.30 0.00 0.00 0.02 0.68 0.00
#> TCGA.93.A4JP.01 2 0.0000 0.753 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7160.01 2 0.4700 0.735 0.00 0.60 0.00 0.00 0.06 0.34
#> TCGA.93.7348.01 5 0.2094 0.717 0.02 0.00 0.08 0.00 0.90 0.00
#> TCGA.55.A48Z.01 4 0.5438 0.416 0.28 0.00 0.00 0.56 0.16 0.00
#> TCGA.55.6980.01 2 0.4700 0.735 0.00 0.60 0.00 0.00 0.06 0.34
#> TCGA.50.5936.01 4 0.5922 -0.055 0.00 0.22 0.00 0.44 0.00 0.34
#> TCGA.55.8621.01 5 0.3697 0.705 0.06 0.00 0.04 0.00 0.82 0.08
#> TCGA.NC.A5HJ.01 2 0.0000 0.753 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M5.01 2 0.0000 0.753 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M6.01 5 0.3631 0.691 0.04 0.00 0.04 0.00 0.82 0.10
#> TCGA.MP.A4TJ.01 5 0.3834 0.676 0.02 0.00 0.20 0.02 0.76 0.00
#> TCGA.97.7553.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7728.01 5 0.3797 0.373 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.44.6774.01 3 0.0547 0.942 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.49.AAQV.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7030.01 2 0.3756 0.735 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.38.A44F.01 2 0.3756 0.735 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.50.5045.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M2.01 2 0.0000 0.753 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6970.01 3 0.2581 0.845 0.00 0.00 0.86 0.00 0.02 0.12
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.99.8033.01 4 0.4243 0.557 0.10 0.00 0.00 0.68 0.22 0.00 0.00
#> TCGA.MP.A4TH.01 3 0.0504 0.881 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.6971.01 3 0.0000 0.886 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.8177.01 5 0.2512 0.549 0.10 0.00 0.00 0.04 0.86 0.00 0.00
#> TCGA.93.A4JP.01 6 0.3221 0.710 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.S2.AA1A.01 1 0.1006 0.954 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.78.7160.01 6 0.0000 0.671 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.93.7348.01 5 0.0504 0.656 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.55.A48Z.01 4 0.7034 0.564 0.10 0.34 0.00 0.38 0.04 0.00 0.14
#> TCGA.55.6980.01 6 0.0000 0.671 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5936.01 7 0.3221 0.000 0.00 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.55.8621.01 5 0.3722 0.605 0.00 0.04 0.00 0.18 0.76 0.00 0.02
#> TCGA.NC.A5HJ.01 6 0.3221 0.710 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.97.A4M5.01 6 0.3221 0.710 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.97.A4M6.01 5 0.3863 0.596 0.00 0.04 0.00 0.20 0.74 0.00 0.02
#> TCGA.MP.A4TJ.01 5 0.3307 0.575 0.00 0.00 0.24 0.00 0.74 0.00 0.02
#> TCGA.97.7553.01 1 0.0504 0.961 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.55.7728.01 5 0.4418 0.482 0.00 0.00 0.30 0.00 0.62 0.00 0.08
#> TCGA.44.6774.01 3 0.0000 0.886 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AAQV.01 1 0.1006 0.954 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.75.7030.01 6 0.1433 0.671 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.38.A44F.01 6 0.1433 0.671 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.50.5045.01 1 0.0504 0.961 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.95.A4VP.01 1 0.0863 0.949 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.97.A4M2.01 6 0.3221 0.710 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.55.6970.01 3 0.3841 0.639 0.00 0.28 0.68 0.04 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.99.8033.01 8 0.6772 -0.3916 0.14 0.04 0.00 0.3 0.14 0.00 0.00 0.38
#> TCGA.MP.A4TH.01 3 0.0471 0.8718 0.00 0.00 0.98 0.0 0.00 0.00 0.02 0.00
#> TCGA.55.6971.01 3 0.0471 0.8794 0.00 0.00 0.98 0.0 0.00 0.00 0.00 0.02
#> TCGA.97.8177.01 2 0.4759 0.1918 0.14 0.50 0.00 0.0 0.00 0.00 0.00 0.36
#> TCGA.93.A4JP.01 6 0.0000 0.6690 0.00 0.00 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.S2.AA1A.01 1 0.2719 0.8313 0.80 0.00 0.00 0.0 0.18 0.00 0.00 0.02
#> TCGA.78.7160.01 6 0.5325 0.6176 0.00 0.00 0.00 0.1 0.26 0.56 0.00 0.08
#> TCGA.93.7348.01 2 0.3272 0.2004 0.00 0.58 0.00 0.0 0.00 0.00 0.00 0.42
#> TCGA.55.A48Z.01 4 0.1887 0.0000 0.06 0.04 0.00 0.9 0.00 0.00 0.00 0.00
#> TCGA.55.6980.01 6 0.5325 0.6176 0.00 0.00 0.00 0.1 0.26 0.56 0.00 0.08
#> TCGA.50.5936.01 7 0.2114 0.0000 0.00 0.00 0.00 0.0 0.00 0.16 0.84 0.00
#> TCGA.55.8621.01 2 0.0000 0.5255 0.00 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HJ.01 6 0.0000 0.6690 0.00 0.00 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.97.A4M5.01 6 0.1091 0.6690 0.00 0.00 0.00 0.0 0.00 0.94 0.00 0.06
#> TCGA.97.A4M6.01 2 0.0941 0.5171 0.00 0.96 0.00 0.0 0.02 0.00 0.02 0.00
#> TCGA.MP.A4TJ.01 8 0.4971 0.0546 0.00 0.36 0.18 0.0 0.00 0.00 0.00 0.46
#> TCGA.97.7553.01 1 0.0471 0.8536 0.98 0.00 0.00 0.0 0.00 0.00 0.00 0.02
#> TCGA.55.7728.01 8 0.5709 0.1758 0.00 0.28 0.20 0.0 0.02 0.00 0.02 0.48
#> TCGA.44.6774.01 3 0.0471 0.8794 0.00 0.00 0.98 0.0 0.00 0.00 0.00 0.02
#> TCGA.49.AAQV.01 1 0.2856 0.8272 0.78 0.00 0.00 0.0 0.20 0.00 0.00 0.02
#> TCGA.75.7030.01 6 0.3299 0.6176 0.00 0.00 0.00 0.0 0.44 0.56 0.00 0.00
#> TCGA.38.A44F.01 6 0.3299 0.6176 0.00 0.00 0.00 0.0 0.44 0.56 0.00 0.00
#> TCGA.50.5045.01 1 0.0471 0.8536 0.98 0.00 0.00 0.0 0.00 0.00 0.00 0.02
#> TCGA.95.A4VP.01 1 0.2348 0.8339 0.88 0.00 0.00 0.0 0.06 0.00 0.04 0.02
#> TCGA.97.A4M2.01 6 0.1091 0.6690 0.00 0.00 0.00 0.0 0.00 0.94 0.00 0.06
#> TCGA.55.6970.01 3 0.4590 0.6454 0.00 0.00 0.68 0.0 0.16 0.00 0.06 0.10
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 44 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5111 0.489 0.489
#> 3 3 0.968 0.956 0.973 0.2396 0.873 0.741
#> 4 4 0.685 0.838 0.867 0.0983 1.000 1.000
#> 5 5 0.612 0.735 0.787 0.0478 1.000 1.000
#> 6 6 0.601 0.594 0.693 0.0480 0.985 0.959
#> 7 7 0.593 0.305 0.650 0.0400 0.855 0.585
#> 8 8 0.574 0.348 0.663 0.0278 0.902 0.617
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.NJ.A4YI.01 1 0 1 1 0
#> TCGA.MN.A4N1.01 2 0 1 0 1
#> TCGA.55.8207.01 2 0 1 0 1
#> TCGA.62.A46V.01 1 0 1 1 0
#> TCGA.62.A46P.01 2 0 1 0 1
#> TCGA.55.A4DG.01 2 0 1 0 1
#> TCGA.44.A47B.01 2 0 1 0 1
#> TCGA.05.5429.01 2 0 1 0 1
#> TCGA.62.A46R.01 1 0 1 1 0
#> TCGA.78.7535.01 2 0 1 0 1
#> TCGA.97.A4M0.01 1 0 1 1 0
#> TCGA.50.5933.01 2 0 1 0 1
#> TCGA.55.7907.01 2 0 1 0 1
#> TCGA.55.8511.01 1 0 1 1 0
#> TCGA.99.8025.01 1 0 1 1 0
#> TCGA.55.7283.01 1 0 1 1 0
#> TCGA.44.8117.01 1 0 1 1 0
#> TCGA.05.4405.01 1 0 1 1 0
#> TCGA.49.6745.01 2 0 1 0 1
#> TCGA.86.8673.01 2 0 1 0 1
#> TCGA.69.7765.01 2 0 1 0 1
#> TCGA.95.8494.01 2 0 1 0 1
#> TCGA.44.A47A.01 1 0 1 1 0
#> TCGA.55.8090.01 2 0 1 0 1
#> TCGA.55.7903.01 2 0 1 0 1
#> TCGA.78.7153.01 1 0 1 1 0
#> TCGA.55.7227.01 2 0 1 0 1
#> TCGA.86.A456.01 1 0 1 1 0
#> TCGA.38.4632.01 2 0 1 0 1
#> TCGA.69.7974.01 1 0 1 1 0
#> TCGA.55.7727.01 2 0 1 0 1
#> TCGA.78.8655.01 1 0 1 1 0
#> TCGA.55.7914.01 1 0 1 1 0
#> TCGA.62.A472.01 2 0 1 0 1
#> TCGA.97.7554.01 1 0 1 1 0
#> TCGA.55.7576.01 2 0 1 0 1
#> TCGA.93.8067.01 2 0 1 0 1
#> TCGA.69.A59K.01 1 0 1 1 0
#> TCGA.95.7567.01 2 0 1 0 1
#> TCGA.49.AARN.01 1 0 1 1 0
#> TCGA.91.6836.01 1 0 1 1 0
#> TCGA.44.7659.01 2 0 1 0 1
#> TCGA.71.8520.01 1 0 1 1 0
#> TCGA.05.4425.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.NJ.A4YI.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.MN.A4N1.01 3 0.0892 0.919 0 0.02 0.98
#> TCGA.55.8207.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.62.A46V.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.62.A46P.01 2 0.0892 0.949 0 0.98 0.02
#> TCGA.55.A4DG.01 3 0.2537 0.923 0 0.08 0.92
#> TCGA.44.A47B.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.05.5429.01 2 0.0892 0.949 0 0.98 0.02
#> TCGA.62.A46R.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.78.7535.01 3 0.0892 0.919 0 0.02 0.98
#> TCGA.97.A4M0.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.50.5933.01 3 0.2959 0.913 0 0.10 0.90
#> TCGA.55.7907.01 3 0.5560 0.663 0 0.30 0.70
#> TCGA.55.8511.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.99.8025.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.7283.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.44.8117.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.05.4405.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.49.6745.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.86.8673.01 2 0.1529 0.944 0 0.96 0.04
#> TCGA.69.7765.01 2 0.3686 0.828 0 0.86 0.14
#> TCGA.95.8494.01 2 0.2066 0.919 0 0.94 0.06
#> TCGA.44.A47A.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.8090.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.55.7903.01 2 0.4796 0.712 0 0.78 0.22
#> TCGA.78.7153.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.7227.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.86.A456.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.38.4632.01 3 0.1529 0.927 0 0.04 0.96
#> TCGA.69.7974.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.7727.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.78.8655.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.7914.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.62.A472.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.97.7554.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.7576.01 3 0.1529 0.925 0 0.04 0.96
#> TCGA.93.8067.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.69.A59K.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.95.7567.01 3 0.2959 0.913 0 0.10 0.90
#> TCGA.49.AARN.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.91.6836.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.44.7659.01 2 0.0000 0.961 0 1.00 0.00
#> TCGA.71.8520.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.05.4425.01 1 0.0000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.NJ.A4YI.01 1 0.3801 0.826 0.78 0.00 0.00 0.22
#> TCGA.MN.A4N1.01 3 0.2345 0.872 0.00 0.00 0.90 0.10
#> TCGA.55.8207.01 2 0.3935 0.814 0.00 0.84 0.06 0.10
#> TCGA.62.A46V.01 1 0.2011 0.888 0.92 0.00 0.00 0.08
#> TCGA.62.A46P.01 2 0.3610 0.806 0.00 0.80 0.00 0.20
#> TCGA.55.A4DG.01 3 0.1913 0.882 0.00 0.02 0.94 0.04
#> TCGA.44.A47B.01 2 0.1637 0.861 0.00 0.94 0.00 0.06
#> TCGA.05.5429.01 2 0.6201 0.641 0.00 0.62 0.08 0.30
#> TCGA.62.A46R.01 1 0.0707 0.890 0.98 0.00 0.00 0.02
#> TCGA.78.7535.01 3 0.2921 0.859 0.00 0.00 0.86 0.14
#> TCGA.97.A4M0.01 1 0.2921 0.867 0.86 0.00 0.00 0.14
#> TCGA.50.5933.01 3 0.3198 0.856 0.00 0.08 0.88 0.04
#> TCGA.55.7907.01 3 0.6594 0.661 0.00 0.14 0.62 0.24
#> TCGA.55.8511.01 1 0.3610 0.837 0.80 0.00 0.00 0.20
#> TCGA.99.8025.01 1 0.2647 0.877 0.88 0.00 0.00 0.12
#> TCGA.55.7283.01 1 0.2345 0.885 0.90 0.00 0.00 0.10
#> TCGA.44.8117.01 1 0.3975 0.812 0.76 0.00 0.00 0.24
#> TCGA.05.4405.01 1 0.2345 0.876 0.90 0.00 0.00 0.10
#> TCGA.49.6745.01 2 0.1211 0.861 0.00 0.96 0.04 0.00
#> TCGA.86.8673.01 2 0.4894 0.797 0.00 0.78 0.10 0.12
#> TCGA.69.7765.01 2 0.4522 0.576 0.00 0.68 0.32 0.00
#> TCGA.95.8494.01 2 0.3335 0.825 0.00 0.86 0.12 0.02
#> TCGA.44.A47A.01 1 0.3172 0.860 0.84 0.00 0.00 0.16
#> TCGA.55.8090.01 2 0.0000 0.868 0.00 1.00 0.00 0.00
#> TCGA.55.7903.01 2 0.5062 0.598 0.00 0.68 0.30 0.02
#> TCGA.78.7153.01 1 0.3172 0.860 0.84 0.00 0.00 0.16
#> TCGA.55.7227.01 2 0.0000 0.868 0.00 1.00 0.00 0.00
#> TCGA.86.A456.01 1 0.1211 0.888 0.96 0.00 0.00 0.04
#> TCGA.38.4632.01 3 0.2921 0.872 0.00 0.00 0.86 0.14
#> TCGA.69.7974.01 1 0.2921 0.863 0.86 0.00 0.00 0.14
#> TCGA.55.7727.01 2 0.0707 0.867 0.00 0.98 0.00 0.02
#> TCGA.78.8655.01 1 0.3172 0.860 0.84 0.00 0.00 0.16
#> TCGA.55.7914.01 1 0.2921 0.868 0.86 0.00 0.00 0.14
#> TCGA.62.A472.01 2 0.0000 0.868 0.00 1.00 0.00 0.00
#> TCGA.97.7554.01 1 0.3801 0.825 0.78 0.00 0.00 0.22
#> TCGA.55.7576.01 3 0.0707 0.884 0.00 0.02 0.98 0.00
#> TCGA.93.8067.01 2 0.2647 0.843 0.00 0.88 0.00 0.12
#> TCGA.69.A59K.01 1 0.1637 0.887 0.94 0.00 0.00 0.06
#> TCGA.95.7567.01 3 0.2706 0.859 0.00 0.08 0.90 0.02
#> TCGA.49.AARN.01 1 0.2647 0.873 0.88 0.00 0.00 0.12
#> TCGA.91.6836.01 1 0.2647 0.877 0.88 0.00 0.00 0.12
#> TCGA.44.7659.01 2 0.0000 0.868 0.00 1.00 0.00 0.00
#> TCGA.71.8520.01 1 0.2921 0.867 0.86 0.00 0.00 0.14
#> TCGA.05.4425.01 1 0.2921 0.874 0.86 0.00 0.00 0.14
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.NJ.A4YI.01 4 0.262 0.769 0.10 0.00 0.00 0.88 0.02
#> TCGA.MN.A4N1.01 3 0.422 0.732 0.12 0.00 0.78 0.00 0.10
#> TCGA.55.8207.01 2 0.608 0.598 0.04 0.64 0.10 0.00 0.22
#> TCGA.62.A46V.01 4 0.352 0.790 0.14 0.00 0.00 0.82 0.04
#> TCGA.62.A46P.01 2 0.400 0.701 0.02 0.74 0.00 0.00 0.24
#> TCGA.55.A4DG.01 3 0.244 0.784 0.00 0.04 0.90 0.00 0.06
#> TCGA.44.A47B.01 2 0.233 0.774 0.02 0.90 0.00 0.00 0.08
#> TCGA.05.5429.01 2 0.597 0.543 0.08 0.58 0.02 0.00 0.32
#> TCGA.62.A46R.01 4 0.273 0.825 0.16 0.00 0.00 0.84 0.00
#> TCGA.78.7535.01 3 0.600 0.688 0.18 0.02 0.64 0.00 0.16
#> TCGA.97.A4M0.01 4 0.423 0.761 0.42 0.00 0.00 0.58 0.00
#> TCGA.50.5933.01 3 0.455 0.741 0.02 0.10 0.78 0.00 0.10
#> TCGA.55.7907.01 3 0.709 0.498 0.04 0.18 0.50 0.00 0.28
#> TCGA.55.8511.01 4 0.202 0.769 0.10 0.00 0.00 0.90 0.00
#> TCGA.99.8025.01 4 0.327 0.809 0.22 0.00 0.00 0.78 0.00
#> TCGA.55.7283.01 4 0.342 0.819 0.24 0.00 0.00 0.76 0.00
#> TCGA.44.8117.01 4 0.228 0.762 0.12 0.00 0.00 0.88 0.00
#> TCGA.05.4405.01 4 0.228 0.819 0.12 0.00 0.00 0.88 0.00
#> TCGA.49.6745.01 2 0.165 0.780 0.00 0.94 0.04 0.00 0.02
#> TCGA.86.8673.01 2 0.677 0.525 0.04 0.56 0.16 0.00 0.24
#> TCGA.69.7765.01 2 0.492 0.458 0.00 0.62 0.34 0.00 0.04
#> TCGA.95.8494.01 2 0.535 0.580 0.00 0.66 0.22 0.00 0.12
#> TCGA.44.A47A.01 4 0.423 0.756 0.42 0.00 0.00 0.58 0.00
#> TCGA.55.8090.01 2 0.104 0.784 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.7903.01 2 0.484 0.506 0.00 0.64 0.32 0.00 0.04
#> TCGA.78.7153.01 4 0.418 0.765 0.40 0.00 0.00 0.60 0.00
#> TCGA.55.7227.01 2 0.000 0.788 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.A456.01 4 0.173 0.819 0.08 0.00 0.00 0.92 0.00
#> TCGA.38.4632.01 3 0.275 0.765 0.08 0.00 0.88 0.00 0.04
#> TCGA.69.7974.01 4 0.104 0.793 0.04 0.00 0.00 0.96 0.00
#> TCGA.55.7727.01 2 0.201 0.786 0.00 0.92 0.02 0.00 0.06
#> TCGA.78.8655.01 4 0.423 0.761 0.42 0.00 0.00 0.58 0.00
#> TCGA.55.7914.01 4 0.413 0.780 0.38 0.00 0.00 0.62 0.00
#> TCGA.62.A472.01 2 0.122 0.787 0.00 0.96 0.02 0.00 0.02
#> TCGA.97.7554.01 4 0.141 0.786 0.06 0.00 0.00 0.94 0.00
#> TCGA.55.7576.01 3 0.335 0.774 0.02 0.08 0.86 0.00 0.04
#> TCGA.93.8067.01 2 0.252 0.776 0.00 0.86 0.00 0.00 0.14
#> TCGA.69.A59K.01 4 0.201 0.815 0.06 0.00 0.00 0.92 0.02
#> TCGA.95.7567.01 3 0.475 0.711 0.02 0.14 0.76 0.00 0.08
#> TCGA.49.AARN.01 4 0.389 0.802 0.32 0.00 0.00 0.68 0.00
#> TCGA.91.6836.01 4 0.443 0.726 0.20 0.00 0.00 0.74 0.06
#> TCGA.44.7659.01 2 0.122 0.788 0.00 0.96 0.02 0.00 0.02
#> TCGA.71.8520.01 4 0.406 0.783 0.36 0.00 0.00 0.64 0.00
#> TCGA.05.4425.01 4 0.426 0.771 0.44 0.00 0.00 0.56 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.NJ.A4YI.01 4 0.5387 0.569 0.00 0.00 0.06 0.60 0.30 0.04
#> TCGA.MN.A4N1.01 1 0.3997 0.512 0.78 0.00 0.14 0.00 0.02 0.06
#> TCGA.55.8207.01 2 0.6975 0.401 0.08 0.58 0.14 0.00 0.08 0.12
#> TCGA.62.A46V.01 4 0.4345 0.708 0.00 0.00 0.06 0.74 0.18 0.02
#> TCGA.62.A46P.01 2 0.5035 0.538 0.02 0.74 0.06 0.00 0.08 0.10
#> TCGA.55.A4DG.01 1 0.3592 0.632 0.74 0.00 0.24 0.00 0.00 0.02
#> TCGA.44.A47B.01 2 0.3567 0.551 0.00 0.80 0.00 0.00 0.10 0.10
#> TCGA.05.5429.01 6 0.6208 0.000 0.12 0.28 0.06 0.00 0.00 0.54
#> TCGA.62.A46R.01 4 0.2048 0.743 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.78.7535.01 1 0.5352 0.397 0.64 0.00 0.08 0.00 0.04 0.24
#> TCGA.97.A4M0.01 4 0.3647 0.691 0.00 0.00 0.00 0.64 0.36 0.00
#> TCGA.50.5933.01 1 0.4222 0.605 0.70 0.02 0.26 0.00 0.00 0.02
#> TCGA.55.7907.01 1 0.7071 0.275 0.42 0.08 0.36 0.00 0.02 0.12
#> TCGA.55.8511.01 4 0.3819 0.610 0.00 0.00 0.00 0.70 0.28 0.02
#> TCGA.99.8025.01 4 0.2581 0.722 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.55.7283.01 4 0.2793 0.729 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.44.8117.01 4 0.4326 0.603 0.00 0.00 0.02 0.68 0.28 0.02
#> TCGA.05.4405.01 4 0.3315 0.716 0.00 0.00 0.00 0.78 0.20 0.02
#> TCGA.49.6745.01 2 0.3475 0.642 0.06 0.80 0.14 0.00 0.00 0.00
#> TCGA.86.8673.01 2 0.6105 0.420 0.04 0.64 0.18 0.00 0.06 0.08
#> TCGA.69.7765.01 2 0.5979 0.435 0.14 0.60 0.22 0.00 0.02 0.02
#> TCGA.95.8494.01 2 0.5345 0.547 0.10 0.68 0.18 0.00 0.02 0.02
#> TCGA.44.A47A.01 4 0.3706 0.684 0.00 0.00 0.00 0.62 0.38 0.00
#> TCGA.55.8090.01 2 0.0547 0.677 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.7903.01 2 0.5628 0.266 0.22 0.54 0.24 0.00 0.00 0.00
#> TCGA.78.7153.01 4 0.3756 0.676 0.00 0.00 0.00 0.60 0.40 0.00
#> TCGA.55.7227.01 2 0.0547 0.677 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.86.A456.01 4 0.2581 0.730 0.00 0.00 0.02 0.86 0.12 0.00
#> TCGA.38.4632.01 1 0.1480 0.592 0.94 0.00 0.04 0.00 0.02 0.00
#> TCGA.69.7974.01 4 0.2793 0.674 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.55.7727.01 2 0.3045 0.682 0.06 0.86 0.06 0.00 0.00 0.02
#> TCGA.78.8655.01 4 0.3756 0.676 0.00 0.00 0.00 0.60 0.40 0.00
#> TCGA.55.7914.01 4 0.4765 0.688 0.00 0.00 0.04 0.64 0.30 0.02
#> TCGA.62.A472.01 2 0.0547 0.683 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.97.7554.01 4 0.3819 0.610 0.00 0.00 0.00 0.70 0.28 0.02
#> TCGA.55.7576.01 1 0.4265 0.587 0.66 0.04 0.30 0.00 0.00 0.00
#> TCGA.93.8067.01 2 0.4798 0.628 0.06 0.76 0.08 0.00 0.02 0.08
#> TCGA.69.A59K.01 4 0.3787 0.705 0.00 0.00 0.10 0.78 0.12 0.00
#> TCGA.95.7567.01 1 0.5626 0.459 0.54 0.10 0.34 0.00 0.00 0.02
#> TCGA.49.AARN.01 4 0.3198 0.720 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.91.6836.01 4 0.6012 0.607 0.00 0.00 0.16 0.60 0.18 0.06
#> TCGA.44.7659.01 2 0.1092 0.689 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.71.8520.01 4 0.4482 0.697 0.00 0.00 0.04 0.60 0.36 0.00
#> TCGA.05.4425.01 4 0.5049 0.698 0.00 0.00 0.06 0.62 0.30 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.NJ.A4YI.01 7 0.504 0.4647 0.00 0.00 0.02 0.36 0.00 0.08 0.54
#> TCGA.MN.A4N1.01 1 0.553 -0.0052 0.54 0.00 0.24 0.00 0.20 0.02 0.00
#> TCGA.55.8207.01 3 0.647 0.0000 0.06 0.38 0.42 0.00 0.04 0.10 0.00
#> TCGA.62.A46V.01 4 0.584 -0.0621 0.00 0.00 0.06 0.48 0.02 0.06 0.38
#> TCGA.62.A46P.01 6 0.432 0.0355 0.02 0.38 0.02 0.00 0.00 0.58 0.00
#> TCGA.55.A4DG.01 1 0.291 0.3016 0.80 0.02 0.00 0.00 0.18 0.00 0.00
#> TCGA.44.A47B.01 2 0.378 0.2873 0.00 0.72 0.02 0.00 0.02 0.24 0.00
#> TCGA.05.5429.01 6 0.764 0.2014 0.06 0.22 0.08 0.00 0.16 0.44 0.04
#> TCGA.62.A46R.01 4 0.466 -0.1314 0.00 0.00 0.02 0.54 0.04 0.00 0.40
#> TCGA.78.7535.01 5 0.329 0.0000 0.34 0.00 0.00 0.00 0.66 0.00 0.00
#> TCGA.97.A4M0.01 4 0.251 0.5695 0.00 0.00 0.04 0.86 0.00 0.00 0.10
#> TCGA.50.5933.01 1 0.277 0.4237 0.86 0.08 0.00 0.00 0.04 0.02 0.00
#> TCGA.55.7907.01 1 0.750 0.2324 0.48 0.10 0.10 0.00 0.14 0.16 0.02
#> TCGA.55.8511.01 7 0.352 0.6234 0.00 0.00 0.02 0.28 0.00 0.00 0.70
#> TCGA.99.8025.01 7 0.442 0.1982 0.00 0.00 0.02 0.46 0.02 0.00 0.50
#> TCGA.55.7283.01 4 0.407 0.3347 0.00 0.00 0.00 0.66 0.02 0.02 0.30
#> TCGA.44.8117.01 7 0.305 0.6118 0.00 0.00 0.02 0.20 0.00 0.00 0.78
#> TCGA.05.4405.01 4 0.352 -0.0151 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.49.6745.01 2 0.436 0.4717 0.12 0.74 0.06 0.00 0.00 0.08 0.00
#> TCGA.86.8673.01 2 0.711 0.1429 0.12 0.50 0.08 0.00 0.06 0.22 0.02
#> TCGA.69.7765.01 2 0.534 0.2783 0.28 0.60 0.04 0.00 0.02 0.06 0.00
#> TCGA.95.8494.01 2 0.606 0.2199 0.28 0.52 0.04 0.00 0.02 0.14 0.00
#> TCGA.44.A47A.01 4 0.251 0.5677 0.00 0.00 0.00 0.86 0.04 0.00 0.10
#> TCGA.55.8090.01 2 0.251 0.4718 0.00 0.88 0.02 0.00 0.04 0.06 0.00
#> TCGA.55.7903.01 2 0.581 0.0901 0.36 0.50 0.06 0.00 0.02 0.06 0.00
#> TCGA.78.7153.01 4 0.101 0.5686 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.55.7227.01 2 0.101 0.4871 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.86.A456.01 7 0.399 0.4065 0.00 0.00 0.00 0.48 0.02 0.00 0.50
#> TCGA.38.4632.01 1 0.509 0.0505 0.64 0.00 0.08 0.00 0.22 0.06 0.00
#> TCGA.69.7974.01 7 0.382 0.5745 0.00 0.00 0.02 0.36 0.00 0.00 0.62
#> TCGA.55.7727.01 2 0.509 0.3884 0.10 0.70 0.02 0.00 0.08 0.10 0.00
#> TCGA.78.8655.01 4 0.000 0.5616 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7914.01 4 0.419 0.5120 0.00 0.00 0.04 0.72 0.04 0.00 0.20
#> TCGA.62.A472.01 2 0.101 0.4871 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.97.7554.01 7 0.319 0.6160 0.00 0.00 0.00 0.22 0.00 0.02 0.76
#> TCGA.55.7576.01 1 0.469 0.3806 0.74 0.04 0.10 0.00 0.08 0.04 0.00
#> TCGA.93.8067.01 2 0.346 0.0491 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.69.A59K.01 4 0.536 -0.3005 0.00 0.00 0.06 0.46 0.02 0.02 0.44
#> TCGA.95.7567.01 1 0.606 0.3221 0.62 0.16 0.02 0.00 0.10 0.08 0.02
#> TCGA.49.AARN.01 4 0.339 0.4593 0.00 0.00 0.04 0.76 0.00 0.00 0.20
#> TCGA.91.6836.01 7 0.589 0.1263 0.00 0.00 0.16 0.34 0.00 0.04 0.46
#> TCGA.44.7659.01 2 0.380 0.4548 0.08 0.80 0.02 0.00 0.02 0.08 0.00
#> TCGA.71.8520.01 4 0.286 0.5230 0.00 0.00 0.02 0.84 0.02 0.00 0.12
#> TCGA.05.4425.01 4 0.493 0.4508 0.00 0.00 0.06 0.70 0.06 0.02 0.16
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.NJ.A4YI.01 7 0.2947 0.5295 0.00 0.06 0.00 0.06 0.00 0.04 0.84 0.00
#> TCGA.MN.A4N1.01 1 0.5321 0.0508 0.54 0.08 0.02 0.00 0.32 0.04 0.00 0.00
#> TCGA.55.8207.01 3 0.4642 0.0000 0.06 0.00 0.60 0.00 0.04 0.00 0.00 0.30
#> TCGA.62.A46V.01 7 0.3975 0.4113 0.00 0.08 0.00 0.26 0.00 0.00 0.66 0.00
#> TCGA.62.A46P.01 8 0.6538 -0.0882 0.04 0.02 0.26 0.00 0.02 0.28 0.00 0.38
#> TCGA.55.A4DG.01 1 0.4781 0.4490 0.72 0.08 0.02 0.00 0.06 0.02 0.00 0.10
#> TCGA.44.A47B.01 8 0.4313 0.3528 0.02 0.00 0.06 0.02 0.00 0.20 0.00 0.70
#> TCGA.05.5429.01 6 0.5125 0.0000 0.08 0.04 0.00 0.00 0.02 0.60 0.00 0.26
#> TCGA.62.A46R.01 7 0.4004 0.0436 0.00 0.04 0.00 0.46 0.00 0.00 0.50 0.00
#> TCGA.78.7535.01 5 0.2856 0.0000 0.20 0.00 0.02 0.00 0.78 0.00 0.00 0.00
#> TCGA.97.A4M0.01 4 0.3170 0.5623 0.00 0.04 0.00 0.76 0.00 0.00 0.20 0.00
#> TCGA.50.5933.01 1 0.3986 0.4580 0.74 0.00 0.08 0.00 0.04 0.00 0.00 0.14
#> TCGA.55.7907.01 1 0.8068 0.1537 0.32 0.22 0.10 0.00 0.12 0.16 0.00 0.08
#> TCGA.55.8511.01 7 0.2725 0.5594 0.00 0.04 0.00 0.14 0.00 0.00 0.82 0.00
#> TCGA.99.8025.01 4 0.5301 0.1011 0.00 0.16 0.02 0.42 0.00 0.00 0.40 0.00
#> TCGA.55.7283.01 4 0.4141 0.2557 0.00 0.06 0.00 0.56 0.00 0.00 0.38 0.00
#> TCGA.44.8117.01 7 0.2648 0.5127 0.00 0.08 0.00 0.08 0.00 0.00 0.84 0.00
#> TCGA.05.4405.01 7 0.3943 0.1773 0.00 0.04 0.00 0.40 0.00 0.00 0.56 0.00
#> TCGA.49.6745.01 8 0.4034 0.4701 0.12 0.04 0.06 0.00 0.02 0.00 0.00 0.76
#> TCGA.86.8673.01 8 0.7203 0.0803 0.16 0.04 0.10 0.00 0.04 0.26 0.00 0.40
#> TCGA.69.7765.01 8 0.5619 0.2221 0.36 0.02 0.04 0.00 0.06 0.02 0.00 0.50
#> TCGA.95.8494.01 8 0.5026 0.3518 0.22 0.04 0.06 0.00 0.00 0.04 0.00 0.64
#> TCGA.44.A47A.01 4 0.2224 0.6058 0.00 0.02 0.00 0.86 0.00 0.00 0.12 0.00
#> TCGA.55.8090.01 8 0.2348 0.5046 0.00 0.00 0.02 0.00 0.06 0.04 0.00 0.88
#> TCGA.55.7903.01 8 0.4933 0.2466 0.36 0.02 0.06 0.00 0.00 0.02 0.00 0.54
#> TCGA.78.7153.01 4 0.2623 0.6158 0.00 0.06 0.00 0.84 0.00 0.00 0.10 0.00
#> TCGA.55.7227.01 8 0.1408 0.5052 0.00 0.00 0.02 0.00 0.02 0.02 0.00 0.94
#> TCGA.86.A456.01 7 0.4412 0.4388 0.00 0.12 0.00 0.28 0.00 0.00 0.60 0.00
#> TCGA.38.4632.01 1 0.5040 0.2305 0.62 0.08 0.04 0.00 0.24 0.02 0.00 0.00
#> TCGA.69.7974.01 7 0.3170 0.5463 0.00 0.04 0.00 0.20 0.00 0.00 0.76 0.00
#> TCGA.55.7727.01 8 0.3663 0.4867 0.06 0.00 0.10 0.00 0.00 0.06 0.00 0.78
#> TCGA.78.8655.01 4 0.2407 0.6105 0.00 0.06 0.00 0.86 0.00 0.00 0.08 0.00
#> TCGA.55.7914.01 4 0.4345 0.4943 0.00 0.12 0.02 0.68 0.00 0.00 0.18 0.00
#> TCGA.62.A472.01 8 0.0471 0.5135 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.97.7554.01 7 0.2547 0.5438 0.00 0.04 0.00 0.12 0.00 0.00 0.84 0.00
#> TCGA.55.7576.01 1 0.4647 0.3999 0.68 0.02 0.02 0.00 0.16 0.00 0.00 0.12
#> TCGA.93.8067.01 8 0.6597 0.1253 0.06 0.02 0.20 0.00 0.04 0.20 0.00 0.48
#> TCGA.69.A59K.01 7 0.4299 0.4440 0.00 0.14 0.00 0.22 0.00 0.00 0.64 0.00
#> TCGA.95.7567.01 1 0.5192 0.4240 0.62 0.20 0.02 0.00 0.00 0.04 0.00 0.12
#> TCGA.49.AARN.01 4 0.4786 0.1605 0.00 0.14 0.00 0.48 0.00 0.00 0.38 0.00
#> TCGA.91.6836.01 7 0.5402 0.2293 0.00 0.26 0.00 0.24 0.02 0.00 0.48 0.00
#> TCGA.44.7659.01 8 0.3048 0.5003 0.02 0.00 0.08 0.00 0.02 0.04 0.00 0.84
#> TCGA.71.8520.01 4 0.4033 0.5556 0.00 0.12 0.00 0.68 0.00 0.00 0.20 0.00
#> TCGA.05.4425.01 4 0.5505 0.4593 0.00 0.12 0.04 0.62 0.02 0.02 0.18 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-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 '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 0.3816 0.619 0.619
#> 3 3 0.738 0.945 0.913 0.6329 0.700 0.515
#> 4 4 0.811 0.810 0.937 0.1393 0.848 0.595
#> 5 5 0.789 0.831 0.857 0.0810 0.876 0.587
#> 6 6 0.789 0.755 0.873 0.0641 1.000 1.000
#> 7 7 0.781 0.428 0.751 0.0314 0.914 0.640
#> 8 8 0.800 0.436 0.756 0.0260 0.914 0.591
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.NJ.A4YI.01 2 0 1 0 1
#> TCGA.62.A46V.01 2 0 1 0 1
#> TCGA.62.A46R.01 1 0 1 1 0
#> TCGA.97.A4M0.01 2 0 1 0 1
#> TCGA.55.8511.01 1 0 1 1 0
#> TCGA.99.8025.01 1 0 1 1 0
#> TCGA.55.7283.01 2 0 1 0 1
#> TCGA.44.8117.01 1 0 1 1 0
#> TCGA.05.4405.01 2 0 1 0 1
#> TCGA.44.A47A.01 2 0 1 0 1
#> TCGA.78.7153.01 2 0 1 0 1
#> TCGA.86.A456.01 2 0 1 0 1
#> TCGA.69.7974.01 2 0 1 0 1
#> TCGA.78.8655.01 2 0 1 0 1
#> TCGA.55.7914.01 2 0 1 0 1
#> TCGA.97.7554.01 1 0 1 1 0
#> TCGA.69.A59K.01 2 0 1 0 1
#> TCGA.49.AARN.01 2 0 1 0 1
#> TCGA.91.6836.01 2 0 1 0 1
#> TCGA.71.8520.01 2 0 1 0 1
#> TCGA.05.4425.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.NJ.A4YI.01 3 0.480 0.765 0.00 0.22 0.78
#> TCGA.62.A46V.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.62.A46R.01 1 0.000 0.973 1.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.55.8511.01 1 0.000 0.973 1.00 0.00 0.00
#> TCGA.99.8025.01 1 0.254 0.960 0.92 0.08 0.00
#> TCGA.55.7283.01 3 0.000 0.895 0.00 0.00 1.00
#> TCGA.44.8117.01 1 0.254 0.960 0.92 0.08 0.00
#> TCGA.05.4405.01 3 0.000 0.895 0.00 0.00 1.00
#> TCGA.44.A47A.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.78.7153.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.86.A456.01 3 0.000 0.895 0.00 0.00 1.00
#> TCGA.69.7974.01 3 0.000 0.895 0.00 0.00 1.00
#> TCGA.78.8655.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.55.7914.01 3 0.000 0.895 0.00 0.00 1.00
#> TCGA.97.7554.01 1 0.000 0.973 1.00 0.00 0.00
#> TCGA.69.A59K.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.49.AARN.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.91.6836.01 2 0.556 1.000 0.00 0.70 0.30
#> TCGA.71.8520.01 3 0.480 0.765 0.00 0.22 0.78
#> TCGA.05.4425.01 2 0.556 1.000 0.00 0.70 0.30
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.NJ.A4YI.01 4 0.2345 0.000 0.00 0.00 0.10 0.90
#> TCGA.62.A46V.01 2 0.0707 0.891 0.00 0.98 0.02 0.00
#> TCGA.62.A46R.01 1 0.0000 0.943 1.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0707 0.891 0.00 0.98 0.02 0.00
#> TCGA.55.8511.01 1 0.0000 0.943 1.00 0.00 0.00 0.00
#> TCGA.99.8025.01 1 0.3037 0.913 0.88 0.02 0.00 0.10
#> TCGA.55.7283.01 3 0.0000 0.921 0.00 0.00 1.00 0.00
#> TCGA.44.8117.01 1 0.3037 0.913 0.88 0.02 0.00 0.10
#> TCGA.05.4405.01 3 0.0000 0.921 0.00 0.00 1.00 0.00
#> TCGA.44.A47A.01 2 0.0707 0.891 0.00 0.98 0.02 0.00
#> TCGA.78.7153.01 2 0.0707 0.891 0.00 0.98 0.02 0.00
#> TCGA.86.A456.01 3 0.0000 0.921 0.00 0.00 1.00 0.00
#> TCGA.69.7974.01 3 0.0000 0.921 0.00 0.00 1.00 0.00
#> TCGA.78.8655.01 2 0.4994 -0.018 0.00 0.52 0.48 0.00
#> TCGA.55.7914.01 3 0.0000 0.921 0.00 0.00 1.00 0.00
#> TCGA.97.7554.01 1 0.0000 0.943 1.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 3 0.3400 0.766 0.00 0.18 0.82 0.00
#> TCGA.49.AARN.01 3 0.3400 0.766 0.00 0.18 0.82 0.00
#> TCGA.91.6836.01 2 0.0707 0.891 0.00 0.98 0.02 0.00
#> TCGA.71.8520.01 3 0.0707 0.898 0.00 0.00 0.98 0.02
#> TCGA.05.4425.01 2 0.0707 0.891 0.00 0.98 0.02 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.NJ.A4YI.01 4 0.0609 0.000 0.0 0.00 0.02 0.98 0.00
#> TCGA.62.A46V.01 2 0.0000 0.996 0.0 1.00 0.00 0.00 0.00
#> TCGA.62.A46R.01 1 0.0000 0.885 1.0 0.00 0.00 0.00 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.996 0.0 1.00 0.00 0.00 0.00
#> TCGA.55.8511.01 1 0.2438 0.849 0.9 0.00 0.04 0.00 0.06
#> TCGA.99.8025.01 1 0.3109 0.848 0.8 0.00 0.00 0.00 0.20
#> TCGA.55.7283.01 3 0.1043 0.821 0.0 0.04 0.96 0.00 0.00
#> TCGA.44.8117.01 1 0.3513 0.848 0.8 0.00 0.00 0.02 0.18
#> TCGA.05.4405.01 5 0.5131 0.854 0.0 0.04 0.42 0.00 0.54
#> TCGA.44.A47A.01 2 0.0000 0.996 0.0 1.00 0.00 0.00 0.00
#> TCGA.78.7153.01 2 0.0000 0.996 0.0 1.00 0.00 0.00 0.00
#> TCGA.86.A456.01 5 0.5131 0.854 0.0 0.04 0.42 0.00 0.54
#> TCGA.69.7974.01 3 0.2438 0.827 0.0 0.04 0.90 0.00 0.06
#> TCGA.78.8655.01 3 0.3109 0.630 0.0 0.20 0.80 0.00 0.00
#> TCGA.55.7914.01 5 0.5131 0.854 0.0 0.04 0.42 0.00 0.54
#> TCGA.97.7554.01 1 0.0000 0.885 1.0 0.00 0.00 0.00 0.00
#> TCGA.69.A59K.01 3 0.2797 0.852 0.0 0.06 0.88 0.00 0.06
#> TCGA.49.AARN.01 3 0.2797 0.852 0.0 0.06 0.88 0.00 0.06
#> TCGA.91.6836.01 2 0.0609 0.980 0.0 0.98 0.00 0.00 0.02
#> TCGA.71.8520.01 5 0.4398 0.634 0.0 0.00 0.24 0.04 0.72
#> TCGA.05.4425.01 2 0.0000 0.996 0.0 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.NJ.A4YI.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.62.A46V.01 2 0.0000 0.952 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.62.A46R.01 1 0.0000 0.819 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.97.A4M0.01 2 0.0000 0.952 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.55.8511.01 1 0.2190 0.783 0.90 0.00 0.04 0.06 0.00 0
#> TCGA.99.8025.01 1 0.4503 0.743 0.68 0.00 0.08 0.24 0.00 0
#> TCGA.55.7283.01 3 0.3475 0.733 0.00 0.00 0.80 0.06 0.14 0
#> TCGA.44.8117.01 1 0.4360 0.743 0.68 0.00 0.06 0.26 0.00 0
#> TCGA.05.4405.01 5 0.0000 0.823 0.00 0.00 0.00 0.00 1.00 0
#> TCGA.44.A47A.01 2 0.1267 0.936 0.00 0.94 0.00 0.06 0.00 0
#> TCGA.78.7153.01 2 0.0000 0.952 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.86.A456.01 5 0.0000 0.823 0.00 0.00 0.00 0.00 1.00 0
#> TCGA.69.7974.01 3 0.3864 0.482 0.00 0.00 0.52 0.00 0.48 0
#> TCGA.78.8655.01 3 0.4279 0.693 0.00 0.06 0.78 0.08 0.08 0
#> TCGA.55.7914.01 5 0.0547 0.815 0.00 0.00 0.00 0.02 0.98 0
#> TCGA.97.7554.01 1 0.0000 0.819 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.69.A59K.01 3 0.3950 0.787 0.00 0.04 0.72 0.00 0.24 0
#> TCGA.49.AARN.01 3 0.3950 0.787 0.00 0.04 0.72 0.00 0.24 0
#> TCGA.91.6836.01 2 0.2350 0.870 0.00 0.88 0.02 0.10 0.00 0
#> TCGA.71.8520.01 5 0.3828 0.418 0.00 0.00 0.00 0.44 0.56 0
#> TCGA.05.4425.01 2 0.1267 0.936 0.00 0.94 0.00 0.06 0.00 0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.NJ.A4YI.01 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.62.A46V.01 2 0.0000 0.8493 0.00 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.62.A46R.01 1 0.0000 0.7151 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.97.A4M0.01 2 0.0000 0.8493 0.00 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.55.8511.01 1 0.3519 0.5944 0.74 0.00 0.04 0.22 0.00 0 0.00
#> TCGA.99.8025.01 1 0.4939 0.6234 0.56 0.00 0.30 0.14 0.00 0 0.00
#> TCGA.55.7283.01 3 0.5342 0.6993 0.00 0.00 0.42 0.18 0.40 0 0.00
#> TCGA.44.8117.01 1 0.5055 0.6234 0.56 0.00 0.26 0.18 0.00 0 0.00
#> TCGA.05.4405.01 5 0.3525 0.2190 0.00 0.00 0.00 0.00 0.56 0 0.44
#> TCGA.44.A47A.01 2 0.2422 0.7884 0.00 0.82 0.18 0.00 0.00 0 0.00
#> TCGA.78.7153.01 2 0.0000 0.8493 0.00 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.86.A456.01 5 0.3525 0.2190 0.00 0.00 0.00 0.00 0.56 0 0.44
#> TCGA.69.7974.01 5 0.0000 0.0896 0.00 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.78.8655.01 3 0.3413 0.7008 0.00 0.00 0.62 0.00 0.38 0 0.00
#> TCGA.55.7914.01 5 0.4701 0.1340 0.00 0.00 0.02 0.04 0.50 0 0.44
#> TCGA.97.7554.01 1 0.0000 0.7151 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.69.A59K.01 5 0.3685 -0.5039 0.00 0.00 0.32 0.02 0.66 0 0.00
#> TCGA.49.AARN.01 5 0.3685 -0.5039 0.00 0.00 0.32 0.02 0.66 0 0.00
#> TCGA.91.6836.01 2 0.3294 0.5435 0.00 0.66 0.00 0.34 0.00 0 0.00
#> TCGA.71.8520.01 7 0.0863 0.0000 0.00 0.00 0.00 0.04 0.00 0 0.96
#> TCGA.05.4425.01 2 0.2422 0.7884 0.00 0.82 0.18 0.00 0.00 0 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.NJ.A4YI.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.62.A46V.01 2 0.2650 0.579 0.00 0.76 0.00 0.24 0.00 0 0.00 0.00
#> TCGA.62.A46R.01 1 0.0471 0.705 0.98 0.00 0.02 0.00 0.00 0 0.00 0.00
#> TCGA.97.A4M0.01 2 0.2650 0.579 0.00 0.76 0.00 0.24 0.00 0 0.00 0.00
#> TCGA.55.8511.01 1 0.4467 0.512 0.66 0.00 0.12 0.20 0.00 0 0.02 0.00
#> TCGA.99.8025.01 1 0.5717 0.623 0.58 0.00 0.08 0.06 0.06 0 0.22 0.00
#> TCGA.55.7283.01 3 0.2852 0.000 0.00 0.00 0.72 0.00 0.00 0 0.00 0.28
#> TCGA.44.8117.01 1 0.5844 0.623 0.58 0.00 0.14 0.04 0.08 0 0.16 0.00
#> TCGA.05.4405.01 5 0.3404 0.831 0.00 0.00 0.04 0.00 0.72 0 0.00 0.24
#> TCGA.44.A47A.01 2 0.1091 0.517 0.00 0.94 0.00 0.00 0.00 0 0.00 0.06
#> TCGA.78.7153.01 2 0.2650 0.579 0.00 0.76 0.00 0.24 0.00 0 0.00 0.00
#> TCGA.86.A456.01 5 0.3404 0.831 0.00 0.00 0.04 0.00 0.72 0 0.00 0.24
#> TCGA.69.7974.01 8 0.3757 0.185 0.00 0.00 0.06 0.00 0.26 0 0.00 0.68
#> TCGA.78.8655.01 8 0.7156 -0.221 0.00 0.24 0.16 0.12 0.00 0 0.10 0.38
#> TCGA.55.7914.01 5 0.1341 0.605 0.00 0.00 0.00 0.00 0.92 0 0.00 0.08
#> TCGA.97.7554.01 1 0.0000 0.705 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.69.A59K.01 8 0.0000 0.490 0.00 0.00 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.49.AARN.01 8 0.0000 0.490 0.00 0.00 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.91.6836.01 4 0.3193 0.000 0.00 0.38 0.00 0.62 0.00 0 0.00 0.00
#> TCGA.71.8520.01 7 0.3083 0.000 0.00 0.00 0.00 0.00 0.34 0 0.66 0.00
#> TCGA.05.4425.01 2 0.1091 0.517 0.00 0.94 0.00 0.00 0.00 0 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 93 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.999 1.000 0.4926 0.508 0.508
#> 3 3 1.000 0.970 0.987 0.3197 0.751 0.550
#> 4 4 1.000 0.945 0.979 0.1507 0.756 0.422
#> 5 5 1.000 0.970 0.987 0.0532 0.925 0.721
#> 6 6 0.832 0.814 0.911 0.0376 0.891 0.560
#> 7 7 0.835 0.774 0.890 0.0106 0.997 0.981
#> 8 8 0.845 0.730 0.875 0.0137 0.972 0.847
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.69.8453.01 1 0.000 1.000 1.00 0.00
#> TCGA.53.A4EZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.J2.A4AG.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.AAR4.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6984.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.6744.01 1 0.000 1.000 1.00 0.00
#> TCGA.L9.A743.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.6562.01 2 0.000 0.999 0.00 1.00
#> TCGA.86.8074.01 2 0.000 0.999 0.00 1.00
#> TCGA.39.5011.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8619.01 1 0.000 1.000 1.00 0.00
#> TCGA.69.8253.01 2 0.000 0.999 0.00 1.00
#> TCGA.91.6849.01 2 0.000 0.999 0.00 1.00
#> TCGA.69.8254.01 2 0.000 0.999 0.00 1.00
#> TCGA.L4.A4E5.01 2 0.242 0.958 0.04 0.96
#> TCGA.44.6775.01 1 0.000 1.000 1.00 0.00
#> TCGA.MP.A4T9.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.7714.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.7815.01 1 0.000 1.000 1.00 0.00
#> TCGA.05.5423.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.6985.01 1 0.000 1.000 1.00 0.00
#> TCGA.93.7347.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.6777.01 1 0.000 1.000 1.00 0.00
#> TCGA.99.7458.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.7938.01 2 0.000 0.999 0.00 1.00
#> TCGA.85.6560.01 1 0.000 1.000 1.00 0.00
#> TCGA.L9.A50W.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.8460.01 2 0.000 0.999 0.00 1.00
#> TCGA.67.6217.01 2 0.000 0.999 0.00 1.00
#> TCGA.86.8671.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.6592.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.7661.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.6767.01 1 0.000 1.000 1.00 0.00
#> TCGA.69.7761.01 1 0.000 1.000 1.00 0.00
#> TCGA.91.6835.01 1 0.000 1.000 1.00 0.00
#> TCGA.95.A4VN.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.A47F.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.5942.01 2 0.000 0.999 0.00 1.00
#> TCGA.80.5608.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.A491.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.6146.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.7552.01 1 0.000 1.000 1.00 0.00
#> TCGA.91.7771.01 2 0.000 0.999 0.00 1.00
#> TCGA.86.8359.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8301.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8089.01 1 0.000 1.000 1.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.8459.01 1 0.000 1.000 1.00 0.00
#> TCGA.73.7499.01 2 0.000 0.999 0.00 1.00
#> TCGA.MP.A4T7.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.8171.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.8457.01 2 0.000 0.999 0.00 1.00
#> TCGA.53.7626.01 1 0.000 1.000 1.00 0.00
#> TCGA.69.7980.01 2 0.000 0.999 0.00 1.00
#> TCGA.86.8668.01 2 0.000 0.999 0.00 1.00
#> TCGA.MP.A4T4.01 1 0.000 1.000 1.00 0.00
#> TCGA.93.A4JO.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.8510.01 1 0.000 1.000 1.00 0.00
#> TCGA.49.AARO.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.8076.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5044.01 1 0.000 1.000 1.00 0.00
#> TCGA.64.5781.01 1 0.000 1.000 1.00 0.00
#> TCGA.NJ.A4YF.01 2 0.000 0.999 0.00 1.00
#> TCGA.49.AAR3.01 1 0.000 1.000 1.00 0.00
#> TCGA.69.7760.01 2 0.000 0.999 0.00 1.00
#> TCGA.49.4512.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.A4M3.01 2 0.000 0.999 0.00 1.00
#> TCGA.99.8028.01 1 0.000 1.000 1.00 0.00
#> TCGA.NJ.A7XG.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.A48X.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.6594.01 2 0.000 0.999 0.00 1.00
#> TCGA.78.7537.01 2 0.000 0.999 0.00 1.00
#> TCGA.85.A513.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5935.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.6981.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.7941.01 2 0.000 0.999 0.00 1.00
#> TCGA.67.4679.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.5941.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8174.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.7725.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.6983.01 2 0.000 0.999 0.00 1.00
#> TCGA.O2.A52Q.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6978.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.A48Y.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.6595.01 1 0.000 1.000 1.00 0.00
#> TCGA.91.8497.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.5049.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.A4M7.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.7662.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5068.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6987.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.7145.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.6593.01 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.69.8453.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.53.A4EZ.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.J2.A4AG.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.49.AAR4.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.55.6984.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.49.6744.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.L9.A743.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.86.6562.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.86.8074.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.39.5011.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.55.8619.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.69.8253.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.91.6849.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.69.8254.01 2 0.5397 0.627 0.00 0.72 0.28
#> TCGA.L4.A4E5.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.44.6775.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.MP.A4T9.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.86.7714.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.55.7815.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.05.5423.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.55.6985.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.93.7347.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.44.6777.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.99.7458.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.97.7938.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.85.6560.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.L9.A50W.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.50.8460.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.67.6217.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.86.8671.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.50.6592.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.44.7661.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.49.6767.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.69.7761.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.91.6835.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.95.A4VN.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.44.A47F.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.50.5942.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.80.5608.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.55.A491.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.44.6146.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.97.7552.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.91.7771.01 3 0.4002 0.803 0.00 0.16 0.84
#> TCGA.86.8359.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.55.8301.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.55.8089.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.50.8459.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.73.7499.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.MP.A4T7.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.97.8171.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.50.8457.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.53.7626.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.69.7980.01 3 0.2537 0.908 0.00 0.08 0.92
#> TCGA.86.8668.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.MP.A4T4.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.93.A4JO.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.55.8510.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.49.AARO.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.86.8076.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.50.5044.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.64.5781.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.NJ.A4YF.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.49.AAR3.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.49.4512.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.97.A4M3.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.99.8028.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.NJ.A7XG.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.55.A48X.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.50.6594.01 2 0.6126 0.357 0.00 0.60 0.40
#> TCGA.78.7537.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.85.A513.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.50.5935.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.55.6981.01 3 0.2066 0.917 0.06 0.00 0.94
#> TCGA.97.7941.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.67.4679.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.50.5941.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.97.8174.01 2 0.4291 0.777 0.00 0.82 0.18
#> TCGA.55.7725.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.55.6983.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.O2.A52Q.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.55.6978.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.55.A48Y.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.50.6595.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0892 0.970 0.00 0.02 0.98
#> TCGA.50.5049.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.97.A4M7.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.44.7662.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.50.5068.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.55.6987.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.78.7145.01 2 0.0000 0.960 0.00 1.00 0.00
#> TCGA.50.6593.01 3 0.0000 0.987 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.69.8453.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.53.A4EZ.01 4 0.2345 0.8700 0.00 0.00 0.10 0.90
#> TCGA.J2.A4AG.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.49.AAR4.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.55.6984.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.49.6744.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.L9.A743.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.86.6562.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.86.8074.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.39.5011.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.55.8619.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.69.8253.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.91.6849.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.69.8254.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.L4.A4E5.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.44.6775.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.MP.A4T9.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.86.7714.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.55.7815.01 4 0.0707 0.9440 0.02 0.00 0.00 0.98
#> TCGA.05.5423.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.55.6985.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.93.7347.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.44.6777.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.99.7458.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.97.7938.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.85.6560.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.50.8460.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.67.6217.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.86.8671.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.50.6592.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.44.7661.01 1 0.0707 0.9422 0.98 0.00 0.00 0.02
#> TCGA.49.6767.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.69.7761.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.91.6835.01 1 0.4948 0.2267 0.56 0.00 0.00 0.44
#> TCGA.95.A4VN.01 4 0.4977 0.0751 0.46 0.00 0.00 0.54
#> TCGA.44.A47F.01 3 0.1211 0.9606 0.00 0.04 0.96 0.00
#> TCGA.50.5942.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.80.5608.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.55.A491.01 4 0.4624 0.4860 0.00 0.00 0.34 0.66
#> TCGA.44.6146.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.97.7552.01 1 0.4713 0.4423 0.64 0.00 0.00 0.36
#> TCGA.91.7771.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.86.8359.01 4 0.0707 0.9456 0.00 0.00 0.02 0.98
#> TCGA.55.8301.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.55.8089.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.50.8459.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.73.7499.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.MP.A4T7.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.97.8171.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.50.8457.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.53.7626.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.69.7980.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.86.8668.01 3 0.1211 0.9606 0.00 0.04 0.96 0.00
#> TCGA.MP.A4T4.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.55.8510.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.49.AARO.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.86.8076.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.50.5044.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.64.5781.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.49.AAR3.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.49.4512.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.97.A4M3.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.99.8028.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.NJ.A7XG.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.55.A48X.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.50.6594.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.78.7537.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.85.A513.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.50.5935.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.55.6981.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.97.7941.01 3 0.1211 0.9606 0.00 0.04 0.96 0.00
#> TCGA.67.4679.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.50.5941.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.97.8174.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.55.7725.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.55.6983.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.O2.A52Q.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.55.6978.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.50.6595.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0000 0.9943 0.00 0.00 1.00 0.00
#> TCGA.50.5049.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.44.7662.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.50.5068.01 4 0.0000 0.9609 0.00 0.00 0.00 1.00
#> TCGA.55.6987.01 1 0.0000 0.9611 1.00 0.00 0.00 0.00
#> TCGA.78.7145.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.50.6593.01 4 0.1637 0.9104 0.00 0.00 0.06 0.94
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.69.8453.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.53.A4EZ.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
#> TCGA.J2.A4AG.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.49.AAR4.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6984.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.49.6744.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.L9.A743.01 1 0.0609 0.946 0.98 0.00 0.00 0.02 0.00
#> TCGA.86.6562.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
#> TCGA.86.8074.01 5 0.0609 0.972 0.00 0.00 0.02 0.00 0.98
#> TCGA.39.5011.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8619.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.69.8253.01 2 0.1043 0.960 0.00 0.96 0.04 0.00 0.00
#> TCGA.91.6849.01 2 0.1410 0.941 0.00 0.94 0.06 0.00 0.00
#> TCGA.69.8254.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.L4.A4E5.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.6775.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.MP.A4T9.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.86.7714.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7815.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.05.5423.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6985.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.93.7347.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.44.6777.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.99.7458.01 3 0.0609 0.978 0.00 0.00 0.98 0.00 0.02
#> TCGA.97.7938.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.6560.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A50W.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.8460.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.67.6217.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8671.01 1 0.2020 0.863 0.90 0.00 0.00 0.10 0.00
#> TCGA.50.6592.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 1 0.4287 0.180 0.54 0.00 0.00 0.46 0.00
#> TCGA.49.6767.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7761.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6835.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.95.A4VN.01 4 0.0609 0.974 0.02 0.00 0.00 0.98 0.00
#> TCGA.44.A47F.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5942.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.80.5608.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.A491.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.6146.01 2 0.1410 0.940 0.00 0.94 0.06 0.00 0.00
#> TCGA.97.7552.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.91.7771.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8359.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.8301.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.8089.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.73.7499.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
#> TCGA.MP.A4T7.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.8171.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.8457.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.53.7626.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.69.7980.01 5 0.1732 0.918 0.00 0.00 0.08 0.00 0.92
#> TCGA.86.8668.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.MP.A4T4.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 1 0.2020 0.863 0.90 0.00 0.00 0.10 0.00
#> TCGA.55.8510.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.49.AARO.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8076.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5044.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.64.5781.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.AAR3.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.A4M3.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A7XG.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A48X.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.6594.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7537.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.A513.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.5935.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6981.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.97.7941.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.67.4679.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5941.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.97.8174.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7725.01 2 0.1043 0.960 0.00 0.96 0.04 0.00 0.00
#> TCGA.55.6983.01 3 0.0609 0.978 0.00 0.00 0.98 0.00 0.02
#> TCGA.O2.A52Q.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.50.6595.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5049.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 4 0.0609 0.984 0.00 0.00 0.00 0.98 0.02
#> TCGA.44.7662.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 4 0.0000 0.993 0.00 0.00 0.00 1.00 0.00
#> TCGA.55.6987.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7145.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6593.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.69.8453.01 6 0.2631 0.8210 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.53.A4EZ.01 6 0.2941 0.5216 0.00 0.00 0.00 0.00 0.22 0.78
#> TCGA.J2.A4AG.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.AAR4.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6984.01 6 0.2631 0.8210 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.49.6744.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.L9.A743.01 4 0.3198 0.6487 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.86.6562.01 5 0.2631 0.7002 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.86.8074.01 5 0.1480 0.7007 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.39.5011.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8619.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.8253.01 2 0.3706 0.5107 0.00 0.62 0.38 0.00 0.00 0.00
#> TCGA.91.6849.01 2 0.3828 0.4080 0.00 0.56 0.44 0.00 0.00 0.00
#> TCGA.69.8254.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.L4.A4E5.01 5 0.2631 0.7002 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.44.6775.01 6 0.2631 0.8210 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.MP.A4T9.01 6 0.2631 0.8210 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.86.7714.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.05.5423.01 3 0.0547 0.8346 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.55.6985.01 6 0.2631 0.8210 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.93.7347.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6777.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.99.7458.01 6 0.2793 0.6644 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.97.7938.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.6560.01 1 0.2260 0.8074 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.L9.A50W.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.8460.01 3 0.3706 0.4314 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.67.6217.01 3 0.3578 0.5241 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.86.8671.01 4 0.2454 0.7871 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.50.6592.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 4 0.2260 0.8114 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.49.6767.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7761.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6835.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.A4VN.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A47F.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5942.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.80.5608.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A491.01 6 0.0000 0.7444 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.6146.01 2 0.4632 0.3535 0.00 0.52 0.44 0.00 0.04 0.00
#> TCGA.97.7552.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.7771.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8359.01 6 0.2631 0.5754 0.00 0.00 0.00 0.00 0.18 0.82
#> TCGA.55.8301.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8089.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.73.7499.01 6 0.0000 0.7444 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MP.A4T7.01 3 0.2793 0.6928 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.97.8171.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.8457.01 3 0.3578 0.5241 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.53.7626.01 6 0.2631 0.8210 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.69.7980.01 5 0.3711 0.5568 0.00 0.00 0.26 0.00 0.72 0.02
#> TCGA.86.8668.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4T4.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 4 0.2454 0.7871 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.55.8510.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.AARO.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8076.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5044.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.64.5781.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 5 0.2631 0.7002 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.49.AAR3.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.97.A4M3.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.2048 0.8363 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.NJ.A7XG.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48X.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6594.01 5 0.3864 0.1356 0.00 0.00 0.48 0.00 0.52 0.00
#> TCGA.78.7537.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A513.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5935.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6981.01 6 0.3409 0.6776 0.00 0.00 0.00 0.30 0.00 0.70
#> TCGA.97.7941.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.4679.01 2 0.0000 0.8432 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5941.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.97.8174.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7725.01 2 0.3706 0.5107 0.00 0.62 0.38 0.00 0.00 0.00
#> TCGA.55.6983.01 6 0.3409 0.5006 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.O2.A52Q.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.6595.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5049.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 6 0.2631 0.8210 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.44.7662.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5068.01 4 0.0000 0.9564 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6987.01 1 0.0000 0.9808 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7145.01 5 0.4337 0.0112 0.00 0.48 0.02 0.00 0.50 0.00
#> TCGA.50.6593.01 6 0.0000 0.7444 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.69.8453.01 6 0.2803 0.7601 0.00 0.00 0.00 0.10 0.00 0.84 0.06
#> TCGA.53.A4EZ.01 6 0.4487 0.3674 0.00 0.00 0.00 0.00 0.08 0.60 0.32
#> TCGA.J2.A4AG.01 4 0.0504 0.9169 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.49.AAR4.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6984.01 6 0.2803 0.7601 0.00 0.00 0.00 0.10 0.00 0.84 0.06
#> TCGA.49.6744.01 4 0.1166 0.9028 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.L9.A743.01 4 0.3307 0.6490 0.24 0.00 0.00 0.74 0.00 0.00 0.02
#> TCGA.86.6562.01 5 0.4681 0.5734 0.00 0.00 0.00 0.00 0.58 0.10 0.32
#> TCGA.86.8074.01 5 0.0504 0.5372 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.39.5011.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8619.01 4 0.0000 0.9182 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.8253.01 2 0.2945 0.3725 0.00 0.74 0.26 0.00 0.00 0.00 0.00
#> TCGA.91.6849.01 2 0.3496 -0.1693 0.00 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.69.8254.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.L4.A4E5.01 5 0.4783 0.5647 0.00 0.00 0.00 0.00 0.54 0.10 0.36
#> TCGA.44.6775.01 6 0.2259 0.7668 0.00 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.MP.A4T9.01 6 0.2259 0.7668 0.00 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.86.7714.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 4 0.0504 0.9152 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.05.5423.01 3 0.0863 0.8644 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.55.6985.01 6 0.2906 0.7574 0.00 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.93.7347.01 4 0.1166 0.9028 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.44.6777.01 4 0.1166 0.9028 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.99.7458.01 6 0.3186 0.5586 0.00 0.00 0.22 0.00 0.00 0.76 0.02
#> TCGA.97.7938.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.6560.01 1 0.3517 0.5974 0.70 0.00 0.00 0.28 0.00 0.00 0.02
#> TCGA.L9.A50W.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8460.01 3 0.3307 0.6647 0.00 0.00 0.74 0.00 0.00 0.24 0.02
#> TCGA.67.6217.01 3 0.3186 0.6876 0.00 0.00 0.76 0.00 0.00 0.22 0.02
#> TCGA.86.8671.01 4 0.2745 0.7582 0.16 0.00 0.00 0.82 0.00 0.00 0.02
#> TCGA.50.6592.01 1 0.1006 0.9402 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.44.7661.01 4 0.2745 0.7582 0.16 0.00 0.00 0.82 0.00 0.00 0.02
#> TCGA.49.6767.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7761.01 1 0.1363 0.9273 0.94 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.91.6835.01 4 0.0504 0.9152 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.95.A4VN.01 4 0.0504 0.9152 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.44.A47F.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5942.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.80.5608.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A491.01 6 0.2421 0.7113 0.00 0.00 0.00 0.02 0.02 0.88 0.08
#> TCGA.44.6146.01 7 0.6179 0.0000 0.00 0.32 0.24 0.00 0.04 0.00 0.40
#> TCGA.97.7552.01 4 0.0504 0.9152 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.91.7771.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8359.01 6 0.4338 0.4323 0.00 0.00 0.00 0.00 0.08 0.64 0.28
#> TCGA.55.8301.01 4 0.0000 0.9182 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8089.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 4 0.2572 0.8519 0.00 0.00 0.00 0.86 0.00 0.08 0.06
#> TCGA.73.7499.01 6 0.3208 0.6533 0.00 0.00 0.02 0.00 0.04 0.82 0.12
#> TCGA.MP.A4T7.01 3 0.2259 0.7684 0.00 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.97.8171.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8457.01 3 0.2906 0.7443 0.00 0.00 0.80 0.00 0.00 0.18 0.02
#> TCGA.53.7626.01 6 0.2906 0.7574 0.00 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.69.7980.01 5 0.3263 0.4901 0.00 0.00 0.12 0.00 0.80 0.00 0.08
#> TCGA.86.8668.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4T4.01 1 0.1664 0.9101 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.93.A4JO.01 4 0.2745 0.7582 0.16 0.00 0.00 0.82 0.00 0.00 0.02
#> TCGA.55.8510.01 4 0.0504 0.9152 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.49.AARO.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8076.01 4 0.0504 0.9169 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.50.5044.01 4 0.1166 0.9028 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.64.5781.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 5 0.4737 0.5740 0.00 0.00 0.00 0.00 0.56 0.10 0.34
#> TCGA.49.AAR3.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.0504 0.8832 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.97.A4M3.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.2569 0.8160 0.84 0.00 0.00 0.14 0.00 0.00 0.02
#> TCGA.NJ.A7XG.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48X.01 4 0.1166 0.9028 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.50.6594.01 5 0.4191 0.2710 0.00 0.00 0.30 0.00 0.64 0.00 0.06
#> TCGA.78.7537.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A513.01 4 0.0863 0.9120 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.50.5935.01 2 0.0504 0.8350 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.55.6981.01 6 0.3307 0.6943 0.00 0.00 0.00 0.24 0.00 0.74 0.02
#> TCGA.97.7941.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.4679.01 2 0.0000 0.8584 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5941.01 4 0.0863 0.9120 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.97.8174.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 2 0.2945 0.3725 0.00 0.74 0.26 0.00 0.00 0.00 0.00
#> TCGA.55.6983.01 6 0.3867 0.2319 0.00 0.00 0.38 0.00 0.00 0.60 0.02
#> TCGA.O2.A52Q.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 1 0.0000 0.9476 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 4 0.1006 0.9181 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.50.6595.01 1 0.1006 0.9402 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.91.8497.01 3 0.0000 0.8931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5049.01 1 0.1006 0.9402 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.97.A4M7.01 6 0.2259 0.7668 0.00 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.44.7662.01 1 0.1006 0.9364 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.50.5068.01 4 0.0000 0.9182 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6987.01 1 0.1006 0.9402 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.78.7145.01 5 0.4778 -0.0614 0.00 0.34 0.02 0.00 0.58 0.00 0.06
#> TCGA.50.6593.01 6 0.1664 0.6993 0.00 0.00 0.00 0.00 0.02 0.92 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.69.8453.01 6 0.3397 0.681757 0.00 0.00 0.00 0.04 0.10 0.80 0.06 0.00
#> TCGA.53.A4EZ.01 8 0.4886 0.203739 0.00 0.00 0.00 0.00 0.04 0.44 0.06 0.46
#> TCGA.J2.A4AG.01 4 0.0808 0.915723 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.49.AAR4.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6984.01 6 0.3397 0.681757 0.00 0.00 0.00 0.04 0.10 0.80 0.06 0.00
#> TCGA.49.6744.01 4 0.1341 0.899154 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.L9.A743.01 4 0.2888 0.745192 0.16 0.00 0.00 0.80 0.00 0.00 0.04 0.00
#> TCGA.86.6562.01 8 0.0941 0.481844 0.00 0.00 0.00 0.00 0.00 0.02 0.02 0.96
#> TCGA.86.8074.01 5 0.3570 0.633199 0.00 0.00 0.02 0.00 0.62 0.00 0.00 0.36
#> TCGA.39.5011.01 1 0.0471 0.933554 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.8619.01 4 0.0471 0.919126 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.69.8253.01 3 0.3658 -0.029713 0.00 0.40 0.58 0.00 0.00 0.00 0.02 0.00
#> TCGA.91.6849.01 3 0.3618 -0.000336 0.00 0.38 0.60 0.00 0.00 0.00 0.02 0.00
#> TCGA.69.8254.01 3 0.0000 0.616380 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L4.A4E5.01 8 0.0000 0.471892 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.44.6775.01 6 0.0808 0.741787 0.00 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.MP.A4T9.01 6 0.0808 0.741787 0.00 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.86.7714.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7815.01 4 0.1275 0.910690 0.02 0.00 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.05.5423.01 3 0.1741 0.574262 0.00 0.00 0.92 0.00 0.04 0.00 0.02 0.02
#> TCGA.55.6985.01 6 0.1765 0.697349 0.00 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.93.7347.01 4 0.1341 0.899154 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.44.6777.01 4 0.0808 0.915723 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.99.7458.01 6 0.4760 0.476588 0.00 0.00 0.16 0.00 0.00 0.62 0.20 0.02
#> TCGA.97.7938.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.6560.01 1 0.2888 0.726122 0.80 0.00 0.00 0.16 0.00 0.00 0.04 0.00
#> TCGA.L9.A50W.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8460.01 3 0.5305 0.291166 0.00 0.00 0.50 0.00 0.00 0.28 0.20 0.02
#> TCGA.67.6217.01 3 0.5244 0.314506 0.00 0.00 0.52 0.00 0.00 0.26 0.20 0.02
#> TCGA.86.8671.01 4 0.1607 0.896880 0.04 0.00 0.00 0.92 0.00 0.00 0.04 0.00
#> TCGA.50.6592.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 4 0.1607 0.896880 0.04 0.00 0.00 0.92 0.00 0.00 0.04 0.00
#> TCGA.49.6767.01 1 0.0471 0.933554 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.69.7761.01 1 0.1275 0.904474 0.94 0.00 0.00 0.02 0.00 0.00 0.04 0.00
#> TCGA.91.6835.01 4 0.0941 0.915835 0.02 0.00 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.95.A4VN.01 4 0.1275 0.910690 0.02 0.00 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.44.A47F.01 3 0.0471 0.606444 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.50.5942.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.80.5608.01 3 0.2407 0.569357 0.00 0.00 0.86 0.00 0.00 0.00 0.08 0.06
#> TCGA.55.A491.01 6 0.2862 0.646118 0.00 0.00 0.00 0.00 0.00 0.82 0.08 0.10
#> TCGA.44.6146.01 7 0.5245 0.000000 0.00 0.10 0.24 0.00 0.08 0.00 0.58 0.00
#> TCGA.97.7552.01 4 0.0941 0.915808 0.02 0.00 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.91.7771.01 3 0.0471 0.617381 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.86.8359.01 8 0.5273 0.218177 0.00 0.00 0.00 0.00 0.06 0.42 0.08 0.44
#> TCGA.55.8301.01 4 0.0471 0.918668 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 1 0.0471 0.933554 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8459.01 4 0.4022 0.728441 0.00 0.00 0.00 0.74 0.10 0.12 0.04 0.00
#> TCGA.73.7499.01 6 0.4213 0.500138 0.00 0.00 0.00 0.00 0.00 0.66 0.18 0.16
#> TCGA.MP.A4T7.01 3 0.5668 0.248391 0.00 0.00 0.46 0.00 0.00 0.26 0.24 0.04
#> TCGA.97.8171.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.8457.01 3 0.5244 0.314506 0.00 0.00 0.52 0.00 0.00 0.26 0.20 0.02
#> TCGA.53.7626.01 6 0.2404 0.680430 0.00 0.00 0.00 0.14 0.00 0.84 0.02 0.00
#> TCGA.69.7980.01 5 0.4756 0.654734 0.00 0.00 0.06 0.00 0.56 0.00 0.04 0.34
#> TCGA.86.8668.01 3 0.0471 0.606444 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.MP.A4T4.01 1 0.1275 0.904452 0.94 0.00 0.00 0.04 0.00 0.00 0.02 0.00
#> TCGA.93.A4JO.01 4 0.1607 0.896880 0.04 0.00 0.00 0.92 0.00 0.00 0.04 0.00
#> TCGA.55.8510.01 4 0.1275 0.910690 0.02 0.00 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.49.AARO.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8076.01 4 0.1091 0.909759 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.50.5044.01 4 0.1765 0.866289 0.00 0.00 0.00 0.88 0.00 0.12 0.00 0.00
#> TCGA.64.5781.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YF.01 8 0.0471 0.470915 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.49.AAR3.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7760.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4512.01 3 0.2025 0.577694 0.00 0.00 0.88 0.00 0.00 0.00 0.10 0.02
#> TCGA.97.A4M3.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 1 0.3594 0.529970 0.68 0.00 0.00 0.28 0.00 0.00 0.04 0.00
#> TCGA.NJ.A7XG.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48X.01 4 0.1341 0.899154 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.50.6594.01 5 0.5610 0.378874 0.00 0.00 0.28 0.00 0.54 0.02 0.06 0.10
#> TCGA.78.7537.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A513.01 4 0.1091 0.909759 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.50.5935.01 2 0.0941 0.943519 0.00 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.55.6981.01 6 0.2981 0.535840 0.00 0.00 0.00 0.22 0.00 0.76 0.02 0.00
#> TCGA.97.7941.01 3 0.0000 0.616380 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.67.4679.01 2 0.0000 0.994542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5941.01 4 0.1091 0.909759 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.97.8174.01 3 0.0000 0.616380 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7725.01 3 0.3658 -0.029713 0.00 0.40 0.58 0.00 0.00 0.00 0.02 0.00
#> TCGA.55.6983.01 6 0.4882 0.438109 0.00 0.00 0.20 0.00 0.00 0.60 0.18 0.02
#> TCGA.O2.A52Q.01 1 0.0471 0.933554 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.6978.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A48Y.01 4 0.0941 0.919995 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.50.6595.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8497.01 3 0.0471 0.617381 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.50.5049.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.97.A4M7.01 6 0.0808 0.741787 0.00 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.44.7662.01 1 0.1607 0.885141 0.92 0.00 0.00 0.04 0.00 0.00 0.04 0.00
#> TCGA.50.5068.01 4 0.0000 0.919600 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6987.01 1 0.0000 0.944097 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7145.01 5 0.4188 0.514889 0.00 0.14 0.04 0.00 0.72 0.00 0.00 0.10
#> TCGA.50.6593.01 6 0.3078 0.671286 0.00 0.00 0.00 0.00 0.02 0.82 0.10 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: Node023. Child nodes: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-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 23 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.993 0.996 0.2969 0.700 0.700
#> 3 3 0.684 0.866 0.922 0.8814 0.573 0.440
#> 4 4 1.000 0.972 0.963 0.2511 0.842 0.626
#> 5 5 0.924 0.962 0.937 0.0768 0.937 0.781
#> 6 6 0.924 0.870 0.917 0.0465 0.988 0.947
#> 7 7 0.867 0.798 0.903 0.0390 0.976 0.889
#> 8 8 0.852 0.709 0.872 0.0213 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] 5
#> attr(,"optional")
#> [1] 2 4
There is also optional best \(k\) = 2 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.49.AAR4.01 1 0.000 0.999 1.00 0.00
#> TCGA.L9.A743.01 1 0.000 0.999 1.00 0.00
#> TCGA.39.5011.01 1 0.000 0.999 1.00 0.00
#> TCGA.85.6560.01 2 0.000 0.973 0.00 1.00
#> TCGA.86.8671.01 1 0.000 0.999 1.00 0.00
#> TCGA.50.6592.01 2 0.242 0.972 0.04 0.96
#> TCGA.44.7661.01 1 0.000 0.999 1.00 0.00
#> TCGA.49.6767.01 1 0.141 0.979 0.98 0.02
#> TCGA.69.7761.01 1 0.000 0.999 1.00 0.00
#> TCGA.55.8089.01 1 0.000 0.999 1.00 0.00
#> TCGA.NJ.A4YQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.MP.A4T4.01 1 0.000 0.999 1.00 0.00
#> TCGA.93.A4JO.01 1 0.000 0.999 1.00 0.00
#> TCGA.49.AARO.01 1 0.000 0.999 1.00 0.00
#> TCGA.64.5781.01 2 0.242 0.972 0.04 0.96
#> TCGA.49.AAR3.01 1 0.000 0.999 1.00 0.00
#> TCGA.99.8028.01 1 0.000 0.999 1.00 0.00
#> TCGA.O2.A52Q.01 2 0.000 0.973 0.00 1.00
#> TCGA.55.6978.01 1 0.000 0.999 1.00 0.00
#> TCGA.50.6595.01 1 0.000 0.999 1.00 0.00
#> TCGA.50.5049.01 1 0.000 0.999 1.00 0.00
#> TCGA.44.7662.01 1 0.000 0.999 1.00 0.00
#> TCGA.55.6987.01 1 0.000 0.999 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.49.AAR4.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.L9.A743.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.39.5011.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.85.6560.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.86.8671.01 2 0.000 0.687 0.00 1.00 0
#> TCGA.50.6592.01 2 0.595 0.695 0.36 0.64 0
#> TCGA.44.7661.01 2 0.000 0.687 0.00 1.00 0
#> TCGA.49.6767.01 2 0.595 0.695 0.36 0.64 0
#> TCGA.69.7761.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.55.8089.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.NJ.A4YQ.01 2 0.595 0.695 0.36 0.64 0
#> TCGA.MP.A4T4.01 2 0.000 0.687 0.00 1.00 0
#> TCGA.93.A4JO.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.49.AARO.01 2 0.595 0.695 0.36 0.64 0
#> TCGA.64.5781.01 2 0.595 0.695 0.36 0.64 0
#> TCGA.49.AAR3.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.99.8028.01 2 0.000 0.687 0.00 1.00 0
#> TCGA.O2.A52Q.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.55.6978.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.50.6595.01 2 0.000 0.687 0.00 1.00 0
#> TCGA.50.5049.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.44.7662.01 1 0.595 1.000 0.64 0.36 0
#> TCGA.55.6987.01 1 0.595 1.000 0.64 0.36 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.49.AAR4.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.39.5011.01 2 0.2647 0.871 0.12 0.88 0.00 0.00
#> TCGA.85.6560.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.86.8671.01 2 0.1211 0.970 0.04 0.96 0.00 0.00
#> TCGA.50.6592.01 4 0.2011 0.994 0.00 0.08 0.00 0.92
#> TCGA.44.7661.01 2 0.1211 0.970 0.04 0.96 0.00 0.00
#> TCGA.49.6767.01 4 0.2345 0.982 0.00 0.10 0.00 0.90
#> TCGA.69.7761.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.55.8089.01 1 0.1637 0.947 0.94 0.00 0.00 0.06
#> TCGA.NJ.A4YQ.01 4 0.2011 0.994 0.00 0.08 0.00 0.92
#> TCGA.MP.A4T4.01 2 0.1211 0.970 0.04 0.96 0.00 0.00
#> TCGA.93.A4JO.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.49.AARO.01 2 0.0707 0.924 0.00 0.98 0.00 0.02
#> TCGA.64.5781.01 4 0.2011 0.994 0.00 0.08 0.00 0.92
#> TCGA.49.AAR3.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.99.8028.01 2 0.1211 0.970 0.04 0.96 0.00 0.00
#> TCGA.O2.A52Q.01 3 0.1411 0.977 0.00 0.02 0.96 0.02
#> TCGA.55.6978.01 1 0.1637 0.947 0.94 0.00 0.00 0.06
#> TCGA.50.6595.01 2 0.1211 0.970 0.04 0.96 0.00 0.00
#> TCGA.50.5049.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.44.7662.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.55.6987.01 1 0.0000 0.987 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.49.AAR4.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
#> TCGA.L9.A743.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
#> TCGA.39.5011.01 2 0.3109 0.797 0.00 0.8 0.00 0.00 0.20
#> TCGA.85.6560.01 3 0.0000 0.988 0.00 0.0 1.00 0.00 0.00
#> TCGA.86.8671.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00
#> TCGA.50.6592.01 4 0.0000 0.926 0.00 0.0 0.00 1.00 0.00
#> TCGA.44.7661.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00
#> TCGA.49.6767.01 4 0.3561 0.758 0.00 0.0 0.00 0.74 0.26
#> TCGA.69.7761.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
#> TCGA.55.8089.01 5 0.4302 1.000 0.48 0.0 0.00 0.00 0.52
#> TCGA.NJ.A4YQ.01 4 0.0000 0.926 0.00 0.0 0.00 1.00 0.00
#> TCGA.MP.A4T4.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00
#> TCGA.93.A4JO.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
#> TCGA.49.AARO.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00
#> TCGA.64.5781.01 4 0.0000 0.926 0.00 0.0 0.00 1.00 0.00
#> TCGA.49.AAR3.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
#> TCGA.99.8028.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00
#> TCGA.O2.A52Q.01 3 0.0609 0.988 0.00 0.0 0.98 0.00 0.02
#> TCGA.55.6978.01 5 0.4302 1.000 0.48 0.0 0.00 0.00 0.52
#> TCGA.50.6595.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00
#> TCGA.50.5049.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
#> TCGA.44.7662.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
#> TCGA.55.6987.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.49.AAR4.01 1 0.1267 0.953 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.L9.A743.01 1 0.0547 0.947 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.39.5011.01 2 0.5235 0.392 0.00 0.52 0.00 0.00 0.10 0.38
#> TCGA.85.6560.01 3 0.0000 0.955 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8671.01 2 0.0000 0.914 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6592.01 4 0.0000 0.914 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7661.01 2 0.0000 0.914 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.6767.01 6 0.3869 0.000 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.69.7761.01 1 0.1267 0.953 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.55.8089.01 5 0.2631 1.000 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.NJ.A4YQ.01 4 0.1807 0.824 0.00 0.02 0.00 0.92 0.06 0.00
#> TCGA.MP.A4T4.01 2 0.0000 0.914 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 1 0.0547 0.947 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.49.AARO.01 2 0.1267 0.873 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.64.5781.01 4 0.0000 0.914 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.AAR3.01 1 0.0000 0.952 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 2 0.0000 0.914 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.O2.A52Q.01 3 0.1480 0.955 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.55.6978.01 5 0.2631 1.000 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.50.6595.01 2 0.0000 0.914 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5049.01 1 0.1267 0.953 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.44.7662.01 1 0.0547 0.947 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.6987.01 1 0.1267 0.953 0.94 0.00 0.00 0.00 0.00 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.49.AAR4.01 1 0.2803 0.856 0.84 0.00 0.0 0.00 0.00 0.06 0.10
#> TCGA.L9.A743.01 1 0.2016 0.817 0.90 0.00 0.0 0.00 0.00 0.04 0.06
#> TCGA.39.5011.01 7 0.3358 0.000 0.00 0.36 0.0 0.00 0.00 0.00 0.64
#> TCGA.85.6560.01 3 0.2159 0.917 0.00 0.00 0.9 0.00 0.06 0.02 0.02
#> TCGA.86.8671.01 2 0.0000 0.940 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.50.6592.01 4 0.0000 0.869 0.00 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.44.7661.01 2 0.0000 0.940 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.49.6767.01 6 0.2572 0.000 0.00 0.00 0.0 0.20 0.00 0.80 0.00
#> TCGA.69.7761.01 1 0.2803 0.856 0.84 0.00 0.0 0.00 0.00 0.06 0.10
#> TCGA.55.8089.01 5 0.1433 1.000 0.08 0.00 0.0 0.00 0.92 0.00 0.00
#> TCGA.NJ.A4YQ.01 4 0.2745 0.745 0.00 0.00 0.0 0.82 0.02 0.00 0.16
#> TCGA.MP.A4T4.01 2 0.0000 0.940 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 1 0.2016 0.817 0.90 0.00 0.0 0.00 0.00 0.04 0.06
#> TCGA.49.AARO.01 2 0.2745 0.674 0.00 0.82 0.0 0.00 0.02 0.00 0.16
#> TCGA.64.5781.01 4 0.0504 0.865 0.00 0.00 0.0 0.98 0.00 0.00 0.02
#> TCGA.49.AAR3.01 1 0.0000 0.845 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 2 0.0000 0.940 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.O2.A52Q.01 3 0.0000 0.917 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.55.6978.01 5 0.1433 1.000 0.08 0.00 0.0 0.00 0.92 0.00 0.00
#> TCGA.50.6595.01 2 0.0000 0.940 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.50.5049.01 1 0.2803 0.856 0.84 0.00 0.0 0.00 0.00 0.06 0.10
#> TCGA.44.7662.01 1 0.3011 0.758 0.82 0.00 0.0 0.00 0.00 0.12 0.06
#> TCGA.55.6987.01 1 0.2803 0.856 0.84 0.00 0.0 0.00 0.00 0.06 0.10
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.49.AAR4.01 1 0.0000 0.832 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A743.01 1 0.2938 0.787 0.70 0.00 0.30 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5011.01 7 0.5138 0.000 0.00 0.24 0.32 0.00 0.00 0.00 0.44 0.00
#> TCGA.85.6560.01 8 0.3483 0.789 0.00 0.00 0.00 0.00 0.02 0.04 0.18 0.76
#> TCGA.86.8671.01 2 0.0941 0.859 0.00 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.50.6592.01 4 0.0000 0.780 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7661.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.6767.01 6 0.1091 0.000 0.00 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.69.7761.01 1 0.0000 0.832 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8089.01 5 0.0808 0.732 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.NJ.A4YQ.01 4 0.3746 0.545 0.00 0.00 0.32 0.64 0.00 0.00 0.04 0.00
#> TCGA.MP.A4T4.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.93.A4JO.01 1 0.2938 0.787 0.70 0.00 0.30 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARO.01 2 0.3746 0.400 0.00 0.64 0.32 0.00 0.00 0.00 0.04 0.00
#> TCGA.64.5781.01 4 0.0471 0.776 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.49.AAR3.01 1 0.2406 0.816 0.80 0.00 0.20 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8028.01 2 0.0941 0.859 0.00 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.O2.A52Q.01 8 0.0000 0.789 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.6978.01 5 0.3675 0.732 0.04 0.00 0.00 0.00 0.66 0.00 0.30 0.00
#> TCGA.50.6595.01 2 0.0000 0.875 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5049.01 1 0.0000 0.832 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.7662.01 1 0.4233 0.704 0.60 0.00 0.34 0.00 0.00 0.02 0.04 0.00
#> TCGA.55.6987.01 1 0.0000 0.832 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node023. Child nodes: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0234"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.43362 0.567 0.567
#> 3 3 1.000 1.000 1.000 0.10502 0.954 0.920
#> 4 4 1.000 0.999 0.999 0.20354 0.903 0.814
#> 5 5 1.000 0.988 0.990 0.33901 0.801 0.530
#> 6 6 1.000 0.949 0.995 0.01593 0.991 0.962
#> 7 7 0.947 0.905 0.991 0.01117 0.991 0.961
#> 8 8 0.954 0.848 0.984 0.00789 0.994 0.973
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 4
There is also optional best \(k\) = 2 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.69.8453.01 2 0 1 0 1
#> TCGA.J2.A4AG.01 1 0 1 1 0
#> TCGA.55.6984.01 1 0 1 1 0
#> TCGA.49.6744.01 1 0 1 1 0
#> TCGA.55.8619.01 1 0 1 1 0
#> TCGA.44.6775.01 1 0 1 1 0
#> TCGA.MP.A4T9.01 1 0 1 1 0
#> TCGA.55.7815.01 2 0 1 0 1
#> TCGA.55.6985.01 1 0 1 1 0
#> TCGA.93.7347.01 1 0 1 1 0
#> TCGA.44.6777.01 1 0 1 1 0
#> TCGA.91.6835.01 1 0 1 1 0
#> TCGA.95.A4VN.01 1 0 1 1 0
#> TCGA.97.7552.01 2 0 1 0 1
#> TCGA.55.8301.01 2 0 1 0 1
#> TCGA.50.8459.01 2 0 1 0 1
#> TCGA.53.7626.01 1 0 1 1 0
#> TCGA.55.8510.01 1 0 1 1 0
#> TCGA.86.8076.01 2 0 1 0 1
#> TCGA.50.5044.01 1 0 1 1 0
#> TCGA.55.A48X.01 1 0 1 1 0
#> TCGA.85.A513.01 1 0 1 1 0
#> TCGA.55.6981.01 1 0 1 1 0
#> TCGA.50.5941.01 1 0 1 1 0
#> TCGA.55.A48Y.01 2 0 1 0 1
#> TCGA.97.A4M7.01 2 0 1 0 1
#> TCGA.50.5068.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.69.8453.01 3 0 1 0 0 1
#> TCGA.J2.A4AG.01 1 0 1 1 0 0
#> TCGA.55.6984.01 1 0 1 1 0 0
#> TCGA.49.6744.01 1 0 1 1 0 0
#> TCGA.55.8619.01 1 0 1 1 0 0
#> TCGA.44.6775.01 1 0 1 1 0 0
#> TCGA.MP.A4T9.01 1 0 1 1 0 0
#> TCGA.55.7815.01 2 0 1 0 1 0
#> TCGA.55.6985.01 1 0 1 1 0 0
#> TCGA.93.7347.01 1 0 1 1 0 0
#> TCGA.44.6777.01 1 0 1 1 0 0
#> TCGA.91.6835.01 1 0 1 1 0 0
#> TCGA.95.A4VN.01 1 0 1 1 0 0
#> TCGA.97.7552.01 3 0 1 0 0 1
#> TCGA.55.8301.01 2 0 1 0 1 0
#> TCGA.50.8459.01 3 0 1 0 0 1
#> TCGA.53.7626.01 1 0 1 1 0 0
#> TCGA.55.8510.01 1 0 1 1 0 0
#> TCGA.86.8076.01 3 0 1 0 0 1
#> TCGA.50.5044.01 1 0 1 1 0 0
#> TCGA.55.A48X.01 1 0 1 1 0 0
#> TCGA.85.A513.01 1 0 1 1 0 0
#> TCGA.55.6981.01 1 0 1 1 0 0
#> TCGA.50.5941.01 1 0 1 1 0 0
#> TCGA.55.A48Y.01 2 0 1 0 1 0
#> TCGA.97.A4M7.01 2 0 1 0 1 0
#> TCGA.50.5068.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.69.8453.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.J2.A4AG.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.55.6984.01 4 0.0000 1.000 0.00 0 0 1.00
#> TCGA.49.6744.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.55.8619.01 4 0.0000 1.000 0.00 0 0 1.00
#> TCGA.44.6775.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.MP.A4T9.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.55.7815.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.55.6985.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.93.7347.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.44.6777.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.91.6835.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.95.A4VN.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.97.7552.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.55.8301.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.50.8459.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.53.7626.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.55.8510.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.86.8076.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.50.5044.01 1 0.0707 0.980 0.98 0 0 0.02
#> TCGA.55.A48X.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.85.A513.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.55.6981.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.50.5941.01 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.55.A48Y.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.97.A4M7.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.50.5068.01 1 0.0000 0.999 1.00 0 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.69.8453.01 3 0.0000 0.995 0.00 0 1.00 0 0.00
#> TCGA.J2.A4AG.01 5 0.0609 1.000 0.02 0 0.00 0 0.98
#> TCGA.55.6984.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.49.6744.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.55.8619.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.44.6775.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.MP.A4T9.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.55.7815.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.55.6985.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.93.7347.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.44.6777.01 5 0.0609 1.000 0.02 0 0.00 0 0.98
#> TCGA.91.6835.01 5 0.0609 1.000 0.02 0 0.00 0 0.98
#> TCGA.95.A4VN.01 5 0.0609 1.000 0.02 0 0.00 0 0.98
#> TCGA.97.7552.01 3 0.0000 0.995 0.00 0 1.00 0 0.00
#> TCGA.55.8301.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.50.8459.01 3 0.0000 0.995 0.00 0 1.00 0 0.00
#> TCGA.53.7626.01 1 0.2280 0.844 0.88 0 0.00 0 0.12
#> TCGA.55.8510.01 5 0.0609 1.000 0.02 0 0.00 0 0.98
#> TCGA.86.8076.01 3 0.0609 0.984 0.00 0 0.98 0 0.02
#> TCGA.50.5044.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.55.A48X.01 5 0.0609 1.000 0.02 0 0.00 0 0.98
#> TCGA.85.A513.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.55.6981.01 5 0.0609 1.000 0.02 0 0.00 0 0.98
#> TCGA.50.5941.01 1 0.0000 0.984 1.00 0 0.00 0 0.00
#> TCGA.55.A48Y.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.97.A4M7.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.50.5068.01 1 0.0000 0.984 1.00 0 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.69.8453.01 3 0.000 1.000 0.00 0 1 0 0.00 0
#> TCGA.J2.A4AG.01 5 0.000 1.000 0.00 0 0 0 1.00 0
#> TCGA.55.6984.01 4 0.000 1.000 0.00 0 0 1 0.00 0
#> TCGA.49.6744.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.55.8619.01 4 0.000 1.000 0.00 0 0 1 0.00 0
#> TCGA.44.6775.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.MP.A4T9.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.55.7815.01 2 0.000 1.000 0.00 1 0 0 0.00 0
#> TCGA.55.6985.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.93.7347.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.44.6777.01 5 0.000 1.000 0.00 0 0 0 1.00 0
#> TCGA.91.6835.01 5 0.000 1.000 0.00 0 0 0 1.00 0
#> TCGA.95.A4VN.01 5 0.000 1.000 0.00 0 0 0 1.00 0
#> TCGA.97.7552.01 3 0.000 1.000 0.00 0 1 0 0.00 0
#> TCGA.55.8301.01 2 0.000 1.000 0.00 1 0 0 0.00 0
#> TCGA.50.8459.01 3 0.000 1.000 0.00 0 1 0 0.00 0
#> TCGA.53.7626.01 1 0.226 0.805 0.86 0 0 0 0.14 0
#> TCGA.55.8510.01 5 0.000 1.000 0.00 0 0 0 1.00 0
#> TCGA.86.8076.01 6 0.000 0.000 0.00 0 0 0 0.00 1
#> TCGA.50.5044.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.55.A48X.01 5 0.000 1.000 0.00 0 0 0 1.00 0
#> TCGA.85.A513.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.55.6981.01 5 0.000 1.000 0.00 0 0 0 1.00 0
#> TCGA.50.5941.01 1 0.000 0.980 1.00 0 0 0 0.00 0
#> TCGA.55.A48Y.01 2 0.000 1.000 0.00 1 0 0 0.00 0
#> TCGA.97.A4M7.01 2 0.000 1.000 0.00 1 0 0 0.00 0
#> TCGA.50.5068.01 1 0.000 0.980 1.00 0 0 0 0.00 0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.69.8453.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0 0.00
#> TCGA.J2.A4AG.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0.00
#> TCGA.55.6984.01 4 0.0000 1.000 0.00 0.00 0 1 0.00 0 0.00
#> TCGA.49.6744.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
#> TCGA.55.8619.01 4 0.0000 1.000 0.00 0.00 0 1 0.00 0 0.00
#> TCGA.44.6775.01 1 0.0504 0.955 0.98 0.00 0 0 0.02 0 0.00
#> TCGA.MP.A4T9.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
#> TCGA.55.7815.01 2 0.0504 0.980 0.00 0.98 0 0 0.00 0 0.02
#> TCGA.55.6985.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
#> TCGA.93.7347.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
#> TCGA.44.6777.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0.00
#> TCGA.91.6835.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0.00
#> TCGA.95.A4VN.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0.00
#> TCGA.97.7552.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0 0.00
#> TCGA.55.8301.01 7 0.0504 0.000 0.00 0.02 0 0 0.00 0 0.98
#> TCGA.50.8459.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0 0.00
#> TCGA.53.7626.01 1 0.2422 0.748 0.82 0.00 0 0 0.18 0 0.00
#> TCGA.55.8510.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0.00
#> TCGA.86.8076.01 6 0.0000 0.000 0.00 0.00 0 0 0.00 1 0.00
#> TCGA.50.5044.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
#> TCGA.55.A48X.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0.00
#> TCGA.85.A513.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
#> TCGA.55.6981.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0.00
#> TCGA.50.5941.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
#> TCGA.55.A48Y.01 2 0.0000 0.990 0.00 1.00 0 0 0.00 0 0.00
#> TCGA.97.A4M7.01 2 0.0000 0.990 0.00 1.00 0 0 0.00 0 0.00
#> TCGA.50.5068.01 1 0.0000 0.972 1.00 0.00 0 0 0.00 0 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.69.8453.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0 0 0.00
#> TCGA.J2.A4AG.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0 0.00
#> TCGA.55.6984.01 4 0.0000 1.000 0.00 0.00 0 1 0.00 0 0 0.00
#> TCGA.49.6744.01 1 0.0000 0.947 1.00 0.00 0 0 0.00 0 0 0.00
#> TCGA.55.8619.01 4 0.0000 1.000 0.00 0.00 0 1 0.00 0 0 0.00
#> TCGA.44.6775.01 1 0.1091 0.899 0.94 0.00 0 0 0.06 0 0 0.00
#> TCGA.MP.A4T9.01 1 0.0000 0.947 1.00 0.00 0 0 0.00 0 0 0.00
#> TCGA.55.7815.01 2 0.0000 0.938 0.00 1.00 0 0 0.00 0 0 0.00
#> TCGA.55.6985.01 1 0.0471 0.934 0.98 0.00 0 0 0.02 0 0 0.00
#> TCGA.93.7347.01 1 0.0000 0.947 1.00 0.00 0 0 0.00 0 0 0.00
#> TCGA.44.6777.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0 0.00
#> TCGA.91.6835.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0 0.00
#> TCGA.95.A4VN.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0 0.00
#> TCGA.97.7552.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0 0 0.00
#> TCGA.55.8301.01 7 0.0000 0.000 0.00 0.00 0 0 0.00 0 1 0.00
#> TCGA.50.8459.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0 0 0.00
#> TCGA.53.7626.01 1 0.2938 0.562 0.70 0.00 0 0 0.30 0 0 0.00
#> TCGA.55.8510.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0 0.00
#> TCGA.86.8076.01 6 0.0000 0.000 0.00 0.00 0 0 0.00 1 0 0.00
#> TCGA.50.5044.01 1 0.0000 0.947 1.00 0.00 0 0 0.00 0 0 0.00
#> TCGA.55.A48X.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0 0.00
#> TCGA.85.A513.01 1 0.0000 0.947 1.00 0.00 0 0 0.00 0 0 0.00
#> TCGA.55.6981.01 5 0.0000 1.000 0.00 0.00 0 0 1.00 0 0 0.00
#> TCGA.50.5941.01 1 0.0000 0.947 1.00 0.00 0 0 0.00 0 0 0.00
#> TCGA.55.A48Y.01 8 0.0000 0.000 0.00 0.00 0 0 0.00 0 0 1.00
#> TCGA.97.A4M7.01 2 0.1091 0.936 0.00 0.94 0 0 0.00 0 0 0.06
#> TCGA.50.5068.01 1 0.0000 0.947 1.00 0.00 0 0 0.00 0 0 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 80 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4866 0.514 0.514
#> 3 3 0.704 0.901 0.833 0.2955 0.821 0.651
#> 4 4 0.556 0.491 0.735 0.1135 0.935 0.814
#> 5 5 0.588 0.539 0.705 0.0829 0.840 0.520
#> 6 6 0.649 0.642 0.727 0.0582 0.891 0.581
#> 7 7 0.634 0.544 0.670 0.0202 0.958 0.800
#> 8 8 0.647 0.282 0.608 0.0364 0.913 0.589
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.44.4112.01 2 0 1 0 1
#> TCGA.NJ.A4YP.01 1 0 1 1 0
#> TCGA.86.8278.01 2 0 1 0 1
#> TCGA.49.AARQ.01 2 0 1 0 1
#> TCGA.62.A46U.01 2 0 1 0 1
#> TCGA.MP.A4T8.01 1 0 1 1 0
#> TCGA.MP.A4SY.01 1 0 1 1 0
#> TCGA.93.A4JN.01 1 0 1 1 0
#> TCGA.86.A4JF.01 1 0 1 1 0
#> TCGA.63.6202.01 1 0 1 1 0
#> TCGA.MP.A4TI.01 1 0 1 1 0
#> TCGA.MP.A4TC.01 1 0 1 1 0
#> TCGA.05.4410.01 1 0 1 1 0
#> TCGA.62.A46Y.01 2 0 1 0 1
#> TCGA.50.6597.01 2 0 1 0 1
#> TCGA.MP.A4SW.01 1 0 1 1 0
#> TCGA.67.6216.01 2 0 1 0 1
#> TCGA.55.8203.01 2 0 1 0 1
#> TCGA.44.2668.01 1 0 1 1 0
#> TCGA.L9.A444.01 2 0 1 0 1
#> TCGA.44.A47G.01 2 0 1 0 1
#> TCGA.44.2665.01 2 0 1 0 1
#> TCGA.44.2666.01 1 0 1 1 0
#> TCGA.55.A494.01 2 0 1 0 1
#> TCGA.75.5125.01 1 0 1 1 0
#> TCGA.55.7911.01 2 0 1 0 1
#> TCGA.55.6712.01 1 0 1 1 0
#> TCGA.95.7948.01 2 0 1 0 1
#> TCGA.55.7281.01 2 0 1 0 1
#> TCGA.38.6178.01 2 0 1 0 1
#> TCGA.75.5122.01 1 0 1 1 0
#> TCGA.L9.A443.01 2 0 1 0 1
#> TCGA.86.7701.01 1 0 1 1 0
#> TCGA.52.7812.01 1 0 1 1 0
#> TCGA.78.8660.01 1 0 1 1 0
#> TCGA.MP.A4TK.01 2 0 1 0 1
#> TCGA.78.7540.01 2 0 1 0 1
#> TCGA.69.7763.01 1 0 1 1 0
#> TCGA.J2.A4AE.01 2 0 1 0 1
#> TCGA.50.6590.01 2 0 1 0 1
#> TCGA.MN.A4N5.01 1 0 1 1 0
#> TCGA.69.7978.01 1 0 1 1 0
#> TCGA.MP.A4TD.01 1 0 1 1 0
#> TCGA.83.5908.01 2 0 1 0 1
#> TCGA.NJ.A4YG.01 1 0 1 1 0
#> TCGA.44.3918.01 2 0 1 0 1
#> TCGA.55.7574.01 2 0 1 0 1
#> TCGA.44.2656.01 1 0 1 1 0
#> TCGA.78.7158.01 2 0 1 0 1
#> TCGA.86.8056.01 2 0 1 0 1
#> TCGA.97.8175.01 2 0 1 0 1
#> TCGA.97.8547.01 2 0 1 0 1
#> TCGA.44.6147.01 2 0 1 0 1
#> TCGA.77.8007.01 1 0 1 1 0
#> TCGA.86.8073.01 1 0 1 1 0
#> TCGA.91.6828.01 1 0 1 1 0
#> TCGA.38.7271.01 2 0 1 0 1
#> TCGA.78.7143.01 2 0 1 0 1
#> TCGA.75.6205.01 2 0 1 0 1
#> TCGA.55.A493.01 2 0 1 0 1
#> TCGA.75.5126.01 2 0 1 0 1
#> TCGA.67.6215.01 2 0 1 0 1
#> TCGA.55.6982.01 2 0 1 0 1
#> TCGA.55.6986.01 2 0 1 0 1
#> TCGA.49.6761.01 2 0 1 0 1
#> TCGA.MP.A4T6.01 2 0 1 0 1
#> TCGA.44.6779.01 2 0 1 0 1
#> TCGA.86.A4P7.01 2 0 1 0 1
#> TCGA.73.4658.01 2 0 1 0 1
#> TCGA.05.4417.01 2 0 1 0 1
#> TCGA.95.8039.01 1 0 1 1 0
#> TCGA.80.5607.01 2 0 1 0 1
#> TCGA.62.8395.01 2 0 1 0 1
#> TCGA.86.8672.01 1 0 1 1 0
#> TCGA.64.5815.01 1 0 1 1 0
#> TCGA.97.8172.01 2 0 1 0 1
#> TCGA.05.5715.01 2 0 1 0 1
#> TCGA.44.7672.01 2 0 1 0 1
#> TCGA.78.7152.01 1 0 1 1 0
#> TCGA.55.8302.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.4112.01 3 0.1529 0.931 0.00 0.04 0.96
#> TCGA.NJ.A4YP.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.86.8278.01 2 0.6192 0.903 0.00 0.58 0.42
#> TCGA.49.AARQ.01 3 0.1529 0.931 0.00 0.04 0.96
#> TCGA.62.A46U.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.MP.A4T8.01 1 0.4291 0.890 0.82 0.18 0.00
#> TCGA.MP.A4SY.01 1 0.2066 0.890 0.94 0.06 0.00
#> TCGA.93.A4JN.01 1 0.4555 0.887 0.80 0.20 0.00
#> TCGA.86.A4JF.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.63.6202.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.MP.A4TI.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.MP.A4TC.01 1 0.4555 0.887 0.80 0.20 0.00
#> TCGA.05.4410.01 1 0.3686 0.893 0.86 0.14 0.00
#> TCGA.62.A46Y.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.50.6597.01 2 0.6244 0.885 0.00 0.56 0.44
#> TCGA.MP.A4SW.01 1 0.4555 0.887 0.80 0.20 0.00
#> TCGA.67.6216.01 2 0.6280 0.856 0.00 0.54 0.46
#> TCGA.55.8203.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.44.2668.01 1 0.4291 0.890 0.82 0.18 0.00
#> TCGA.L9.A444.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.44.A47G.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.44.2665.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.44.2666.01 1 0.2066 0.890 0.94 0.06 0.00
#> TCGA.55.A494.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.75.5125.01 1 0.3686 0.893 0.86 0.14 0.00
#> TCGA.55.7911.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.55.6712.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.95.7948.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.55.7281.01 2 0.6244 0.885 0.00 0.56 0.44
#> TCGA.38.6178.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.75.5122.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.L9.A443.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.86.7701.01 1 0.4291 0.890 0.82 0.18 0.00
#> TCGA.52.7812.01 1 0.4555 0.887 0.80 0.20 0.00
#> TCGA.78.8660.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.MP.A4TK.01 2 0.6302 0.741 0.00 0.52 0.48
#> TCGA.78.7540.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.69.7763.01 1 0.3340 0.895 0.88 0.12 0.00
#> TCGA.J2.A4AE.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.50.6590.01 3 0.2537 0.879 0.00 0.08 0.92
#> TCGA.MN.A4N5.01 1 0.4002 0.894 0.84 0.16 0.00
#> TCGA.69.7978.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.MP.A4TD.01 1 0.3340 0.895 0.88 0.12 0.00
#> TCGA.83.5908.01 2 0.6045 0.921 0.00 0.62 0.38
#> TCGA.NJ.A4YG.01 1 0.4555 0.887 0.80 0.20 0.00
#> TCGA.44.3918.01 3 0.2537 0.879 0.00 0.08 0.92
#> TCGA.55.7574.01 3 0.4796 0.501 0.00 0.22 0.78
#> TCGA.44.2656.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.78.7158.01 2 0.5948 0.934 0.00 0.64 0.36
#> TCGA.86.8056.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.97.8175.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.97.8547.01 2 0.6244 0.885 0.00 0.56 0.44
#> TCGA.44.6147.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.77.8007.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.86.8073.01 1 0.4555 0.887 0.80 0.20 0.00
#> TCGA.91.6828.01 1 0.3340 0.895 0.88 0.12 0.00
#> TCGA.38.7271.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.78.7143.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.75.6205.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.55.A493.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.75.5126.01 3 0.0892 0.944 0.00 0.02 0.98
#> TCGA.67.6215.01 2 0.6244 0.885 0.00 0.56 0.44
#> TCGA.55.6982.01 3 0.1529 0.931 0.00 0.04 0.96
#> TCGA.55.6986.01 2 0.6126 0.913 0.00 0.60 0.40
#> TCGA.49.6761.01 2 0.6126 0.900 0.00 0.60 0.40
#> TCGA.MP.A4T6.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.44.6779.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.86.A4P7.01 2 0.5948 0.933 0.00 0.64 0.36
#> TCGA.73.4658.01 2 0.5835 0.937 0.00 0.66 0.34
#> TCGA.05.4417.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.95.8039.01 1 0.2537 0.878 0.92 0.08 0.00
#> TCGA.80.5607.01 2 0.6192 0.903 0.00 0.58 0.42
#> TCGA.62.8395.01 2 0.6045 0.924 0.00 0.62 0.38
#> TCGA.86.8672.01 1 0.3686 0.857 0.86 0.14 0.00
#> TCGA.64.5815.01 1 0.1529 0.889 0.96 0.04 0.00
#> TCGA.97.8172.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.05.5715.01 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.44.7672.01 2 0.5948 0.933 0.00 0.64 0.36
#> TCGA.78.7152.01 1 0.4555 0.887 0.80 0.20 0.00
#> TCGA.55.8302.01 1 0.4555 0.887 0.80 0.20 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.44.4112.01 3 0.2335 0.7778 0.00 0.02 0.92 0.06
#> TCGA.NJ.A4YP.01 1 0.5570 -0.8272 0.54 0.02 0.00 0.44
#> TCGA.86.8278.01 2 0.4277 0.6787 0.00 0.72 0.28 0.00
#> TCGA.49.AARQ.01 3 0.3972 0.7347 0.00 0.08 0.84 0.08
#> TCGA.62.A46U.01 2 0.7357 0.7151 0.00 0.50 0.18 0.32
#> TCGA.MP.A4T8.01 1 0.2011 0.5758 0.92 0.08 0.00 0.00
#> TCGA.MP.A4SY.01 1 0.4332 0.3320 0.80 0.04 0.00 0.16
#> TCGA.93.A4JN.01 1 0.1211 0.5824 0.96 0.04 0.00 0.00
#> TCGA.86.A4JF.01 1 0.4994 -0.9423 0.52 0.00 0.00 0.48
#> TCGA.63.6202.01 4 0.5000 1.0000 0.50 0.00 0.00 0.50
#> TCGA.MP.A4TI.01 1 0.5000 -1.0000 0.50 0.00 0.00 0.50
#> TCGA.MP.A4TC.01 1 0.1211 0.5880 0.96 0.04 0.00 0.00
#> TCGA.05.4410.01 1 0.3335 0.5623 0.86 0.12 0.00 0.02
#> TCGA.62.A46Y.01 2 0.4553 0.7429 0.00 0.78 0.18 0.04
#> TCGA.50.6597.01 2 0.5392 0.6705 0.00 0.68 0.28 0.04
#> TCGA.MP.A4SW.01 1 0.0707 0.5879 0.98 0.02 0.00 0.00
#> TCGA.67.6216.01 2 0.5062 0.6384 0.00 0.68 0.30 0.02
#> TCGA.55.8203.01 3 0.1211 0.7868 0.00 0.00 0.96 0.04
#> TCGA.44.2668.01 1 0.2011 0.5792 0.92 0.08 0.00 0.00
#> TCGA.L9.A444.01 2 0.7357 0.7151 0.00 0.50 0.18 0.32
#> TCGA.44.A47G.01 2 0.7357 0.7151 0.00 0.50 0.18 0.32
#> TCGA.44.2665.01 3 0.2830 0.7705 0.00 0.06 0.90 0.04
#> TCGA.44.2666.01 1 0.4332 0.3320 0.80 0.04 0.00 0.16
#> TCGA.55.A494.01 3 0.5327 0.5897 0.00 0.22 0.72 0.06
#> TCGA.75.5125.01 1 0.4731 0.3357 0.78 0.06 0.00 0.16
#> TCGA.55.7911.01 2 0.7414 0.7052 0.00 0.48 0.18 0.34
#> TCGA.55.6712.01 4 0.5000 1.0000 0.50 0.00 0.00 0.50
#> TCGA.95.7948.01 3 0.3037 0.7752 0.00 0.02 0.88 0.10
#> TCGA.55.7281.01 2 0.4936 0.6620 0.00 0.70 0.28 0.02
#> TCGA.38.6178.01 3 0.2011 0.7832 0.00 0.00 0.92 0.08
#> TCGA.75.5122.01 1 0.5000 -1.0000 0.50 0.00 0.00 0.50
#> TCGA.L9.A443.01 3 0.2011 0.7806 0.00 0.00 0.92 0.08
#> TCGA.86.7701.01 1 0.2011 0.5758 0.92 0.08 0.00 0.00
#> TCGA.52.7812.01 1 0.2011 0.5678 0.92 0.08 0.00 0.00
#> TCGA.78.8660.01 1 0.5000 -1.0000 0.50 0.00 0.00 0.50
#> TCGA.MP.A4TK.01 3 0.7610 -0.2712 0.00 0.32 0.46 0.22
#> TCGA.78.7540.01 3 0.1211 0.7871 0.00 0.00 0.96 0.04
#> TCGA.69.7763.01 1 0.3037 0.5608 0.88 0.10 0.00 0.02
#> TCGA.J2.A4AE.01 2 0.5594 0.7428 0.00 0.72 0.18 0.10
#> TCGA.50.6590.01 3 0.6049 0.5215 0.00 0.12 0.68 0.20
#> TCGA.MN.A4N5.01 1 0.3037 0.5608 0.88 0.10 0.00 0.02
#> TCGA.69.7978.01 1 0.5000 -1.0000 0.50 0.00 0.00 0.50
#> TCGA.MP.A4TD.01 1 0.3037 0.5608 0.88 0.10 0.00 0.02
#> TCGA.83.5908.01 2 0.7699 0.4743 0.00 0.40 0.38 0.22
#> TCGA.NJ.A4YG.01 1 0.1211 0.5754 0.96 0.04 0.00 0.00
#> TCGA.44.3918.01 3 0.5661 0.5713 0.00 0.08 0.70 0.22
#> TCGA.55.7574.01 3 0.6286 0.4437 0.00 0.14 0.66 0.20
#> TCGA.44.2656.01 4 0.5000 1.0000 0.50 0.00 0.00 0.50
#> TCGA.78.7158.01 2 0.5147 0.7359 0.00 0.74 0.20 0.06
#> TCGA.86.8056.01 3 0.4755 0.6134 0.00 0.20 0.76 0.04
#> TCGA.97.8175.01 2 0.6686 0.7398 0.00 0.62 0.18 0.20
#> TCGA.97.8547.01 2 0.5062 0.6384 0.00 0.68 0.30 0.02
#> TCGA.44.6147.01 3 0.1211 0.7861 0.00 0.00 0.96 0.04
#> TCGA.77.8007.01 1 0.5000 -1.0000 0.50 0.00 0.00 0.50
#> TCGA.86.8073.01 1 0.1637 0.5832 0.94 0.06 0.00 0.00
#> TCGA.91.6828.01 1 0.3037 0.5608 0.88 0.10 0.00 0.02
#> TCGA.38.7271.01 2 0.7357 0.7151 0.00 0.50 0.18 0.32
#> TCGA.78.7143.01 3 0.2830 0.7683 0.00 0.06 0.90 0.04
#> TCGA.75.6205.01 2 0.7493 0.7021 0.00 0.48 0.20 0.32
#> TCGA.55.A493.01 2 0.7550 0.6980 0.00 0.48 0.22 0.30
#> TCGA.75.5126.01 3 0.4949 0.6393 0.00 0.06 0.76 0.18
#> TCGA.67.6215.01 2 0.5062 0.6384 0.00 0.68 0.30 0.02
#> TCGA.55.6982.01 3 0.1411 0.7843 0.00 0.02 0.96 0.02
#> TCGA.55.6986.01 2 0.3801 0.7126 0.00 0.78 0.22 0.00
#> TCGA.49.6761.01 3 0.7684 -0.4263 0.00 0.36 0.42 0.22
#> TCGA.MP.A4T6.01 3 0.2345 0.7795 0.00 0.00 0.90 0.10
#> TCGA.44.6779.01 2 0.7493 0.7021 0.00 0.48 0.20 0.32
#> TCGA.86.A4P7.01 2 0.4939 0.7322 0.00 0.74 0.22 0.04
#> TCGA.73.4658.01 2 0.7414 0.7052 0.00 0.48 0.18 0.34
#> TCGA.05.4417.01 3 0.0707 0.7872 0.00 0.00 0.98 0.02
#> TCGA.95.8039.01 1 0.4936 -0.0926 0.70 0.02 0.00 0.28
#> TCGA.80.5607.01 2 0.4134 0.6939 0.00 0.74 0.26 0.00
#> TCGA.62.8395.01 2 0.5147 0.7359 0.00 0.74 0.20 0.06
#> TCGA.86.8672.01 4 0.5000 1.0000 0.50 0.00 0.00 0.50
#> TCGA.64.5815.01 1 0.4332 0.3320 0.80 0.04 0.00 0.16
#> TCGA.97.8172.01 3 0.1637 0.7847 0.00 0.00 0.94 0.06
#> TCGA.05.5715.01 3 0.3198 0.7625 0.00 0.04 0.88 0.08
#> TCGA.44.7672.01 2 0.7274 0.6957 0.00 0.54 0.24 0.22
#> TCGA.78.7152.01 1 0.1637 0.5879 0.94 0.06 0.00 0.00
#> TCGA.55.8302.01 1 0.0707 0.5879 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.44.4112.01 3 0.3627 0.7767 0.02 0.10 0.84 0.00 0.04
#> TCGA.NJ.A4YP.01 4 0.3099 0.6773 0.04 0.00 0.04 0.88 0.04
#> TCGA.86.8278.01 5 0.5173 0.3326 0.00 0.46 0.04 0.00 0.50
#> TCGA.49.AARQ.01 3 0.6496 0.6893 0.14 0.12 0.64 0.00 0.10
#> TCGA.62.A46U.01 2 0.2331 0.5807 0.02 0.90 0.00 0.00 0.08
#> TCGA.MP.A4T8.01 1 0.6759 0.8051 0.52 0.00 0.04 0.32 0.12
#> TCGA.MP.A4SY.01 4 0.6200 -0.1588 0.32 0.00 0.00 0.52 0.16
#> TCGA.93.A4JN.01 1 0.5498 0.7902 0.58 0.00 0.00 0.34 0.08
#> TCGA.86.A4JF.01 4 0.2331 0.6991 0.02 0.00 0.00 0.90 0.08
#> TCGA.63.6202.01 4 0.0609 0.7319 0.00 0.00 0.00 0.98 0.02
#> TCGA.MP.A4TI.01 4 0.0000 0.7338 0.00 0.00 0.00 1.00 0.00
#> TCGA.MP.A4TC.01 1 0.5393 0.8056 0.62 0.00 0.04 0.32 0.02
#> TCGA.05.4410.01 1 0.6038 0.8000 0.56 0.00 0.02 0.34 0.08
#> TCGA.62.A46Y.01 2 0.3796 0.3730 0.00 0.70 0.00 0.00 0.30
#> TCGA.50.6597.01 2 0.5695 -0.3470 0.02 0.48 0.04 0.00 0.46
#> TCGA.MP.A4SW.01 1 0.4540 0.8155 0.64 0.00 0.00 0.34 0.02
#> TCGA.67.6216.01 5 0.5131 0.4396 0.00 0.42 0.04 0.00 0.54
#> TCGA.55.8203.01 3 0.4420 0.7790 0.04 0.08 0.80 0.00 0.08
#> TCGA.44.2668.01 1 0.5705 0.7975 0.60 0.00 0.02 0.32 0.06
#> TCGA.L9.A444.01 2 0.0000 0.6135 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A47G.01 2 0.0609 0.6094 0.00 0.98 0.00 0.00 0.02
#> TCGA.44.2665.01 3 0.6743 0.5300 0.08 0.08 0.56 0.00 0.28
#> TCGA.44.2666.01 4 0.6200 -0.1588 0.32 0.00 0.00 0.52 0.16
#> TCGA.55.A494.01 5 0.7015 -0.1687 0.08 0.08 0.38 0.00 0.46
#> TCGA.75.5125.01 4 0.6350 -0.5032 0.42 0.00 0.00 0.42 0.16
#> TCGA.55.7911.01 2 0.1410 0.6001 0.00 0.94 0.00 0.00 0.06
#> TCGA.55.6712.01 4 0.0000 0.7338 0.00 0.00 0.00 1.00 0.00
#> TCGA.95.7948.01 3 0.6047 0.6791 0.12 0.08 0.68 0.00 0.12
#> TCGA.55.7281.01 5 0.5588 0.4778 0.02 0.38 0.04 0.00 0.56
#> TCGA.38.6178.01 3 0.4281 0.7761 0.10 0.08 0.80 0.00 0.02
#> TCGA.75.5122.01 4 0.1043 0.7257 0.00 0.00 0.00 0.96 0.04
#> TCGA.L9.A443.01 3 0.4115 0.7837 0.06 0.08 0.82 0.00 0.04
#> TCGA.86.7701.01 1 0.6693 0.8072 0.54 0.00 0.04 0.30 0.12
#> TCGA.52.7812.01 1 0.6400 0.7490 0.54 0.00 0.02 0.32 0.12
#> TCGA.78.8660.01 4 0.0609 0.7230 0.02 0.00 0.00 0.98 0.00
#> TCGA.MP.A4TK.01 2 0.6894 0.3050 0.10 0.58 0.22 0.00 0.10
#> TCGA.78.7540.01 3 0.2927 0.7892 0.02 0.08 0.88 0.00 0.02
#> TCGA.69.7763.01 1 0.6623 0.7824 0.52 0.00 0.04 0.34 0.10
#> TCGA.J2.A4AE.01 2 0.3424 0.4183 0.00 0.76 0.00 0.00 0.24
#> TCGA.50.6590.01 3 0.7535 0.3431 0.10 0.34 0.44 0.00 0.12
#> TCGA.MN.A4N5.01 1 0.6254 0.7775 0.50 0.00 0.00 0.34 0.16
#> TCGA.69.7978.01 4 0.0609 0.7233 0.02 0.00 0.00 0.98 0.00
#> TCGA.MP.A4TD.01 1 0.6564 0.7865 0.54 0.00 0.04 0.32 0.10
#> TCGA.83.5908.01 2 0.6296 0.4101 0.10 0.66 0.12 0.00 0.12
#> TCGA.NJ.A4YG.01 1 0.6043 0.7521 0.54 0.00 0.00 0.32 0.14
#> TCGA.44.3918.01 3 0.5997 0.5708 0.06 0.30 0.60 0.00 0.04
#> TCGA.55.7574.01 2 0.7105 0.1517 0.10 0.50 0.32 0.00 0.08
#> TCGA.44.2656.01 4 0.0000 0.7338 0.00 0.00 0.00 1.00 0.00
#> TCGA.78.7158.01 2 0.3796 0.3618 0.00 0.70 0.00 0.00 0.30
#> TCGA.86.8056.01 5 0.6539 -0.0943 0.04 0.08 0.42 0.00 0.46
#> TCGA.97.8175.01 2 0.2020 0.5697 0.00 0.90 0.00 0.00 0.10
#> TCGA.97.8547.01 5 0.5095 0.4717 0.00 0.40 0.04 0.00 0.56
#> TCGA.44.6147.01 3 0.4115 0.7807 0.06 0.08 0.82 0.00 0.04
#> TCGA.77.8007.01 4 0.0000 0.7338 0.00 0.00 0.00 1.00 0.00
#> TCGA.86.8073.01 1 0.4840 0.8089 0.64 0.00 0.04 0.32 0.00
#> TCGA.91.6828.01 1 0.6623 0.7824 0.52 0.00 0.04 0.34 0.10
#> TCGA.38.7271.01 2 0.1216 0.6144 0.02 0.96 0.00 0.00 0.02
#> TCGA.78.7143.01 3 0.4690 0.7653 0.04 0.08 0.78 0.00 0.10
#> TCGA.75.6205.01 2 0.2438 0.6014 0.06 0.90 0.00 0.00 0.04
#> TCGA.55.A493.01 2 0.3697 0.5610 0.08 0.82 0.00 0.00 0.10
#> TCGA.75.5126.01 3 0.7053 0.5159 0.08 0.22 0.56 0.00 0.14
#> TCGA.67.6215.01 5 0.5588 0.4778 0.02 0.38 0.04 0.00 0.56
#> TCGA.55.6982.01 3 0.4389 0.7769 0.06 0.10 0.80 0.00 0.04
#> TCGA.55.6986.01 2 0.4818 -0.2207 0.00 0.52 0.02 0.00 0.46
#> TCGA.49.6761.01 2 0.6000 0.3501 0.06 0.64 0.24 0.00 0.06
#> TCGA.MP.A4T6.01 3 0.4527 0.7667 0.12 0.08 0.78 0.00 0.02
#> TCGA.44.6779.01 2 0.2438 0.6014 0.06 0.90 0.00 0.00 0.04
#> TCGA.86.A4P7.01 2 0.4252 0.3931 0.02 0.70 0.00 0.00 0.28
#> TCGA.73.4658.01 2 0.1410 0.6001 0.00 0.94 0.00 0.00 0.06
#> TCGA.05.4417.01 3 0.3765 0.7877 0.04 0.08 0.84 0.00 0.04
#> TCGA.95.8039.01 4 0.5892 0.1956 0.22 0.00 0.00 0.60 0.18
#> TCGA.80.5607.01 2 0.4818 -0.2669 0.00 0.52 0.02 0.00 0.46
#> TCGA.62.8395.01 2 0.3684 0.3642 0.00 0.72 0.00 0.00 0.28
#> TCGA.86.8672.01 4 0.0609 0.7233 0.02 0.00 0.00 0.98 0.00
#> TCGA.64.5815.01 4 0.6275 -0.1332 0.30 0.00 0.00 0.52 0.18
#> TCGA.97.8172.01 3 0.3700 0.7774 0.02 0.08 0.84 0.00 0.06
#> TCGA.05.5715.01 3 0.6251 0.6912 0.12 0.08 0.66 0.00 0.14
#> TCGA.44.7672.01 2 0.4225 0.5558 0.06 0.80 0.02 0.00 0.12
#> TCGA.78.7152.01 1 0.5012 0.8262 0.64 0.00 0.02 0.32 0.02
#> TCGA.55.8302.01 1 0.6400 0.7637 0.54 0.00 0.02 0.32 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.4112.01 3 0.2345 0.7476 0.02 0.02 0.90 0.06 0.00 0.00
#> TCGA.NJ.A4YP.01 4 0.5835 0.6492 0.06 0.06 0.00 0.52 0.00 0.36
#> TCGA.86.8278.01 5 0.1267 0.6896 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.49.AARQ.01 3 0.4259 0.7071 0.06 0.06 0.80 0.06 0.02 0.00
#> TCGA.62.A46U.01 2 0.5846 0.4432 0.02 0.54 0.00 0.14 0.30 0.00
#> TCGA.MP.A4T8.01 6 0.5073 0.6930 0.14 0.16 0.00 0.02 0.00 0.68
#> TCGA.MP.A4SY.01 6 0.2581 0.6372 0.00 0.02 0.00 0.12 0.00 0.86
#> TCGA.93.A4JN.01 6 0.2350 0.7542 0.10 0.00 0.00 0.02 0.00 0.88
#> TCGA.86.A4JF.01 4 0.4420 0.8196 0.04 0.00 0.00 0.62 0.00 0.34
#> TCGA.63.6202.01 4 0.3309 0.9316 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.MP.A4TI.01 4 0.3198 0.9381 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.MP.A4TC.01 6 0.2790 0.7430 0.14 0.00 0.00 0.02 0.00 0.84
#> TCGA.05.4410.01 6 0.5455 0.6681 0.26 0.04 0.00 0.08 0.00 0.62
#> TCGA.62.A46Y.01 5 0.3523 0.5801 0.00 0.18 0.00 0.04 0.78 0.00
#> TCGA.50.6597.01 5 0.3942 0.6590 0.06 0.10 0.00 0.04 0.80 0.00
#> TCGA.MP.A4SW.01 6 0.1807 0.7541 0.06 0.00 0.00 0.02 0.00 0.92
#> TCGA.67.6216.01 5 0.1807 0.6826 0.02 0.06 0.00 0.00 0.92 0.00
#> TCGA.55.8203.01 3 0.3321 0.7099 0.08 0.00 0.82 0.00 0.10 0.00
#> TCGA.44.2668.01 6 0.2882 0.7364 0.10 0.02 0.00 0.02 0.00 0.86
#> TCGA.L9.A444.01 2 0.4067 0.6269 0.00 0.70 0.00 0.04 0.26 0.00
#> TCGA.44.A47G.01 2 0.4222 0.6071 0.02 0.70 0.00 0.02 0.26 0.00
#> TCGA.44.2665.01 3 0.6817 0.6015 0.22 0.08 0.54 0.02 0.14 0.00
#> TCGA.44.2666.01 6 0.2581 0.6372 0.00 0.02 0.00 0.12 0.00 0.86
#> TCGA.55.A494.01 5 0.7588 -0.1120 0.22 0.06 0.30 0.04 0.38 0.00
#> TCGA.75.5125.01 6 0.3111 0.6476 0.02 0.02 0.00 0.12 0.00 0.84
#> TCGA.55.7911.01 2 0.5331 0.5661 0.02 0.62 0.00 0.10 0.26 0.00
#> TCGA.55.6712.01 4 0.3198 0.9381 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.95.7948.01 3 0.4328 0.6650 0.46 0.00 0.52 0.02 0.00 0.00
#> TCGA.55.7281.01 5 0.3163 0.6362 0.14 0.00 0.00 0.04 0.82 0.00
#> TCGA.38.6178.01 3 0.3819 0.7267 0.28 0.02 0.70 0.00 0.00 0.00
#> TCGA.75.5122.01 4 0.3409 0.9186 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.L9.A443.01 3 0.3324 0.7516 0.08 0.02 0.84 0.06 0.00 0.00
#> TCGA.86.7701.01 6 0.5226 0.6959 0.18 0.14 0.00 0.02 0.00 0.66
#> TCGA.52.7812.01 6 0.2190 0.7337 0.06 0.04 0.00 0.00 0.00 0.90
#> TCGA.78.8660.01 4 0.3198 0.9381 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.MP.A4TK.01 2 0.7257 0.5392 0.10 0.54 0.16 0.06 0.14 0.00
#> TCGA.78.7540.01 3 0.1267 0.7706 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.69.7763.01 6 0.5529 0.6613 0.16 0.12 0.00 0.06 0.00 0.66
#> TCGA.J2.A4AE.01 5 0.4982 0.5013 0.02 0.20 0.00 0.10 0.68 0.00
#> TCGA.50.6590.01 2 0.7366 0.0634 0.16 0.42 0.32 0.06 0.04 0.00
#> TCGA.MN.A4N5.01 6 0.5157 0.6746 0.14 0.10 0.00 0.06 0.00 0.70
#> TCGA.69.7978.01 4 0.3309 0.9316 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.MP.A4TD.01 6 0.5679 0.6587 0.18 0.12 0.00 0.06 0.00 0.64
#> TCGA.83.5908.01 2 0.7166 0.5639 0.10 0.54 0.10 0.06 0.20 0.00
#> TCGA.NJ.A4YG.01 6 0.0547 0.7523 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.44.3918.01 3 0.4962 0.4565 0.02 0.28 0.64 0.06 0.00 0.00
#> TCGA.55.7574.01 2 0.7121 0.3789 0.08 0.50 0.28 0.06 0.08 0.00
#> TCGA.44.2656.01 4 0.3198 0.9381 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.78.7158.01 5 0.3985 0.5809 0.00 0.14 0.00 0.10 0.76 0.00
#> TCGA.86.8056.01 5 0.6446 -0.1407 0.16 0.00 0.40 0.04 0.40 0.00
#> TCGA.97.8175.01 2 0.5544 0.2976 0.02 0.50 0.00 0.08 0.40 0.00
#> TCGA.97.8547.01 5 0.1865 0.6881 0.04 0.04 0.00 0.00 0.92 0.00
#> TCGA.44.6147.01 3 0.4121 0.7205 0.22 0.06 0.72 0.00 0.00 0.00
#> TCGA.77.8007.01 4 0.3309 0.9316 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.86.8073.01 6 0.2454 0.7421 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.91.6828.01 6 0.5362 0.6635 0.14 0.12 0.00 0.06 0.00 0.68
#> TCGA.38.7271.01 2 0.3309 0.6206 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.78.7143.01 3 0.4444 0.6857 0.08 0.02 0.74 0.00 0.16 0.00
#> TCGA.75.6205.01 2 0.5077 0.6386 0.02 0.66 0.02 0.04 0.26 0.00
#> TCGA.55.A493.01 2 0.6020 0.6007 0.08 0.62 0.02 0.06 0.22 0.00
#> TCGA.75.5126.01 3 0.6840 0.2020 0.12 0.34 0.46 0.06 0.02 0.00
#> TCGA.67.6215.01 5 0.2094 0.6857 0.08 0.00 0.00 0.02 0.90 0.00
#> TCGA.55.6982.01 3 0.1092 0.7602 0.02 0.02 0.96 0.00 0.00 0.00
#> TCGA.55.6986.01 5 0.1480 0.6921 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.49.6761.01 2 0.6682 0.3584 0.00 0.38 0.36 0.04 0.22 0.00
#> TCGA.MP.A4T6.01 3 0.4199 0.6983 0.38 0.00 0.60 0.02 0.00 0.00
#> TCGA.44.6779.01 2 0.5364 0.6381 0.02 0.64 0.02 0.06 0.26 0.00
#> TCGA.86.A4P7.01 5 0.3711 0.4445 0.00 0.26 0.02 0.00 0.72 0.00
#> TCGA.73.4658.01 2 0.5113 0.5835 0.02 0.64 0.00 0.08 0.26 0.00
#> TCGA.05.4417.01 3 0.0547 0.7635 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.95.8039.01 6 0.4798 0.1939 0.08 0.00 0.00 0.30 0.00 0.62
#> TCGA.80.5607.01 5 0.1807 0.6882 0.00 0.06 0.00 0.02 0.92 0.00
#> TCGA.62.8395.01 5 0.3985 0.5809 0.00 0.14 0.00 0.10 0.76 0.00
#> TCGA.86.8672.01 4 0.3198 0.9381 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.64.5815.01 6 0.2790 0.6140 0.00 0.02 0.00 0.14 0.00 0.84
#> TCGA.97.8172.01 3 0.1807 0.7647 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.05.5715.01 3 0.4609 0.6751 0.42 0.04 0.54 0.00 0.00 0.00
#> TCGA.44.7672.01 2 0.4758 0.5633 0.00 0.58 0.06 0.00 0.36 0.00
#> TCGA.78.7152.01 6 0.2350 0.7555 0.10 0.00 0.00 0.02 0.00 0.88
#> TCGA.55.8302.01 6 0.2345 0.7416 0.06 0.02 0.00 0.02 0.00 0.90
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.44.4112.01 3 0.3798 0.4729 0.08 0.08 0.80 0.00 0.00 0.02 0.02
#> TCGA.NJ.A4YP.01 4 0.5682 0.5442 0.06 0.00 0.00 0.66 0.08 0.10 0.10
#> TCGA.86.8278.01 5 0.4992 0.7596 0.10 0.28 0.00 0.00 0.60 0.02 0.00
#> TCGA.49.AARQ.01 3 0.6572 0.3084 0.12 0.08 0.54 0.00 0.02 0.22 0.02
#> TCGA.62.A46U.01 2 0.3734 0.5039 0.04 0.78 0.00 0.00 0.14 0.04 0.00
#> TCGA.MP.A4T8.01 7 0.7250 0.5995 0.02 0.00 0.02 0.14 0.14 0.24 0.44
#> TCGA.MP.A4SY.01 7 0.5830 0.4174 0.06 0.00 0.00 0.32 0.00 0.12 0.50
#> TCGA.93.A4JN.01 7 0.2376 0.6989 0.00 0.00 0.00 0.12 0.00 0.02 0.86
#> TCGA.86.A4JF.01 4 0.3208 0.7682 0.12 0.00 0.00 0.82 0.00 0.04 0.02
#> TCGA.63.6202.01 4 0.1505 0.8577 0.02 0.00 0.00 0.94 0.02 0.02 0.00
#> TCGA.MP.A4TI.01 4 0.0000 0.8727 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TC.01 7 0.4644 0.6769 0.02 0.00 0.00 0.12 0.00 0.18 0.68
#> TCGA.05.4410.01 7 0.5806 0.6266 0.00 0.00 0.00 0.16 0.04 0.30 0.50
#> TCGA.62.A46Y.01 5 0.3909 0.6681 0.00 0.40 0.00 0.00 0.58 0.02 0.00
#> TCGA.50.6597.01 5 0.3661 0.7426 0.02 0.22 0.00 0.00 0.74 0.02 0.00
#> TCGA.MP.A4SW.01 7 0.3011 0.6965 0.00 0.00 0.00 0.12 0.00 0.06 0.82
#> TCGA.67.6216.01 5 0.5234 0.7237 0.12 0.20 0.02 0.00 0.64 0.02 0.00
#> TCGA.55.8203.01 3 0.3257 0.5294 0.02 0.04 0.84 0.00 0.08 0.00 0.02
#> TCGA.44.2668.01 7 0.5469 0.6483 0.04 0.00 0.00 0.12 0.00 0.28 0.56
#> TCGA.L9.A444.01 2 0.1664 0.6589 0.02 0.92 0.00 0.00 0.06 0.00 0.00
#> TCGA.44.A47G.01 2 0.1928 0.6269 0.00 0.90 0.00 0.00 0.08 0.02 0.00
#> TCGA.44.2665.01 1 0.5625 -0.1506 0.46 0.06 0.40 0.00 0.08 0.00 0.00
#> TCGA.44.2666.01 7 0.5830 0.4174 0.06 0.00 0.00 0.32 0.00 0.12 0.50
#> TCGA.55.A494.01 3 0.7384 0.1643 0.16 0.04 0.36 0.00 0.34 0.02 0.08
#> TCGA.75.5125.01 7 0.6057 0.5084 0.04 0.00 0.00 0.26 0.00 0.24 0.46
#> TCGA.55.7911.01 2 0.3000 0.5795 0.04 0.84 0.00 0.00 0.10 0.02 0.00
#> TCGA.55.6712.01 4 0.0000 0.8727 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.95.7948.01 3 0.5802 0.3625 0.36 0.04 0.46 0.00 0.00 0.14 0.00
#> TCGA.55.7281.01 5 0.5500 0.6738 0.04 0.18 0.02 0.00 0.66 0.02 0.08
#> TCGA.38.6178.01 3 0.5107 0.3770 0.28 0.04 0.60 0.00 0.00 0.08 0.00
#> TCGA.75.5122.01 4 0.1860 0.8477 0.02 0.00 0.00 0.92 0.02 0.04 0.00
#> TCGA.L9.A443.01 3 0.4357 0.5138 0.08 0.04 0.76 0.00 0.00 0.10 0.02
#> TCGA.86.7701.01 7 0.6517 0.6086 0.00 0.00 0.00 0.14 0.14 0.28 0.44
#> TCGA.52.7812.01 7 0.6141 0.6423 0.04 0.00 0.04 0.12 0.00 0.26 0.54
#> TCGA.78.8660.01 4 0.0000 0.8727 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TK.01 2 0.4681 -0.0164 0.32 0.58 0.10 0.00 0.00 0.00 0.00
#> TCGA.78.7540.01 3 0.2857 0.5398 0.04 0.04 0.86 0.00 0.00 0.06 0.00
#> TCGA.69.7763.01 7 0.6307 0.6054 0.00 0.00 0.00 0.16 0.12 0.22 0.50
#> TCGA.J2.A4AE.01 5 0.4701 0.5387 0.04 0.44 0.00 0.00 0.50 0.02 0.00
#> TCGA.50.6590.01 1 0.5539 0.6218 0.38 0.38 0.24 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N5.01 7 0.6412 0.6314 0.06 0.00 0.00 0.18 0.04 0.18 0.54
#> TCGA.69.7978.01 4 0.0000 0.8727 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TD.01 7 0.6450 0.5961 0.00 0.00 0.00 0.16 0.12 0.26 0.46
#> TCGA.83.5908.01 2 0.4191 0.1913 0.30 0.64 0.06 0.00 0.00 0.00 0.00
#> TCGA.NJ.A4YG.01 7 0.4079 0.6798 0.04 0.00 0.00 0.12 0.00 0.08 0.76
#> TCGA.44.3918.01 3 0.5537 -0.2430 0.08 0.40 0.48 0.00 0.00 0.02 0.02
#> TCGA.55.7574.01 2 0.5875 -0.4261 0.24 0.44 0.30 0.00 0.02 0.00 0.00
#> TCGA.44.2656.01 4 0.0000 0.8727 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7158.01 5 0.4524 0.6765 0.04 0.34 0.00 0.00 0.60 0.02 0.00
#> TCGA.86.8056.01 3 0.6914 0.1781 0.08 0.04 0.40 0.00 0.38 0.02 0.08
#> TCGA.97.8175.01 2 0.4211 0.1872 0.04 0.68 0.00 0.00 0.26 0.02 0.00
#> TCGA.97.8547.01 5 0.4939 0.7409 0.14 0.20 0.00 0.00 0.64 0.02 0.00
#> TCGA.44.6147.01 3 0.4718 0.2461 0.32 0.06 0.60 0.00 0.00 0.02 0.00
#> TCGA.77.8007.01 4 0.0504 0.8695 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.86.8073.01 7 0.4644 0.6794 0.02 0.00 0.00 0.12 0.00 0.18 0.68
#> TCGA.91.6828.01 7 0.7073 0.5911 0.04 0.00 0.00 0.16 0.14 0.20 0.46
#> TCGA.38.7271.01 2 0.1166 0.6505 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.78.7143.01 3 0.5125 0.4737 0.04 0.04 0.68 0.00 0.18 0.06 0.00
#> TCGA.75.6205.01 2 0.0863 0.6586 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.2422 0.5494 0.18 0.82 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5126.01 1 0.5539 0.6218 0.38 0.38 0.24 0.00 0.00 0.00 0.00
#> TCGA.67.6215.01 5 0.3526 0.7471 0.06 0.18 0.00 0.00 0.76 0.00 0.00
#> TCGA.55.6982.01 3 0.2803 0.4514 0.10 0.06 0.84 0.00 0.00 0.00 0.00
#> TCGA.55.6986.01 5 0.4795 0.7688 0.08 0.28 0.00 0.00 0.62 0.02 0.00
#> TCGA.49.6761.01 2 0.6087 0.0999 0.12 0.54 0.26 0.00 0.06 0.00 0.02
#> TCGA.MP.A4T6.01 3 0.5535 0.4128 0.30 0.04 0.54 0.00 0.00 0.12 0.00
#> TCGA.44.6779.01 2 0.0863 0.6586 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 5 0.4692 0.5502 0.08 0.42 0.00 0.00 0.50 0.00 0.00
#> TCGA.73.4658.01 2 0.1928 0.6328 0.00 0.90 0.00 0.00 0.08 0.02 0.00
#> TCGA.05.4417.01 3 0.2857 0.5186 0.06 0.04 0.86 0.00 0.04 0.00 0.00
#> TCGA.95.8039.01 4 0.6435 -0.0181 0.10 0.00 0.00 0.48 0.02 0.10 0.30
#> TCGA.80.5607.01 5 0.4992 0.7596 0.10 0.28 0.00 0.00 0.60 0.02 0.00
#> TCGA.62.8395.01 5 0.4461 0.6879 0.04 0.32 0.00 0.00 0.62 0.02 0.00
#> TCGA.86.8672.01 4 0.2016 0.8188 0.04 0.00 0.00 0.90 0.00 0.06 0.00
#> TCGA.64.5815.01 7 0.6232 0.3629 0.10 0.00 0.00 0.34 0.00 0.12 0.44
#> TCGA.97.8172.01 3 0.2706 0.5362 0.02 0.04 0.88 0.00 0.04 0.00 0.02
#> TCGA.05.5715.01 3 0.5083 0.4116 0.34 0.04 0.56 0.00 0.00 0.06 0.00
#> TCGA.44.7672.01 2 0.3867 0.4965 0.12 0.74 0.00 0.00 0.14 0.00 0.00
#> TCGA.78.7152.01 7 0.3263 0.6938 0.00 0.00 0.00 0.12 0.00 0.08 0.80
#> TCGA.55.8302.01 7 0.5293 0.6481 0.02 0.00 0.00 0.12 0.00 0.32 0.54
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.44.4112.01 3 0.3135 0.35572 0.12 0.02 0.82 0.00 0.00 0.02 0.00 0.02
#> TCGA.NJ.A4YP.01 7 0.6429 -0.10763 0.20 0.00 0.00 0.34 0.02 0.00 0.36 0.08
#> TCGA.86.8278.01 5 0.0808 0.63336 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.49.AARQ.01 3 0.6262 0.16519 0.28 0.02 0.52 0.02 0.02 0.08 0.00 0.06
#> TCGA.62.A46U.01 2 0.4523 0.41924 0.10 0.70 0.00 0.00 0.10 0.10 0.00 0.00
#> TCGA.MP.A4T8.01 7 0.2020 0.35475 0.00 0.02 0.00 0.00 0.00 0.06 0.90 0.02
#> TCGA.MP.A4SY.01 8 0.6252 0.41598 0.20 0.00 0.00 0.06 0.02 0.00 0.32 0.40
#> TCGA.93.A4JN.01 7 0.5329 -0.23785 0.12 0.00 0.00 0.00 0.00 0.04 0.46 0.38
#> TCGA.86.A4JF.01 4 0.5171 0.53765 0.20 0.00 0.00 0.58 0.00 0.00 0.18 0.04
#> TCGA.63.6202.01 4 0.1563 0.94172 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.MP.A4TI.01 4 0.1563 0.94172 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.MP.A4TC.01 7 0.4886 -0.22454 0.06 0.00 0.00 0.00 0.00 0.04 0.46 0.44
#> TCGA.05.4410.01 7 0.5511 0.19646 0.06 0.00 0.00 0.06 0.00 0.06 0.60 0.22
#> TCGA.62.A46Y.01 5 0.4199 0.37153 0.00 0.32 0.00 0.00 0.60 0.08 0.00 0.00
#> TCGA.50.6597.01 5 0.5037 0.51643 0.00 0.14 0.00 0.00 0.54 0.30 0.00 0.02
#> TCGA.MP.A4SW.01 7 0.5048 -0.22082 0.08 0.00 0.00 0.00 0.00 0.04 0.48 0.40
#> TCGA.67.6216.01 5 0.0808 0.63336 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.55.8203.01 3 0.2914 0.26965 0.00 0.00 0.84 0.00 0.04 0.04 0.00 0.08
#> TCGA.44.2668.01 8 0.4968 0.22532 0.02 0.00 0.00 0.02 0.00 0.06 0.38 0.52
#> TCGA.L9.A444.01 2 0.2348 0.48840 0.06 0.88 0.00 0.00 0.04 0.02 0.00 0.00
#> TCGA.44.A47G.01 2 0.1947 0.52005 0.00 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.44.2665.01 3 0.7182 -0.14242 0.12 0.02 0.40 0.00 0.26 0.14 0.00 0.06
#> TCGA.44.2666.01 8 0.6252 0.41598 0.20 0.00 0.00 0.06 0.02 0.00 0.32 0.40
#> TCGA.55.A494.01 5 0.6601 -0.27186 0.00 0.00 0.28 0.00 0.30 0.22 0.00 0.20
#> TCGA.75.5125.01 8 0.4673 0.45269 0.08 0.00 0.00 0.02 0.00 0.00 0.34 0.56
#> TCGA.55.7911.01 2 0.2947 0.51583 0.06 0.84 0.00 0.00 0.06 0.04 0.00 0.00
#> TCGA.55.6712.01 4 0.1563 0.94172 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.95.7948.01 6 0.6464 0.00000 0.02 0.00 0.34 0.08 0.12 0.42 0.00 0.02
#> TCGA.55.7281.01 5 0.4337 0.57977 0.00 0.04 0.00 0.00 0.70 0.10 0.00 0.16
#> TCGA.38.6178.01 3 0.4943 0.05637 0.08 0.02 0.64 0.04 0.00 0.22 0.00 0.00
#> TCGA.75.5122.01 4 0.2025 0.92900 0.02 0.00 0.00 0.88 0.00 0.00 0.10 0.00
#> TCGA.L9.A443.01 3 0.3830 0.19703 0.08 0.02 0.74 0.00 0.00 0.16 0.00 0.00
#> TCGA.86.7701.01 7 0.2807 0.35247 0.02 0.00 0.00 0.00 0.02 0.06 0.86 0.04
#> TCGA.52.7812.01 8 0.4367 0.40865 0.02 0.00 0.00 0.00 0.02 0.02 0.34 0.60
#> TCGA.78.8660.01 4 0.2025 0.93104 0.02 0.00 0.00 0.88 0.00 0.00 0.10 0.00
#> TCGA.MP.A4TK.01 2 0.5641 -0.57883 0.36 0.44 0.06 0.00 0.14 0.00 0.00 0.00
#> TCGA.78.7540.01 3 0.2674 0.36144 0.04 0.00 0.86 0.00 0.00 0.06 0.00 0.04
#> TCGA.69.7763.01 7 0.1741 0.37412 0.00 0.00 0.00 0.04 0.02 0.00 0.92 0.02
#> TCGA.J2.A4AE.01 2 0.4680 -0.14240 0.00 0.48 0.00 0.00 0.40 0.12 0.00 0.00
#> TCGA.50.6590.01 1 0.6543 0.83320 0.36 0.34 0.16 0.00 0.12 0.02 0.00 0.00
#> TCGA.MN.A4N5.01 7 0.4245 0.23244 0.14 0.00 0.00 0.06 0.00 0.00 0.72 0.08
#> TCGA.69.7978.01 4 0.1563 0.94172 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.MP.A4TD.01 7 0.2071 0.37346 0.00 0.00 0.00 0.04 0.02 0.00 0.90 0.04
#> TCGA.83.5908.01 2 0.5723 -0.54867 0.34 0.44 0.06 0.00 0.16 0.00 0.00 0.00
#> TCGA.NJ.A4YG.01 7 0.5308 -0.37911 0.18 0.00 0.00 0.00 0.00 0.02 0.48 0.32
#> TCGA.44.3918.01 3 0.5244 0.02336 0.20 0.26 0.52 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.7574.01 3 0.6658 -0.72112 0.30 0.26 0.32 0.00 0.10 0.00 0.00 0.02
#> TCGA.44.2656.01 4 0.1563 0.94172 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.78.7158.01 5 0.5190 0.31848 0.00 0.32 0.00 0.00 0.42 0.26 0.00 0.00
#> TCGA.86.8056.01 5 0.6400 -0.18269 0.00 0.00 0.30 0.00 0.36 0.16 0.00 0.18
#> TCGA.97.8175.01 2 0.4318 0.13789 0.00 0.60 0.00 0.00 0.30 0.10 0.00 0.00
#> TCGA.97.8547.01 5 0.0808 0.63336 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.44.6147.01 3 0.4937 0.24307 0.12 0.02 0.68 0.02 0.00 0.14 0.00 0.02
#> TCGA.77.8007.01 4 0.1563 0.94172 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.86.8073.01 7 0.4886 -0.22454 0.06 0.00 0.00 0.00 0.00 0.04 0.46 0.44
#> TCGA.91.6828.01 7 0.3264 0.34973 0.02 0.02 0.00 0.04 0.00 0.06 0.84 0.02
#> TCGA.38.7271.01 2 0.3078 0.49506 0.06 0.82 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.78.7143.01 3 0.5435 0.00425 0.06 0.00 0.56 0.00 0.08 0.28 0.00 0.02
#> TCGA.75.6205.01 2 0.3154 0.37112 0.16 0.78 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.5264 -0.33164 0.30 0.50 0.02 0.00 0.18 0.00 0.00 0.00
#> TCGA.75.5126.01 1 0.7245 0.84085 0.34 0.28 0.20 0.00 0.12 0.04 0.00 0.02
#> TCGA.67.6215.01 5 0.4096 0.59554 0.00 0.06 0.00 0.00 0.68 0.24 0.00 0.02
#> TCGA.55.6982.01 3 0.2807 0.39747 0.10 0.04 0.84 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.6986.01 5 0.1341 0.62724 0.00 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.49.6761.01 2 0.6554 -0.19220 0.20 0.36 0.32 0.00 0.10 0.02 0.00 0.00
#> TCGA.MP.A4T6.01 3 0.4325 -0.35741 0.02 0.00 0.56 0.04 0.00 0.38 0.00 0.00
#> TCGA.44.6779.01 2 0.3299 0.35994 0.18 0.76 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.86.A4P7.01 5 0.3922 0.27844 0.06 0.30 0.00 0.00 0.64 0.00 0.00 0.00
#> TCGA.73.4658.01 2 0.2947 0.51583 0.06 0.84 0.00 0.00 0.06 0.04 0.00 0.00
#> TCGA.05.4417.01 3 0.0941 0.37763 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.95.8039.01 7 0.6655 -0.21415 0.22 0.00 0.00 0.26 0.00 0.00 0.26 0.26
#> TCGA.80.5607.01 5 0.1091 0.63159 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.62.8395.01 5 0.5116 0.38919 0.00 0.28 0.00 0.00 0.46 0.26 0.00 0.00
#> TCGA.86.8672.01 4 0.3397 0.85445 0.06 0.00 0.00 0.80 0.00 0.00 0.10 0.04
#> TCGA.64.5815.01 8 0.6408 0.34076 0.22 0.00 0.00 0.14 0.00 0.00 0.28 0.36
#> TCGA.97.8172.01 3 0.2484 0.28423 0.02 0.00 0.86 0.00 0.00 0.10 0.00 0.02
#> TCGA.05.5715.01 3 0.6489 -0.52789 0.04 0.00 0.48 0.04 0.12 0.28 0.00 0.04
#> TCGA.44.7672.01 2 0.5496 0.13433 0.14 0.50 0.02 0.00 0.32 0.00 0.00 0.02
#> TCGA.78.7152.01 7 0.4779 -0.04370 0.08 0.00 0.00 0.00 0.00 0.04 0.60 0.28
#> TCGA.55.8302.01 8 0.4834 0.27758 0.04 0.00 0.00 0.00 0.00 0.06 0.38 0.52
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: Node024. Child nodes: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0242"]
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 48 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 0.999 1.000 0.40432 0.597 0.597
#> 3 3 1.000 1.000 1.000 0.59930 0.637 0.447
#> 4 4 0.900 0.833 0.932 0.06059 0.993 0.980
#> 5 5 0.771 0.550 0.840 0.06430 0.982 0.949
#> 6 6 0.739 0.716 0.733 0.04866 0.852 0.563
#> 7 7 0.714 0.632 0.817 0.03807 0.934 0.712
#> 8 8 0.691 0.605 0.718 0.00526 0.950 0.773
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.44.4112.01 2 0.000 0.999 0.00 1.00
#> TCGA.86.8278.01 2 0.000 0.999 0.00 1.00
#> TCGA.49.AARQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.62.A46U.01 2 0.000 0.999 0.00 1.00
#> TCGA.62.A46Y.01 2 0.000 0.999 0.00 1.00
#> TCGA.50.6597.01 1 0.000 1.000 1.00 0.00
#> TCGA.67.6216.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.8203.01 2 0.000 0.999 0.00 1.00
#> TCGA.L9.A444.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.A47G.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.2665.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.A494.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7911.01 2 0.000 0.999 0.00 1.00
#> TCGA.95.7948.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.7281.01 2 0.000 0.999 0.00 1.00
#> TCGA.38.6178.01 2 0.000 0.999 0.00 1.00
#> TCGA.L9.A443.01 1 0.000 1.000 1.00 0.00
#> TCGA.MP.A4TK.01 2 0.000 0.999 0.00 1.00
#> TCGA.78.7540.01 1 0.000 1.000 1.00 0.00
#> TCGA.J2.A4AE.01 2 0.141 0.980 0.02 0.98
#> TCGA.50.6590.01 2 0.000 0.999 0.00 1.00
#> TCGA.83.5908.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.3918.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.7574.01 2 0.000 0.999 0.00 1.00
#> TCGA.78.7158.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.8056.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8175.01 2 0.000 0.999 0.00 1.00
#> TCGA.97.8547.01 2 0.000 0.999 0.00 1.00
#> TCGA.44.6147.01 2 0.000 0.999 0.00 1.00
#> TCGA.38.7271.01 2 0.000 0.999 0.00 1.00
#> TCGA.78.7143.01 1 0.000 1.000 1.00 0.00
#> TCGA.75.6205.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.A493.01 2 0.000 0.999 0.00 1.00
#> TCGA.75.5126.01 2 0.000 0.999 0.00 1.00
#> TCGA.67.6215.01 1 0.000 1.000 1.00 0.00
#> TCGA.55.6982.01 2 0.000 0.999 0.00 1.00
#> TCGA.55.6986.01 2 0.000 0.999 0.00 1.00
#> TCGA.49.6761.01 2 0.000 0.999 0.00 1.00
#> TCGA.MP.A4T6.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.6779.01 2 0.000 0.999 0.00 1.00
#> TCGA.86.A4P7.01 2 0.000 0.999 0.00 1.00
#> TCGA.73.4658.01 2 0.000 0.999 0.00 1.00
#> TCGA.05.4417.01 2 0.000 0.999 0.00 1.00
#> TCGA.80.5607.01 2 0.000 0.999 0.00 1.00
#> TCGA.62.8395.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8172.01 2 0.000 0.999 0.00 1.00
#> TCGA.05.5715.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.7672.01 2 0.000 0.999 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.4112.01 3 0 1 0 0 1
#> TCGA.86.8278.01 3 0 1 0 0 1
#> TCGA.49.AARQ.01 3 0 1 0 0 1
#> TCGA.62.A46U.01 2 0 1 0 1 0
#> TCGA.62.A46Y.01 3 0 1 0 0 1
#> TCGA.50.6597.01 3 0 1 0 0 1
#> TCGA.67.6216.01 3 0 1 0 0 1
#> TCGA.55.8203.01 3 0 1 0 0 1
#> TCGA.L9.A444.01 2 0 1 0 1 0
#> TCGA.44.A47G.01 2 0 1 0 1 0
#> TCGA.44.2665.01 3 0 1 0 0 1
#> TCGA.55.A494.01 1 0 1 1 0 0
#> TCGA.55.7911.01 2 0 1 0 1 0
#> TCGA.95.7948.01 1 0 1 1 0 0
#> TCGA.55.7281.01 3 0 1 0 0 1
#> TCGA.38.6178.01 3 0 1 0 0 1
#> TCGA.L9.A443.01 3 0 1 0 0 1
#> TCGA.MP.A4TK.01 2 0 1 0 1 0
#> TCGA.78.7540.01 1 0 1 1 0 0
#> TCGA.J2.A4AE.01 3 0 1 0 0 1
#> TCGA.50.6590.01 2 0 1 0 1 0
#> TCGA.83.5908.01 2 0 1 0 1 0
#> TCGA.44.3918.01 2 0 1 0 1 0
#> TCGA.55.7574.01 2 0 1 0 1 0
#> TCGA.78.7158.01 1 0 1 1 0 0
#> TCGA.86.8056.01 3 0 1 0 0 1
#> TCGA.97.8175.01 3 0 1 0 0 1
#> TCGA.97.8547.01 3 0 1 0 0 1
#> TCGA.44.6147.01 3 0 1 0 0 1
#> TCGA.38.7271.01 2 0 1 0 1 0
#> TCGA.78.7143.01 1 0 1 1 0 0
#> TCGA.75.6205.01 2 0 1 0 1 0
#> TCGA.55.A493.01 2 0 1 0 1 0
#> TCGA.75.5126.01 2 0 1 0 1 0
#> TCGA.67.6215.01 1 0 1 1 0 0
#> TCGA.55.6982.01 3 0 1 0 0 1
#> TCGA.55.6986.01 3 0 1 0 0 1
#> TCGA.49.6761.01 2 0 1 0 1 0
#> TCGA.MP.A4T6.01 1 0 1 1 0 0
#> TCGA.44.6779.01 2 0 1 0 1 0
#> TCGA.86.A4P7.01 2 0 1 0 1 0
#> TCGA.73.4658.01 2 0 1 0 1 0
#> TCGA.05.4417.01 3 0 1 0 0 1
#> TCGA.80.5607.01 3 0 1 0 0 1
#> TCGA.62.8395.01 1 0 1 1 0 0
#> TCGA.97.8172.01 3 0 1 0 0 1
#> TCGA.05.5715.01 1 0 1 1 0 0
#> TCGA.44.7672.01 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.44.4112.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.86.8278.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.49.AARQ.01 3 0.5428 0.417 0.38 0.00 0.60 0.02
#> TCGA.62.A46U.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.62.A46Y.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.50.6597.01 3 0.5428 0.417 0.38 0.00 0.60 0.02
#> TCGA.67.6216.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.55.8203.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.L9.A444.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.44.A47G.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.44.2665.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.55.A494.01 1 0.4790 0.913 0.62 0.00 0.00 0.38
#> TCGA.55.7911.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.95.7948.01 1 0.4790 0.913 0.62 0.00 0.00 0.38
#> TCGA.55.7281.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.38.6178.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.L9.A443.01 3 0.5428 0.417 0.38 0.00 0.60 0.02
#> TCGA.MP.A4TK.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.78.7540.01 4 0.5570 0.000 0.44 0.00 0.02 0.54
#> TCGA.J2.A4AE.01 3 0.3335 0.776 0.12 0.00 0.86 0.02
#> TCGA.50.6590.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.83.5908.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.44.3918.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.55.7574.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.78.7158.01 1 0.4790 0.913 0.62 0.00 0.00 0.38
#> TCGA.86.8056.01 3 0.5428 0.417 0.38 0.00 0.60 0.02
#> TCGA.97.8175.01 3 0.2706 0.808 0.00 0.02 0.90 0.08
#> TCGA.97.8547.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.44.6147.01 3 0.2011 0.828 0.00 0.00 0.92 0.08
#> TCGA.38.7271.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.78.7143.01 1 0.4624 0.893 0.66 0.00 0.00 0.34
#> TCGA.75.6205.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.55.A493.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.75.5126.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.67.6215.01 1 0.4790 0.913 0.62 0.00 0.00 0.38
#> TCGA.55.6982.01 3 0.2011 0.828 0.00 0.00 0.92 0.08
#> TCGA.55.6986.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.49.6761.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.MP.A4T6.01 1 0.4624 0.893 0.66 0.00 0.00 0.34
#> TCGA.44.6779.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
#> TCGA.86.A4P7.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.73.4658.01 2 0.2011 0.949 0.00 0.92 0.00 0.08
#> TCGA.05.4417.01 3 0.2011 0.828 0.00 0.00 0.92 0.08
#> TCGA.80.5607.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.62.8395.01 1 0.0707 0.166 0.98 0.00 0.00 0.02
#> TCGA.97.8172.01 3 0.0000 0.878 0.00 0.00 1.00 0.00
#> TCGA.05.5715.01 1 0.4790 0.913 0.62 0.00 0.00 0.38
#> TCGA.44.7672.01 2 0.0000 0.959 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.4112.01 3 0.1043 0.6186 0.00 0.00 0.96 0.00 0.04
#> TCGA.86.8278.01 3 0.0609 0.6174 0.00 0.00 0.98 0.00 0.02
#> TCGA.49.AARQ.01 5 0.5173 0.0000 0.00 0.00 0.46 0.04 0.50
#> TCGA.62.A46U.01 2 0.3796 0.7369 0.00 0.70 0.00 0.00 0.30
#> TCGA.62.A46Y.01 3 0.1043 0.6187 0.00 0.00 0.96 0.00 0.04
#> TCGA.50.6597.01 3 0.5157 -0.8619 0.00 0.00 0.52 0.04 0.44
#> TCGA.67.6216.01 3 0.1043 0.5987 0.00 0.00 0.96 0.00 0.04
#> TCGA.55.8203.01 3 0.0609 0.6265 0.00 0.00 0.98 0.00 0.02
#> TCGA.L9.A444.01 2 0.4182 0.6783 0.00 0.60 0.00 0.00 0.40
#> TCGA.44.A47G.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.2665.01 3 0.0000 0.6263 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.A494.01 1 0.0000 0.8745 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7911.01 2 0.3561 0.7522 0.00 0.74 0.00 0.00 0.26
#> TCGA.95.7948.01 1 0.1410 0.8426 0.94 0.00 0.00 0.00 0.06
#> TCGA.55.7281.01 3 0.0609 0.6174 0.00 0.00 0.98 0.00 0.02
#> TCGA.38.6178.01 3 0.0609 0.6174 0.00 0.00 0.98 0.00 0.02
#> TCGA.L9.A443.01 3 0.5457 -0.9046 0.00 0.00 0.48 0.06 0.46
#> TCGA.MP.A4TK.01 2 0.4060 0.7041 0.00 0.64 0.00 0.00 0.36
#> TCGA.78.7540.01 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00
#> TCGA.J2.A4AE.01 3 0.3561 -0.0563 0.00 0.00 0.74 0.00 0.26
#> TCGA.50.6590.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.83.5908.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.3918.01 2 0.4726 0.6597 0.00 0.58 0.02 0.00 0.40
#> TCGA.55.7574.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7158.01 1 0.0000 0.8745 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8056.01 3 0.5157 -0.8619 0.00 0.00 0.52 0.04 0.44
#> TCGA.97.8175.01 3 0.4675 0.3340 0.00 0.02 0.60 0.00 0.38
#> TCGA.97.8547.01 3 0.1043 0.5992 0.00 0.00 0.96 0.00 0.04
#> TCGA.44.6147.01 3 0.4060 0.3778 0.00 0.00 0.64 0.00 0.36
#> TCGA.38.7271.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7143.01 1 0.3106 0.8257 0.84 0.00 0.00 0.02 0.14
#> TCGA.75.6205.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.5126.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.67.6215.01 1 0.1216 0.8693 0.96 0.00 0.00 0.02 0.02
#> TCGA.55.6982.01 3 0.4060 0.3778 0.00 0.00 0.64 0.00 0.36
#> TCGA.55.6986.01 3 0.0000 0.6263 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.6761.01 2 0.4726 0.6597 0.00 0.58 0.02 0.00 0.40
#> TCGA.MP.A4T6.01 1 0.3319 0.8139 0.82 0.00 0.00 0.02 0.16
#> TCGA.44.6779.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 2 0.4675 0.6750 0.00 0.60 0.02 0.00 0.38
#> TCGA.73.4658.01 2 0.3684 0.7458 0.00 0.72 0.00 0.00 0.28
#> TCGA.05.4417.01 3 0.4060 0.3778 0.00 0.00 0.64 0.00 0.36
#> TCGA.80.5607.01 3 0.0609 0.6161 0.00 0.00 0.98 0.00 0.02
#> TCGA.62.8395.01 1 0.5156 0.5700 0.62 0.00 0.00 0.06 0.32
#> TCGA.97.8172.01 3 0.0609 0.6265 0.00 0.00 0.98 0.00 0.02
#> TCGA.05.5715.01 1 0.0000 0.8745 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7672.01 2 0.0000 0.8068 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.4112.01 3 0.1267 0.810 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.86.8278.01 3 0.1267 0.806 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.49.AARQ.01 5 0.3309 0.828 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.62.A46U.01 6 0.3797 0.786 0.00 0.42 0.00 0.00 0.00 0.58
#> TCGA.62.A46Y.01 3 0.0547 0.830 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.50.6597.01 5 0.3819 0.834 0.00 0.00 0.28 0.00 0.70 0.02
#> TCGA.67.6216.01 3 0.1556 0.783 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.55.8203.01 3 0.1092 0.824 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.L9.A444.01 6 0.3756 0.798 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.44.A47G.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2665.01 3 0.1556 0.819 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.55.A494.01 1 0.2474 0.719 0.88 0.00 0.00 0.00 0.04 0.08
#> TCGA.55.7911.01 6 0.3869 0.643 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.95.7948.01 1 0.4360 0.533 0.68 0.00 0.00 0.00 0.06 0.26
#> TCGA.55.7281.01 3 0.0547 0.828 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.38.6178.01 3 0.0937 0.831 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.L9.A443.01 5 0.3711 0.716 0.00 0.00 0.26 0.00 0.72 0.02
#> TCGA.MP.A4TK.01 6 0.3828 0.765 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.78.7540.01 4 0.0937 0.000 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.J2.A4AE.01 5 0.3851 0.658 0.00 0.00 0.46 0.00 0.54 0.00
#> TCGA.50.6590.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.83.5908.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.3918.01 6 0.3756 0.798 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.55.7574.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 1 0.2474 0.719 0.88 0.00 0.00 0.00 0.04 0.08
#> TCGA.86.8056.01 5 0.4078 0.835 0.00 0.00 0.34 0.00 0.64 0.02
#> TCGA.97.8175.01 6 0.3851 -0.179 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.97.8547.01 3 0.1814 0.805 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.44.6147.01 3 0.3819 0.571 0.00 0.00 0.70 0.00 0.02 0.28
#> TCGA.38.7271.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7143.01 1 0.4926 0.694 0.72 0.00 0.00 0.06 0.14 0.08
#> TCGA.75.6205.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.5126.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.67.6215.01 1 0.2403 0.746 0.90 0.00 0.00 0.02 0.04 0.04
#> TCGA.55.6982.01 3 0.3916 0.544 0.00 0.00 0.68 0.00 0.02 0.30
#> TCGA.55.6986.01 3 0.0937 0.820 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.49.6761.01 6 0.3756 0.798 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.MP.A4T6.01 1 0.4733 0.703 0.74 0.00 0.00 0.06 0.12 0.08
#> TCGA.44.6779.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P7.01 6 0.3797 0.790 0.00 0.42 0.00 0.00 0.00 0.58
#> TCGA.73.4658.01 2 0.3869 -0.711 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.05.4417.01 3 0.3819 0.571 0.00 0.00 0.70 0.00 0.02 0.28
#> TCGA.80.5607.01 3 0.1807 0.810 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.62.8395.01 1 0.6015 0.475 0.52 0.00 0.00 0.06 0.34 0.08
#> TCGA.97.8172.01 3 0.0547 0.830 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.05.5715.01 1 0.0547 0.745 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.44.7672.01 2 0.0000 0.917 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.44.4112.01 3 0.1363 0.6974 0.00 0.00 0.94 0 0.00 0.02 0.04
#> TCGA.86.8278.01 3 0.2421 0.6757 0.00 0.00 0.88 0 0.08 0.02 0.02
#> TCGA.49.AARQ.01 5 0.3358 0.7195 0.00 0.00 0.36 0 0.64 0.00 0.00
#> TCGA.62.A46U.01 6 0.2572 0.8055 0.00 0.20 0.00 0 0.00 0.80 0.00
#> TCGA.62.A46Y.01 3 0.0504 0.6996 0.00 0.00 0.98 0 0.02 0.00 0.00
#> TCGA.50.6597.01 5 0.3496 0.7159 0.00 0.00 0.42 0 0.58 0.00 0.00
#> TCGA.67.6216.01 3 0.2509 0.6401 0.00 0.00 0.88 0 0.06 0.04 0.02
#> TCGA.55.8203.01 3 0.0863 0.6939 0.00 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.L9.A444.01 6 0.2259 0.8196 0.00 0.16 0.00 0 0.00 0.84 0.00
#> TCGA.44.A47G.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.44.2665.01 3 0.3940 0.5989 0.00 0.00 0.78 0 0.08 0.06 0.08
#> TCGA.55.A494.01 1 0.0000 0.5432 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.55.7911.01 6 0.3047 0.7456 0.00 0.28 0.00 0 0.00 0.72 0.00
#> TCGA.95.7948.01 1 0.5386 0.3335 0.60 0.00 0.00 0 0.10 0.06 0.24
#> TCGA.55.7281.01 3 0.1664 0.6786 0.00 0.00 0.92 0 0.06 0.00 0.02
#> TCGA.38.6178.01 3 0.1006 0.6985 0.00 0.00 0.96 0 0.02 0.00 0.02
#> TCGA.L9.A443.01 5 0.4825 0.3486 0.00 0.00 0.16 0 0.66 0.02 0.16
#> TCGA.MP.A4TK.01 6 0.2259 0.8196 0.00 0.16 0.00 0 0.00 0.84 0.00
#> TCGA.78.7540.01 4 0.0000 0.0000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.J2.A4AE.01 3 0.3755 -0.2659 0.00 0.00 0.64 0 0.34 0.02 0.00
#> TCGA.50.6590.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.83.5908.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.44.3918.01 6 0.2081 0.8120 0.00 0.14 0.00 0 0.00 0.86 0.00
#> TCGA.55.7574.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.78.7158.01 1 0.0000 0.5432 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.86.8056.01 5 0.3994 0.6083 0.00 0.00 0.48 0 0.50 0.02 0.00
#> TCGA.97.8175.01 6 0.3780 0.5375 0.00 0.02 0.24 0 0.02 0.72 0.00
#> TCGA.97.8547.01 3 0.3656 0.6113 0.00 0.00 0.80 0 0.08 0.04 0.08
#> TCGA.44.6147.01 3 0.3994 -0.0591 0.00 0.00 0.50 0 0.02 0.48 0.00
#> TCGA.38.7271.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.78.7143.01 7 0.4381 0.7668 0.36 0.00 0.00 0 0.06 0.00 0.58
#> TCGA.75.6205.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.75.5126.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.67.6215.01 1 0.3546 -0.4031 0.54 0.00 0.00 0 0.00 0.00 0.46
#> TCGA.55.6982.01 6 0.4954 0.0170 0.00 0.00 0.40 0 0.04 0.52 0.04
#> TCGA.55.6986.01 3 0.1860 0.6759 0.00 0.00 0.92 0 0.02 0.04 0.02
#> TCGA.49.6761.01 6 0.2081 0.8120 0.00 0.14 0.00 0 0.00 0.86 0.00
#> TCGA.MP.A4T6.01 7 0.4381 0.7668 0.36 0.00 0.00 0 0.06 0.00 0.58
#> TCGA.44.6779.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.86.A4P7.01 6 0.2422 0.8176 0.00 0.18 0.00 0 0.00 0.82 0.00
#> TCGA.73.4658.01 6 0.3047 0.7456 0.00 0.28 0.00 0 0.00 0.72 0.00
#> TCGA.05.4417.01 3 0.3985 0.0369 0.00 0.00 0.52 0 0.02 0.46 0.00
#> TCGA.80.5607.01 3 0.2509 0.6562 0.00 0.00 0.88 0 0.06 0.04 0.02
#> TCGA.62.8395.01 7 0.4883 0.6028 0.20 0.00 0.00 0 0.20 0.00 0.60
#> TCGA.97.8172.01 3 0.0863 0.6939 0.00 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.05.5715.01 1 0.3139 0.1183 0.70 0.00 0.00 0 0.00 0.00 0.30
#> TCGA.44.7672.01 2 0.0000 1.0000 0.00 1.00 0.00 0 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.44.4112.01 3 0.2071 0.6761 0.00 0.00 0.90 0 0.02 0.04 0.00 0.04
#> TCGA.86.8278.01 3 0.3385 0.6166 0.00 0.00 0.76 0 0.16 0.00 0.00 0.08
#> TCGA.49.AARQ.01 5 0.6587 0.0299 0.00 0.00 0.16 0 0.40 0.02 0.14 0.28
#> TCGA.62.A46U.01 6 0.3318 0.8331 0.00 0.46 0.00 0 0.00 0.54 0.00 0.00
#> TCGA.62.A46Y.01 3 0.1275 0.6863 0.00 0.00 0.94 0 0.04 0.02 0.00 0.00
#> TCGA.50.6597.01 5 0.6426 0.3399 0.00 0.00 0.30 0 0.34 0.00 0.14 0.22
#> TCGA.67.6216.01 3 0.3170 0.5789 0.00 0.00 0.76 0 0.20 0.00 0.00 0.04
#> TCGA.55.8203.01 3 0.1275 0.6812 0.00 0.00 0.94 0 0.04 0.02 0.00 0.00
#> TCGA.L9.A444.01 6 0.4239 0.8189 0.00 0.30 0.00 0 0.02 0.64 0.02 0.02
#> TCGA.44.A47G.01 2 0.0000 0.9776 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.44.2665.01 3 0.4605 0.5606 0.00 0.00 0.68 0 0.10 0.02 0.02 0.18
#> TCGA.55.A494.01 1 0.0000 0.6323 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.55.7911.01 6 0.3714 0.8285 0.00 0.44 0.00 0 0.02 0.54 0.00 0.00
#> TCGA.95.7948.01 5 0.6321 -0.3446 0.30 0.00 0.00 0 0.42 0.18 0.08 0.02
#> TCGA.55.7281.01 3 0.1563 0.6713 0.00 0.00 0.90 0 0.10 0.00 0.00 0.00
#> TCGA.38.6178.01 3 0.2265 0.6792 0.00 0.00 0.88 0 0.08 0.00 0.02 0.02
#> TCGA.L9.A443.01 8 0.3744 0.0000 0.00 0.00 0.06 0 0.00 0.02 0.18 0.74
#> TCGA.MP.A4TK.01 6 0.3272 0.8513 0.00 0.42 0.00 0 0.00 0.58 0.00 0.00
#> TCGA.78.7540.01 4 0.0000 0.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.J2.A4AE.01 3 0.5743 -0.4080 0.00 0.00 0.42 0 0.36 0.00 0.06 0.16
#> TCGA.50.6590.01 2 0.0000 0.9776 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.83.5908.01 2 0.0808 0.9423 0.00 0.96 0.00 0 0.00 0.04 0.00 0.00
#> TCGA.44.3918.01 6 0.4074 0.7878 0.00 0.26 0.02 0 0.02 0.68 0.00 0.02
#> TCGA.55.7574.01 2 0.0000 0.9776 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.78.7158.01 1 0.0000 0.6323 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.86.8056.01 5 0.6179 0.3507 0.00 0.00 0.34 0 0.38 0.00 0.14 0.14
#> TCGA.97.8175.01 3 0.3737 0.2611 0.00 0.00 0.50 0 0.00 0.48 0.02 0.00
#> TCGA.97.8547.01 3 0.4293 0.5550 0.00 0.00 0.68 0 0.10 0.02 0.00 0.20
#> TCGA.44.6147.01 3 0.3941 0.5209 0.00 0.00 0.68 0 0.00 0.26 0.04 0.02
#> TCGA.38.7271.01 2 0.0000 0.9776 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.78.7143.01 7 0.2938 0.6831 0.30 0.00 0.00 0 0.00 0.00 0.70 0.00
#> TCGA.75.6205.01 2 0.0000 0.9776 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.55.A493.01 2 0.0000 0.9776 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.75.5126.01 2 0.0808 0.9423 0.00 0.96 0.00 0 0.00 0.04 0.00 0.00
#> TCGA.67.6215.01 1 0.3329 -0.2702 0.52 0.00 0.00 0 0.00 0.00 0.48 0.00
#> TCGA.55.6982.01 3 0.4702 0.5265 0.00 0.00 0.64 0 0.00 0.22 0.04 0.10
#> TCGA.55.6986.01 3 0.2547 0.6504 0.00 0.00 0.84 0 0.12 0.00 0.00 0.04
#> TCGA.49.6761.01 6 0.2852 0.8144 0.00 0.28 0.00 0 0.00 0.72 0.00 0.00
#> TCGA.MP.A4T6.01 7 0.3083 0.6285 0.34 0.00 0.00 0 0.00 0.00 0.66 0.00
#> TCGA.44.6779.01 2 0.1091 0.9161 0.00 0.94 0.00 0 0.00 0.06 0.00 0.00
#> TCGA.86.A4P7.01 6 0.3690 0.8492 0.00 0.42 0.00 0 0.00 0.56 0.02 0.00
#> TCGA.73.4658.01 6 0.3329 0.8048 0.00 0.48 0.00 0 0.00 0.52 0.00 0.00
#> TCGA.05.4417.01 3 0.3843 0.5414 0.00 0.00 0.70 0 0.00 0.24 0.04 0.02
#> TCGA.80.5607.01 3 0.2888 0.6136 0.00 0.00 0.80 0 0.16 0.00 0.00 0.04
#> TCGA.62.8395.01 7 0.2807 0.5412 0.10 0.00 0.00 0 0.02 0.00 0.84 0.04
#> TCGA.97.8172.01 3 0.0471 0.6848 0.00 0.00 0.98 0 0.00 0.02 0.00 0.00
#> TCGA.05.5715.01 1 0.2650 0.4799 0.76 0.00 0.00 0 0.00 0.00 0.24 0.00
#> TCGA.44.7672.01 2 0.0000 0.9776 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: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node041 , Node042 , Node043 , Node051 , Node052 , Node061 , Node062-leaf , Node071 , Node072 , Node073 .
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 48 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 0.2844 0.716 0.716
#> 3 3 0.929 0.922 0.965 1.2256 0.653 0.516
#> 4 4 0.774 0.874 0.912 0.1446 0.766 0.460
#> 5 5 0.800 0.779 0.882 0.0547 0.973 0.900
#> 6 6 0.876 0.796 0.892 0.0492 0.945 0.775
#> 7 7 0.872 0.761 0.890 0.0103 0.981 0.909
#> 8 8 0.868 0.704 0.868 0.0233 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.62.A470.01 2 0 1 0 1
#> TCGA.44.6778.01 2 0 1 0 1
#> TCGA.69.8255.01 2 0 1 0 1
#> TCGA.91.6847.01 1 0 1 1 0
#> TCGA.44.6144.01 2 0 1 0 1
#> TCGA.86.7955.01 2 0 1 0 1
#> TCGA.56.7223.01 1 0 1 1 0
#> TCGA.55.8507.01 2 0 1 0 1
#> TCGA.37.5819.01 2 0 1 0 1
#> TCGA.86.8054.01 2 0 1 0 1
#> TCGA.85.A510.01 2 0 1 0 1
#> TCGA.85.8352.01 1 0 1 1 0
#> TCGA.64.5775.01 2 0 1 0 1
#> TCGA.50.5946.02 2 0 1 0 1
#> TCGA.43.7658.01 1 0 1 1 0
#> TCGA.55.8514.01 2 0 1 0 1
#> TCGA.78.7155.01 2 0 1 0 1
#> TCGA.44.7669.01 2 0 1 0 1
#> TCGA.49.AAR2.01 2 0 1 0 1
#> TCGA.64.5774.01 2 0 1 0 1
#> TCGA.55.8094.01 2 0 1 0 1
#> TCGA.22.5481.01 1 0 1 1 0
#> TCGA.22.5483.01 1 0 1 1 0
#> TCGA.75.6211.01 2 0 1 0 1
#> TCGA.75.7031.01 2 0 1 0 1
#> TCGA.44.8119.01 2 0 1 0 1
#> TCGA.55.A4DF.01 2 0 1 0 1
#> TCGA.78.8662.01 2 0 1 0 1
#> TCGA.78.7220.01 2 0 1 0 1
#> TCGA.44.5644.01 2 0 1 0 1
#> TCGA.50.6591.01 1 0 1 1 0
#> TCGA.L9.A7SV.01 2 0 1 0 1
#> TCGA.80.5611.01 2 0 1 0 1
#> TCGA.49.6742.01 2 0 1 0 1
#> TCGA.62.A46O.01 2 0 1 0 1
#> TCGA.39.5034.01 2 0 1 0 1
#> TCGA.55.8620.01 2 0 1 0 1
#> TCGA.55.7570.01 2 0 1 0 1
#> TCGA.55.5899.01 2 0 1 0 1
#> TCGA.62.8399.01 2 0 1 0 1
#> TCGA.91.8499.01 2 0 1 0 1
#> TCGA.78.7150.01 2 0 1 0 1
#> TCGA.55.A490.01 2 0 1 0 1
#> TCGA.55.6969.01 2 0 1 0 1
#> TCGA.21.5787.01 2 0 1 0 1
#> TCGA.78.7536.01 2 0 1 0 1
#> TCGA.50.5946.01 2 0 1 0 1
#> TCGA.O2.A5IB.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.62.A470.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.44.6778.01 2 0.613 0.446 0 0.60 0.40
#> TCGA.69.8255.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.91.6847.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.44.6144.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.86.7955.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.56.7223.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.55.8507.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.37.5819.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.86.8054.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.85.A510.01 2 0.613 0.446 0 0.60 0.40
#> TCGA.85.8352.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.64.5775.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.50.5946.02 2 0.000 0.913 0 1.00 0.00
#> TCGA.43.7658.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.55.8514.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.78.7155.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.44.7669.01 2 0.153 0.886 0 0.96 0.04
#> TCGA.49.AAR2.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.64.5774.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.55.8094.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.22.5481.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.22.5483.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.75.6211.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.75.7031.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.44.8119.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.55.A4DF.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.78.8662.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.78.7220.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.44.5644.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.50.6591.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.L9.A7SV.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.80.5611.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.49.6742.01 2 0.480 0.736 0 0.78 0.22
#> TCGA.62.A46O.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.39.5034.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.55.8620.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.55.7570.01 2 0.480 0.736 0 0.78 0.22
#> TCGA.55.5899.01 2 0.604 0.488 0 0.62 0.38
#> TCGA.62.8399.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.91.8499.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.78.7150.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.55.A490.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.55.6969.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.21.5787.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.78.7536.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.50.5946.01 2 0.000 0.913 0 1.00 0.00
#> TCGA.O2.A5IB.01 1 0.000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.62.A470.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.44.6778.01 3 0.3400 0.790 0.00 0.18 0.82 0.00
#> TCGA.69.8255.01 3 0.0000 0.753 0.00 0.00 1.00 0.00
#> TCGA.91.6847.01 1 0.0707 0.989 0.98 0.00 0.00 0.02
#> TCGA.44.6144.01 3 0.4134 0.751 0.00 0.26 0.74 0.00
#> TCGA.86.7955.01 3 0.0707 0.743 0.00 0.00 0.98 0.02
#> TCGA.56.7223.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.55.8507.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.37.5819.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.86.8054.01 4 0.1211 0.735 0.00 0.00 0.04 0.96
#> TCGA.85.A510.01 3 0.3801 0.743 0.00 0.00 0.78 0.22
#> TCGA.85.8352.01 1 0.0707 0.989 0.98 0.00 0.00 0.02
#> TCGA.64.5775.01 3 0.0707 0.743 0.00 0.00 0.98 0.02
#> TCGA.50.5946.02 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.43.7658.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.55.8514.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.78.7155.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.44.7669.01 3 0.4134 0.751 0.00 0.26 0.74 0.00
#> TCGA.49.AAR2.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.64.5774.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.8094.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.22.5481.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.22.5483.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.75.6211.01 3 0.3801 0.743 0.00 0.00 0.78 0.22
#> TCGA.75.7031.01 3 0.4134 0.751 0.00 0.26 0.74 0.00
#> TCGA.44.8119.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.A4DF.01 4 0.3975 0.857 0.00 0.00 0.24 0.76
#> TCGA.78.8662.01 3 0.3801 0.743 0.00 0.00 0.78 0.22
#> TCGA.78.7220.01 3 0.0000 0.753 0.00 0.00 1.00 0.00
#> TCGA.44.5644.01 4 0.1211 0.735 0.00 0.00 0.04 0.96
#> TCGA.50.6591.01 1 0.0707 0.989 0.98 0.00 0.00 0.02
#> TCGA.L9.A7SV.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.80.5611.01 4 0.3975 0.857 0.00 0.00 0.24 0.76
#> TCGA.49.6742.01 3 0.3801 0.779 0.00 0.22 0.78 0.00
#> TCGA.62.A46O.01 3 0.0000 0.753 0.00 0.00 1.00 0.00
#> TCGA.39.5034.01 3 0.3801 0.743 0.00 0.00 0.78 0.22
#> TCGA.55.8620.01 4 0.3975 0.857 0.00 0.00 0.24 0.76
#> TCGA.55.7570.01 3 0.3801 0.779 0.00 0.22 0.78 0.00
#> TCGA.55.5899.01 3 0.3610 0.785 0.00 0.20 0.80 0.00
#> TCGA.62.8399.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.91.8499.01 4 0.3975 0.857 0.00 0.00 0.24 0.76
#> TCGA.78.7150.01 4 0.4907 0.700 0.00 0.00 0.42 0.58
#> TCGA.55.A490.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.55.6969.01 3 0.2647 0.594 0.00 0.00 0.88 0.12
#> TCGA.21.5787.01 4 0.4907 0.700 0.00 0.00 0.42 0.58
#> TCGA.78.7536.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.50.5946.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.O2.A5IB.01 1 0.0000 0.994 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.62.A470.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.6778.01 3 0.2438 0.716 0.00 0.06 0.90 0.04 0.00
#> TCGA.69.8255.01 3 0.3731 0.686 0.00 0.00 0.80 0.16 0.04
#> TCGA.91.6847.01 1 0.1216 0.973 0.96 0.00 0.00 0.02 0.02
#> TCGA.44.6144.01 3 0.2929 0.648 0.00 0.18 0.82 0.00 0.00
#> TCGA.86.7955.01 3 0.5597 0.523 0.00 0.00 0.64 0.16 0.20
#> TCGA.56.7223.01 1 0.0000 0.984 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8507.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.37.5819.01 2 0.0609 0.979 0.00 0.98 0.02 0.00 0.00
#> TCGA.86.8054.01 5 0.5232 0.163 0.00 0.00 0.06 0.34 0.60
#> TCGA.85.A510.01 3 0.4106 0.607 0.00 0.02 0.80 0.04 0.14
#> TCGA.85.8352.01 1 0.1216 0.973 0.96 0.00 0.00 0.02 0.02
#> TCGA.64.5775.01 3 0.5733 0.498 0.00 0.00 0.62 0.16 0.22
#> TCGA.50.5946.02 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.43.7658.01 1 0.0000 0.984 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8514.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7155.01 2 0.0609 0.979 0.00 0.98 0.02 0.00 0.00
#> TCGA.44.7669.01 3 0.2732 0.670 0.00 0.16 0.84 0.00 0.00
#> TCGA.49.AAR2.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.64.5774.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8094.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5481.01 1 0.0000 0.984 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5483.01 1 0.0000 0.984 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6211.01 3 0.3922 0.578 0.00 0.00 0.78 0.04 0.18
#> TCGA.75.7031.01 3 0.2732 0.670 0.00 0.16 0.84 0.00 0.00
#> TCGA.44.8119.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.A4DF.01 4 0.3106 0.707 0.00 0.00 0.02 0.84 0.14
#> TCGA.78.8662.01 5 0.5673 -0.141 0.00 0.00 0.42 0.08 0.50
#> TCGA.78.7220.01 3 0.4373 0.641 0.00 0.00 0.76 0.16 0.08
#> TCGA.44.5644.01 5 0.4263 0.395 0.00 0.00 0.06 0.18 0.76
#> TCGA.50.6591.01 1 0.1648 0.963 0.94 0.00 0.00 0.02 0.04
#> TCGA.L9.A7SV.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.80.5611.01 4 0.1732 0.723 0.00 0.00 0.08 0.92 0.00
#> TCGA.49.6742.01 3 0.5270 0.671 0.00 0.06 0.74 0.12 0.08
#> TCGA.62.A46O.01 3 0.5733 0.498 0.00 0.00 0.62 0.16 0.22
#> TCGA.39.5034.01 3 0.3521 0.600 0.00 0.00 0.82 0.04 0.14
#> TCGA.55.8620.01 4 0.3319 0.704 0.00 0.00 0.02 0.82 0.16
#> TCGA.55.7570.01 3 0.2012 0.723 0.00 0.06 0.92 0.00 0.02
#> TCGA.55.5899.01 3 0.2797 0.720 0.00 0.06 0.88 0.00 0.06
#> TCGA.62.8399.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.8499.01 4 0.4360 0.618 0.00 0.00 0.02 0.68 0.30
#> TCGA.78.7150.01 4 0.2516 0.690 0.00 0.00 0.14 0.86 0.00
#> TCGA.55.A490.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.6969.01 3 0.2929 0.644 0.00 0.00 0.82 0.18 0.00
#> TCGA.21.5787.01 4 0.2516 0.690 0.00 0.00 0.14 0.86 0.00
#> TCGA.78.7536.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5946.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.O2.A5IB.01 1 0.0000 0.984 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.62.A470.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6778.01 3 0.0000 0.7875 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.69.8255.01 3 0.3797 0.0508 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.91.6847.01 1 0.0547 0.9872 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.44.6144.01 3 0.0000 0.7875 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.7955.01 6 0.2048 0.7092 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.56.7223.01 1 0.0000 0.9924 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8507.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.37.5819.01 2 0.3475 0.7577 0.00 0.80 0.14 0.06 0.00 0.00
#> TCGA.86.8054.01 5 0.0937 0.9732 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.85.A510.01 3 0.1807 0.7667 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.85.8352.01 1 0.0547 0.9872 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.64.5775.01 6 0.2048 0.7092 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.50.5946.02 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.7658.01 1 0.0000 0.9924 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8514.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7155.01 2 0.1480 0.9261 0.00 0.94 0.04 0.02 0.00 0.00
#> TCGA.44.7669.01 3 0.0000 0.7875 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AAR2.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.64.5774.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8094.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5481.01 1 0.0000 0.9924 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5483.01 1 0.0000 0.9924 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6211.01 3 0.2190 0.7532 0.00 0.00 0.90 0.00 0.04 0.06
#> TCGA.75.7031.01 3 0.1267 0.7724 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.44.8119.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.A4DF.01 4 0.3163 0.6317 0.00 0.00 0.00 0.82 0.14 0.04
#> TCGA.78.8662.01 6 0.4758 0.2273 0.00 0.00 0.06 0.00 0.36 0.58
#> TCGA.78.7220.01 6 0.3756 0.4347 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.44.5644.01 5 0.0547 0.9734 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.50.6591.01 1 0.0547 0.9872 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.L9.A7SV.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.80.5611.01 4 0.3647 0.6929 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.49.6742.01 6 0.3851 0.2923 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.62.A46O.01 6 0.2048 0.7092 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.39.5034.01 3 0.1807 0.7667 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.55.8620.01 4 0.3351 0.6254 0.00 0.00 0.00 0.80 0.16 0.04
#> TCGA.55.7570.01 3 0.3076 0.5511 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.55.5899.01 3 0.3409 0.4339 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.62.8399.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.8499.01 4 0.4200 0.4678 0.00 0.00 0.00 0.74 0.14 0.12
#> TCGA.78.7150.01 4 0.3647 0.6929 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.55.A490.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6969.01 3 0.3982 0.5473 0.00 0.00 0.74 0.20 0.00 0.06
#> TCGA.21.5787.01 4 0.3647 0.6929 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.78.7536.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5946.01 2 0.0000 0.9802 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.O2.A5IB.01 1 0.0000 0.9924 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.62.A470.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.6778.01 3 0.0504 0.7216 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.69.8255.01 3 0.2945 0.5689 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.91.6847.01 1 0.1006 0.9403 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.44.6144.01 3 0.0504 0.7234 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.86.7955.01 6 0.2163 0.6958 0.00 0.00 0.10 0.00 0.00 0.88 0.02
#> TCGA.56.7223.01 1 0.0000 0.9546 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8507.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.37.5819.01 2 0.3263 0.7564 0.00 0.80 0.12 0.00 0.00 0.00 0.08
#> TCGA.86.8054.01 5 0.2163 0.7922 0.00 0.00 0.02 0.10 0.88 0.00 0.00
#> TCGA.85.A510.01 3 0.2512 0.6713 0.00 0.00 0.86 0.00 0.04 0.00 0.10
#> TCGA.85.8352.01 1 0.1363 0.9315 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.64.5775.01 6 0.3058 0.6638 0.00 0.00 0.08 0.00 0.00 0.82 0.10
#> TCGA.50.5946.02 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.7658.01 1 0.0000 0.9546 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8514.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7155.01 2 0.1006 0.9462 0.00 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.44.7669.01 3 0.0504 0.7234 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.49.AAR2.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.5774.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8094.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5481.01 1 0.0000 0.9546 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5483.01 1 0.0000 0.9546 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6211.01 3 0.3404 0.6645 0.00 0.00 0.82 0.00 0.04 0.08 0.06
#> TCGA.75.7031.01 3 0.1664 0.7062 0.00 0.02 0.92 0.00 0.00 0.00 0.06
#> TCGA.44.8119.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A4DF.01 4 0.0000 0.7733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.8662.01 6 0.4824 0.3185 0.00 0.00 0.04 0.00 0.16 0.68 0.12
#> TCGA.78.7220.01 6 0.3558 -0.1644 0.00 0.00 0.48 0.00 0.00 0.52 0.00
#> TCGA.44.5644.01 5 0.3887 0.8031 0.00 0.00 0.04 0.02 0.80 0.06 0.08
#> TCGA.50.6591.01 1 0.4358 0.7425 0.74 0.00 0.00 0.00 0.12 0.08 0.06
#> TCGA.L9.A7SV.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.80.5611.01 4 0.2081 0.8637 0.00 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.49.6742.01 3 0.3558 0.0398 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.62.A46O.01 6 0.1433 0.6987 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.39.5034.01 3 0.2512 0.6713 0.00 0.00 0.86 0.00 0.04 0.00 0.10
#> TCGA.55.8620.01 4 0.0000 0.7733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7570.01 3 0.2832 0.5883 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.55.5899.01 3 0.4214 0.2186 0.00 0.00 0.56 0.00 0.00 0.40 0.04
#> TCGA.62.8399.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.8499.01 7 0.3459 0.0000 0.00 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.78.7150.01 4 0.2081 0.8637 0.00 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.55.A490.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6969.01 3 0.3755 0.4332 0.00 0.00 0.64 0.34 0.00 0.02 0.00
#> TCGA.21.5787.01 4 0.2081 0.8637 0.00 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.78.7536.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5946.01 2 0.0000 0.9819 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.O2.A5IB.01 1 0.0000 0.9546 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.62.A470.01 2 0.0471 0.9411 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.44.6778.01 3 0.0000 0.6298 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.8255.01 3 0.3514 0.3926 0.00 0.00 0.64 0.00 0.00 0.02 0.00 0.34
#> TCGA.91.6847.01 1 0.2025 0.8967 0.88 0.00 0.00 0.00 0.02 0.10 0.00 0.00
#> TCGA.44.6144.01 3 0.0000 0.6298 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7955.01 8 0.0941 0.6237 0.00 0.00 0.02 0.00 0.00 0.00 0.02 0.96
#> TCGA.56.7223.01 1 0.0000 0.9376 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8507.01 2 0.0471 0.9411 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.37.5819.01 2 0.4841 0.2400 0.00 0.50 0.16 0.00 0.00 0.34 0.00 0.00
#> TCGA.86.8054.01 5 0.0471 0.6728 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.85.A510.01 3 0.3142 0.4474 0.00 0.00 0.64 0.00 0.00 0.36 0.00 0.00
#> TCGA.85.8352.01 1 0.2025 0.8967 0.88 0.00 0.00 0.00 0.02 0.10 0.00 0.00
#> TCGA.64.5775.01 8 0.3299 0.5227 0.00 0.00 0.00 0.00 0.00 0.18 0.06 0.76
#> TCGA.50.5946.02 2 0.0000 0.9423 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.7658.01 1 0.0000 0.9376 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8514.01 2 0.0471 0.9411 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.78.7155.01 2 0.2725 0.7816 0.00 0.82 0.04 0.00 0.00 0.14 0.00 0.00
#> TCGA.44.7669.01 3 0.0471 0.6283 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.49.AAR2.01 2 0.0000 0.9423 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.5774.01 2 0.0000 0.9423 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8094.01 2 0.0000 0.9423 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5481.01 1 0.0000 0.9376 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5483.01 1 0.0000 0.9376 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6211.01 3 0.4578 0.4822 0.00 0.00 0.70 0.00 0.02 0.08 0.16 0.04
#> TCGA.75.7031.01 3 0.2756 0.5381 0.00 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.44.8119.01 2 0.0000 0.9423 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.A4DF.01 4 0.0000 0.9220 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.8662.01 8 0.4590 0.3563 0.00 0.00 0.00 0.00 0.06 0.10 0.16 0.68
#> TCGA.78.7220.01 8 0.3737 -0.2804 0.00 0.00 0.48 0.00 0.00 0.02 0.00 0.50
#> TCGA.44.5644.01 5 0.3970 0.6854 0.00 0.00 0.00 0.00 0.72 0.08 0.18 0.02
#> TCGA.50.6591.01 1 0.2981 0.8006 0.76 0.00 0.00 0.00 0.02 0.22 0.00 0.00
#> TCGA.L9.A7SV.01 2 0.0000 0.9423 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.80.5611.01 4 0.0808 0.9410 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.49.6742.01 3 0.3333 0.0641 0.00 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.62.A46O.01 8 0.0471 0.6296 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.39.5034.01 3 0.3142 0.4474 0.00 0.00 0.64 0.00 0.00 0.36 0.00 0.00
#> TCGA.55.8620.01 4 0.0808 0.8979 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.55.7570.01 3 0.2938 0.4508 0.00 0.00 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.55.5899.01 3 0.4040 0.2703 0.00 0.00 0.58 0.00 0.00 0.02 0.02 0.38
#> TCGA.62.8399.01 2 0.0471 0.9411 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.91.8499.01 7 0.2756 0.0000 0.00 0.00 0.00 0.26 0.00 0.00 0.74 0.00
#> TCGA.78.7150.01 4 0.1275 0.9393 0.00 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.55.A490.01 2 0.0471 0.9411 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.55.6969.01 3 0.3374 0.4242 0.00 0.00 0.68 0.30 0.00 0.02 0.00 0.00
#> TCGA.21.5787.01 4 0.1275 0.9393 0.00 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.78.7536.01 2 0.0000 0.9423 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5946.01 2 0.0471 0.9411 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.O2.A5IB.01 1 0.0000 0.9376 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node041 , Node042 , Node043 , Node051 , Node052 , Node061 , Node062-leaf , Node071 , Node072 , Node073 .
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 83 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 0.5065 0.494 0.494
#> 3 3 1.000 0.973 0.989 0.2894 0.807 0.627
#> 4 4 0.799 0.656 0.856 0.1224 0.862 0.634
#> 5 5 0.824 0.826 0.901 0.0691 0.869 0.568
#> 6 6 0.858 0.757 0.881 0.0356 0.974 0.880
#> 7 7 0.867 0.743 0.854 0.0143 0.981 0.906
#> 8 8 0.867 0.703 0.828 0.0215 0.961 0.802
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.22.4613.01 2 0 1 0 1
#> TCGA.90.7769.01 1 0 1 1 0
#> TCGA.77.A5G3.01 1 0 1 1 0
#> TCGA.58.A46N.01 1 0 1 1 0
#> TCGA.34.7107.01 1 0 1 1 0
#> TCGA.56.7823.01 2 0 1 0 1
#> TCGA.58.8391.01 1 0 1 1 0
#> TCGA.85.A4QR.01 2 0 1 0 1
#> TCGA.77.8128.01 2 0 1 0 1
#> TCGA.22.4601.01 1 0 1 1 0
#> TCGA.22.4593.01 2 0 1 0 1
#> TCGA.34.5240.01 1 0 1 1 0
#> TCGA.63.5131.01 2 0 1 0 1
#> TCGA.77.8009.01 1 0 1 1 0
#> TCGA.77.8153.01 2 0 1 0 1
#> TCGA.56.8083.01 2 0 1 0 1
#> TCGA.77.A5G6.01 1 0 1 1 0
#> TCGA.56.A4BX.01 2 0 1 0 1
#> TCGA.NC.A5HG.01 2 0 1 0 1
#> TCGA.33.A5GW.01 1 0 1 1 0
#> TCGA.63.5128.01 1 0 1 1 0
#> TCGA.63.A5MU.01 2 0 1 0 1
#> TCGA.34.5231.01 2 0 1 0 1
#> TCGA.33.AASD.01 1 0 1 1 0
#> TCGA.NC.A5HP.01 1 0 1 1 0
#> TCGA.39.5037.01 1 0 1 1 0
#> TCGA.37.A5EN.01 1 0 1 1 0
#> TCGA.77.8148.01 2 0 1 0 1
#> TCGA.18.5592.01 1 0 1 1 0
#> TCGA.92.7341.01 1 0 1 1 0
#> TCGA.56.7582.01 1 0 1 1 0
#> TCGA.43.6143.01 2 0 1 0 1
#> TCGA.34.8456.01 2 0 1 0 1
#> TCGA.56.7222.01 2 0 1 0 1
#> TCGA.94.8490.01 1 0 1 1 0
#> TCGA.22.5482.01 1 0 1 1 0
#> TCGA.46.6026.01 2 0 1 0 1
#> TCGA.85.7710.01 1 0 1 1 0
#> TCGA.43.A474.01 2 0 1 0 1
#> TCGA.22.5473.01 1 0 1 1 0
#> TCGA.77.8154.01 2 0 1 0 1
#> TCGA.22.5491.01 1 0 1 1 0
#> TCGA.77.7139.01 2 0 1 0 1
#> TCGA.58.8392.01 2 0 1 0 1
#> TCGA.63.7023.01 2 0 1 0 1
#> TCGA.33.AASJ.01 1 0 1 1 0
#> TCGA.85.8070.01 2 0 1 0 1
#> TCGA.98.A53A.01 1 0 1 1 0
#> TCGA.NC.A5HT.01 2 0 1 0 1
#> TCGA.43.6770.01 2 0 1 0 1
#> TCGA.34.5929.01 2 0 1 0 1
#> TCGA.77.7140.01 2 0 1 0 1
#> TCGA.NC.A5HF.01 2 0 1 0 1
#> TCGA.63.A5MB.01 1 0 1 1 0
#> TCGA.34.5927.01 2 0 1 0 1
#> TCGA.NC.A5HN.01 2 0 1 0 1
#> TCGA.77.8150.01 1 0 1 1 0
#> TCGA.18.5595.01 1 0 1 1 0
#> TCGA.79.5596.01 2 0 1 0 1
#> TCGA.63.A5ML.01 1 0 1 1 0
#> TCGA.22.5477.01 1 0 1 1 0
#> TCGA.85.8071.01 2 0 1 0 1
#> TCGA.77.8143.01 2 0 1 0 1
#> TCGA.77.6845.01 1 0 1 1 0
#> TCGA.56.7730.01 1 0 1 1 0
#> TCGA.56.7579.01 2 0 1 0 1
#> TCGA.63.A5MH.01 2 0 1 0 1
#> TCGA.58.8390.01 2 0 1 0 1
#> TCGA.39.5027.01 2 0 1 0 1
#> TCGA.22.5485.01 1 0 1 1 0
#> TCGA.33.4583.01 1 0 1 1 0
#> TCGA.MF.A522.01 1 0 1 1 0
#> TCGA.70.6723.01 1 0 1 1 0
#> TCGA.68.7755.01 1 0 1 1 0
#> TCGA.NC.A5HH.01 2 0 1 0 1
#> TCGA.NK.A5CR.01 2 0 1 0 1
#> TCGA.77.6844.01 2 0 1 0 1
#> TCGA.56.8082.01 2 0 1 0 1
#> TCGA.L3.A524.01 1 0 1 1 0
#> TCGA.85.A5B5.01 1 0 1 1 0
#> TCGA.63.A5MY.01 2 0 1 0 1
#> TCGA.85.A512.01 1 0 1 1 0
#> TCGA.85.8354.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.22.4613.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.90.7769.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.77.A5G3.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.58.A46N.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.34.7107.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.56.7823.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.58.8391.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.85.A4QR.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.8128.01 3 0.3340 0.843 0.00 0.12 0.88
#> TCGA.22.4601.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.22.4593.01 2 0.6045 0.381 0.00 0.62 0.38
#> TCGA.34.5240.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.63.5131.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.8009.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.77.8153.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.56.8083.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.A5G6.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.56.A4BX.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.NC.A5HG.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.33.A5GW.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.63.5128.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.63.A5MU.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.34.5231.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.33.AASD.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.NC.A5HP.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.39.5037.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.37.A5EN.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.77.8148.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.18.5592.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.92.7341.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.56.7582.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.43.6143.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.34.8456.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.56.7222.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.94.8490.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.22.5482.01 1 0.0892 0.979 0.98 0.00 0.02
#> TCGA.46.6026.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.85.7710.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.43.A474.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.22.5473.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.77.8154.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.22.5491.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.77.7139.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.58.8392.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.63.7023.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.33.AASJ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.85.8070.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.98.A53A.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.NC.A5HT.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.43.6770.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.34.5929.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.7140.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.NC.A5HF.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.63.A5MB.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.34.5927.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.NC.A5HN.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.8150.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.18.5595.01 3 0.5948 0.433 0.36 0.00 0.64
#> TCGA.79.5596.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.63.A5ML.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.22.5477.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.8143.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.6845.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.56.7730.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.56.7579.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.63.A5MH.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.58.8390.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.39.5027.01 3 0.0000 0.970 0.00 0.00 1.00
#> TCGA.22.5485.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.33.4583.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.MF.A522.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.70.6723.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.68.7755.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.NC.A5HH.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.NK.A5CR.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.77.6844.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.56.8082.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.L3.A524.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.85.A5B5.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.63.A5MY.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.85.A512.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.85.8354.01 3 0.0000 0.970 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.22.4613.01 3 0.0000 0.5680 0.00 0.00 1.00 0.00
#> TCGA.90.7769.01 1 0.1637 0.8527 0.94 0.00 0.00 0.06
#> TCGA.77.A5G3.01 1 0.4994 0.2262 0.52 0.00 0.00 0.48
#> TCGA.58.A46N.01 1 0.4713 0.4892 0.64 0.00 0.00 0.36
#> TCGA.34.7107.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.56.7823.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.58.8391.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.85.A4QR.01 2 0.4948 0.3297 0.00 0.56 0.44 0.00
#> TCGA.77.8128.01 3 0.0000 0.5680 0.00 0.00 1.00 0.00
#> TCGA.22.4601.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.22.4593.01 3 0.2335 0.5683 0.00 0.06 0.92 0.02
#> TCGA.34.5240.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.63.5131.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.77.8009.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.77.8153.01 3 0.4790 0.4295 0.00 0.00 0.62 0.38
#> TCGA.56.8083.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.77.A5G6.01 4 0.4713 0.1433 0.00 0.00 0.36 0.64
#> TCGA.56.A4BX.01 3 0.3801 0.5081 0.00 0.22 0.78 0.00
#> TCGA.NC.A5HG.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.33.A5GW.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.63.5128.01 4 0.4855 0.0886 0.40 0.00 0.00 0.60
#> TCGA.63.A5MU.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.34.5231.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HP.01 1 0.4994 0.2262 0.52 0.00 0.00 0.48
#> TCGA.39.5037.01 4 0.4790 0.1293 0.00 0.00 0.38 0.62
#> TCGA.37.A5EN.01 4 0.4855 0.0886 0.40 0.00 0.00 0.60
#> TCGA.77.8148.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.18.5592.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.92.7341.01 1 0.1637 0.8527 0.94 0.00 0.00 0.06
#> TCGA.56.7582.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.43.6143.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.34.8456.01 3 0.4790 0.4295 0.00 0.00 0.62 0.38
#> TCGA.56.7222.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.94.8490.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.22.5482.01 4 0.2647 0.5383 0.12 0.00 0.00 0.88
#> TCGA.46.6026.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.85.7710.01 1 0.4994 0.2262 0.52 0.00 0.00 0.48
#> TCGA.43.A474.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.22.5473.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.77.8154.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.22.5491.01 4 0.2011 0.5278 0.00 0.00 0.08 0.92
#> TCGA.77.7139.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.58.8392.01 3 0.0000 0.5680 0.00 0.00 1.00 0.00
#> TCGA.63.7023.01 3 0.4790 0.4295 0.00 0.00 0.62 0.38
#> TCGA.33.AASJ.01 1 0.4713 0.4892 0.64 0.00 0.00 0.36
#> TCGA.85.8070.01 3 0.4790 0.4295 0.00 0.00 0.62 0.38
#> TCGA.98.A53A.01 4 0.4713 0.1433 0.00 0.00 0.36 0.64
#> TCGA.NC.A5HT.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.43.6770.01 3 0.4790 0.4295 0.00 0.00 0.62 0.38
#> TCGA.34.5929.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.77.7140.01 3 0.4790 0.4295 0.00 0.00 0.62 0.38
#> TCGA.NC.A5HF.01 3 0.3172 0.5536 0.00 0.16 0.84 0.00
#> TCGA.63.A5MB.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.34.5927.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.NC.A5HN.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.77.8150.01 4 0.2011 0.5278 0.00 0.00 0.08 0.92
#> TCGA.18.5595.01 4 0.0707 0.5425 0.02 0.00 0.00 0.98
#> TCGA.79.5596.01 3 0.4907 0.0469 0.00 0.42 0.58 0.00
#> TCGA.63.A5ML.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.22.5477.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.77.8143.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.77.6845.01 1 0.1211 0.8636 0.96 0.00 0.00 0.04
#> TCGA.56.7730.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.56.7579.01 3 0.4855 0.1120 0.00 0.40 0.60 0.00
#> TCGA.63.A5MH.01 3 0.4948 0.3466 0.00 0.00 0.56 0.44
#> TCGA.58.8390.01 2 0.4713 0.5060 0.00 0.64 0.36 0.00
#> TCGA.39.5027.01 3 0.4790 0.4295 0.00 0.00 0.62 0.38
#> TCGA.22.5485.01 4 0.4855 0.0886 0.40 0.00 0.00 0.60
#> TCGA.33.4583.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.MF.A522.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.70.6723.01 1 0.1637 0.8527 0.94 0.00 0.00 0.06
#> TCGA.68.7755.01 1 0.1637 0.8527 0.94 0.00 0.00 0.06
#> TCGA.NC.A5HH.01 2 0.4406 0.5975 0.00 0.70 0.30 0.00
#> TCGA.NK.A5CR.01 3 0.2921 0.5593 0.00 0.14 0.86 0.00
#> TCGA.77.6844.01 2 0.0000 0.9283 0.00 1.00 0.00 0.00
#> TCGA.56.8082.01 2 0.4713 0.5060 0.00 0.64 0.36 0.00
#> TCGA.L3.A524.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.85.A5B5.01 1 0.4994 0.2262 0.52 0.00 0.00 0.48
#> TCGA.63.A5MY.01 3 0.4406 0.3681 0.00 0.30 0.70 0.00
#> TCGA.85.A512.01 1 0.0000 0.8826 1.00 0.00 0.00 0.00
#> TCGA.85.8354.01 4 0.3400 0.4523 0.00 0.00 0.18 0.82
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.22.4613.01 3 0.2732 0.676 0.00 0.00 0.84 0.00 0.16
#> TCGA.90.7769.01 1 0.3796 0.540 0.70 0.00 0.00 0.30 0.00
#> TCGA.77.A5G3.01 4 0.3684 0.708 0.28 0.00 0.00 0.72 0.00
#> TCGA.58.A46N.01 4 0.3684 0.708 0.28 0.00 0.00 0.72 0.00
#> TCGA.34.7107.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.7823.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.58.8391.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4QR.01 3 0.2873 0.792 0.00 0.12 0.86 0.02 0.00
#> TCGA.77.8128.01 3 0.0000 0.820 0.00 0.00 1.00 0.00 0.00
#> TCGA.22.4601.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.4593.01 3 0.1216 0.816 0.00 0.00 0.96 0.02 0.02
#> TCGA.34.5240.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.5131.01 2 0.0609 0.970 0.00 0.98 0.00 0.02 0.00
#> TCGA.77.8009.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8153.01 5 0.3319 0.814 0.00 0.00 0.16 0.02 0.82
#> TCGA.56.8083.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.A5G6.01 5 0.3274 0.724 0.00 0.00 0.00 0.22 0.78
#> TCGA.56.A4BX.01 3 0.0000 0.820 0.00 0.00 1.00 0.00 0.00
#> TCGA.NC.A5HG.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.33.A5GW.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.5128.01 4 0.1732 0.722 0.08 0.00 0.00 0.92 0.00
#> TCGA.63.A5MU.01 2 0.0609 0.970 0.00 0.98 0.00 0.02 0.00
#> TCGA.34.5231.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HP.01 4 0.3684 0.708 0.28 0.00 0.00 0.72 0.00
#> TCGA.39.5037.01 5 0.3274 0.724 0.00 0.00 0.00 0.22 0.78
#> TCGA.37.A5EN.01 4 0.1410 0.714 0.06 0.00 0.00 0.94 0.00
#> TCGA.77.8148.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.18.5592.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.92.7341.01 1 0.3274 0.698 0.78 0.00 0.00 0.22 0.00
#> TCGA.56.7582.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.6143.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.34.8456.01 5 0.3513 0.826 0.00 0.00 0.18 0.02 0.80
#> TCGA.56.7222.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.94.8490.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5482.01 4 0.1216 0.675 0.02 0.00 0.00 0.96 0.02
#> TCGA.46.6026.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.7710.01 4 0.3684 0.708 0.28 0.00 0.00 0.72 0.00
#> TCGA.43.A474.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5473.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8154.01 2 0.3690 0.690 0.00 0.78 0.20 0.02 0.00
#> TCGA.22.5491.01 4 0.4060 0.178 0.00 0.00 0.00 0.64 0.36
#> TCGA.77.7139.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.58.8392.01 3 0.3684 0.469 0.00 0.00 0.72 0.00 0.28
#> TCGA.63.7023.01 5 0.3513 0.826 0.00 0.00 0.18 0.02 0.80
#> TCGA.33.AASJ.01 4 0.3684 0.708 0.28 0.00 0.00 0.72 0.00
#> TCGA.85.8070.01 5 0.3106 0.814 0.00 0.00 0.14 0.02 0.84
#> TCGA.98.A53A.01 5 0.3274 0.724 0.00 0.00 0.00 0.22 0.78
#> TCGA.NC.A5HT.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.43.6770.01 5 0.3513 0.826 0.00 0.00 0.18 0.02 0.80
#> TCGA.34.5929.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7140.01 5 0.3319 0.814 0.00 0.00 0.16 0.02 0.82
#> TCGA.NC.A5HF.01 3 0.0000 0.820 0.00 0.00 1.00 0.00 0.00
#> TCGA.63.A5MB.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.34.5927.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HN.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8150.01 4 0.4126 0.124 0.00 0.00 0.00 0.62 0.38
#> TCGA.18.5595.01 4 0.2732 0.560 0.00 0.00 0.00 0.84 0.16
#> TCGA.79.5596.01 3 0.1732 0.817 0.00 0.08 0.92 0.00 0.00
#> TCGA.63.A5ML.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5477.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8143.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.6845.01 1 0.2020 0.850 0.90 0.00 0.00 0.10 0.00
#> TCGA.56.7730.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.7579.01 3 0.1410 0.823 0.00 0.06 0.94 0.00 0.00
#> TCGA.63.A5MH.01 5 0.2077 0.804 0.00 0.00 0.04 0.04 0.92
#> TCGA.58.8390.01 3 0.4132 0.683 0.00 0.26 0.72 0.02 0.00
#> TCGA.39.5027.01 5 0.3319 0.829 0.00 0.00 0.16 0.02 0.82
#> TCGA.22.5485.01 4 0.1410 0.714 0.06 0.00 0.00 0.94 0.00
#> TCGA.33.4583.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.MF.A522.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.70.6723.01 1 0.3274 0.698 0.78 0.00 0.00 0.22 0.00
#> TCGA.68.7755.01 1 0.3274 0.698 0.78 0.00 0.00 0.22 0.00
#> TCGA.NC.A5HH.01 3 0.4540 0.546 0.00 0.34 0.64 0.02 0.00
#> TCGA.NK.A5CR.01 3 0.1043 0.816 0.00 0.00 0.96 0.00 0.04
#> TCGA.77.6844.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.8082.01 3 0.4132 0.683 0.00 0.26 0.72 0.02 0.00
#> TCGA.L3.A524.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A5B5.01 4 0.3684 0.708 0.28 0.00 0.00 0.72 0.00
#> TCGA.63.A5MY.01 3 0.1648 0.818 0.00 0.00 0.94 0.02 0.04
#> TCGA.85.A512.01 1 0.0000 0.943 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8354.01 5 0.3424 0.699 0.00 0.00 0.00 0.24 0.76
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.22.4613.01 5 0.5586 0.136 0.00 0.00 0.42 0.00 0.44 0.14
#> TCGA.90.7769.01 1 0.3706 0.557 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.77.A5G3.01 4 0.1807 0.730 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.58.A46N.01 4 0.1814 0.692 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.34.7107.01 1 0.0547 0.903 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.56.7823.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.58.8391.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4QR.01 3 0.2350 0.851 0.00 0.02 0.88 0.00 0.00 0.10
#> TCGA.77.8128.01 3 0.2790 0.762 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.22.4601.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.4593.01 3 0.2094 0.850 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.34.5240.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.5131.01 2 0.0937 0.965 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.77.8009.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8153.01 5 0.3499 0.427 0.00 0.00 0.00 0.00 0.68 0.32
#> TCGA.56.8083.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5G6.01 5 0.4503 0.257 0.00 0.00 0.00 0.08 0.68 0.24
#> TCGA.56.A4BX.01 3 0.1480 0.850 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.NC.A5HG.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.A5GW.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.5128.01 4 0.1814 0.703 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.63.A5MU.01 2 0.0937 0.965 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.34.5231.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HP.01 4 0.1807 0.730 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.39.5037.01 5 0.3321 0.352 0.00 0.00 0.00 0.10 0.82 0.08
#> TCGA.37.A5EN.01 4 0.1814 0.709 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.77.8148.01 2 0.1267 0.951 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.18.5592.01 1 0.0547 0.903 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.92.7341.01 1 0.3409 0.687 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.56.7582.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.6143.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.34.8456.01 5 0.0000 0.574 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.56.7222.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.94.8490.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5482.01 4 0.3198 0.593 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.46.6026.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.7710.01 4 0.1807 0.730 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.43.A474.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5473.01 1 0.2260 0.835 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.77.8154.01 3 0.5195 0.432 0.00 0.36 0.54 0.00 0.00 0.10
#> TCGA.22.5491.01 4 0.4631 0.379 0.00 0.00 0.00 0.62 0.06 0.32
#> TCGA.77.7139.01 2 0.1267 0.951 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.58.8392.01 5 0.4863 0.403 0.00 0.00 0.20 0.00 0.66 0.14
#> TCGA.63.7023.01 5 0.0000 0.574 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.33.AASJ.01 4 0.1556 0.717 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.85.8070.01 5 0.4482 0.383 0.00 0.00 0.04 0.00 0.60 0.36
#> TCGA.98.A53A.01 5 0.4503 0.257 0.00 0.00 0.00 0.08 0.68 0.24
#> TCGA.NC.A5HT.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.6770.01 5 0.0547 0.577 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.34.5929.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7140.01 5 0.3916 0.438 0.00 0.00 0.02 0.00 0.68 0.30
#> TCGA.NC.A5HF.01 3 0.1480 0.850 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.63.A5MB.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5927.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HN.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8150.01 4 0.4758 0.290 0.00 0.00 0.00 0.58 0.06 0.36
#> TCGA.18.5595.01 4 0.3409 0.543 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.79.5596.01 3 0.1092 0.856 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.63.A5ML.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5477.01 1 0.2631 0.806 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8143.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.6845.01 1 0.3309 0.711 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.56.7730.01 1 0.0547 0.903 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.56.7579.01 3 0.0547 0.857 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.63.A5MH.01 5 0.3198 0.394 0.00 0.00 0.00 0.00 0.74 0.26
#> TCGA.58.8390.01 3 0.3073 0.822 0.00 0.08 0.84 0.00 0.00 0.08
#> TCGA.39.5027.01 5 0.0547 0.577 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.22.5485.01 4 0.2941 0.628 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.33.4583.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MF.A522.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.70.6723.01 1 0.4002 0.637 0.66 0.00 0.00 0.32 0.00 0.02
#> TCGA.68.7755.01 1 0.3409 0.687 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.NC.A5HH.01 3 0.3321 0.805 0.00 0.10 0.82 0.00 0.00 0.08
#> TCGA.NK.A5CR.01 3 0.2981 0.761 0.00 0.00 0.82 0.00 0.02 0.16
#> TCGA.77.6844.01 2 0.0937 0.965 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.56.8082.01 3 0.3073 0.822 0.00 0.08 0.84 0.00 0.00 0.08
#> TCGA.L3.A524.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A5B5.01 4 0.1267 0.732 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.63.A5MY.01 3 0.1814 0.831 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.85.A512.01 1 0.0000 0.909 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8354.01 6 0.5618 0.000 0.00 0.00 0.00 0.16 0.34 0.50
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.22.4613.01 7 0.6337 0.434 0.00 0.00 0.30 0.00 0.18 0.08 0.44
#> TCGA.90.7769.01 1 0.4356 0.438 0.56 0.00 0.00 0.40 0.00 0.02 0.02
#> TCGA.77.A5G3.01 4 0.1166 0.706 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.58.A46N.01 4 0.2421 0.674 0.08 0.00 0.00 0.88 0.00 0.02 0.02
#> TCGA.34.7107.01 1 0.1006 0.882 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.56.7823.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.58.8391.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4QR.01 3 0.1433 0.770 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.77.8128.01 3 0.4309 0.533 0.00 0.00 0.68 0.00 0.00 0.12 0.20
#> TCGA.22.4601.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.4593.01 3 0.3244 0.720 0.00 0.00 0.78 0.00 0.04 0.18 0.00
#> TCGA.34.5240.01 1 0.0504 0.890 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.63.5131.01 2 0.1363 0.952 0.00 0.94 0.02 0.00 0.00 0.04 0.00
#> TCGA.77.8009.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8153.01 7 0.1166 0.638 0.00 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.56.8083.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5G6.01 5 0.2906 0.650 0.00 0.00 0.00 0.02 0.80 0.18 0.00
#> TCGA.56.A4BX.01 3 0.2422 0.747 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.NC.A5HG.01 2 0.0504 0.978 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.33.A5GW.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.5128.01 4 0.2081 0.550 0.00 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.63.A5MU.01 2 0.1860 0.935 0.00 0.92 0.04 0.00 0.02 0.02 0.00
#> TCGA.34.5231.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HP.01 4 0.1166 0.706 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.39.5037.01 5 0.4079 0.634 0.00 0.00 0.00 0.08 0.76 0.12 0.04
#> TCGA.37.A5EN.01 4 0.1886 0.556 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.77.8148.01 2 0.1006 0.967 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.18.5592.01 1 0.0504 0.890 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.92.7341.01 1 0.3755 0.595 0.64 0.00 0.00 0.34 0.00 0.00 0.02
#> TCGA.56.7582.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.6143.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.8456.01 5 0.2832 0.675 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.56.7222.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.8490.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5482.01 4 0.3221 0.113 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.46.6026.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.7710.01 4 0.1166 0.706 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.43.A474.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5473.01 1 0.2745 0.793 0.82 0.00 0.00 0.16 0.00 0.00 0.02
#> TCGA.77.8154.01 3 0.4569 0.469 0.00 0.28 0.64 0.00 0.02 0.06 0.00
#> TCGA.22.5491.01 6 0.4875 0.590 0.00 0.00 0.00 0.44 0.10 0.46 0.00
#> TCGA.77.7139.01 2 0.1006 0.967 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.58.8392.01 7 0.6381 0.381 0.00 0.00 0.20 0.00 0.28 0.08 0.44
#> TCGA.63.7023.01 5 0.2832 0.675 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.33.AASJ.01 4 0.2159 0.698 0.06 0.00 0.00 0.90 0.00 0.02 0.02
#> TCGA.85.8070.01 7 0.1928 0.610 0.00 0.00 0.00 0.00 0.02 0.08 0.90
#> TCGA.98.A53A.01 5 0.2906 0.650 0.00 0.00 0.00 0.02 0.80 0.18 0.00
#> TCGA.NC.A5HT.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.6770.01 5 0.3047 0.628 0.00 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.34.5929.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7140.01 7 0.1166 0.638 0.00 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.NC.A5HF.01 3 0.1671 0.772 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.63.A5MB.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5927.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HN.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8150.01 6 0.5132 0.574 0.00 0.00 0.00 0.44 0.02 0.46 0.08
#> TCGA.18.5595.01 4 0.3558 -0.533 0.00 0.00 0.00 0.52 0.00 0.48 0.00
#> TCGA.79.5596.01 3 0.1886 0.747 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.63.A5ML.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5477.01 1 0.2745 0.793 0.82 0.00 0.00 0.16 0.00 0.00 0.02
#> TCGA.85.8071.01 2 0.0504 0.978 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.77.8143.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.6845.01 1 0.3517 0.677 0.70 0.00 0.00 0.28 0.00 0.00 0.02
#> TCGA.56.7730.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7579.01 3 0.0863 0.775 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.63.A5MH.01 5 0.3186 0.590 0.00 0.00 0.00 0.00 0.76 0.22 0.02
#> TCGA.58.8390.01 3 0.2572 0.750 0.00 0.06 0.86 0.00 0.00 0.08 0.00
#> TCGA.39.5027.01 5 0.2945 0.656 0.00 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.22.5485.01 4 0.2945 0.298 0.00 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.33.4583.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MF.A522.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.70.6723.01 1 0.3413 0.555 0.62 0.00 0.00 0.38 0.00 0.00 0.00
#> TCGA.68.7755.01 1 0.3815 0.564 0.62 0.00 0.00 0.36 0.00 0.00 0.02
#> TCGA.NC.A5HH.01 3 0.2829 0.735 0.00 0.08 0.84 0.00 0.00 0.08 0.00
#> TCGA.NK.A5CR.01 3 0.4902 0.276 0.00 0.00 0.54 0.00 0.00 0.12 0.34
#> TCGA.77.6844.01 2 0.1006 0.967 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.56.8082.01 3 0.2016 0.757 0.00 0.06 0.90 0.00 0.00 0.04 0.00
#> TCGA.L3.A524.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A5B5.01 4 0.1664 0.706 0.06 0.00 0.00 0.92 0.00 0.02 0.00
#> TCGA.63.A5MY.01 3 0.3086 0.721 0.00 0.00 0.80 0.00 0.00 0.16 0.04
#> TCGA.85.A512.01 1 0.0000 0.896 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8354.01 6 0.6634 0.540 0.00 0.00 0.00 0.20 0.12 0.42 0.26
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.22.4613.01 7 0.3774 0.358 0.00 0.00 0.22 0.00 0.00 0.08 0.70 0.00
#> TCGA.90.7769.01 4 0.5903 0.300 0.26 0.00 0.00 0.42 0.02 0.28 0.00 0.02
#> TCGA.77.A5G3.01 4 0.0000 0.647 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.58.A46N.01 4 0.3537 0.608 0.00 0.00 0.00 0.72 0.02 0.24 0.00 0.02
#> TCGA.34.7107.01 1 0.2725 0.758 0.82 0.00 0.00 0.04 0.00 0.14 0.00 0.00
#> TCGA.56.7823.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.58.8391.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4QR.01 3 0.1804 0.789 0.00 0.02 0.90 0.00 0.00 0.08 0.00 0.00
#> TCGA.77.8128.01 3 0.3909 0.712 0.00 0.00 0.70 0.00 0.00 0.12 0.18 0.00
#> TCGA.22.4601.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.4593.01 3 0.2569 0.735 0.00 0.00 0.82 0.00 0.16 0.02 0.00 0.00
#> TCGA.34.5240.01 1 0.1947 0.777 0.86 0.00 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.63.5131.01 2 0.1275 0.948 0.00 0.94 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.77.8009.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8153.01 7 0.5770 0.410 0.00 0.00 0.00 0.00 0.08 0.18 0.50 0.24
#> TCGA.56.8083.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5G6.01 5 0.3922 0.869 0.00 0.00 0.00 0.00 0.64 0.00 0.30 0.06
#> TCGA.56.A4BX.01 3 0.3450 0.758 0.00 0.00 0.76 0.00 0.00 0.12 0.12 0.00
#> TCGA.NC.A5HG.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.A5GW.01 1 0.1091 0.816 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.63.5128.01 4 0.3879 0.505 0.00 0.00 0.00 0.74 0.02 0.10 0.00 0.14
#> TCGA.63.A5MU.01 2 0.1275 0.948 0.00 0.94 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.34.5231.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.0471 0.827 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.NC.A5HP.01 4 0.0000 0.647 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5037.01 7 0.4757 -0.162 0.00 0.00 0.00 0.00 0.20 0.00 0.56 0.24
#> TCGA.37.A5EN.01 4 0.2114 0.420 0.00 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.77.8148.01 2 0.0941 0.964 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.18.5592.01 1 0.2856 0.734 0.78 0.00 0.00 0.02 0.00 0.20 0.00 0.00
#> TCGA.92.7341.01 1 0.5301 0.112 0.42 0.00 0.00 0.40 0.02 0.16 0.00 0.00
#> TCGA.56.7582.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.6143.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.8456.01 7 0.2114 0.423 0.00 0.00 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.56.7222.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.8490.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5482.01 8 0.3862 0.610 0.00 0.00 0.00 0.36 0.00 0.04 0.00 0.60
#> TCGA.46.6026.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.7710.01 4 0.1275 0.608 0.00 0.00 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.43.A474.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5473.01 1 0.4849 0.433 0.54 0.00 0.00 0.22 0.00 0.24 0.00 0.00
#> TCGA.77.8154.01 3 0.3757 0.544 0.00 0.26 0.68 0.00 0.00 0.06 0.00 0.00
#> TCGA.22.5491.01 8 0.3528 0.747 0.00 0.00 0.00 0.18 0.08 0.00 0.00 0.74
#> TCGA.77.7139.01 2 0.0941 0.964 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.58.8392.01 7 0.2623 0.439 0.00 0.00 0.10 0.00 0.00 0.06 0.84 0.00
#> TCGA.63.7023.01 7 0.2114 0.423 0.00 0.00 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.33.AASJ.01 4 0.3537 0.608 0.00 0.00 0.00 0.72 0.02 0.24 0.00 0.02
#> TCGA.85.8070.01 7 0.5634 0.320 0.00 0.00 0.00 0.00 0.04 0.38 0.40 0.18
#> TCGA.98.A53A.01 5 0.3922 0.869 0.00 0.00 0.00 0.00 0.64 0.00 0.30 0.06
#> TCGA.NC.A5HT.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.6770.01 7 0.1947 0.445 0.00 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.34.5929.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7140.01 7 0.5693 0.419 0.00 0.00 0.00 0.00 0.08 0.18 0.52 0.22
#> TCGA.NC.A5HF.01 3 0.1804 0.794 0.00 0.00 0.90 0.00 0.00 0.08 0.02 0.00
#> TCGA.63.A5MB.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5927.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HN.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8150.01 8 0.2725 0.719 0.00 0.00 0.00 0.14 0.04 0.00 0.00 0.82
#> TCGA.18.5595.01 8 0.3873 0.749 0.00 0.00 0.00 0.20 0.06 0.02 0.00 0.72
#> TCGA.79.5596.01 3 0.3879 0.763 0.00 0.02 0.74 0.00 0.00 0.14 0.10 0.00
#> TCGA.63.A5ML.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5477.01 1 0.4849 0.433 0.54 0.00 0.00 0.22 0.00 0.24 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8143.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.6845.01 1 0.5301 0.122 0.42 0.00 0.00 0.40 0.02 0.16 0.00 0.00
#> TCGA.56.7730.01 1 0.2265 0.793 0.88 0.00 0.00 0.02 0.02 0.08 0.00 0.00
#> TCGA.56.7579.01 3 0.2348 0.799 0.00 0.02 0.88 0.00 0.00 0.06 0.04 0.00
#> TCGA.63.A5MH.01 5 0.3303 0.746 0.00 0.00 0.02 0.00 0.76 0.02 0.20 0.00
#> TCGA.58.8390.01 3 0.2807 0.787 0.00 0.04 0.84 0.00 0.02 0.10 0.00 0.00
#> TCGA.39.5027.01 7 0.1947 0.445 0.00 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.22.5485.01 8 0.3943 0.553 0.00 0.00 0.00 0.40 0.00 0.04 0.00 0.56
#> TCGA.33.4583.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MF.A522.01 1 0.0471 0.827 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.70.6723.01 4 0.5350 0.229 0.28 0.00 0.00 0.54 0.06 0.12 0.00 0.00
#> TCGA.68.7755.01 1 0.5301 0.112 0.42 0.00 0.00 0.40 0.02 0.16 0.00 0.00
#> TCGA.NC.A5HH.01 3 0.3314 0.763 0.00 0.08 0.80 0.00 0.02 0.10 0.00 0.00
#> TCGA.NK.A5CR.01 3 0.4770 0.662 0.00 0.00 0.62 0.00 0.00 0.18 0.18 0.02
#> TCGA.77.6844.01 2 0.0471 0.976 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.56.8082.01 3 0.2807 0.787 0.00 0.04 0.84 0.00 0.02 0.10 0.00 0.00
#> TCGA.L3.A524.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A5B5.01 4 0.2484 0.640 0.00 0.00 0.00 0.86 0.02 0.10 0.00 0.02
#> TCGA.63.A5MY.01 3 0.3095 0.696 0.00 0.00 0.74 0.00 0.00 0.24 0.02 0.00
#> TCGA.85.A512.01 1 0.0000 0.830 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8354.01 8 0.3319 0.507 0.00 0.00 0.00 0.02 0.08 0.06 0.02 0.82
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: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 34 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.4996 0.501 0.501
#> 3 3 0.704 0.825 0.893 0.3217 0.770 0.563
#> 4 4 0.778 0.882 0.872 0.1219 0.856 0.593
#> 5 5 0.798 0.805 0.856 0.0689 1.000 1.000
#> 6 6 0.794 0.668 0.764 0.0394 0.936 0.745
#> 7 7 0.784 0.449 0.716 0.0352 0.891 0.512
#> 8 8 0.792 0.650 0.714 0.0223 0.941 0.637
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.90.7769.01 1 0 1 1 0
#> TCGA.77.A5G3.01 1 0 1 1 0
#> TCGA.58.A46N.01 1 0 1 1 0
#> TCGA.34.7107.01 2 0 1 0 1
#> TCGA.58.8391.01 1 0 1 1 0
#> TCGA.22.4601.01 2 0 1 0 1
#> TCGA.34.5240.01 2 0 1 0 1
#> TCGA.77.8009.01 2 0 1 0 1
#> TCGA.33.A5GW.01 1 0 1 1 0
#> TCGA.63.5128.01 1 0 1 1 0
#> TCGA.33.AASD.01 1 0 1 1 0
#> TCGA.NC.A5HP.01 2 0 1 0 1
#> TCGA.37.A5EN.01 1 0 1 1 0
#> TCGA.18.5592.01 2 0 1 0 1
#> TCGA.92.7341.01 1 0 1 1 0
#> TCGA.56.7582.01 2 0 1 0 1
#> TCGA.94.8490.01 1 0 1 1 0
#> TCGA.22.5482.01 1 0 1 1 0
#> TCGA.85.7710.01 2 0 1 0 1
#> TCGA.22.5473.01 1 0 1 1 0
#> TCGA.33.AASJ.01 2 0 1 0 1
#> TCGA.63.A5MB.01 2 0 1 0 1
#> TCGA.63.A5ML.01 2 0 1 0 1
#> TCGA.22.5477.01 2 0 1 0 1
#> TCGA.77.6845.01 1 0 1 1 0
#> TCGA.56.7730.01 1 0 1 1 0
#> TCGA.22.5485.01 1 0 1 1 0
#> TCGA.33.4583.01 2 0 1 0 1
#> TCGA.MF.A522.01 1 0 1 1 0
#> TCGA.70.6723.01 1 0 1 1 0
#> TCGA.68.7755.01 1 0 1 1 0
#> TCGA.L3.A524.01 1 0 1 1 0
#> TCGA.85.A5B5.01 1 0 1 1 0
#> TCGA.85.A512.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.90.7769.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.77.A5G3.01 3 0.369 0.775 0.14 0.00 0.86
#> TCGA.58.A46N.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.34.7107.01 2 0.556 0.770 0.00 0.70 0.30
#> TCGA.58.8391.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.22.4601.01 2 0.207 0.804 0.00 0.94 0.06
#> TCGA.34.5240.01 2 0.540 0.783 0.00 0.72 0.28
#> TCGA.77.8009.01 2 0.000 0.845 0.00 1.00 0.00
#> TCGA.33.A5GW.01 3 0.254 0.760 0.08 0.00 0.92
#> TCGA.63.5128.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.NC.A5HP.01 3 0.480 0.436 0.00 0.22 0.78
#> TCGA.37.A5EN.01 3 0.595 0.577 0.36 0.00 0.64
#> TCGA.18.5592.01 2 0.556 0.770 0.00 0.70 0.30
#> TCGA.92.7341.01 3 0.595 0.577 0.36 0.00 0.64
#> TCGA.56.7582.01 2 0.000 0.845 0.00 1.00 0.00
#> TCGA.94.8490.01 3 0.369 0.775 0.14 0.00 0.86
#> TCGA.22.5482.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.85.7710.01 2 0.540 0.783 0.00 0.72 0.28
#> TCGA.22.5473.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.33.AASJ.01 2 0.556 0.770 0.00 0.70 0.30
#> TCGA.63.A5MB.01 2 0.000 0.845 0.00 1.00 0.00
#> TCGA.63.A5ML.01 2 0.000 0.845 0.00 1.00 0.00
#> TCGA.22.5477.01 3 0.480 0.436 0.00 0.22 0.78
#> TCGA.77.6845.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.56.7730.01 1 0.400 0.764 0.84 0.00 0.16
#> TCGA.22.5485.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.33.4583.01 2 0.254 0.838 0.00 0.92 0.08
#> TCGA.MF.A522.01 3 0.254 0.760 0.08 0.00 0.92
#> TCGA.70.6723.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.68.7755.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.L3.A524.01 3 0.540 0.654 0.28 0.00 0.72
#> TCGA.85.A5B5.01 1 0.000 0.984 1.00 0.00 0.00
#> TCGA.85.A512.01 2 0.000 0.845 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.90.7769.01 1 0.2011 0.913 0.92 0.00 0.00 0.08
#> TCGA.77.A5G3.01 3 0.1913 0.880 0.02 0.00 0.94 0.04
#> TCGA.58.A46N.01 1 0.0000 0.934 1.00 0.00 0.00 0.00
#> TCGA.34.7107.01 2 0.1211 0.889 0.00 0.96 0.04 0.00
#> TCGA.58.8391.01 1 0.2011 0.913 0.92 0.00 0.00 0.08
#> TCGA.22.4601.01 4 0.3610 0.741 0.00 0.20 0.00 0.80
#> TCGA.34.5240.01 2 0.0000 0.906 0.00 1.00 0.00 0.00
#> TCGA.77.8009.01 4 0.5355 0.934 0.00 0.36 0.02 0.62
#> TCGA.33.A5GW.01 3 0.5006 0.852 0.02 0.04 0.78 0.16
#> TCGA.63.5128.01 1 0.0000 0.934 1.00 0.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.1211 0.926 0.96 0.00 0.00 0.04
#> TCGA.NC.A5HP.01 2 0.3400 0.761 0.00 0.82 0.18 0.00
#> TCGA.37.A5EN.01 3 0.1637 0.892 0.06 0.00 0.94 0.00
#> TCGA.18.5592.01 2 0.0000 0.906 0.00 1.00 0.00 0.00
#> TCGA.92.7341.01 3 0.1637 0.892 0.06 0.00 0.94 0.00
#> TCGA.56.7582.01 4 0.4713 0.931 0.00 0.36 0.00 0.64
#> TCGA.94.8490.01 3 0.1913 0.880 0.02 0.00 0.94 0.04
#> TCGA.22.5482.01 1 0.0707 0.931 0.98 0.00 0.00 0.02
#> TCGA.85.7710.01 2 0.0000 0.906 0.00 1.00 0.00 0.00
#> TCGA.22.5473.01 1 0.2011 0.913 0.92 0.00 0.00 0.08
#> TCGA.33.AASJ.01 2 0.0000 0.906 0.00 1.00 0.00 0.00
#> TCGA.63.A5MB.01 4 0.5355 0.934 0.00 0.36 0.02 0.62
#> TCGA.63.A5ML.01 4 0.4713 0.931 0.00 0.36 0.00 0.64
#> TCGA.22.5477.01 2 0.2921 0.796 0.00 0.86 0.14 0.00
#> TCGA.77.6845.01 1 0.0000 0.934 1.00 0.00 0.00 0.00
#> TCGA.56.7730.01 3 0.4088 0.815 0.14 0.00 0.82 0.04
#> TCGA.22.5485.01 1 0.0000 0.934 1.00 0.00 0.00 0.00
#> TCGA.33.4583.01 2 0.1913 0.850 0.00 0.94 0.02 0.04
#> TCGA.MF.A522.01 3 0.5006 0.852 0.02 0.04 0.78 0.16
#> TCGA.70.6723.01 1 0.5151 0.740 0.76 0.00 0.14 0.10
#> TCGA.68.7755.01 1 0.0000 0.934 1.00 0.00 0.00 0.00
#> TCGA.L3.A524.01 3 0.4731 0.862 0.06 0.00 0.78 0.16
#> TCGA.85.A5B5.01 1 0.5151 0.740 0.76 0.00 0.14 0.10
#> TCGA.85.A512.01 4 0.5355 0.934 0.00 0.36 0.02 0.62
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.90.7769.01 1 0.3421 0.814 0.84 0.00 0.08 0.08 0.00
#> TCGA.77.A5G3.01 5 0.3274 0.715 0.00 0.00 0.22 0.00 0.78
#> TCGA.58.A46N.01 1 0.0609 0.841 0.98 0.00 0.02 0.00 0.00
#> TCGA.34.7107.01 2 0.0609 0.917 0.00 0.98 0.02 0.00 0.00
#> TCGA.58.8391.01 1 0.3421 0.814 0.84 0.00 0.08 0.08 0.00
#> TCGA.22.4601.01 4 0.3868 0.905 0.00 0.06 0.14 0.80 0.00
#> TCGA.34.5240.01 2 0.1410 0.906 0.00 0.94 0.06 0.00 0.00
#> TCGA.77.8009.01 4 0.2020 0.949 0.00 0.10 0.00 0.90 0.00
#> TCGA.33.A5GW.01 5 0.4060 0.709 0.00 0.00 0.36 0.00 0.64
#> TCGA.63.5128.01 1 0.0609 0.841 0.98 0.00 0.02 0.00 0.00
#> TCGA.33.AASD.01 1 0.1648 0.822 0.94 0.00 0.04 0.02 0.00
#> TCGA.NC.A5HP.01 2 0.3922 0.802 0.00 0.78 0.18 0.00 0.04
#> TCGA.37.A5EN.01 5 0.0000 0.791 0.00 0.00 0.00 0.00 1.00
#> TCGA.18.5592.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.92.7341.01 5 0.0000 0.791 0.00 0.00 0.00 0.00 1.00
#> TCGA.56.7582.01 4 0.3697 0.944 0.00 0.10 0.08 0.82 0.00
#> TCGA.94.8490.01 5 0.3274 0.715 0.00 0.00 0.22 0.00 0.78
#> TCGA.22.5482.01 1 0.3110 0.820 0.86 0.00 0.06 0.08 0.00
#> TCGA.85.7710.01 2 0.0609 0.917 0.00 0.98 0.02 0.00 0.00
#> TCGA.22.5473.01 1 0.3421 0.814 0.84 0.00 0.08 0.08 0.00
#> TCGA.33.AASJ.01 2 0.0609 0.916 0.00 0.98 0.02 0.00 0.00
#> TCGA.63.A5MB.01 4 0.2020 0.949 0.00 0.10 0.00 0.90 0.00
#> TCGA.63.A5ML.01 4 0.3697 0.944 0.00 0.10 0.08 0.82 0.00
#> TCGA.22.5477.01 2 0.3521 0.851 0.00 0.82 0.14 0.00 0.04
#> TCGA.77.6845.01 1 0.0609 0.841 0.98 0.00 0.02 0.00 0.00
#> TCGA.56.7730.01 5 0.1043 0.778 0.00 0.00 0.04 0.00 0.96
#> TCGA.22.5485.01 1 0.0609 0.841 0.98 0.00 0.02 0.00 0.00
#> TCGA.33.4583.01 2 0.2280 0.839 0.00 0.88 0.00 0.12 0.00
#> TCGA.MF.A522.01 5 0.4060 0.709 0.00 0.00 0.36 0.00 0.64
#> TCGA.70.6723.01 1 0.6530 0.229 0.44 0.00 0.20 0.00 0.36
#> TCGA.68.7755.01 1 0.0000 0.840 1.00 0.00 0.00 0.00 0.00
#> TCGA.L3.A524.01 5 0.4060 0.709 0.00 0.00 0.36 0.00 0.64
#> TCGA.85.A5B5.01 1 0.6530 0.229 0.44 0.00 0.20 0.00 0.36
#> TCGA.85.A512.01 4 0.2020 0.949 0.00 0.10 0.00 0.90 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.90.7769.01 1 0.3706 0.685 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.77.A5G3.01 3 0.4845 -0.154 0.00 0.00 0.54 0.00 0.40 0.06
#> TCGA.58.A46N.01 1 0.0937 0.726 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.34.7107.01 2 0.2094 0.832 0.00 0.90 0.08 0.00 0.00 0.02
#> TCGA.58.8391.01 1 0.3797 0.669 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.22.4601.01 4 0.1267 0.840 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.34.5240.01 2 0.3163 0.804 0.00 0.82 0.04 0.00 0.00 0.14
#> TCGA.77.8009.01 4 0.3156 0.896 0.00 0.02 0.00 0.80 0.00 0.18
#> TCGA.33.A5GW.01 5 0.0547 0.723 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.63.5128.01 1 0.0000 0.740 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.AASD.01 1 0.3982 0.613 0.74 0.00 0.06 0.00 0.00 0.20
#> TCGA.NC.A5HP.01 2 0.4993 0.582 0.00 0.56 0.36 0.00 0.00 0.08
#> TCGA.37.A5EN.01 5 0.3309 0.715 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.18.5592.01 2 0.0000 0.837 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.92.7341.01 5 0.3309 0.715 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.56.7582.01 4 0.0547 0.888 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.94.8490.01 3 0.4845 -0.154 0.00 0.00 0.54 0.00 0.40 0.06
#> TCGA.22.5482.01 1 0.3756 0.680 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.85.7710.01 2 0.1807 0.834 0.00 0.92 0.06 0.00 0.00 0.02
#> TCGA.22.5473.01 1 0.3797 0.669 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.33.AASJ.01 2 0.1092 0.835 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.63.A5MB.01 4 0.3156 0.896 0.00 0.02 0.00 0.80 0.00 0.18
#> TCGA.63.A5ML.01 4 0.0547 0.888 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.22.5477.01 2 0.4737 0.745 0.00 0.68 0.16 0.00 0.00 0.16
#> TCGA.77.6845.01 1 0.0000 0.740 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7730.01 5 0.3409 0.703 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.22.5485.01 1 0.0000 0.740 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.4583.01 2 0.3660 0.704 0.00 0.78 0.00 0.06 0.00 0.16
#> TCGA.MF.A522.01 5 0.1092 0.709 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.70.6723.01 3 0.4328 0.146 0.46 0.00 0.52 0.00 0.00 0.02
#> TCGA.68.7755.01 1 0.1480 0.742 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.L3.A524.01 5 0.0937 0.741 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.85.A5B5.01 3 0.4337 0.106 0.48 0.00 0.50 0.00 0.00 0.02
#> TCGA.85.A512.01 4 0.3156 0.896 0.00 0.02 0.00 0.80 0.00 0.18
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.90.7769.01 1 0.1166 0.718 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.77.A5G3.01 3 0.2313 0.411 0.00 0.00 0.88 0.00 0.00 0.06 0.06
#> TCGA.58.A46N.01 7 0.4622 0.480 0.38 0.00 0.00 0.00 0.02 0.04 0.56
#> TCGA.34.7107.01 2 0.1433 0.430 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.58.8391.01 1 0.0504 0.754 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.22.4601.01 4 0.0863 0.769 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.34.5240.01 2 0.3943 -0.607 0.00 0.56 0.00 0.00 0.00 0.42 0.02
#> TCGA.77.8009.01 4 0.4965 0.798 0.00 0.00 0.00 0.66 0.04 0.18 0.12
#> TCGA.33.A5GW.01 5 0.2081 0.794 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.63.5128.01 7 0.3413 0.535 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.33.AASD.01 1 0.5408 -0.367 0.46 0.00 0.00 0.00 0.04 0.08 0.42
#> TCGA.NC.A5HP.01 2 0.5115 -0.115 0.00 0.48 0.38 0.00 0.00 0.14 0.00
#> TCGA.37.A5EN.01 3 0.4269 0.351 0.02 0.00 0.60 0.00 0.36 0.00 0.02
#> TCGA.18.5592.01 2 0.0863 0.428 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.92.7341.01 3 0.4269 0.351 0.02 0.00 0.60 0.00 0.36 0.00 0.02
#> TCGA.56.7582.01 4 0.0000 0.793 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.94.8490.01 3 0.2313 0.411 0.00 0.00 0.88 0.00 0.00 0.06 0.06
#> TCGA.22.5482.01 1 0.0504 0.748 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.85.7710.01 2 0.1718 0.439 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.22.5473.01 1 0.0504 0.754 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.33.AASJ.01 2 0.2081 0.306 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.63.A5MB.01 4 0.4965 0.798 0.00 0.00 0.00 0.66 0.04 0.18 0.12
#> TCGA.63.A5ML.01 4 0.0000 0.793 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5477.01 6 0.4692 0.000 0.00 0.42 0.08 0.00 0.00 0.50 0.00
#> TCGA.77.6845.01 7 0.3413 0.535 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.56.7730.01 3 0.4269 0.351 0.02 0.00 0.60 0.00 0.36 0.00 0.02
#> TCGA.22.5485.01 7 0.3413 0.535 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.33.4583.01 2 0.5368 0.194 0.00 0.68 0.00 0.06 0.04 0.12 0.10
#> TCGA.MF.A522.01 5 0.2081 0.794 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.70.6723.01 7 0.7230 0.163 0.10 0.00 0.26 0.00 0.06 0.16 0.42
#> TCGA.68.7755.01 7 0.3525 0.415 0.44 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.L3.A524.01 5 0.3815 0.453 0.02 0.00 0.36 0.00 0.62 0.00 0.00
#> TCGA.85.A5B5.01 7 0.7022 0.268 0.10 0.00 0.20 0.00 0.06 0.16 0.48
#> TCGA.85.A512.01 4 0.4965 0.798 0.00 0.00 0.00 0.66 0.04 0.18 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.90.7769.01 1 0.3015 0.9292 0.68 0.00 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.77.A5G3.01 3 0.6342 0.3272 0.16 0.00 0.48 0.00 0.08 0.24 0.00 0.04
#> TCGA.58.A46N.01 7 0.3080 0.7630 0.02 0.00 0.00 0.00 0.06 0.02 0.84 0.06
#> TCGA.34.7107.01 2 0.3048 0.4809 0.02 0.84 0.00 0.00 0.02 0.04 0.00 0.08
#> TCGA.58.8391.01 1 0.3291 0.9556 0.70 0.00 0.02 0.00 0.00 0.00 0.28 0.00
#> TCGA.22.4601.01 4 0.5369 0.6843 0.00 0.00 0.00 0.54 0.22 0.04 0.00 0.20
#> TCGA.34.5240.01 6 0.4125 0.5788 0.02 0.44 0.00 0.00 0.02 0.52 0.00 0.00
#> TCGA.77.8009.01 4 0.0000 0.7753 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.A5GW.01 5 0.3658 0.9776 0.02 0.00 0.40 0.00 0.58 0.00 0.00 0.00
#> TCGA.63.5128.01 7 0.0000 0.8983 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.33.AASD.01 7 0.4134 0.6829 0.08 0.00 0.00 0.00 0.08 0.06 0.76 0.02
#> TCGA.NC.A5HP.01 2 0.7161 -0.0758 0.14 0.32 0.00 0.00 0.10 0.32 0.00 0.12
#> TCGA.37.A5EN.01 3 0.0000 0.4952 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.18.5592.01 2 0.0471 0.4827 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.92.7341.01 3 0.0471 0.4804 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.56.7582.01 4 0.4835 0.7576 0.02 0.00 0.00 0.64 0.10 0.02 0.00 0.22
#> TCGA.94.8490.01 3 0.6342 0.3272 0.16 0.00 0.48 0.00 0.08 0.24 0.00 0.04
#> TCGA.22.5482.01 1 0.4106 0.9231 0.64 0.00 0.02 0.00 0.04 0.00 0.30 0.00
#> TCGA.85.7710.01 2 0.2348 0.5076 0.04 0.88 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.22.5473.01 1 0.3291 0.9556 0.70 0.00 0.02 0.00 0.00 0.00 0.28 0.00
#> TCGA.33.AASJ.01 2 0.2267 0.2394 0.00 0.82 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.63.A5MB.01 4 0.0000 0.7753 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5ML.01 4 0.4835 0.7576 0.02 0.00 0.00 0.64 0.10 0.02 0.00 0.22
#> TCGA.22.5477.01 6 0.2756 0.6335 0.00 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.77.6845.01 7 0.0000 0.8983 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.56.7730.01 3 0.0000 0.4952 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5485.01 7 0.0000 0.8983 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.33.4583.01 2 0.3291 0.2793 0.02 0.70 0.00 0.28 0.00 0.00 0.00 0.00
#> TCGA.MF.A522.01 5 0.3237 0.9776 0.00 0.00 0.40 0.00 0.60 0.00 0.00 0.00
#> TCGA.70.6723.01 8 0.4412 0.9636 0.00 0.00 0.28 0.00 0.00 0.00 0.12 0.60
#> TCGA.68.7755.01 7 0.0471 0.8848 0.02 0.00 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.L3.A524.01 3 0.2938 -0.3341 0.00 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.85.A5B5.01 8 0.4482 0.9642 0.00 0.00 0.26 0.00 0.00 0.00 0.14 0.60
#> TCGA.85.A512.01 4 0.0471 0.7640 0.02 0.00 0.00 0.98 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: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.950 0.981 0.5048 0.497 0.497
#> 3 3 1.000 0.987 0.991 0.2553 0.843 0.692
#> 4 4 1.000 0.911 0.977 0.0550 0.970 0.918
#> 5 5 0.894 0.828 0.915 0.0346 0.987 0.962
#> 6 6 0.764 0.585 0.858 0.0586 0.953 0.856
#> 7 7 0.734 0.633 0.828 0.0362 0.957 0.860
#> 8 8 0.751 0.475 0.785 0.0336 0.901 0.664
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.56.7823.01 2 0.000 0.974 0.00 1.00
#> TCGA.85.A4QR.01 2 0.000 0.974 0.00 1.00
#> TCGA.22.4593.01 2 0.000 0.974 0.00 1.00
#> TCGA.63.5131.01 2 0.981 0.247 0.42 0.58
#> TCGA.56.8083.01 1 0.327 0.933 0.94 0.06
#> TCGA.56.A4BX.01 2 0.000 0.974 0.00 1.00
#> TCGA.NC.A5HG.01 2 0.000 0.974 0.00 1.00
#> TCGA.63.A5MU.01 2 0.000 0.974 0.00 1.00
#> TCGA.34.5231.01 2 0.000 0.974 0.00 1.00
#> TCGA.77.8148.01 1 0.000 0.984 1.00 0.00
#> TCGA.43.6143.01 1 0.529 0.866 0.88 0.12
#> TCGA.56.7222.01 2 0.000 0.974 0.00 1.00
#> TCGA.46.6026.01 2 0.000 0.974 0.00 1.00
#> TCGA.43.A474.01 2 0.000 0.974 0.00 1.00
#> TCGA.77.8154.01 2 0.000 0.974 0.00 1.00
#> TCGA.77.7139.01 2 0.000 0.974 0.00 1.00
#> TCGA.NC.A5HT.01 2 0.000 0.974 0.00 1.00
#> TCGA.34.5929.01 2 0.000 0.974 0.00 1.00
#> TCGA.NC.A5HF.01 1 0.000 0.984 1.00 0.00
#> TCGA.34.5927.01 2 0.000 0.974 0.00 1.00
#> TCGA.NC.A5HN.01 2 0.000 0.974 0.00 1.00
#> TCGA.79.5596.01 1 0.000 0.984 1.00 0.00
#> TCGA.85.8071.01 2 0.000 0.974 0.00 1.00
#> TCGA.77.8143.01 1 0.000 0.984 1.00 0.00
#> TCGA.56.7579.01 1 0.000 0.984 1.00 0.00
#> TCGA.58.8390.01 1 0.000 0.984 1.00 0.00
#> TCGA.NC.A5HH.01 1 0.000 0.984 1.00 0.00
#> TCGA.NK.A5CR.01 1 0.000 0.984 1.00 0.00
#> TCGA.77.6844.01 1 0.000 0.984 1.00 0.00
#> TCGA.56.8082.01 1 0.000 0.984 1.00 0.00
#> TCGA.63.A5MY.01 1 0.000 0.984 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.56.7823.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.85.A4QR.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.22.4593.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.63.5131.01 3 0.207 0.967 0.06 0.0 0.94
#> TCGA.56.8083.01 3 0.207 0.967 0.06 0.0 0.94
#> TCGA.56.A4BX.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.NC.A5HG.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.63.A5MU.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.34.5231.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.77.8148.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.43.6143.01 3 0.207 0.967 0.06 0.0 0.94
#> TCGA.56.7222.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.46.6026.01 2 0.296 0.897 0.00 0.9 0.10
#> TCGA.43.A474.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.77.8154.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.77.7139.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.NC.A5HT.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.34.5929.01 3 0.000 0.953 0.00 0.0 1.00
#> TCGA.NC.A5HF.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.34.5927.01 3 0.000 0.953 0.00 0.0 1.00
#> TCGA.NC.A5HN.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.79.5596.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.85.8071.01 2 0.000 0.993 0.00 1.0 0.00
#> TCGA.77.8143.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.56.7579.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.58.8390.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.NC.A5HH.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.NK.A5CR.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.77.6844.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.56.8082.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.63.A5MY.01 1 0.000 1.000 1.00 0.0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.56.7823.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.85.A4QR.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.22.4593.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.63.5131.01 3 0.1913 0.806 0.00 0.04 0.94 0.02
#> TCGA.56.8083.01 3 0.0000 0.831 0.00 0.00 1.00 0.00
#> TCGA.56.A4BX.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.NC.A5HG.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.63.A5MU.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.34.5231.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.77.8148.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.43.6143.01 3 0.0707 0.827 0.00 0.00 0.98 0.02
#> TCGA.56.7222.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.46.6026.01 4 0.0000 0.000 0.00 0.00 0.00 1.00
#> TCGA.43.A474.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.77.8154.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.77.7139.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.NC.A5HT.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.34.5929.01 3 0.1211 0.827 0.00 0.00 0.96 0.04
#> TCGA.NC.A5HF.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.34.5927.01 3 0.4994 0.134 0.00 0.00 0.52 0.48
#> TCGA.NC.A5HN.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.79.5596.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.77.8143.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.56.7579.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.58.8390.01 1 0.0707 0.979 0.98 0.00 0.02 0.00
#> TCGA.NC.A5HH.01 1 0.0707 0.979 0.98 0.00 0.02 0.00
#> TCGA.NK.A5CR.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.77.6844.01 1 0.1637 0.942 0.94 0.00 0.06 0.00
#> TCGA.56.8082.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.63.A5MY.01 1 0.0000 0.990 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.56.7823.01 2 0.1043 0.968 0.00 0.96 0.04 0.00 0.00
#> TCGA.85.A4QR.01 2 0.0609 0.981 0.00 0.98 0.02 0.00 0.00
#> TCGA.22.4593.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.5131.01 3 0.6296 0.300 0.00 0.16 0.48 0.00 0.36
#> TCGA.56.8083.01 3 0.4262 0.543 0.00 0.00 0.56 0.00 0.44
#> TCGA.56.A4BX.01 2 0.0609 0.981 0.00 0.98 0.02 0.00 0.00
#> TCGA.NC.A5HG.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5MU.01 2 0.0609 0.981 0.00 0.98 0.02 0.00 0.00
#> TCGA.34.5231.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8148.01 1 0.1648 0.878 0.94 0.00 0.04 0.02 0.00
#> TCGA.43.6143.01 3 0.4126 0.575 0.00 0.00 0.62 0.00 0.38
#> TCGA.56.7222.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.46.6026.01 4 0.0609 0.000 0.00 0.00 0.00 0.98 0.02
#> TCGA.43.A474.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8154.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7139.01 2 0.1043 0.968 0.00 0.96 0.04 0.00 0.00
#> TCGA.NC.A5HT.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.34.5929.01 5 0.1043 0.599 0.00 0.00 0.04 0.00 0.96
#> TCGA.NC.A5HF.01 1 0.1410 0.878 0.94 0.00 0.06 0.00 0.00
#> TCGA.34.5927.01 5 0.3513 0.657 0.00 0.00 0.02 0.18 0.80
#> TCGA.NC.A5HN.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.79.5596.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8143.01 1 0.1732 0.874 0.92 0.00 0.08 0.00 0.00
#> TCGA.56.7579.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00
#> TCGA.58.8390.01 1 0.3796 0.723 0.70 0.00 0.30 0.00 0.00
#> TCGA.NC.A5HH.01 1 0.3983 0.678 0.66 0.00 0.34 0.00 0.00
#> TCGA.NK.A5CR.01 1 0.0609 0.886 0.98 0.00 0.00 0.02 0.00
#> TCGA.77.6844.01 1 0.2929 0.816 0.82 0.00 0.18 0.00 0.00
#> TCGA.56.8082.01 1 0.3319 0.823 0.82 0.00 0.16 0.02 0.00
#> TCGA.63.A5MY.01 1 0.0609 0.886 0.98 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.56.7823.01 2 0.4265 0.798 0.00 0.76 0.08 0.00 0.02 0.14
#> TCGA.85.A4QR.01 2 0.3795 0.833 0.00 0.80 0.06 0.00 0.02 0.12
#> TCGA.22.4593.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.5131.01 3 0.3045 0.414 0.00 0.06 0.86 0.00 0.02 0.06
#> TCGA.56.8083.01 3 0.2793 0.349 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.56.A4BX.01 2 0.3324 0.857 0.00 0.84 0.06 0.00 0.02 0.08
#> TCGA.NC.A5HG.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MU.01 2 0.2725 0.879 0.00 0.88 0.04 0.00 0.02 0.06
#> TCGA.34.5231.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8148.01 1 0.2581 0.565 0.86 0.00 0.02 0.00 0.00 0.12
#> TCGA.43.6143.01 3 0.2350 0.440 0.00 0.00 0.88 0.00 0.10 0.02
#> TCGA.56.7222.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.46.6026.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.43.A474.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8154.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7139.01 2 0.4502 0.776 0.00 0.74 0.10 0.00 0.02 0.14
#> TCGA.NC.A5HT.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.34.5929.01 5 0.2048 0.647 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.NC.A5HF.01 1 0.0547 0.655 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.34.5927.01 5 0.5730 0.603 0.00 0.00 0.10 0.18 0.64 0.08
#> TCGA.NC.A5HN.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.79.5596.01 1 0.0000 0.663 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8071.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8143.01 1 0.4552 0.028 0.64 0.00 0.00 0.00 0.06 0.30
#> TCGA.56.7579.01 1 0.1092 0.632 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.58.8390.01 1 0.4420 -0.625 0.62 0.00 0.04 0.00 0.00 0.34
#> TCGA.NC.A5HH.01 6 0.4651 0.000 0.48 0.00 0.04 0.00 0.00 0.48
#> TCGA.NK.A5CR.01 1 0.0547 0.659 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.77.6844.01 3 0.5957 -0.223 0.38 0.00 0.40 0.00 0.00 0.22
#> TCGA.56.8082.01 1 0.4834 0.192 0.64 0.00 0.10 0.00 0.00 0.26
#> TCGA.63.A5MY.01 1 0.0000 0.663 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.56.7823.01 2 0.329 0.6869 0.34 0.66 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4QR.01 2 0.314 0.7265 0.30 0.70 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.4593.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.5131.01 3 0.639 0.2701 0.38 0.04 0.44 0.00 0.10 0.02 0.02
#> TCGA.56.8083.01 3 0.136 0.5814 0.02 0.00 0.94 0.00 0.04 0.00 0.00
#> TCGA.56.A4BX.01 2 0.283 0.7679 0.24 0.76 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HG.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MU.01 2 0.294 0.7569 0.26 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5231.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8148.01 7 0.238 0.5942 0.12 0.00 0.00 0.00 0.00 0.02 0.86
#> TCGA.43.6143.01 3 0.101 0.5989 0.02 0.00 0.96 0.00 0.02 0.00 0.00
#> TCGA.56.7222.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.46.6026.01 4 0.000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.43.A474.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8154.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7139.01 2 0.350 0.5870 0.42 0.58 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HT.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5929.01 5 0.117 0.5756 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.NC.A5HF.01 7 0.166 0.6373 0.00 0.00 0.00 0.00 0.02 0.06 0.92
#> TCGA.34.5927.01 5 0.634 0.5576 0.12 0.00 0.16 0.08 0.58 0.06 0.00
#> TCGA.NC.A5HN.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.79.5596.01 7 0.101 0.6611 0.02 0.00 0.00 0.00 0.00 0.02 0.96
#> TCGA.85.8071.01 2 0.000 0.8758 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8143.01 7 0.569 0.1763 0.22 0.00 0.00 0.00 0.02 0.26 0.50
#> TCGA.56.7579.01 7 0.251 0.6277 0.04 0.00 0.00 0.00 0.02 0.06 0.88
#> TCGA.58.8390.01 6 0.413 0.6822 0.04 0.00 0.00 0.00 0.00 0.60 0.36
#> TCGA.NC.A5HH.01 6 0.319 0.7135 0.00 0.00 0.02 0.00 0.00 0.76 0.22
#> TCGA.NK.A5CR.01 7 0.000 0.6636 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.77.6844.01 7 0.687 -0.0798 0.36 0.00 0.10 0.00 0.02 0.16 0.36
#> TCGA.56.8082.01 7 0.438 0.3031 0.36 0.00 0.00 0.00 0.00 0.06 0.58
#> TCGA.63.A5MY.01 7 0.000 0.6636 0.00 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.56.7823.01 8 0.3318 -0.0532 0.00 0.46 0.00 0 0.00 0.00 0.00 0.54
#> TCGA.85.A4QR.01 2 0.3318 0.0285 0.00 0.54 0.00 0 0.00 0.00 0.00 0.46
#> TCGA.22.4593.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.63.5131.01 8 0.6848 -0.3538 0.08 0.02 0.24 0 0.06 0.14 0.00 0.46
#> TCGA.56.8083.01 3 0.4019 0.6847 0.00 0.00 0.74 0 0.14 0.06 0.00 0.06
#> TCGA.56.A4BX.01 2 0.3237 0.2239 0.00 0.60 0.00 0 0.00 0.00 0.00 0.40
#> TCGA.NC.A5HG.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.63.A5MU.01 2 0.3142 0.3151 0.00 0.64 0.00 0 0.00 0.00 0.00 0.36
#> TCGA.34.5231.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.77.8148.01 7 0.2725 0.6161 0.00 0.00 0.00 0 0.00 0.04 0.82 0.14
#> TCGA.43.6143.01 3 0.0471 0.7035 0.00 0.00 0.98 0 0.00 0.00 0.00 0.02
#> TCGA.56.7222.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.46.6026.01 4 0.0000 0.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.43.A474.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.77.8154.01 2 0.0471 0.8246 0.00 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.77.7139.01 8 0.3318 -0.0512 0.00 0.46 0.00 0 0.00 0.00 0.00 0.54
#> TCGA.NC.A5HT.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.34.5929.01 5 0.6539 0.4423 0.22 0.00 0.06 0 0.48 0.10 0.00 0.14
#> TCGA.NC.A5HF.01 7 0.2807 0.6361 0.04 0.00 0.00 0 0.00 0.10 0.84 0.02
#> TCGA.34.5927.01 5 0.1091 0.4218 0.00 0.00 0.06 0 0.94 0.00 0.00 0.00
#> TCGA.NC.A5HN.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.79.5596.01 7 0.0941 0.7286 0.02 0.00 0.00 0 0.00 0.02 0.96 0.00
#> TCGA.85.8071.01 2 0.0000 0.8410 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.77.8143.01 1 0.3922 0.0000 0.64 0.00 0.00 0 0.00 0.06 0.30 0.00
#> TCGA.56.7579.01 7 0.2071 0.6859 0.04 0.00 0.02 0 0.00 0.04 0.90 0.00
#> TCGA.58.8390.01 6 0.4770 0.5955 0.04 0.00 0.02 0 0.00 0.52 0.40 0.02
#> TCGA.NC.A5HH.01 6 0.3504 0.5850 0.04 0.00 0.00 0 0.00 0.70 0.26 0.00
#> TCGA.NK.A5CR.01 7 0.0000 0.7369 0.00 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.77.6844.01 8 0.7368 -0.4049 0.08 0.00 0.16 0 0.00 0.22 0.24 0.30
#> TCGA.56.8082.01 7 0.5342 -0.1124 0.04 0.00 0.00 0 0.00 0.12 0.44 0.40
#> TCGA.63.A5MY.01 7 0.0000 0.7369 0.00 0.00 0.00 0 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: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 18 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 0.4711 0.529 0.529
#> 3 3 0.680 0.753 0.886 0.3661 0.869 0.753
#> 4 4 0.667 0.823 0.821 0.1226 0.739 0.420
#> 5 5 0.673 0.854 0.813 0.0874 0.948 0.784
#> 6 6 0.647 0.606 0.808 0.0383 0.967 0.828
#> 7 7 0.843 0.581 0.772 0.0594 0.974 0.833
#> 8 8 0.869 0.626 0.830 0.0218 0.961 0.739
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.22.4613.01 1 0 1 1 0
#> TCGA.77.8128.01 1 0 1 1 0
#> TCGA.77.8153.01 1 0 1 1 0
#> TCGA.77.A5G6.01 2 0 1 0 1
#> TCGA.39.5037.01 1 0 1 1 0
#> TCGA.34.8456.01 1 0 1 1 0
#> TCGA.22.5491.01 2 0 1 0 1
#> TCGA.58.8392.01 1 0 1 1 0
#> TCGA.63.7023.01 2 0 1 0 1
#> TCGA.85.8070.01 1 0 1 1 0
#> TCGA.98.A53A.01 2 0 1 0 1
#> TCGA.43.6770.01 1 0 1 1 0
#> TCGA.77.7140.01 1 0 1 1 0
#> TCGA.77.8150.01 1 0 1 1 0
#> TCGA.18.5595.01 2 0 1 0 1
#> TCGA.63.A5MH.01 2 0 1 0 1
#> TCGA.39.5027.01 1 0 1 1 0
#> TCGA.85.8354.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.22.4613.01 1 0.619 0.454 0.58 0.00 0.42
#> TCGA.77.8128.01 1 0.000 0.754 1.00 0.00 0.00
#> TCGA.77.8153.01 1 0.000 0.754 1.00 0.00 0.00
#> TCGA.77.A5G6.01 2 0.000 0.952 0.00 1.00 0.00
#> TCGA.39.5037.01 3 0.000 0.817 0.00 0.00 1.00
#> TCGA.34.8456.01 3 0.334 0.789 0.12 0.00 0.88
#> TCGA.22.5491.01 2 0.369 0.889 0.00 0.86 0.14
#> TCGA.58.8392.01 1 0.619 0.454 0.58 0.00 0.42
#> TCGA.63.7023.01 2 0.334 0.902 0.00 0.88 0.12
#> TCGA.85.8070.01 1 0.000 0.754 1.00 0.00 0.00
#> TCGA.98.A53A.01 2 0.000 0.952 0.00 1.00 0.00
#> TCGA.43.6770.01 1 0.619 0.454 0.58 0.00 0.42
#> TCGA.77.7140.01 1 0.000 0.754 1.00 0.00 0.00
#> TCGA.77.8150.01 1 0.000 0.754 1.00 0.00 0.00
#> TCGA.18.5595.01 2 0.000 0.952 0.00 1.00 0.00
#> TCGA.63.A5MH.01 2 0.000 0.952 0.00 1.00 0.00
#> TCGA.39.5027.01 1 0.619 0.454 0.58 0.00 0.42
#> TCGA.85.8354.01 1 0.000 0.754 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.22.4613.01 3 0.000 0.700 0.00 0.00 1.00 0.00
#> TCGA.77.8128.01 1 0.471 0.880 0.64 0.00 0.36 0.00
#> TCGA.77.8153.01 1 0.657 0.871 0.58 0.00 0.32 0.10
#> TCGA.77.A5G6.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.39.5037.01 3 0.761 0.473 0.32 0.00 0.46 0.22
#> TCGA.34.8456.01 3 0.749 0.492 0.32 0.00 0.48 0.20
#> TCGA.22.5491.01 4 0.498 0.960 0.00 0.46 0.00 0.54
#> TCGA.58.8392.01 3 0.000 0.700 0.00 0.00 1.00 0.00
#> TCGA.63.7023.01 4 0.499 0.958 0.00 0.48 0.00 0.52
#> TCGA.85.8070.01 1 0.767 0.750 0.46 0.00 0.28 0.26
#> TCGA.98.A53A.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.43.6770.01 3 0.000 0.700 0.00 0.00 1.00 0.00
#> TCGA.77.7140.01 1 0.657 0.871 0.58 0.00 0.32 0.10
#> TCGA.77.8150.01 1 0.471 0.880 0.64 0.00 0.36 0.00
#> TCGA.18.5595.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.63.A5MH.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.39.5027.01 3 0.000 0.700 0.00 0.00 1.00 0.00
#> TCGA.85.8354.01 1 0.471 0.880 0.64 0.00 0.36 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.22.4613.01 3 0.6146 0.993 0.24 0.00 0.56 0.00 0.20
#> TCGA.77.8128.01 1 0.0609 0.683 0.98 0.00 0.02 0.00 0.00
#> TCGA.77.8153.01 1 0.5854 0.694 0.60 0.24 0.16 0.00 0.00
#> TCGA.77.A5G6.01 2 0.3983 0.940 0.00 0.66 0.00 0.34 0.00
#> TCGA.39.5037.01 5 0.0000 0.947 0.00 0.00 0.00 0.00 1.00
#> TCGA.34.8456.01 5 0.1043 0.945 0.00 0.00 0.04 0.00 0.96
#> TCGA.22.5491.01 4 0.1648 0.936 0.00 0.00 0.02 0.94 0.04
#> TCGA.58.8392.01 3 0.6682 0.979 0.24 0.02 0.54 0.00 0.20
#> TCGA.63.7023.01 4 0.0000 0.935 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.8070.01 1 0.6766 0.557 0.40 0.30 0.30 0.00 0.00
#> TCGA.98.A53A.01 2 0.3983 0.940 0.00 0.66 0.00 0.34 0.00
#> TCGA.43.6770.01 3 0.6146 0.993 0.24 0.00 0.56 0.00 0.20
#> TCGA.77.7140.01 1 0.5854 0.694 0.60 0.24 0.16 0.00 0.00
#> TCGA.77.8150.01 1 0.0609 0.683 0.98 0.00 0.02 0.00 0.00
#> TCGA.18.5595.01 2 0.5659 0.837 0.00 0.58 0.10 0.32 0.00
#> TCGA.63.A5MH.01 2 0.4540 0.930 0.00 0.64 0.02 0.34 0.00
#> TCGA.39.5027.01 3 0.6146 0.993 0.24 0.00 0.56 0.00 0.20
#> TCGA.85.8354.01 1 0.0000 0.686 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.22.4613.01 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8128.01 1 0.5992 -0.242 0.42 0.00 0.24 0.00 0.00 0.34
#> TCGA.77.8153.01 1 0.2793 0.387 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.77.A5G6.01 2 0.0000 0.882 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5037.01 5 0.0937 0.854 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.34.8456.01 5 0.2790 0.859 0.00 0.00 0.14 0.00 0.84 0.02
#> TCGA.22.5491.01 4 0.5569 0.855 0.00 0.24 0.00 0.62 0.10 0.04
#> TCGA.58.8392.01 3 0.2474 0.867 0.00 0.00 0.88 0.08 0.00 0.04
#> TCGA.63.7023.01 4 0.3309 0.849 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.85.8070.01 1 0.4375 0.108 0.78 0.00 0.02 0.12 0.04 0.04
#> TCGA.98.A53A.01 2 0.0000 0.882 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.6770.01 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7140.01 1 0.2793 0.387 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.77.8150.01 1 0.6023 -0.196 0.42 0.00 0.26 0.00 0.00 0.32
#> TCGA.18.5595.01 2 0.1807 0.844 0.02 0.92 0.00 0.00 0.00 0.06
#> TCGA.63.A5MH.01 2 0.2941 0.708 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.39.5027.01 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8354.01 6 0.6696 0.000 0.24 0.00 0.18 0.08 0.00 0.50
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.22.4613.01 3 0.0000 0.928 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8128.01 7 0.4283 0.000 0.48 0.00 0.04 0.00 0.00 0.00 0.48
#> TCGA.77.8153.01 1 0.0863 0.294 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.77.A5G6.01 2 0.0504 0.865 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.39.5037.01 5 0.0504 0.985 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.34.8456.01 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.22.5491.01 4 0.2259 0.984 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.58.8392.01 3 0.3670 0.761 0.00 0.00 0.76 0.10 0.00 0.14 0.00
#> TCGA.63.7023.01 4 0.2745 0.984 0.00 0.16 0.00 0.82 0.00 0.00 0.02
#> TCGA.85.8070.01 1 0.4505 0.102 0.50 0.00 0.00 0.06 0.00 0.00 0.44
#> TCGA.98.A53A.01 2 0.0504 0.865 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.43.6770.01 3 0.0000 0.928 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7140.01 1 0.0863 0.294 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.77.8150.01 1 0.4266 -0.935 0.52 0.00 0.04 0.00 0.00 0.00 0.44
#> TCGA.18.5595.01 2 0.3606 0.641 0.00 0.68 0.00 0.00 0.00 0.30 0.02
#> TCGA.63.A5MH.01 2 0.1363 0.843 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.39.5027.01 3 0.0000 0.928 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8354.01 6 0.5622 0.000 0.24 0.00 0.02 0.00 0.00 0.52 0.22
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.22.4613.01 3 0.0471 0.859 0.00 0.00 0.98 0.00 0.0 0.00 0.02 0.00
#> TCGA.77.8128.01 1 0.6362 0.407 0.52 0.00 0.06 0.10 0.0 0.18 0.00 0.14
#> TCGA.77.8153.01 1 0.0808 0.489 0.96 0.00 0.04 0.00 0.0 0.00 0.00 0.00
#> TCGA.77.A5G6.01 2 0.0000 0.788 0.00 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.39.5037.01 5 0.1804 0.921 0.00 0.00 0.00 0.08 0.9 0.00 0.00 0.02
#> TCGA.34.8456.01 5 0.0000 0.921 0.00 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.22.5491.01 7 0.3980 0.837 0.02 0.02 0.00 0.10 0.0 0.06 0.78 0.02
#> TCGA.58.8392.01 3 0.4621 0.540 0.00 0.00 0.58 0.32 0.0 0.02 0.00 0.08
#> TCGA.63.7023.01 7 0.0471 0.837 0.00 0.02 0.00 0.00 0.0 0.00 0.98 0.00
#> TCGA.85.8070.01 8 0.3272 0.000 0.42 0.00 0.00 0.00 0.0 0.00 0.00 0.58
#> TCGA.98.A53A.01 2 0.0000 0.788 0.00 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.43.6770.01 3 0.0000 0.863 0.00 0.00 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.77.7140.01 1 0.0808 0.489 0.96 0.00 0.04 0.00 0.0 0.00 0.00 0.00
#> TCGA.77.8150.01 1 0.6313 0.407 0.52 0.00 0.06 0.08 0.0 0.18 0.00 0.16
#> TCGA.18.5595.01 2 0.5347 0.609 0.02 0.62 0.00 0.06 0.0 0.16 0.00 0.14
#> TCGA.63.A5MH.01 2 0.3083 0.643 0.00 0.66 0.00 0.34 0.0 0.00 0.00 0.00
#> TCGA.39.5027.01 3 0.0000 0.863 0.00 0.00 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.85.8354.01 6 0.2981 0.000 0.22 0.00 0.02 0.00 0.0 0.76 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node041 , Node042 , Node043 , Node051 , Node052 , Node061 , Node062-leaf , Node071 , Node072 , Node073 .
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 89 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4877 0.513 0.513
#> 3 3 0.577 0.582 0.808 0.2831 0.899 0.803
#> 4 4 0.509 0.546 0.606 0.0897 0.856 0.682
#> 5 5 0.489 0.232 0.635 0.0907 0.843 0.606
#> 6 6 0.505 0.240 0.555 0.0611 0.887 0.654
#> 7 7 0.565 0.209 0.529 0.0355 0.839 0.475
#> 8 8 0.574 0.225 0.451 0.0307 0.843 0.408
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.44.2659.11 1 0 1 1 0
#> TCGA.43.3920.11 2 0 1 0 1
#> TCGA.44.5645.11 1 0 1 1 0
#> TCGA.44.2665.11 1 0 1 1 0
#> TCGA.22.5473.11 2 0 1 0 1
#> TCGA.22.5482.11 2 0 1 0 1
#> TCGA.39.5030.11 1 0 1 1 0
#> TCGA.22.5489.11 2 0 1 0 1
#> TCGA.44.2662.11 2 0 1 0 1
#> TCGA.50.5930.11 2 0 1 0 1
#> TCGA.22.5474.11 2 0 1 0 1
#> TCGA.22.5492.11 1 0 1 1 0
#> TCGA.22.5485.11 1 0 1 1 0
#> TCGA.33.4583.11 2 0 1 0 1
#> TCGA.22.5491.11 2 0 1 0 1
#> TCGA.44.6146.11 2 0 1 0 1
#> TCGA.98.A53C.01 1 0 1 1 0
#> TCGA.43.6771.11 2 0 1 0 1
#> TCGA.39.5011.11 1 0 1 1 0
#> TCGA.39.5021.11 2 0 1 0 1
#> TCGA.34.5929.11 1 0 1 1 0
#> TCGA.55.7816.01 1 0 1 1 0
#> TCGA.39.5019.11 2 0 1 0 1
#> TCGA.50.6593.11 1 0 1 1 0
#> TCGA.22.4613.11 1 0 1 1 0
#> TCGA.56.8623.01 2 0 1 0 1
#> TCGA.44.2656.11 2 0 1 0 1
#> TCGA.44.6778.11 2 0 1 0 1
#> TCGA.38.4631.11 1 0 1 1 0
#> TCGA.33.4579.11 1 0 1 1 0
#> TCGA.86.A4P8.01 1 0 1 1 0
#> TCGA.33.4586.11 2 0 1 0 1
#> TCGA.39.5039.11 2 0 1 0 1
#> TCGA.38.4632.11 2 0 1 0 1
#> TCGA.44.2655.11 1 0 1 1 0
#> TCGA.33.4582.11 2 0 1 0 1
#> TCGA.50.5939.11 2 0 1 0 1
#> TCGA.75.6203.01 1 0 1 1 0
#> TCGA.18.4721.11 2 0 1 0 1
#> TCGA.50.6594.11 1 0 1 1 0
#> TCGA.49.4488.11 1 0 1 1 0
#> TCGA.22.5477.11 2 0 1 0 1
#> TCGA.39.5035.11 1 0 1 1 0
#> TCGA.44.6145.11 1 0 1 1 0
#> TCGA.18.5595.11 2 0 1 0 1
#> TCGA.50.5935.11 1 0 1 1 0
#> TCGA.22.5478.11 2 0 1 0 1
#> TCGA.49.6745.11 2 0 1 0 1
#> TCGA.49.AARR.01 2 0 1 0 1
#> TCGA.18.5592.11 2 0 1 0 1
#> TCGA.85.A4PA.01 2 0 1 0 1
#> TCGA.99.AA5R.01 1 0 1 1 0
#> TCGA.73.4676.11 2 0 1 0 1
#> TCGA.60.2697.01 2 0 1 0 1
#> TCGA.43.5668.11 2 0 1 0 1
#> TCGA.L4.A4E6.01 2 0 1 0 1
#> TCGA.73.4658.11 1 0 1 1 0
#> TCGA.43.3394.11 2 0 1 0 1
#> TCGA.39.5016.11 2 0 1 0 1
#> TCGA.90.6837.01 2 0 1 0 1
#> TCGA.44.6148.11 2 0 1 0 1
#> TCGA.50.6592.11 1 0 1 1 0
#> TCGA.50.5933.11 2 0 1 0 1
#> TCGA.98.A53D.01 2 0 1 0 1
#> TCGA.44.2668.11 2 0 1 0 1
#> TCGA.39.5034.11 1 0 1 1 0
#> TCGA.98.A53H.01 1 0 1 1 0
#> TCGA.39.5036.11 2 0 1 0 1
#> TCGA.22.4599.11 1 0 1 1 0
#> TCGA.39.5031.11 1 0 1 1 0
#> TCGA.50.5936.11 2 0 1 0 1
#> TCGA.22.5471.11 2 0 1 0 1
#> TCGA.50.5932.11 2 0 1 0 1
#> TCGA.22.5480.11 1 0 1 1 0
#> TCGA.50.5931.11 1 0 1 1 0
#> TCGA.22.4601.11 1 0 1 1 0
#> TCGA.77.A5FZ.01 2 0 1 0 1
#> TCGA.33.4589.11 1 0 1 1 0
#> TCGA.18.3417.11 2 0 1 0 1
#> TCGA.44.6144.11 2 0 1 0 1
#> TCGA.39.5029.11 2 0 1 0 1
#> TCGA.44.6147.11 1 0 1 1 0
#> TCGA.22.5472.11 2 0 1 0 1
#> TCGA.44.5643.11 2 0 1 0 1
#> TCGA.55.8513.01 1 0 1 1 0
#> TCGA.05.5420.11 2 0 1 0 1
#> TCGA.33.4566.11 2 0 1 0 1
#> TCGA.39.5037.11 2 0 1 0 1
#> TCGA.50.6591.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.2659.11 1 0.3686 0.9313 0.86 0.00 0.14
#> TCGA.43.3920.11 2 0.6192 -0.1197 0.00 0.58 0.42
#> TCGA.44.5645.11 1 0.2959 0.9402 0.90 0.00 0.10
#> TCGA.44.2665.11 1 0.4291 0.9258 0.82 0.00 0.18
#> TCGA.22.5473.11 2 0.4555 0.5126 0.00 0.80 0.20
#> TCGA.22.5482.11 2 0.2537 0.5658 0.00 0.92 0.08
#> TCGA.39.5030.11 1 0.2537 0.9405 0.92 0.00 0.08
#> TCGA.22.5489.11 2 0.6302 -0.3386 0.00 0.52 0.48
#> TCGA.44.2662.11 2 0.5016 0.4406 0.00 0.76 0.24
#> TCGA.50.5930.11 3 0.6302 0.3906 0.00 0.48 0.52
#> TCGA.22.5474.11 2 0.4796 0.4855 0.00 0.78 0.22
#> TCGA.22.5492.11 1 0.1529 0.9411 0.96 0.00 0.04
#> TCGA.22.5485.11 1 0.3340 0.9469 0.88 0.00 0.12
#> TCGA.33.4583.11 2 0.2537 0.5782 0.00 0.92 0.08
#> TCGA.22.5491.11 2 0.6280 -0.2056 0.00 0.54 0.46
#> TCGA.44.6146.11 3 0.6192 0.5247 0.00 0.42 0.58
#> TCGA.98.A53C.01 1 0.2537 0.9413 0.92 0.00 0.08
#> TCGA.43.6771.11 2 0.1529 0.5817 0.00 0.96 0.04
#> TCGA.39.5011.11 1 0.2066 0.9450 0.94 0.00 0.06
#> TCGA.39.5021.11 2 0.6280 -0.3056 0.00 0.54 0.46
#> TCGA.34.5929.11 1 0.2066 0.9377 0.94 0.00 0.06
#> TCGA.55.7816.01 1 0.2066 0.9377 0.94 0.00 0.06
#> TCGA.39.5019.11 2 0.5016 0.4808 0.00 0.76 0.24
#> TCGA.50.6593.11 1 0.4002 0.9279 0.84 0.00 0.16
#> TCGA.22.4613.11 1 0.2066 0.9422 0.94 0.00 0.06
#> TCGA.56.8623.01 2 0.3340 0.5673 0.00 0.88 0.12
#> TCGA.44.2656.11 2 0.3686 0.5711 0.00 0.86 0.14
#> TCGA.44.6778.11 3 0.5216 0.7298 0.00 0.26 0.74
#> TCGA.38.4631.11 1 0.2537 0.9385 0.92 0.00 0.08
#> TCGA.33.4579.11 1 0.0892 0.9472 0.98 0.00 0.02
#> TCGA.86.A4P8.01 1 0.4002 0.9203 0.84 0.00 0.16
#> TCGA.33.4586.11 2 0.1529 0.5760 0.00 0.96 0.04
#> TCGA.39.5039.11 2 0.5016 0.4054 0.00 0.76 0.24
#> TCGA.38.4632.11 3 0.5216 0.7298 0.00 0.26 0.74
#> TCGA.44.2655.11 1 0.4291 0.9209 0.82 0.00 0.18
#> TCGA.33.4582.11 2 0.5397 0.3814 0.00 0.72 0.28
#> TCGA.50.5939.11 2 0.5948 0.1098 0.00 0.64 0.36
#> TCGA.75.6203.01 1 0.2066 0.9450 0.94 0.00 0.06
#> TCGA.18.4721.11 2 0.1529 0.5789 0.00 0.96 0.04
#> TCGA.50.6594.11 1 0.2537 0.9427 0.92 0.00 0.08
#> TCGA.49.4488.11 1 0.4002 0.9279 0.84 0.00 0.16
#> TCGA.22.5477.11 2 0.5216 0.4384 0.00 0.74 0.26
#> TCGA.39.5035.11 1 0.4002 0.9270 0.84 0.00 0.16
#> TCGA.44.6145.11 1 0.1529 0.9478 0.96 0.00 0.04
#> TCGA.18.5595.11 2 0.6309 -0.4042 0.00 0.50 0.50
#> TCGA.50.5935.11 1 0.3340 0.9371 0.88 0.00 0.12
#> TCGA.22.5478.11 2 0.6192 -0.0869 0.00 0.58 0.42
#> TCGA.49.6745.11 3 0.6244 0.5371 0.00 0.44 0.56
#> TCGA.49.AARR.01 3 0.5216 0.7298 0.00 0.26 0.74
#> TCGA.18.5592.11 2 0.4002 0.5265 0.00 0.84 0.16
#> TCGA.85.A4PA.01 3 0.6309 0.2605 0.00 0.50 0.50
#> TCGA.99.AA5R.01 1 0.2537 0.9386 0.92 0.00 0.08
#> TCGA.73.4676.11 2 0.5948 0.0798 0.00 0.64 0.36
#> TCGA.60.2697.01 2 0.2537 0.5787 0.00 0.92 0.08
#> TCGA.43.5668.11 2 0.2066 0.5721 0.00 0.94 0.06
#> TCGA.L4.A4E6.01 2 0.4796 0.4534 0.00 0.78 0.22
#> TCGA.73.4658.11 1 0.2537 0.9443 0.92 0.00 0.08
#> TCGA.43.3394.11 3 0.5835 0.5840 0.00 0.34 0.66
#> TCGA.39.5016.11 2 0.2959 0.5707 0.00 0.90 0.10
#> TCGA.90.6837.01 2 0.2066 0.5796 0.00 0.94 0.06
#> TCGA.44.6148.11 2 0.6302 -0.3465 0.00 0.52 0.48
#> TCGA.50.6592.11 1 0.4002 0.9270 0.84 0.00 0.16
#> TCGA.50.5933.11 2 0.3686 0.5320 0.00 0.86 0.14
#> TCGA.98.A53D.01 2 0.6302 -0.3434 0.00 0.52 0.48
#> TCGA.44.2668.11 2 0.6192 -0.0917 0.00 0.58 0.42
#> TCGA.39.5034.11 1 0.2537 0.9402 0.92 0.00 0.08
#> TCGA.98.A53H.01 1 0.2959 0.9389 0.90 0.00 0.10
#> TCGA.39.5036.11 2 0.2959 0.5692 0.00 0.90 0.10
#> TCGA.22.4599.11 1 0.1529 0.9446 0.96 0.00 0.04
#> TCGA.39.5031.11 1 0.2537 0.9434 0.92 0.00 0.08
#> TCGA.50.5936.11 2 0.2959 0.5741 0.00 0.90 0.10
#> TCGA.22.5471.11 2 0.2959 0.5557 0.00 0.90 0.10
#> TCGA.50.5932.11 2 0.6045 -0.1266 0.00 0.62 0.38
#> TCGA.22.5480.11 1 0.2066 0.9422 0.94 0.00 0.06
#> TCGA.50.5931.11 1 0.3686 0.9277 0.86 0.00 0.14
#> TCGA.22.4601.11 1 0.2066 0.9422 0.94 0.00 0.06
#> TCGA.77.A5FZ.01 2 0.2066 0.5796 0.00 0.94 0.06
#> TCGA.33.4589.11 1 0.2537 0.9459 0.92 0.00 0.08
#> TCGA.18.3417.11 2 0.0892 0.5780 0.00 0.98 0.02
#> TCGA.44.6144.11 2 0.6244 -0.1891 0.00 0.56 0.44
#> TCGA.39.5029.11 2 0.6309 -0.3296 0.00 0.50 0.50
#> TCGA.44.6147.11 1 0.0892 0.9450 0.98 0.00 0.02
#> TCGA.22.5472.11 2 0.5560 0.4308 0.00 0.70 0.30
#> TCGA.44.5643.11 3 0.5216 0.7298 0.00 0.26 0.74
#> TCGA.55.8513.01 1 0.4291 0.9209 0.82 0.00 0.18
#> TCGA.05.5420.11 2 0.5948 0.1205 0.00 0.64 0.36
#> TCGA.33.4566.11 2 0.4796 0.5300 0.00 0.78 0.22
#> TCGA.39.5037.11 2 0.1529 0.5852 0.00 0.96 0.04
#> TCGA.50.6591.11 1 0.1529 0.9457 0.96 0.00 0.04
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.44.2659.11 1 0.515 0.8424 0.74 0.00 0.20 0.06
#> TCGA.43.3920.11 2 0.283 0.4813 0.00 0.90 0.06 0.04
#> TCGA.44.5645.11 1 0.562 0.8178 0.64 0.00 0.32 0.04
#> TCGA.44.2665.11 1 0.495 0.8356 0.76 0.00 0.18 0.06
#> TCGA.22.5473.11 4 0.549 0.5800 0.00 0.40 0.02 0.58
#> TCGA.22.5482.11 4 0.471 0.7608 0.00 0.36 0.00 0.64
#> TCGA.39.5030.11 1 0.596 0.8227 0.68 0.00 0.22 0.10
#> TCGA.22.5489.11 2 0.461 0.2761 0.00 0.80 0.10 0.10
#> TCGA.44.2662.11 2 0.449 0.4589 0.00 0.80 0.06 0.14
#> TCGA.50.5930.11 2 0.549 0.2972 0.00 0.72 0.08 0.20
#> TCGA.22.5474.11 4 0.579 0.7521 0.00 0.36 0.04 0.60
#> TCGA.22.5492.11 1 0.241 0.8378 0.92 0.00 0.04 0.04
#> TCGA.22.5485.11 1 0.320 0.8518 0.88 0.00 0.08 0.04
#> TCGA.33.4583.11 2 0.549 -0.0448 0.00 0.58 0.02 0.40
#> TCGA.22.5491.11 2 0.494 0.3431 0.00 0.74 0.04 0.22
#> TCGA.44.6146.11 2 0.361 0.4823 0.00 0.86 0.08 0.06
#> TCGA.98.A53C.01 1 0.506 0.8411 0.68 0.00 0.30 0.02
#> TCGA.43.6771.11 2 0.506 0.2134 0.00 0.68 0.02 0.30
#> TCGA.39.5011.11 1 0.423 0.8608 0.82 0.00 0.12 0.06
#> TCGA.39.5021.11 2 0.385 0.4418 0.00 0.82 0.02 0.16
#> TCGA.34.5929.11 1 0.334 0.8288 0.86 0.00 0.02 0.12
#> TCGA.55.7816.01 1 0.385 0.8294 0.82 0.00 0.02 0.16
#> TCGA.39.5019.11 2 0.491 -0.0606 0.00 0.58 0.00 0.42
#> TCGA.50.6593.11 1 0.543 0.8241 0.60 0.00 0.38 0.02
#> TCGA.22.4613.11 1 0.201 0.8542 0.92 0.00 0.08 0.00
#> TCGA.56.8623.01 2 0.428 0.4035 0.00 0.78 0.02 0.20
#> TCGA.44.2656.11 2 0.462 0.0869 0.00 0.66 0.00 0.34
#> TCGA.44.6778.11 3 0.718 1.0000 0.00 0.38 0.48 0.14
#> TCGA.38.4631.11 1 0.320 0.8522 0.88 0.00 0.08 0.04
#> TCGA.33.4579.11 1 0.429 0.8607 0.82 0.00 0.10 0.08
#> TCGA.86.A4P8.01 1 0.441 0.8427 0.70 0.00 0.30 0.00
#> TCGA.33.4586.11 4 0.462 0.7630 0.00 0.34 0.00 0.66
#> TCGA.39.5039.11 4 0.479 0.7174 0.00 0.38 0.00 0.62
#> TCGA.38.4632.11 3 0.718 1.0000 0.00 0.38 0.48 0.14
#> TCGA.44.2655.11 1 0.571 0.8290 0.62 0.00 0.34 0.04
#> TCGA.33.4582.11 2 0.334 0.4734 0.00 0.86 0.02 0.12
#> TCGA.50.5939.11 2 0.626 -0.2492 0.00 0.54 0.06 0.40
#> TCGA.75.6203.01 1 0.494 0.8594 0.74 0.00 0.22 0.04
#> TCGA.18.4721.11 4 0.485 0.7373 0.00 0.40 0.00 0.60
#> TCGA.50.6594.11 1 0.579 0.8021 0.60 0.00 0.36 0.04
#> TCGA.49.4488.11 1 0.549 0.8204 0.58 0.00 0.40 0.02
#> TCGA.22.5477.11 2 0.494 0.4485 0.00 0.74 0.04 0.22
#> TCGA.39.5035.11 1 0.361 0.8325 0.86 0.00 0.08 0.06
#> TCGA.44.6145.11 1 0.398 0.8543 0.76 0.00 0.24 0.00
#> TCGA.18.5595.11 2 0.320 0.4516 0.00 0.88 0.08 0.04
#> TCGA.50.5935.11 1 0.462 0.8273 0.66 0.00 0.34 0.00
#> TCGA.22.5478.11 2 0.508 0.4637 0.00 0.76 0.08 0.16
#> TCGA.49.6745.11 2 0.458 0.4290 0.00 0.80 0.08 0.12
#> TCGA.49.AARR.01 3 0.718 1.0000 0.00 0.38 0.48 0.14
#> TCGA.18.5592.11 2 0.385 0.4429 0.00 0.82 0.02 0.16
#> TCGA.85.A4PA.01 2 0.735 -0.3100 0.00 0.52 0.28 0.20
#> TCGA.99.AA5R.01 1 0.579 0.8021 0.60 0.00 0.36 0.04
#> TCGA.73.4676.11 2 0.688 -0.2340 0.00 0.54 0.12 0.34
#> TCGA.60.2697.01 2 0.526 0.3387 0.00 0.70 0.04 0.26
#> TCGA.43.5668.11 4 0.543 0.6897 0.00 0.38 0.02 0.60
#> TCGA.L4.A4E6.01 2 0.692 0.1290 0.00 0.58 0.16 0.26
#> TCGA.73.4658.11 1 0.408 0.8510 0.80 0.00 0.18 0.02
#> TCGA.43.3394.11 2 0.681 -0.6602 0.00 0.56 0.32 0.12
#> TCGA.39.5016.11 2 0.506 0.2588 0.00 0.68 0.02 0.30
#> TCGA.90.6837.01 2 0.498 -0.4148 0.00 0.54 0.00 0.46
#> TCGA.44.6148.11 2 0.164 0.4904 0.00 0.94 0.06 0.00
#> TCGA.50.6592.11 1 0.334 0.8369 0.86 0.00 0.12 0.02
#> TCGA.50.5933.11 4 0.615 0.6657 0.00 0.36 0.06 0.58
#> TCGA.98.A53D.01 2 0.271 0.4374 0.00 0.90 0.08 0.02
#> TCGA.44.2668.11 2 0.599 -0.0716 0.00 0.62 0.06 0.32
#> TCGA.39.5034.11 1 0.234 0.8382 0.92 0.00 0.06 0.02
#> TCGA.98.A53H.01 1 0.428 0.8479 0.72 0.00 0.28 0.00
#> TCGA.39.5036.11 2 0.441 0.2429 0.00 0.70 0.00 0.30
#> TCGA.22.4599.11 1 0.394 0.8611 0.84 0.00 0.10 0.06
#> TCGA.39.5031.11 1 0.452 0.8395 0.68 0.00 0.32 0.00
#> TCGA.50.5936.11 4 0.495 0.6246 0.00 0.44 0.00 0.56
#> TCGA.22.5471.11 4 0.471 0.7538 0.00 0.36 0.00 0.64
#> TCGA.50.5932.11 2 0.632 0.2941 0.00 0.66 0.16 0.18
#> TCGA.22.5480.11 1 0.334 0.8572 0.86 0.00 0.12 0.02
#> TCGA.50.5931.11 1 0.449 0.8470 0.80 0.00 0.14 0.06
#> TCGA.22.4601.11 1 0.361 0.8584 0.86 0.00 0.08 0.06
#> TCGA.77.A5FZ.01 2 0.498 -0.3467 0.00 0.54 0.00 0.46
#> TCGA.33.4589.11 1 0.361 0.8363 0.84 0.00 0.02 0.14
#> TCGA.18.3417.11 4 0.549 0.6877 0.00 0.40 0.02 0.58
#> TCGA.44.6144.11 2 0.713 0.1739 0.00 0.56 0.20 0.24
#> TCGA.39.5029.11 2 0.536 0.2196 0.00 0.62 0.02 0.36
#> TCGA.44.6147.11 1 0.455 0.8612 0.78 0.00 0.18 0.04
#> TCGA.22.5472.11 2 0.539 0.2951 0.00 0.68 0.04 0.28
#> TCGA.44.5643.11 3 0.718 1.0000 0.00 0.38 0.48 0.14
#> TCGA.55.8513.01 1 0.571 0.8307 0.62 0.00 0.34 0.04
#> TCGA.05.5420.11 4 0.683 0.4577 0.00 0.42 0.10 0.48
#> TCGA.33.4566.11 2 0.596 0.0333 0.00 0.54 0.04 0.42
#> TCGA.39.5037.11 2 0.500 -0.5609 0.00 0.50 0.00 0.50
#> TCGA.50.6591.11 1 0.429 0.8484 0.82 0.00 0.08 0.10
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.2659.11 1 0.4767 -0.5770 0.56 0.02 0.00 0.00 0.42
#> TCGA.43.3920.11 2 0.8239 0.3173 0.00 0.40 0.16 0.22 0.22
#> TCGA.44.5645.11 1 0.4733 0.2660 0.78 0.06 0.10 0.00 0.06
#> TCGA.44.2665.11 5 0.4818 0.0000 0.46 0.02 0.00 0.00 0.52
#> TCGA.22.5473.11 4 0.5770 0.0344 0.00 0.32 0.04 0.60 0.04
#> TCGA.22.5482.11 4 0.2616 0.3912 0.00 0.10 0.00 0.88 0.02
#> TCGA.39.5030.11 1 0.6322 0.0799 0.64 0.12 0.06 0.00 0.18
#> TCGA.22.5489.11 3 0.8443 -0.1343 0.00 0.26 0.34 0.22 0.18
#> TCGA.44.2662.11 2 0.6601 0.5212 0.00 0.58 0.04 0.24 0.14
#> TCGA.50.5930.11 4 0.7491 0.2363 0.00 0.12 0.26 0.50 0.12
#> TCGA.22.5474.11 4 0.4312 0.3419 0.00 0.16 0.02 0.78 0.04
#> TCGA.22.5492.11 1 0.5484 -0.1098 0.64 0.12 0.00 0.00 0.24
#> TCGA.22.5485.11 1 0.5700 -0.2042 0.60 0.12 0.00 0.00 0.28
#> TCGA.33.4583.11 2 0.6350 0.4323 0.00 0.42 0.00 0.42 0.16
#> TCGA.22.5491.11 4 0.7334 0.1804 0.00 0.28 0.14 0.50 0.08
#> TCGA.44.6146.11 4 0.8102 0.1885 0.00 0.20 0.24 0.42 0.14
#> TCGA.98.A53C.01 1 0.3627 0.3340 0.84 0.04 0.02 0.00 0.10
#> TCGA.43.6771.11 4 0.6776 -0.0519 0.00 0.34 0.02 0.48 0.16
#> TCGA.39.5011.11 1 0.3977 0.3326 0.82 0.06 0.02 0.00 0.10
#> TCGA.39.5021.11 4 0.6858 0.1987 0.00 0.32 0.06 0.52 0.10
#> TCGA.34.5929.11 1 0.6399 -0.1025 0.58 0.16 0.02 0.00 0.24
#> TCGA.55.7816.01 1 0.6520 -0.1260 0.58 0.12 0.04 0.00 0.26
#> TCGA.39.5019.11 4 0.5588 -0.0836 0.00 0.38 0.04 0.56 0.02
#> TCGA.50.6593.11 1 0.3561 0.1476 0.74 0.00 0.00 0.00 0.26
#> TCGA.22.4613.11 1 0.4312 0.1923 0.78 0.04 0.02 0.00 0.16
#> TCGA.56.8623.01 2 0.4644 0.4909 0.00 0.68 0.00 0.28 0.04
#> TCGA.44.2656.11 2 0.5330 0.3978 0.00 0.52 0.02 0.44 0.02
#> TCGA.44.6778.11 3 0.2616 0.7381 0.00 0.02 0.88 0.10 0.00
#> TCGA.38.4631.11 1 0.5525 0.1068 0.70 0.08 0.04 0.00 0.18
#> TCGA.33.4579.11 1 0.3521 0.2634 0.82 0.04 0.00 0.00 0.14
#> TCGA.86.A4P8.01 1 0.3684 0.1334 0.72 0.00 0.00 0.00 0.28
#> TCGA.33.4586.11 4 0.4373 0.2813 0.00 0.16 0.00 0.76 0.08
#> TCGA.39.5039.11 4 0.3291 0.4345 0.00 0.04 0.00 0.84 0.12
#> TCGA.38.4632.11 3 0.2616 0.7381 0.00 0.02 0.88 0.10 0.00
#> TCGA.44.2655.11 1 0.5092 0.1438 0.68 0.04 0.02 0.00 0.26
#> TCGA.33.4582.11 2 0.4527 0.5635 0.00 0.70 0.00 0.26 0.04
#> TCGA.50.5939.11 4 0.6356 0.4015 0.00 0.06 0.16 0.64 0.14
#> TCGA.75.6203.01 1 0.0609 0.3700 0.98 0.00 0.00 0.00 0.02
#> TCGA.18.4721.11 4 0.2438 0.4259 0.00 0.04 0.00 0.90 0.06
#> TCGA.50.6594.11 1 0.5931 0.1548 0.68 0.06 0.10 0.00 0.16
#> TCGA.49.4488.11 1 0.3109 0.1941 0.80 0.00 0.00 0.00 0.20
#> TCGA.22.5477.11 2 0.6520 0.5262 0.00 0.58 0.04 0.26 0.12
#> TCGA.39.5035.11 1 0.5157 -0.6641 0.52 0.04 0.00 0.00 0.44
#> TCGA.44.6145.11 1 0.3319 0.2576 0.82 0.02 0.00 0.00 0.16
#> TCGA.18.5595.11 2 0.8239 0.2234 0.00 0.40 0.22 0.16 0.22
#> TCGA.50.5935.11 1 0.3627 0.3374 0.84 0.04 0.02 0.00 0.10
#> TCGA.22.5478.11 2 0.8102 0.4342 0.00 0.42 0.14 0.24 0.20
#> TCGA.49.6745.11 4 0.8020 0.1395 0.00 0.18 0.30 0.40 0.12
#> TCGA.49.AARR.01 3 0.2616 0.7381 0.00 0.02 0.88 0.10 0.00
#> TCGA.18.5592.11 2 0.6245 0.5477 0.00 0.58 0.02 0.28 0.12
#> TCGA.85.A4PA.01 3 0.6564 0.0479 0.00 0.12 0.46 0.40 0.02
#> TCGA.99.AA5R.01 1 0.5031 0.2489 0.76 0.06 0.10 0.00 0.08
#> TCGA.73.4676.11 4 0.6982 0.3367 0.00 0.08 0.24 0.56 0.12
#> TCGA.60.2697.01 2 0.6858 0.2857 0.00 0.52 0.06 0.32 0.10
#> TCGA.43.5668.11 4 0.3390 0.4137 0.00 0.06 0.00 0.84 0.10
#> TCGA.L4.A4E6.01 2 0.8255 0.0431 0.00 0.34 0.20 0.32 0.14
#> TCGA.73.4658.11 1 0.4106 0.2887 0.80 0.04 0.02 0.00 0.14
#> TCGA.43.3394.11 3 0.6433 0.5595 0.00 0.12 0.64 0.08 0.16
#> TCGA.39.5016.11 2 0.6148 0.5452 0.00 0.60 0.02 0.26 0.12
#> TCGA.90.6837.01 4 0.4840 -0.1002 0.00 0.32 0.00 0.64 0.04
#> TCGA.44.6148.11 2 0.8265 0.2409 0.00 0.40 0.22 0.20 0.18
#> TCGA.50.6592.11 1 0.4818 -0.7823 0.52 0.02 0.00 0.00 0.46
#> TCGA.50.5933.11 4 0.3946 0.4521 0.00 0.00 0.12 0.80 0.08
#> TCGA.98.A53D.01 2 0.8227 0.3211 0.00 0.40 0.16 0.20 0.24
#> TCGA.44.2668.11 4 0.6867 0.3998 0.00 0.10 0.14 0.60 0.16
#> TCGA.39.5034.11 1 0.5068 -0.1780 0.64 0.06 0.00 0.00 0.30
#> TCGA.98.A53H.01 1 0.3109 0.1963 0.80 0.00 0.00 0.00 0.20
#> TCGA.39.5036.11 2 0.4360 0.5451 0.00 0.68 0.00 0.30 0.02
#> TCGA.22.4599.11 1 0.3878 0.3089 0.82 0.04 0.02 0.00 0.12
#> TCGA.39.5031.11 1 0.3109 0.2716 0.80 0.00 0.00 0.00 0.20
#> TCGA.50.5936.11 4 0.4921 0.0480 0.00 0.34 0.00 0.62 0.04
#> TCGA.22.5471.11 4 0.1410 0.4235 0.00 0.06 0.00 0.94 0.00
#> TCGA.50.5932.11 4 0.7715 0.2622 0.00 0.08 0.28 0.44 0.20
#> TCGA.22.5480.11 1 0.3513 0.1740 0.80 0.02 0.00 0.00 0.18
#> TCGA.50.5931.11 1 0.3796 -0.0615 0.70 0.00 0.00 0.00 0.30
#> TCGA.22.4601.11 1 0.4653 0.2239 0.76 0.06 0.02 0.00 0.16
#> TCGA.77.A5FZ.01 2 0.4798 0.4120 0.00 0.54 0.00 0.44 0.02
#> TCGA.33.4589.11 1 0.5440 0.0474 0.70 0.12 0.02 0.00 0.16
#> TCGA.18.3417.11 4 0.5050 0.2639 0.00 0.18 0.00 0.70 0.12
#> TCGA.44.6144.11 4 0.6912 0.2943 0.00 0.06 0.28 0.54 0.12
#> TCGA.39.5029.11 4 0.7481 0.1264 0.00 0.28 0.16 0.48 0.08
#> TCGA.44.6147.11 1 0.1410 0.3598 0.94 0.00 0.00 0.00 0.06
#> TCGA.22.5472.11 2 0.5588 0.4386 0.00 0.56 0.04 0.38 0.02
#> TCGA.44.5643.11 3 0.2616 0.7381 0.00 0.02 0.88 0.10 0.00
#> TCGA.55.8513.01 1 0.4360 0.1047 0.68 0.02 0.00 0.00 0.30
#> TCGA.05.5420.11 4 0.5196 0.4437 0.00 0.04 0.12 0.74 0.10
#> TCGA.33.4566.11 2 0.5727 0.4579 0.00 0.56 0.10 0.34 0.00
#> TCGA.39.5037.11 4 0.5425 0.2090 0.00 0.32 0.00 0.60 0.08
#> TCGA.50.6591.11 1 0.5440 0.0291 0.70 0.12 0.02 0.00 0.16
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.2659.11 1 0.577 0.14346 0.56 0.00 0.02 0.00 0.14 0.28
#> TCGA.43.3920.11 5 0.664 0.65915 0.00 0.36 0.10 0.10 0.44 0.00
#> TCGA.44.5645.11 1 0.776 -0.02944 0.42 0.00 0.04 0.12 0.16 0.26
#> TCGA.44.2665.11 1 0.599 0.10182 0.52 0.00 0.02 0.00 0.16 0.30
#> TCGA.22.5473.11 2 0.603 0.16208 0.00 0.56 0.06 0.28 0.00 0.10
#> TCGA.22.5482.11 4 0.487 0.40791 0.00 0.32 0.00 0.60 0.00 0.08
#> TCGA.39.5030.11 1 0.700 -0.15217 0.42 0.00 0.02 0.06 0.14 0.36
#> TCGA.22.5489.11 5 0.661 0.55267 0.00 0.36 0.20 0.04 0.40 0.00
#> TCGA.44.2662.11 2 0.561 -0.08409 0.00 0.66 0.08 0.04 0.20 0.02
#> TCGA.50.5930.11 4 0.701 0.11727 0.00 0.32 0.28 0.34 0.06 0.00
#> TCGA.22.5474.11 4 0.598 0.48370 0.00 0.22 0.08 0.60 0.00 0.10
#> TCGA.22.5492.11 6 0.433 0.43769 0.46 0.00 0.02 0.00 0.00 0.52
#> TCGA.22.5485.11 1 0.484 -0.22877 0.54 0.00 0.00 0.00 0.06 0.40
#> TCGA.33.4583.11 2 0.672 0.22232 0.00 0.50 0.00 0.22 0.20 0.08
#> TCGA.22.5491.11 2 0.810 -0.00468 0.00 0.32 0.20 0.30 0.14 0.04
#> TCGA.44.6146.11 4 0.780 0.02138 0.00 0.28 0.24 0.34 0.12 0.02
#> TCGA.98.A53C.01 1 0.448 0.27799 0.70 0.00 0.00 0.00 0.20 0.10
#> TCGA.43.6771.11 4 0.696 0.15440 0.00 0.26 0.02 0.46 0.22 0.04
#> TCGA.39.5011.11 1 0.354 0.19890 0.80 0.00 0.00 0.00 0.08 0.12
#> TCGA.39.5021.11 2 0.812 0.02676 0.00 0.36 0.16 0.20 0.24 0.04
#> TCGA.34.5929.11 6 0.414 0.61336 0.36 0.00 0.02 0.00 0.00 0.62
#> TCGA.55.7816.01 6 0.434 0.47295 0.48 0.00 0.00 0.00 0.02 0.50
#> TCGA.39.5019.11 2 0.521 0.36649 0.00 0.70 0.04 0.18 0.06 0.02
#> TCGA.50.6593.11 1 0.399 0.35217 0.76 0.00 0.00 0.00 0.14 0.10
#> TCGA.22.4613.11 1 0.527 -0.17790 0.56 0.00 0.00 0.00 0.12 0.32
#> TCGA.56.8623.01 2 0.572 0.02162 0.00 0.62 0.02 0.10 0.24 0.02
#> TCGA.44.2656.11 2 0.463 0.35082 0.00 0.70 0.00 0.22 0.06 0.02
#> TCGA.44.6778.11 3 0.235 0.77961 0.00 0.10 0.88 0.00 0.02 0.00
#> TCGA.38.4631.11 1 0.537 -0.31783 0.52 0.00 0.00 0.00 0.12 0.36
#> TCGA.33.4579.11 1 0.382 0.08130 0.74 0.00 0.00 0.00 0.04 0.22
#> TCGA.86.A4P8.01 1 0.379 0.35672 0.78 0.00 0.00 0.00 0.10 0.12
#> TCGA.33.4586.11 4 0.577 0.40844 0.00 0.28 0.00 0.56 0.02 0.14
#> TCGA.39.5039.11 4 0.548 0.51543 0.00 0.12 0.10 0.70 0.02 0.06
#> TCGA.38.4632.11 3 0.235 0.77961 0.00 0.10 0.88 0.00 0.02 0.00
#> TCGA.44.2655.11 1 0.493 0.31967 0.64 0.00 0.00 0.00 0.24 0.12
#> TCGA.33.4582.11 2 0.473 0.04451 0.00 0.68 0.02 0.02 0.26 0.02
#> TCGA.50.5939.11 4 0.625 0.37812 0.00 0.16 0.22 0.56 0.06 0.00
#> TCGA.75.6203.01 1 0.316 0.19080 0.80 0.00 0.00 0.00 0.02 0.18
#> TCGA.18.4721.11 4 0.511 0.47814 0.00 0.22 0.00 0.66 0.02 0.10
#> TCGA.50.6594.11 1 0.774 0.00675 0.44 0.00 0.04 0.12 0.18 0.22
#> TCGA.49.4488.11 1 0.486 0.30881 0.66 0.00 0.00 0.00 0.20 0.14
#> TCGA.22.5477.11 2 0.498 0.21859 0.00 0.68 0.00 0.06 0.22 0.04
#> TCGA.39.5035.11 1 0.511 -0.13156 0.50 0.00 0.02 0.00 0.04 0.44
#> TCGA.44.6145.11 1 0.354 0.32084 0.80 0.00 0.00 0.00 0.08 0.12
#> TCGA.18.5595.11 5 0.682 0.67022 0.00 0.32 0.16 0.04 0.46 0.02
#> TCGA.50.5935.11 1 0.354 0.32553 0.80 0.00 0.00 0.00 0.12 0.08
#> TCGA.22.5478.11 2 0.601 -0.28969 0.00 0.52 0.06 0.08 0.34 0.00
#> TCGA.49.6745.11 2 0.765 -0.07012 0.00 0.30 0.26 0.26 0.18 0.00
#> TCGA.49.AARR.01 3 0.181 0.78121 0.00 0.10 0.90 0.00 0.00 0.00
#> TCGA.18.5592.11 2 0.477 0.00704 0.00 0.64 0.02 0.04 0.30 0.00
#> TCGA.85.A4PA.01 3 0.695 0.24578 0.00 0.24 0.50 0.18 0.06 0.02
#> TCGA.99.AA5R.01 1 0.774 0.00624 0.44 0.00 0.04 0.12 0.18 0.22
#> TCGA.73.4676.11 4 0.586 0.43458 0.00 0.16 0.20 0.60 0.04 0.00
#> TCGA.60.2697.01 2 0.656 0.04465 0.00 0.54 0.04 0.16 0.24 0.02
#> TCGA.43.5668.11 4 0.541 0.49435 0.00 0.14 0.02 0.68 0.02 0.14
#> TCGA.L4.A4E6.01 2 0.731 -0.00352 0.00 0.40 0.16 0.28 0.16 0.00
#> TCGA.73.4658.11 1 0.474 0.12816 0.68 0.00 0.00 0.00 0.16 0.16
#> TCGA.43.3394.11 3 0.503 0.38488 0.00 0.12 0.62 0.00 0.26 0.00
#> TCGA.39.5016.11 2 0.546 0.15442 0.00 0.64 0.04 0.10 0.22 0.00
#> TCGA.90.6837.01 4 0.571 0.30915 0.00 0.38 0.00 0.50 0.02 0.10
#> TCGA.44.6148.11 5 0.730 0.49885 0.00 0.32 0.20 0.12 0.36 0.00
#> TCGA.50.6592.11 1 0.481 -0.00594 0.56 0.00 0.00 0.00 0.06 0.38
#> TCGA.50.5933.11 4 0.522 0.51598 0.00 0.14 0.12 0.70 0.02 0.02
#> TCGA.98.A53D.01 5 0.643 0.67856 0.00 0.38 0.12 0.06 0.44 0.00
#> TCGA.44.2668.11 4 0.698 0.37145 0.00 0.18 0.20 0.52 0.08 0.02
#> TCGA.39.5034.11 1 0.434 -0.52784 0.50 0.00 0.02 0.00 0.00 0.48
#> TCGA.98.A53H.01 1 0.420 0.35199 0.74 0.00 0.00 0.00 0.12 0.14
#> TCGA.39.5036.11 2 0.326 0.28346 0.00 0.84 0.02 0.04 0.10 0.00
#> TCGA.22.4599.11 1 0.393 0.13016 0.76 0.00 0.00 0.00 0.08 0.16
#> TCGA.39.5031.11 1 0.407 0.32618 0.78 0.00 0.02 0.00 0.12 0.08
#> TCGA.50.5936.11 2 0.457 -0.03356 0.00 0.62 0.02 0.34 0.00 0.02
#> TCGA.22.5471.11 4 0.473 0.44788 0.00 0.24 0.00 0.66 0.00 0.10
#> TCGA.50.5932.11 4 0.779 0.20923 0.00 0.14 0.20 0.44 0.18 0.04
#> TCGA.22.5480.11 1 0.468 0.09115 0.68 0.00 0.00 0.00 0.12 0.20
#> TCGA.50.5931.11 1 0.383 0.29028 0.76 0.00 0.02 0.00 0.02 0.20
#> TCGA.22.4601.11 1 0.448 0.07923 0.70 0.00 0.00 0.00 0.10 0.20
#> TCGA.77.A5FZ.01 2 0.521 0.29904 0.00 0.62 0.00 0.28 0.08 0.02
#> TCGA.33.4589.11 1 0.458 -0.33210 0.56 0.00 0.00 0.00 0.04 0.40
#> TCGA.18.3417.11 4 0.631 0.42491 0.00 0.20 0.02 0.60 0.06 0.12
#> TCGA.44.6144.11 4 0.625 0.43501 0.00 0.12 0.24 0.58 0.04 0.02
#> TCGA.39.5029.11 2 0.723 0.21698 0.00 0.52 0.14 0.20 0.10 0.04
#> TCGA.44.6147.11 1 0.316 0.20223 0.82 0.00 0.00 0.00 0.04 0.14
#> TCGA.22.5472.11 2 0.473 0.30961 0.00 0.76 0.04 0.08 0.10 0.02
#> TCGA.44.5643.11 3 0.181 0.78121 0.00 0.10 0.90 0.00 0.00 0.00
#> TCGA.55.8513.01 1 0.504 0.32185 0.68 0.00 0.02 0.00 0.18 0.12
#> TCGA.05.5420.11 4 0.568 0.50336 0.00 0.12 0.12 0.68 0.02 0.06
#> TCGA.33.4566.11 2 0.480 0.34579 0.00 0.76 0.06 0.08 0.08 0.02
#> TCGA.39.5037.11 4 0.575 0.27520 0.00 0.34 0.04 0.54 0.08 0.00
#> TCGA.50.6591.11 1 0.425 0.06313 0.70 0.00 0.00 0.00 0.06 0.24
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.44.2659.11 1 0.4766 0.3168 0.70 0.12 0.12 0.00 0.00 0.06 0.00
#> TCGA.43.3920.11 5 0.4110 0.2430 0.00 0.10 0.04 0.06 0.78 0.02 0.00
#> TCGA.44.5645.11 6 0.4707 0.3774 0.22 0.10 0.02 0.00 0.00 0.66 0.00
#> TCGA.44.2665.11 1 0.5424 0.2852 0.64 0.08 0.22 0.00 0.02 0.02 0.02
#> TCGA.22.5473.11 4 0.6137 -0.0505 0.00 0.40 0.04 0.44 0.06 0.06 0.00
#> TCGA.22.5482.11 4 0.4466 0.4901 0.00 0.06 0.20 0.70 0.00 0.04 0.00
#> TCGA.39.5030.11 6 0.6567 0.3237 0.22 0.10 0.26 0.00 0.00 0.42 0.00
#> TCGA.22.5489.11 5 0.7104 0.1601 0.00 0.10 0.08 0.08 0.56 0.06 0.12
#> TCGA.44.2662.11 5 0.5620 -0.0885 0.00 0.34 0.02 0.10 0.52 0.02 0.00
#> TCGA.50.5930.11 5 0.6386 0.0304 0.00 0.10 0.02 0.38 0.42 0.00 0.08
#> TCGA.22.5474.11 4 0.5626 0.4517 0.00 0.08 0.20 0.64 0.04 0.02 0.02
#> TCGA.22.5492.11 1 0.6382 -0.0970 0.38 0.00 0.28 0.00 0.02 0.30 0.02
#> TCGA.22.5485.11 1 0.5622 0.1180 0.52 0.00 0.24 0.00 0.00 0.22 0.02
#> TCGA.33.4583.11 5 0.7088 -0.1254 0.00 0.22 0.24 0.24 0.30 0.00 0.00
#> TCGA.22.5491.11 5 0.7354 0.1649 0.00 0.16 0.06 0.26 0.44 0.04 0.04
#> TCGA.44.6146.11 5 0.5538 0.1638 0.00 0.08 0.00 0.34 0.52 0.00 0.06
#> TCGA.98.A53C.01 1 0.4524 0.0411 0.60 0.02 0.04 0.00 0.00 0.34 0.00
#> TCGA.43.6771.11 5 0.7150 0.0989 0.00 0.08 0.26 0.24 0.38 0.04 0.00
#> TCGA.39.5011.11 1 0.4828 0.0265 0.56 0.02 0.06 0.00 0.00 0.36 0.00
#> TCGA.39.5021.11 5 0.7555 0.0705 0.00 0.22 0.04 0.30 0.34 0.08 0.02
#> TCGA.34.5929.11 6 0.6022 0.1578 0.30 0.00 0.32 0.00 0.02 0.36 0.00
#> TCGA.55.7816.01 6 0.5619 0.1905 0.30 0.00 0.32 0.00 0.00 0.38 0.00
#> TCGA.39.5019.11 2 0.5778 0.2282 0.00 0.50 0.02 0.34 0.12 0.02 0.00
#> TCGA.50.6593.11 1 0.3541 0.3184 0.80 0.02 0.08 0.00 0.00 0.10 0.00
#> TCGA.22.4613.11 1 0.4487 -0.0140 0.52 0.00 0.06 0.00 0.00 0.42 0.00
#> TCGA.56.8623.01 5 0.6717 -0.2629 0.00 0.38 0.08 0.08 0.40 0.06 0.00
#> TCGA.44.2656.11 2 0.6189 0.3397 0.00 0.46 0.06 0.20 0.28 0.00 0.00
#> TCGA.44.6778.11 7 0.0504 0.7907 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.38.4631.11 6 0.4783 0.1601 0.36 0.00 0.10 0.00 0.00 0.54 0.00
#> TCGA.33.4579.11 6 0.4505 0.1209 0.44 0.00 0.06 0.00 0.00 0.50 0.00
#> TCGA.86.A4P8.01 1 0.3386 0.2811 0.78 0.02 0.02 0.00 0.00 0.18 0.00
#> TCGA.33.4586.11 4 0.4070 0.4677 0.00 0.02 0.30 0.66 0.02 0.00 0.00
#> TCGA.39.5039.11 4 0.4507 0.4964 0.00 0.02 0.12 0.76 0.04 0.04 0.02
#> TCGA.38.4632.11 7 0.0504 0.7907 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.44.2655.11 1 0.2857 0.3334 0.86 0.04 0.06 0.00 0.00 0.04 0.00
#> TCGA.33.4582.11 2 0.4692 0.3862 0.00 0.50 0.00 0.08 0.42 0.00 0.00
#> TCGA.50.5939.11 4 0.4589 0.3669 0.00 0.04 0.00 0.68 0.22 0.00 0.06
#> TCGA.75.6203.01 6 0.4266 0.1302 0.44 0.00 0.04 0.00 0.00 0.52 0.00
#> TCGA.18.4721.11 4 0.3517 0.4838 0.00 0.02 0.28 0.70 0.00 0.00 0.00
#> TCGA.50.6594.11 6 0.5792 0.3071 0.26 0.14 0.06 0.00 0.00 0.54 0.00
#> TCGA.49.4488.11 1 0.2572 0.2650 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.22.5477.11 5 0.6816 -0.3824 0.00 0.36 0.04 0.16 0.38 0.06 0.00
#> TCGA.39.5035.11 1 0.6026 0.2457 0.58 0.08 0.20 0.00 0.00 0.12 0.02
#> TCGA.44.6145.11 1 0.4431 0.2060 0.68 0.04 0.04 0.00 0.00 0.24 0.00
#> TCGA.18.5595.11 5 0.5769 0.1795 0.00 0.16 0.06 0.04 0.66 0.04 0.04
#> TCGA.50.5935.11 1 0.3909 0.0176 0.58 0.00 0.02 0.00 0.00 0.40 0.00
#> TCGA.22.5478.11 5 0.7205 0.0713 0.00 0.12 0.08 0.14 0.54 0.06 0.06
#> TCGA.49.6745.11 5 0.6842 0.1773 0.00 0.12 0.02 0.30 0.46 0.02 0.08
#> TCGA.49.AARR.01 7 0.0504 0.7907 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.18.5592.11 5 0.5516 -0.3236 0.00 0.36 0.00 0.10 0.50 0.04 0.00
#> TCGA.85.A4PA.01 7 0.7835 -0.1337 0.00 0.22 0.04 0.14 0.24 0.02 0.34
#> TCGA.99.AA5R.01 6 0.4908 0.3579 0.26 0.10 0.02 0.00 0.00 0.62 0.00
#> TCGA.73.4676.11 4 0.4928 0.3649 0.00 0.04 0.00 0.64 0.24 0.00 0.08
#> TCGA.60.2697.01 5 0.7642 -0.0862 0.00 0.28 0.14 0.20 0.32 0.06 0.00
#> TCGA.43.5668.11 4 0.4269 0.4356 0.00 0.02 0.36 0.60 0.02 0.00 0.00
#> TCGA.L4.A4E6.01 4 0.7530 0.0510 0.00 0.16 0.08 0.40 0.28 0.02 0.06
#> TCGA.73.4658.11 1 0.4266 -0.0174 0.52 0.00 0.04 0.00 0.00 0.44 0.00
#> TCGA.43.3394.11 7 0.4845 0.4733 0.00 0.02 0.04 0.00 0.30 0.02 0.62
#> TCGA.39.5016.11 2 0.6134 0.4548 0.00 0.50 0.08 0.08 0.32 0.02 0.00
#> TCGA.90.6837.01 4 0.6512 0.1678 0.00 0.10 0.24 0.44 0.22 0.00 0.00
#> TCGA.44.6148.11 5 0.5094 0.2339 0.00 0.14 0.06 0.06 0.70 0.00 0.04
#> TCGA.50.6592.11 1 0.6065 0.2044 0.56 0.06 0.22 0.00 0.00 0.14 0.02
#> TCGA.50.5933.11 4 0.4703 0.4664 0.00 0.04 0.06 0.76 0.08 0.02 0.04
#> TCGA.98.A53D.01 5 0.3831 0.2882 0.00 0.04 0.02 0.06 0.82 0.02 0.04
#> TCGA.44.2668.11 4 0.5474 0.3038 0.00 0.04 0.00 0.56 0.32 0.02 0.06
#> TCGA.39.5034.11 1 0.6177 0.1288 0.52 0.02 0.20 0.00 0.04 0.22 0.00
#> TCGA.98.A53H.01 1 0.2906 0.2767 0.80 0.02 0.00 0.00 0.00 0.18 0.00
#> TCGA.39.5036.11 2 0.6048 0.4815 0.00 0.54 0.04 0.10 0.28 0.04 0.00
#> TCGA.22.4599.11 1 0.4869 0.0168 0.54 0.02 0.06 0.00 0.00 0.38 0.00
#> TCGA.39.5031.11 1 0.4569 0.1399 0.64 0.06 0.02 0.00 0.00 0.28 0.00
#> TCGA.50.5936.11 4 0.6109 0.1805 0.00 0.28 0.04 0.54 0.06 0.08 0.00
#> TCGA.22.5471.11 4 0.3566 0.5003 0.00 0.04 0.16 0.78 0.00 0.02 0.00
#> TCGA.50.5932.11 4 0.6344 0.1856 0.00 0.02 0.10 0.46 0.34 0.00 0.08
#> TCGA.22.5480.11 1 0.5429 -0.0475 0.46 0.02 0.12 0.00 0.00 0.40 0.00
#> TCGA.50.5931.11 1 0.4654 0.2927 0.72 0.06 0.04 0.00 0.02 0.16 0.00
#> TCGA.22.4601.11 1 0.5105 -0.0131 0.50 0.02 0.08 0.00 0.00 0.40 0.00
#> TCGA.77.A5FZ.01 4 0.6610 -0.2487 0.00 0.28 0.10 0.40 0.22 0.00 0.00
#> TCGA.33.4589.11 1 0.5560 -0.1828 0.42 0.00 0.28 0.00 0.00 0.30 0.00
#> TCGA.18.3417.11 4 0.5709 0.2928 0.00 0.04 0.40 0.44 0.12 0.00 0.00
#> TCGA.44.6144.11 4 0.5559 0.3158 0.00 0.00 0.06 0.58 0.24 0.00 0.12
#> TCGA.39.5029.11 4 0.6546 0.0165 0.00 0.32 0.00 0.46 0.12 0.06 0.04
#> TCGA.44.6147.11 6 0.3985 0.0520 0.46 0.00 0.02 0.00 0.00 0.52 0.00
#> TCGA.22.5472.11 2 0.5240 0.4767 0.00 0.58 0.02 0.14 0.26 0.00 0.00
#> TCGA.44.5643.11 7 0.0504 0.7907 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.55.8513.01 1 0.3346 0.3279 0.84 0.06 0.04 0.00 0.02 0.04 0.00
#> TCGA.05.5420.11 4 0.4654 0.4538 0.00 0.02 0.06 0.72 0.16 0.00 0.04
#> TCGA.33.4566.11 2 0.5848 0.5207 0.00 0.58 0.04 0.16 0.20 0.02 0.00
#> TCGA.39.5037.11 4 0.6756 0.0715 0.00 0.20 0.06 0.50 0.18 0.06 0.00
#> TCGA.50.6591.11 1 0.6202 -0.2889 0.36 0.04 0.24 0.00 0.00 0.36 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.44.2659.11 1 0.635 0.079886 0.46 0.06 0.30 0.00 0.00 0.10 0.00 0.08
#> TCGA.43.3920.11 5 0.532 0.162508 0.00 0.02 0.00 0.18 0.62 0.06 0.00 0.12
#> TCGA.44.5645.11 6 0.463 0.727355 0.36 0.00 0.12 0.00 0.00 0.52 0.00 0.00
#> TCGA.44.2665.11 1 0.625 -0.015048 0.44 0.14 0.32 0.00 0.00 0.04 0.00 0.06
#> TCGA.22.5473.11 4 0.730 -0.222111 0.00 0.26 0.00 0.28 0.22 0.02 0.02 0.20
#> TCGA.22.5482.11 2 0.534 0.525978 0.00 0.46 0.00 0.40 0.10 0.02 0.00 0.02
#> TCGA.39.5030.11 6 0.604 0.429501 0.18 0.00 0.28 0.00 0.00 0.44 0.00 0.10
#> TCGA.22.5489.11 5 0.566 0.161831 0.00 0.00 0.00 0.08 0.56 0.24 0.02 0.10
#> TCGA.44.2662.11 5 0.536 0.242140 0.00 0.06 0.00 0.24 0.60 0.06 0.00 0.04
#> TCGA.50.5930.11 4 0.453 0.099819 0.00 0.02 0.02 0.76 0.06 0.02 0.04 0.08
#> TCGA.22.5474.11 4 0.728 -0.319988 0.00 0.28 0.02 0.40 0.14 0.02 0.04 0.10
#> TCGA.22.5492.11 3 0.235 0.587499 0.10 0.00 0.86 0.00 0.00 0.00 0.00 0.04
#> TCGA.22.5485.11 3 0.309 0.549053 0.24 0.00 0.74 0.00 0.00 0.00 0.00 0.02
#> TCGA.33.4583.11 5 0.582 0.233689 0.00 0.22 0.00 0.04 0.56 0.06 0.00 0.12
#> TCGA.22.5491.11 4 0.712 -0.234791 0.00 0.02 0.02 0.46 0.22 0.10 0.04 0.14
#> TCGA.44.6146.11 4 0.639 -0.055252 0.00 0.04 0.02 0.58 0.16 0.04 0.04 0.12
#> TCGA.98.A53C.01 1 0.595 0.229889 0.54 0.00 0.24 0.00 0.00 0.04 0.08 0.10
#> TCGA.43.6771.11 5 0.648 -0.031801 0.00 0.34 0.00 0.10 0.40 0.04 0.00 0.12
#> TCGA.39.5011.11 1 0.562 0.162507 0.50 0.00 0.30 0.00 0.00 0.00 0.10 0.10
#> TCGA.39.5021.11 8 0.776 0.468167 0.00 0.14 0.00 0.24 0.24 0.06 0.04 0.28
#> TCGA.34.5929.11 3 0.416 0.558904 0.10 0.04 0.76 0.00 0.00 0.06 0.00 0.04
#> TCGA.55.7816.01 3 0.537 0.510301 0.18 0.04 0.62 0.00 0.00 0.12 0.00 0.04
#> TCGA.39.5019.11 5 0.659 -0.182013 0.00 0.20 0.00 0.22 0.32 0.00 0.00 0.26
#> TCGA.50.6593.11 1 0.222 0.364699 0.86 0.00 0.00 0.00 0.00 0.02 0.00 0.12
#> TCGA.22.4613.11 3 0.453 0.397978 0.30 0.00 0.62 0.00 0.00 0.02 0.02 0.04
#> TCGA.56.8623.01 5 0.644 0.222955 0.00 0.16 0.06 0.06 0.46 0.00 0.00 0.26
#> TCGA.44.2656.11 4 0.732 -0.053243 0.00 0.08 0.02 0.38 0.32 0.08 0.02 0.10
#> TCGA.44.6778.11 7 0.180 0.756496 0.00 0.00 0.00 0.08 0.02 0.00 0.90 0.00
#> TCGA.38.4631.11 3 0.570 0.191639 0.36 0.00 0.44 0.00 0.00 0.12 0.00 0.08
#> TCGA.33.4579.11 1 0.586 0.223033 0.56 0.02 0.22 0.00 0.00 0.14 0.02 0.04
#> TCGA.86.A4P8.01 1 0.364 0.385347 0.80 0.06 0.08 0.00 0.00 0.02 0.00 0.04
#> TCGA.33.4586.11 2 0.447 0.628472 0.00 0.66 0.00 0.20 0.12 0.02 0.00 0.00
#> TCGA.39.5039.11 2 0.581 0.501071 0.00 0.42 0.00 0.40 0.10 0.02 0.00 0.06
#> TCGA.38.4632.11 7 0.180 0.756496 0.00 0.00 0.00 0.08 0.02 0.00 0.90 0.00
#> TCGA.44.2655.11 1 0.474 0.396162 0.72 0.12 0.06 0.00 0.00 0.02 0.02 0.06
#> TCGA.33.4582.11 5 0.531 0.121761 0.00 0.04 0.00 0.10 0.58 0.02 0.00 0.26
#> TCGA.50.5939.11 4 0.377 0.171941 0.00 0.08 0.02 0.80 0.00 0.02 0.02 0.06
#> TCGA.75.6203.01 1 0.490 0.287100 0.68 0.00 0.14 0.00 0.00 0.08 0.02 0.08
#> TCGA.18.4721.11 2 0.495 0.591904 0.00 0.54 0.00 0.34 0.08 0.04 0.00 0.00
#> TCGA.50.6594.11 6 0.413 0.692143 0.30 0.00 0.08 0.00 0.00 0.62 0.00 0.00
#> TCGA.49.4488.11 1 0.340 0.343568 0.80 0.06 0.00 0.00 0.00 0.10 0.00 0.04
#> TCGA.22.5477.11 5 0.595 0.053727 0.00 0.04 0.00 0.08 0.54 0.10 0.00 0.24
#> TCGA.39.5035.11 3 0.498 0.317916 0.30 0.00 0.58 0.00 0.00 0.02 0.02 0.08
#> TCGA.44.6145.11 1 0.505 0.298634 0.62 0.00 0.20 0.00 0.00 0.10 0.00 0.08
#> TCGA.18.5595.11 5 0.536 0.236951 0.00 0.02 0.00 0.08 0.62 0.18 0.00 0.10
#> TCGA.50.5935.11 1 0.485 0.325398 0.70 0.00 0.10 0.00 0.00 0.04 0.06 0.10
#> TCGA.22.5478.11 5 0.660 0.115095 0.00 0.10 0.00 0.14 0.54 0.08 0.02 0.12
#> TCGA.49.6745.11 4 0.596 -0.057846 0.00 0.02 0.02 0.62 0.12 0.04 0.04 0.14
#> TCGA.49.AARR.01 7 0.180 0.756496 0.00 0.00 0.00 0.08 0.02 0.00 0.90 0.00
#> TCGA.18.5592.11 5 0.491 0.250956 0.00 0.06 0.00 0.04 0.68 0.06 0.00 0.16
#> TCGA.85.A4PA.01 7 0.693 -0.136397 0.00 0.02 0.00 0.32 0.10 0.02 0.34 0.20
#> TCGA.99.AA5R.01 6 0.434 0.708861 0.38 0.00 0.08 0.00 0.00 0.54 0.00 0.00
#> TCGA.73.4676.11 4 0.227 0.249811 0.00 0.00 0.02 0.88 0.00 0.00 0.02 0.08
#> TCGA.60.2697.01 5 0.689 0.142796 0.00 0.18 0.06 0.10 0.38 0.00 0.00 0.28
#> TCGA.43.5668.11 2 0.500 0.543589 0.00 0.62 0.02 0.22 0.12 0.00 0.00 0.02
#> TCGA.L4.A4E6.01 4 0.635 0.106676 0.00 0.06 0.02 0.48 0.26 0.00 0.02 0.16
#> TCGA.73.4658.11 1 0.541 -0.033930 0.48 0.00 0.36 0.00 0.00 0.08 0.00 0.08
#> TCGA.43.3394.11 7 0.652 0.258273 0.00 0.02 0.00 0.06 0.32 0.12 0.44 0.04
#> TCGA.39.5016.11 5 0.624 0.313437 0.00 0.12 0.04 0.02 0.56 0.08 0.00 0.18
#> TCGA.90.6837.01 4 0.597 -0.284567 0.00 0.28 0.00 0.40 0.26 0.06 0.00 0.00
#> TCGA.44.6148.11 5 0.654 0.000716 0.00 0.06 0.04 0.36 0.42 0.08 0.00 0.04
#> TCGA.50.6592.11 1 0.559 -0.102054 0.46 0.02 0.38 0.00 0.00 0.04 0.00 0.10
#> TCGA.50.5933.11 4 0.481 0.060526 0.00 0.16 0.00 0.66 0.08 0.00 0.00 0.10
#> TCGA.98.A53D.01 5 0.484 0.165335 0.00 0.00 0.00 0.20 0.64 0.06 0.00 0.10
#> TCGA.44.2668.11 4 0.474 0.093736 0.00 0.04 0.02 0.74 0.06 0.02 0.02 0.10
#> TCGA.39.5034.11 3 0.349 0.583420 0.14 0.04 0.78 0.00 0.00 0.00 0.00 0.04
#> TCGA.98.A53H.01 1 0.327 0.399843 0.80 0.00 0.12 0.00 0.00 0.06 0.00 0.02
#> TCGA.39.5036.11 5 0.631 0.289803 0.00 0.12 0.04 0.04 0.58 0.10 0.00 0.12
#> TCGA.22.4599.11 1 0.545 -0.078812 0.42 0.00 0.42 0.00 0.00 0.00 0.08 0.08
#> TCGA.39.5031.11 1 0.525 0.103760 0.60 0.00 0.14 0.00 0.00 0.18 0.00 0.08
#> TCGA.50.5936.11 4 0.704 -0.283501 0.00 0.20 0.04 0.40 0.26 0.04 0.00 0.06
#> TCGA.22.5471.11 4 0.548 -0.588184 0.00 0.42 0.00 0.42 0.12 0.02 0.00 0.02
#> TCGA.50.5932.11 4 0.646 0.019050 0.00 0.20 0.02 0.46 0.16 0.00 0.00 0.16
#> TCGA.22.5480.11 1 0.486 -0.014174 0.50 0.00 0.40 0.00 0.00 0.04 0.00 0.06
#> TCGA.50.5931.11 1 0.483 0.271946 0.62 0.02 0.26 0.00 0.00 0.00 0.02 0.08
#> TCGA.22.4601.11 3 0.581 0.142695 0.36 0.00 0.46 0.00 0.00 0.02 0.08 0.08
#> TCGA.77.A5FZ.01 5 0.655 -0.012766 0.00 0.12 0.02 0.34 0.42 0.04 0.00 0.06
#> TCGA.33.4589.11 3 0.604 0.344221 0.28 0.06 0.50 0.00 0.00 0.12 0.00 0.04
#> TCGA.18.3417.11 2 0.558 0.452051 0.00 0.58 0.02 0.14 0.20 0.00 0.00 0.06
#> TCGA.44.6144.11 4 0.490 0.170134 0.00 0.08 0.00 0.68 0.08 0.00 0.02 0.14
#> TCGA.39.5029.11 8 0.733 0.467282 0.00 0.16 0.00 0.32 0.12 0.02 0.06 0.32
#> TCGA.44.6147.11 1 0.527 0.305286 0.62 0.00 0.20 0.00 0.00 0.06 0.02 0.10
#> TCGA.22.5472.11 5 0.655 -0.019168 0.00 0.12 0.00 0.20 0.42 0.00 0.02 0.24
#> TCGA.44.5643.11 7 0.180 0.756496 0.00 0.00 0.00 0.08 0.02 0.00 0.90 0.00
#> TCGA.55.8513.01 1 0.435 0.390154 0.72 0.16 0.06 0.00 0.00 0.00 0.02 0.04
#> TCGA.05.5420.11 4 0.222 0.249377 0.00 0.12 0.00 0.86 0.00 0.00 0.00 0.02
#> TCGA.33.4566.11 5 0.802 0.072620 0.00 0.14 0.04 0.16 0.36 0.08 0.02 0.20
#> TCGA.39.5037.11 4 0.738 -0.059684 0.00 0.10 0.02 0.32 0.26 0.06 0.00 0.24
#> TCGA.50.6591.11 1 0.593 0.023164 0.48 0.00 0.24 0.00 0.00 0.18 0.00 0.10
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node05. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 36 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.797 0.963 0.979 0.4857 0.511 0.511
#> 3 3 0.775 0.850 0.925 0.2945 0.637 0.405
#> 4 4 1.000 0.989 0.996 0.1127 0.822 0.569
#> 5 5 0.832 0.932 0.948 0.1050 0.825 0.498
#> 6 6 0.909 0.900 0.872 0.0665 0.943 0.741
#> 7 7 0.859 0.897 0.896 0.0394 0.957 0.745
#> 8 8 0.829 0.834 0.865 0.0189 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] 6
#> attr(,"optional")
#> [1] 4
There is also optional best \(k\) = 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.44.2659.11 1 0.000 0.978 1.00 0.00
#> TCGA.44.5645.11 1 0.000 0.978 1.00 0.00
#> TCGA.44.2665.11 1 0.000 0.978 1.00 0.00
#> TCGA.39.5030.11 1 0.141 0.967 0.98 0.02
#> TCGA.22.5492.11 1 0.000 0.978 1.00 0.00
#> TCGA.22.5485.11 1 0.141 0.967 0.98 0.02
#> TCGA.98.A53C.01 2 0.000 0.974 0.00 1.00
#> TCGA.39.5011.11 1 0.000 0.978 1.00 0.00
#> TCGA.34.5929.11 1 0.000 0.978 1.00 0.00
#> TCGA.55.7816.01 2 0.000 0.974 0.00 1.00
#> TCGA.50.6593.11 2 0.000 0.974 0.00 1.00
#> TCGA.22.4613.11 1 0.000 0.978 1.00 0.00
#> TCGA.38.4631.11 2 0.402 0.930 0.08 0.92
#> TCGA.33.4579.11 1 0.000 0.978 1.00 0.00
#> TCGA.86.A4P8.01 2 0.000 0.974 0.00 1.00
#> TCGA.44.2655.11 1 0.000 0.978 1.00 0.00
#> TCGA.75.6203.01 2 0.000 0.974 0.00 1.00
#> TCGA.50.6594.11 2 0.402 0.930 0.08 0.92
#> TCGA.49.4488.11 2 0.000 0.974 0.00 1.00
#> TCGA.39.5035.11 2 0.402 0.930 0.08 0.92
#> TCGA.44.6145.11 1 0.469 0.905 0.90 0.10
#> TCGA.50.5935.11 1 0.469 0.905 0.90 0.10
#> TCGA.99.AA5R.01 2 0.000 0.974 0.00 1.00
#> TCGA.73.4658.11 2 0.000 0.974 0.00 1.00
#> TCGA.50.6592.11 1 0.469 0.905 0.90 0.10
#> TCGA.39.5034.11 1 0.469 0.905 0.90 0.10
#> TCGA.98.A53H.01 2 0.000 0.974 0.00 1.00
#> TCGA.22.4599.11 1 0.000 0.978 1.00 0.00
#> TCGA.39.5031.11 1 0.000 0.978 1.00 0.00
#> TCGA.22.5480.11 2 0.402 0.930 0.08 0.92
#> TCGA.50.5931.11 1 0.000 0.978 1.00 0.00
#> TCGA.22.4601.11 1 0.000 0.978 1.00 0.00
#> TCGA.33.4589.11 1 0.000 0.978 1.00 0.00
#> TCGA.44.6147.11 1 0.000 0.978 1.00 0.00
#> TCGA.55.8513.01 2 0.000 0.974 0.00 1.00
#> TCGA.50.6591.11 1 0.000 0.978 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.44.2659.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.44.5645.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.44.2665.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.39.5030.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.22.5492.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.22.5485.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.98.A53C.01 2 0.6045 0.723 0.00 0.62 0.38
#> TCGA.39.5011.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.34.5929.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.55.7816.01 2 0.0000 0.719 0.00 1.00 0.00
#> TCGA.50.6593.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.22.4613.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.38.4631.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.33.4579.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.86.A4P8.01 2 0.0000 0.719 0.00 1.00 0.00
#> TCGA.44.2655.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.75.6203.01 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.50.6594.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.49.4488.11 2 0.0000 0.719 0.00 1.00 0.00
#> TCGA.39.5035.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.44.6145.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.50.5935.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.99.AA5R.01 2 0.6045 0.723 0.00 0.62 0.38
#> TCGA.73.4658.11 2 0.0000 0.719 0.00 1.00 0.00
#> TCGA.50.6592.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.39.5034.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.98.A53H.01 2 0.6045 0.723 0.00 0.62 0.38
#> TCGA.22.4599.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.39.5031.11 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.22.5480.11 3 0.6045 0.873 0.00 0.38 0.62
#> TCGA.50.5931.11 3 0.6045 0.430 0.38 0.00 0.62
#> TCGA.22.4601.11 3 0.6045 0.430 0.38 0.00 0.62
#> TCGA.33.4589.11 1 0.0000 0.998 1.00 0.00 0.00
#> TCGA.44.6147.11 3 0.6045 0.430 0.38 0.00 0.62
#> TCGA.55.8513.01 3 0.6126 0.849 0.00 0.40 0.60
#> TCGA.50.6591.11 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.44.2659.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.44.5645.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.44.2665.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.39.5030.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.22.5492.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.22.5485.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.98.A53C.01 4 0.000 1.000 0.00 0.00 0.00 1
#> TCGA.39.5011.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.34.5929.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.55.7816.01 2 0.000 0.983 0.00 1.00 0.00 0
#> TCGA.50.6593.11 2 0.121 0.949 0.00 0.96 0.04 0
#> TCGA.22.4613.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.38.4631.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.33.4579.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.86.A4P8.01 2 0.000 0.983 0.00 1.00 0.00 0
#> TCGA.44.2655.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.75.6203.01 2 0.121 0.949 0.00 0.96 0.04 0
#> TCGA.50.6594.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.49.4488.11 2 0.000 0.983 0.00 1.00 0.00 0
#> TCGA.39.5035.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.44.6145.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.50.5935.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.99.AA5R.01 2 0.000 0.983 0.00 1.00 0.00 0
#> TCGA.73.4658.11 2 0.000 0.983 0.00 1.00 0.00 0
#> TCGA.50.6592.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.39.5034.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.98.A53H.01 4 0.000 1.000 0.00 0.00 0.00 1
#> TCGA.22.4599.11 3 0.121 0.951 0.04 0.00 0.96 0
#> TCGA.39.5031.11 3 0.121 0.951 0.04 0.00 0.96 0
#> TCGA.22.5480.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.50.5931.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.22.4601.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.33.4589.11 1 0.000 1.000 1.00 0.00 0.00 0
#> TCGA.44.6147.11 3 0.000 0.993 0.00 0.00 1.00 0
#> TCGA.55.8513.01 2 0.000 0.983 0.00 1.00 0.00 0
#> TCGA.50.6591.11 1 0.000 1.000 1.00 0.00 0.00 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.44.2659.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.5645.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2665.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5030.11 3 0.1043 0.912 0.00 0.00 0.96 0.00 0.04
#> TCGA.22.5492.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5485.11 3 0.0609 0.927 0.00 0.00 0.98 0.00 0.02
#> TCGA.98.A53C.01 4 0.1043 0.979 0.00 0.00 0.00 0.96 0.04
#> TCGA.39.5011.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.34.5929.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7816.01 2 0.2020 0.905 0.00 0.90 0.00 0.00 0.10
#> TCGA.50.6593.11 3 0.2516 0.860 0.00 0.14 0.86 0.00 0.00
#> TCGA.22.4613.11 5 0.2732 0.765 0.16 0.00 0.00 0.00 0.84
#> TCGA.38.4631.11 3 0.2020 0.895 0.00 0.10 0.90 0.00 0.00
#> TCGA.33.4579.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4P8.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.2655.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6203.01 3 0.2516 0.860 0.00 0.14 0.86 0.00 0.00
#> TCGA.50.6594.11 3 0.2020 0.895 0.00 0.10 0.90 0.00 0.00
#> TCGA.49.4488.11 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.39.5035.11 3 0.1043 0.924 0.00 0.04 0.96 0.00 0.00
#> TCGA.44.6145.11 3 0.0609 0.927 0.00 0.00 0.98 0.00 0.02
#> TCGA.50.5935.11 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.99.AA5R.01 2 0.2020 0.905 0.00 0.90 0.00 0.00 0.10
#> TCGA.73.4658.11 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6592.11 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.39.5034.11 3 0.0609 0.927 0.00 0.00 0.98 0.00 0.02
#> TCGA.98.A53H.01 4 0.0000 0.979 0.00 0.00 0.00 1.00 0.00
#> TCGA.22.4599.11 5 0.2516 0.909 0.00 0.00 0.14 0.00 0.86
#> TCGA.39.5031.11 5 0.2516 0.909 0.00 0.00 0.14 0.00 0.86
#> TCGA.22.5480.11 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5931.11 5 0.2516 0.909 0.00 0.00 0.14 0.00 0.86
#> TCGA.22.4601.11 5 0.2516 0.909 0.00 0.00 0.14 0.00 0.86
#> TCGA.33.4589.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.6147.11 5 0.2516 0.909 0.00 0.00 0.14 0.00 0.86
#> TCGA.55.8513.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.6591.11 5 0.2929 0.743 0.18 0.00 0.00 0.00 0.82
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.44.2659.11 1 0.3647 0.690 0.64 0.00 0.36 0 0.00 0.00
#> TCGA.44.5645.11 1 0.3647 0.690 0.64 0.00 0.36 0 0.00 0.00
#> TCGA.44.2665.11 1 0.3647 0.690 0.64 0.00 0.36 0 0.00 0.00
#> TCGA.39.5030.11 3 0.4328 0.976 0.00 0.00 0.52 0 0.02 0.46
#> TCGA.22.5492.11 1 0.0000 0.859 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.22.5485.11 3 0.4328 0.976 0.00 0.00 0.52 0 0.02 0.46
#> TCGA.98.A53C.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.39.5011.11 1 0.0000 0.859 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.34.5929.11 1 0.0000 0.859 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.55.7816.01 2 0.0937 0.963 0.00 0.96 0.04 0 0.00 0.00
#> TCGA.50.6593.11 6 0.0937 0.919 0.00 0.04 0.00 0 0.00 0.96
#> TCGA.22.4613.11 5 0.0000 0.913 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.38.4631.11 6 0.0000 0.943 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.33.4579.11 1 0.0000 0.859 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.86.A4P8.01 2 0.0000 0.981 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.44.2655.11 1 0.0000 0.859 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.75.6203.01 6 0.1267 0.890 0.00 0.06 0.00 0 0.00 0.94
#> TCGA.50.6594.11 6 0.0000 0.943 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.49.4488.11 2 0.0000 0.981 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.39.5035.11 3 0.3864 0.968 0.00 0.00 0.52 0 0.00 0.48
#> TCGA.44.6145.11 3 0.3851 0.963 0.00 0.00 0.54 0 0.00 0.46
#> TCGA.50.5935.11 6 0.0547 0.940 0.00 0.00 0.02 0 0.00 0.98
#> TCGA.99.AA5R.01 2 0.1267 0.951 0.00 0.94 0.06 0 0.00 0.00
#> TCGA.73.4658.11 2 0.0000 0.981 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.50.6592.11 6 0.0547 0.940 0.00 0.00 0.02 0 0.00 0.98
#> TCGA.39.5034.11 3 0.4328 0.976 0.00 0.00 0.52 0 0.02 0.46
#> TCGA.98.A53H.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.22.4599.11 5 0.0000 0.913 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.39.5031.11 5 0.0000 0.913 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.22.5480.11 3 0.3864 0.968 0.00 0.00 0.52 0 0.00 0.48
#> TCGA.50.5931.11 5 0.1267 0.891 0.00 0.00 0.06 0 0.94 0.00
#> TCGA.22.4601.11 5 0.0000 0.913 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.33.4589.11 1 0.0000 0.859 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.44.6147.11 5 0.0937 0.901 0.00 0.00 0.04 0 0.96 0.00
#> TCGA.55.8513.01 2 0.0000 0.981 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.50.6591.11 5 0.4246 0.482 0.02 0.00 0.40 0 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.44.2659.11 7 0.3358 0.772 0.36 0.00 0.00 0 0.00 0.00 0.64
#> TCGA.44.5645.11 7 0.3358 0.772 0.36 0.00 0.00 0 0.00 0.00 0.64
#> TCGA.44.2665.11 7 0.3358 0.772 0.36 0.00 0.00 0 0.00 0.00 0.64
#> TCGA.39.5030.11 3 0.1718 0.912 0.00 0.00 0.92 0 0.04 0.04 0.00
#> TCGA.22.5492.11 1 0.0000 0.985 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.22.5485.11 3 0.1433 0.949 0.00 0.00 0.92 0 0.00 0.08 0.00
#> TCGA.98.A53C.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.39.5011.11 1 0.0000 0.985 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.34.5929.11 1 0.0000 0.985 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.55.7816.01 2 0.0000 0.918 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.50.6593.11 6 0.1363 0.868 0.00 0.00 0.02 0 0.00 0.94 0.04
#> TCGA.22.4613.11 5 0.1363 0.909 0.00 0.00 0.02 0 0.94 0.00 0.04
#> TCGA.38.4631.11 6 0.1928 0.902 0.00 0.00 0.08 0 0.00 0.90 0.02
#> TCGA.33.4579.11 1 0.0000 0.985 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.86.A4P8.01 2 0.1166 0.941 0.00 0.94 0.00 0 0.00 0.06 0.00
#> TCGA.44.2655.11 1 0.0000 0.985 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.75.6203.01 6 0.2569 0.814 0.00 0.00 0.02 0 0.00 0.84 0.14
#> TCGA.50.6594.11 6 0.1433 0.901 0.00 0.00 0.08 0 0.00 0.92 0.00
#> TCGA.49.4488.11 2 0.1166 0.941 0.00 0.94 0.00 0 0.00 0.06 0.00
#> TCGA.39.5035.11 3 0.2376 0.951 0.00 0.00 0.86 0 0.00 0.12 0.02
#> TCGA.44.6145.11 3 0.1886 0.947 0.00 0.00 0.88 0 0.00 0.12 0.00
#> TCGA.50.5935.11 6 0.2569 0.866 0.00 0.00 0.14 0 0.02 0.84 0.00
#> TCGA.99.AA5R.01 2 0.1671 0.860 0.00 0.90 0.00 0 0.00 0.00 0.10
#> TCGA.73.4658.11 2 0.1166 0.941 0.00 0.94 0.00 0 0.00 0.06 0.00
#> TCGA.50.6592.11 6 0.3061 0.874 0.00 0.00 0.08 0 0.02 0.84 0.06
#> TCGA.39.5034.11 3 0.2163 0.957 0.00 0.00 0.88 0 0.00 0.10 0.02
#> TCGA.98.A53H.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.22.4599.11 5 0.1006 0.927 0.00 0.00 0.02 0 0.96 0.00 0.02
#> TCGA.39.5031.11 5 0.0504 0.930 0.00 0.00 0.02 0 0.98 0.00 0.00
#> TCGA.22.5480.11 3 0.2376 0.951 0.00 0.00 0.86 0 0.00 0.12 0.02
#> TCGA.50.5931.11 5 0.2769 0.879 0.00 0.00 0.08 0 0.86 0.02 0.04
#> TCGA.22.4601.11 5 0.1363 0.927 0.00 0.00 0.04 0 0.94 0.00 0.02
#> TCGA.33.4589.11 1 0.1505 0.921 0.94 0.00 0.02 0 0.02 0.00 0.02
#> TCGA.44.6147.11 5 0.3000 0.887 0.00 0.00 0.10 0 0.84 0.02 0.04
#> TCGA.55.8513.01 2 0.2829 0.879 0.00 0.84 0.00 0 0.00 0.08 0.08
#> TCGA.50.6591.11 7 0.3139 0.305 0.00 0.00 0.00 0 0.30 0.00 0.70
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.44.2659.11 7 0.4134 0.768 0.30 0.00 0.00 0 0.08 0.00 0.62 0.00
#> TCGA.44.5645.11 7 0.2938 0.755 0.30 0.00 0.00 0 0.00 0.00 0.70 0.00
#> TCGA.44.2665.11 7 0.4134 0.768 0.30 0.00 0.00 0 0.08 0.00 0.62 0.00
#> TCGA.39.5030.11 3 0.1563 0.910 0.00 0.00 0.90 0 0.10 0.00 0.00 0.00
#> TCGA.22.5492.11 1 0.0000 0.913 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.22.5485.11 3 0.1563 0.910 0.00 0.00 0.90 0 0.10 0.00 0.00 0.00
#> TCGA.98.A53C.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.39.5011.11 1 0.0471 0.906 0.98 0.00 0.00 0 0.00 0.02 0.00 0.00
#> TCGA.34.5929.11 1 0.0000 0.913 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.55.7816.01 2 0.0941 0.900 0.00 0.96 0.00 0 0.02 0.02 0.00 0.00
#> TCGA.50.6593.11 6 0.5560 0.745 0.00 0.04 0.10 0 0.06 0.60 0.20 0.00
#> TCGA.22.4613.11 8 0.2864 0.764 0.00 0.00 0.00 0 0.08 0.02 0.06 0.84
#> TCGA.38.4631.11 6 0.1563 0.829 0.00 0.00 0.10 0 0.00 0.90 0.00 0.00
#> TCGA.33.4579.11 1 0.0000 0.913 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.86.A4P8.01 2 0.0000 0.915 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.44.2655.11 1 0.2132 0.805 0.88 0.00 0.00 0 0.08 0.00 0.04 0.00
#> TCGA.75.6203.01 6 0.5448 0.679 0.00 0.04 0.06 0 0.10 0.62 0.18 0.00
#> TCGA.50.6594.11 6 0.3444 0.817 0.00 0.00 0.14 0 0.06 0.78 0.02 0.00
#> TCGA.49.4488.11 2 0.0000 0.915 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.39.5035.11 3 0.0941 0.925 0.00 0.00 0.96 0 0.02 0.00 0.02 0.00
#> TCGA.44.6145.11 3 0.1091 0.916 0.00 0.00 0.94 0 0.06 0.00 0.00 0.00
#> TCGA.50.5935.11 6 0.3434 0.807 0.00 0.00 0.14 0 0.10 0.76 0.00 0.00
#> TCGA.99.AA5R.01 2 0.3637 0.701 0.00 0.70 0.00 0 0.26 0.02 0.02 0.00
#> TCGA.73.4658.11 2 0.0000 0.915 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.50.6592.11 6 0.2623 0.817 0.00 0.00 0.10 0 0.06 0.84 0.00 0.00
#> TCGA.39.5034.11 3 0.0000 0.932 0.00 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.98.A53H.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.22.4599.11 8 0.0941 0.832 0.00 0.00 0.00 0 0.02 0.00 0.02 0.96
#> TCGA.39.5031.11 8 0.0000 0.835 0.00 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.22.5480.11 3 0.0941 0.925 0.00 0.00 0.96 0 0.02 0.00 0.02 0.00
#> TCGA.50.5931.11 8 0.2852 0.749 0.00 0.00 0.00 0 0.28 0.00 0.00 0.72
#> TCGA.22.4601.11 8 0.1341 0.811 0.00 0.00 0.00 0 0.08 0.00 0.00 0.92
#> TCGA.33.4589.11 1 0.3687 0.715 0.78 0.00 0.00 0 0.08 0.08 0.06 0.00
#> TCGA.44.6147.11 8 0.2852 0.749 0.00 0.00 0.00 0 0.28 0.00 0.00 0.72
#> TCGA.55.8513.01 2 0.2132 0.841 0.00 0.88 0.00 0 0.08 0.00 0.04 0.00
#> TCGA.50.6591.11 7 0.4174 0.420 0.02 0.00 0.00 0 0.04 0.02 0.70 0.22
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node05. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-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 53 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 0.795 0.905 0.950 0.3785 0.570 0.570
#> 3 3 1.000 0.951 0.982 0.4781 0.777 0.640
#> 4 4 0.705 0.698 0.819 0.1695 0.921 0.828
#> 5 5 1.000 0.993 0.997 0.1705 0.816 0.548
#> 6 6 1.000 0.959 0.980 0.0453 0.945 0.774
#> 7 7 0.850 0.673 0.808 0.0377 0.914 0.621
#> 8 8 0.876 0.817 0.909 0.0276 0.945 0.698
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] 3 5
There is also optional best \(k\) = 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.43.3920.11 2 0.00 0.813 0.00 1.00
#> TCGA.22.5473.11 1 0.00 1.000 1.00 0.00
#> TCGA.22.5482.11 1 0.00 1.000 1.00 0.00
#> TCGA.22.5489.11 1 0.00 1.000 1.00 0.00
#> TCGA.44.2662.11 1 0.00 1.000 1.00 0.00
#> TCGA.50.5930.11 2 0.00 0.813 0.00 1.00
#> TCGA.22.5474.11 2 0.00 0.813 0.00 1.00
#> TCGA.33.4583.11 1 0.00 1.000 1.00 0.00
#> TCGA.22.5491.11 1 0.00 1.000 1.00 0.00
#> TCGA.44.6146.11 1 0.00 1.000 1.00 0.00
#> TCGA.43.6771.11 2 0.99 0.476 0.44 0.56
#> TCGA.39.5021.11 1 0.00 1.000 1.00 0.00
#> TCGA.39.5019.11 2 0.99 0.476 0.44 0.56
#> TCGA.56.8623.01 2 0.99 0.476 0.44 0.56
#> TCGA.44.2656.11 1 0.00 1.000 1.00 0.00
#> TCGA.44.6778.11 1 0.00 1.000 1.00 0.00
#> TCGA.33.4586.11 1 0.00 1.000 1.00 0.00
#> TCGA.39.5039.11 1 0.00 1.000 1.00 0.00
#> TCGA.38.4632.11 2 0.99 0.476 0.44 0.56
#> TCGA.33.4582.11 1 0.00 1.000 1.00 0.00
#> TCGA.50.5939.11 1 0.00 1.000 1.00 0.00
#> TCGA.18.4721.11 1 0.00 1.000 1.00 0.00
#> TCGA.22.5477.11 1 0.00 1.000 1.00 0.00
#> TCGA.18.5595.11 2 0.00 0.813 0.00 1.00
#> TCGA.22.5478.11 1 0.00 1.000 1.00 0.00
#> TCGA.49.6745.11 1 0.00 1.000 1.00 0.00
#> TCGA.49.AARR.01 2 0.99 0.476 0.44 0.56
#> TCGA.18.5592.11 1 0.00 1.000 1.00 0.00
#> TCGA.85.A4PA.01 2 0.00 0.813 0.00 1.00
#> TCGA.73.4676.11 1 0.00 1.000 1.00 0.00
#> TCGA.60.2697.01 2 0.00 0.813 0.00 1.00
#> TCGA.43.5668.11 1 0.00 1.000 1.00 0.00
#> TCGA.L4.A4E6.01 2 0.00 0.813 0.00 1.00
#> TCGA.43.3394.11 1 0.00 1.000 1.00 0.00
#> TCGA.39.5016.11 1 0.00 1.000 1.00 0.00
#> TCGA.90.6837.01 1 0.00 1.000 1.00 0.00
#> TCGA.44.6148.11 1 0.00 1.000 1.00 0.00
#> TCGA.50.5933.11 1 0.00 1.000 1.00 0.00
#> TCGA.98.A53D.01 2 0.00 0.813 0.00 1.00
#> TCGA.44.2668.11 2 0.00 0.813 0.00 1.00
#> TCGA.39.5036.11 1 0.00 1.000 1.00 0.00
#> TCGA.50.5936.11 1 0.00 1.000 1.00 0.00
#> TCGA.22.5471.11 1 0.00 1.000 1.00 0.00
#> TCGA.50.5932.11 1 0.00 1.000 1.00 0.00
#> TCGA.77.A5FZ.01 2 0.00 0.813 0.00 1.00
#> TCGA.18.3417.11 1 0.00 1.000 1.00 0.00
#> TCGA.44.6144.11 1 0.00 1.000 1.00 0.00
#> TCGA.39.5029.11 1 0.00 1.000 1.00 0.00
#> TCGA.22.5472.11 1 0.00 1.000 1.00 0.00
#> TCGA.44.5643.11 1 0.00 1.000 1.00 0.00
#> TCGA.05.5420.11 1 0.00 1.000 1.00 0.00
#> TCGA.33.4566.11 1 0.00 1.000 1.00 0.00
#> TCGA.39.5037.11 2 0.99 0.476 0.44 0.56
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.43.3920.11 3 0.583 0.463 0.00 0.34 0.66
#> TCGA.22.5473.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.22.5482.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.22.5489.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.44.2662.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.50.5930.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.22.5474.11 2 0.540 0.552 0.00 0.72 0.28
#> TCGA.33.4583.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.22.5491.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.44.6146.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.43.6771.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.39.5021.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.39.5019.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.56.8623.01 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.44.2656.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.44.6778.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.33.4586.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.39.5039.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.38.4632.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.33.4582.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.50.5939.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.18.4721.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.22.5477.11 1 0.583 0.475 0.66 0.34 0.00
#> TCGA.18.5595.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.22.5478.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.49.6745.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.49.AARR.01 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.18.5592.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.85.A4PA.01 3 0.000 0.910 0.00 0.00 1.00
#> TCGA.73.4676.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.60.2697.01 3 0.000 0.910 0.00 0.00 1.00
#> TCGA.43.5668.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.L4.A4E6.01 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.43.3394.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.39.5016.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.90.6837.01 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.44.6148.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.50.5933.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.98.A53D.01 3 0.000 0.910 0.00 0.00 1.00
#> TCGA.44.2668.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.39.5036.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.50.5936.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.22.5471.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.50.5932.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.77.A5FZ.01 3 0.000 0.910 0.00 0.00 1.00
#> TCGA.18.3417.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.44.6144.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.39.5029.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.22.5472.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.44.5643.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.05.5420.11 1 0.000 0.987 1.00 0.00 0.00
#> TCGA.33.4566.11 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.39.5037.11 2 0.000 0.980 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.43.3920.11 4 0.000 0.8903 0.00 0.00 0.00 1.00
#> TCGA.22.5473.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.22.5482.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.22.5489.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.44.2662.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.50.5930.11 4 0.000 0.8903 0.00 0.00 0.00 1.00
#> TCGA.22.5474.11 4 0.000 0.8903 0.00 0.00 0.00 1.00
#> TCGA.33.4583.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.22.5491.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.44.6146.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.43.6771.11 2 0.495 0.5490 0.00 0.56 0.00 0.44
#> TCGA.39.5021.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.39.5019.11 2 0.495 0.5490 0.00 0.56 0.00 0.44
#> TCGA.56.8623.01 2 0.495 0.5490 0.00 0.56 0.00 0.44
#> TCGA.44.2656.11 2 0.495 0.5964 0.00 0.56 0.44 0.00
#> TCGA.44.6778.11 2 0.495 0.5964 0.00 0.56 0.44 0.00
#> TCGA.33.4586.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.39.5039.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.38.4632.11 2 0.495 0.5490 0.00 0.56 0.00 0.44
#> TCGA.33.4582.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.50.5939.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.18.4721.11 1 0.479 0.6772 0.62 0.00 0.38 0.00
#> TCGA.22.5477.11 2 0.495 0.5964 0.00 0.56 0.44 0.00
#> TCGA.18.5595.11 4 0.000 0.8903 0.00 0.00 0.00 1.00
#> TCGA.22.5478.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.49.6745.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.49.AARR.01 2 0.495 0.5490 0.00 0.56 0.00 0.44
#> TCGA.18.5592.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.85.A4PA.01 3 0.495 1.0000 0.00 0.44 0.56 0.00
#> TCGA.73.4676.11 2 0.495 0.5964 0.00 0.56 0.44 0.00
#> TCGA.60.2697.01 3 0.495 1.0000 0.00 0.44 0.56 0.00
#> TCGA.43.5668.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.L4.A4E6.01 4 0.000 0.8903 0.00 0.00 0.00 1.00
#> TCGA.43.3394.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.39.5016.11 2 0.591 0.5581 0.00 0.56 0.04 0.40
#> TCGA.90.6837.01 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.44.6148.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.50.5933.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.98.A53D.01 4 0.485 0.0865 0.00 0.40 0.00 0.60
#> TCGA.44.2668.11 2 0.500 0.4412 0.00 0.50 0.00 0.50
#> TCGA.39.5036.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.50.5936.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.22.5471.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.50.5932.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.77.A5FZ.01 3 0.495 1.0000 0.00 0.44 0.56 0.00
#> TCGA.18.3417.11 2 0.495 0.5964 0.00 0.56 0.44 0.00
#> TCGA.44.6144.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.39.5029.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.22.5472.11 1 0.000 0.7639 1.00 0.00 0.00 0.00
#> TCGA.44.5643.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.05.5420.11 1 0.495 0.6589 0.56 0.00 0.44 0.00
#> TCGA.33.4566.11 2 0.495 0.5964 0.00 0.56 0.44 0.00
#> TCGA.39.5037.11 2 0.495 0.5490 0.00 0.56 0.00 0.44
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.43.3920.11 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.22.5473.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.22.5482.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.22.5489.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.44.2662.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.50.5930.11 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.22.5474.11 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.33.4583.11 5 0.141 0.915 0.06 0.00 0 0.00 0.94
#> TCGA.22.5491.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.44.6146.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.43.6771.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.39.5021.11 1 0.104 0.949 0.96 0.00 0 0.00 0.04
#> TCGA.39.5019.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.56.8623.01 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.44.2656.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.44.6778.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.33.4586.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.39.5039.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.38.4632.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.33.4582.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.50.5939.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.18.4721.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.22.5477.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.18.5595.11 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.22.5478.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.49.6745.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.49.AARR.01 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.18.5592.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.85.A4PA.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.73.4676.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.60.2697.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.43.5668.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.L4.A4E6.01 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.43.3394.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.39.5016.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.90.6837.01 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.44.6148.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.50.5933.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.98.A53D.01 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.44.2668.11 2 0.104 0.955 0.00 0.96 0 0.04 0.00
#> TCGA.39.5036.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.50.5936.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.22.5471.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.50.5932.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.77.A5FZ.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.18.3417.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.44.6144.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.39.5029.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.22.5472.11 5 0.000 0.994 0.00 0.00 0 0.00 1.00
#> TCGA.44.5643.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.05.5420.11 1 0.000 0.997 1.00 0.00 0 0.00 0.00
#> TCGA.33.4566.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
#> TCGA.39.5037.11 2 0.000 0.996 0.00 1.00 0 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.43.3920.11 4 0.0000 0.990 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.22.5473.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.22.5482.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.22.5489.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.44.2662.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.50.5930.11 2 0.0937 0.938 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.22.5474.11 4 0.0000 0.990 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.33.4583.11 5 0.3076 0.632 0.24 0.00 0 0.00 0.76 0.00
#> TCGA.22.5491.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.44.6146.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.43.6771.11 2 0.0000 0.971 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.39.5021.11 1 0.0937 0.955 0.96 0.00 0 0.00 0.04 0.00
#> TCGA.39.5019.11 2 0.0547 0.977 0.00 0.98 0 0.00 0.00 0.02
#> TCGA.56.8623.01 2 0.0937 0.968 0.00 0.96 0 0.00 0.00 0.04
#> TCGA.44.2656.11 6 0.0547 0.929 0.00 0.02 0 0.00 0.00 0.98
#> TCGA.44.6778.11 6 0.0547 0.929 0.00 0.02 0 0.00 0.00 0.98
#> TCGA.33.4586.11 1 0.0547 0.977 0.98 0.00 0 0.00 0.02 0.00
#> TCGA.39.5039.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.38.4632.11 2 0.0547 0.977 0.00 0.98 0 0.00 0.00 0.02
#> TCGA.33.4582.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.50.5939.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.18.4721.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.22.5477.11 6 0.0937 0.891 0.04 0.00 0 0.00 0.00 0.96
#> TCGA.18.5595.11 4 0.0547 0.985 0.00 0.02 0 0.98 0.00 0.00
#> TCGA.22.5478.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.49.6745.11 5 0.0547 0.950 0.02 0.00 0 0.00 0.98 0.00
#> TCGA.49.AARR.01 2 0.0547 0.977 0.00 0.98 0 0.00 0.00 0.02
#> TCGA.18.5592.11 5 0.0547 0.958 0.00 0.00 0 0.00 0.98 0.02
#> TCGA.85.A4PA.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.73.4676.11 6 0.0547 0.915 0.02 0.00 0 0.00 0.00 0.98
#> TCGA.60.2697.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.43.5668.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.L4.A4E6.01 4 0.0547 0.985 0.00 0.02 0 0.98 0.00 0.00
#> TCGA.43.3394.11 5 0.0547 0.958 0.00 0.00 0 0.00 0.98 0.02
#> TCGA.39.5016.11 6 0.3309 0.618 0.00 0.28 0 0.00 0.00 0.72
#> TCGA.90.6837.01 5 0.0547 0.958 0.00 0.00 0 0.00 0.98 0.02
#> TCGA.44.6148.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.50.5933.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.98.A53D.01 4 0.0000 0.990 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.44.2668.11 2 0.0000 0.971 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.39.5036.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.50.5936.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.22.5471.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.50.5932.11 1 0.0547 0.977 0.98 0.00 0 0.00 0.02 0.00
#> TCGA.77.A5FZ.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.18.3417.11 6 0.0547 0.929 0.00 0.02 0 0.00 0.00 0.98
#> TCGA.44.6144.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.39.5029.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.22.5472.11 5 0.0000 0.968 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.44.5643.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.05.5420.11 1 0.0000 0.994 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.33.4566.11 6 0.0547 0.929 0.00 0.02 0 0.00 0.00 0.98
#> TCGA.39.5037.11 2 0.0937 0.968 0.00 0.96 0 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.43.3920.11 4 0.3459 0.7931 0.00 0.00 0 0.60 0.00 0.0 0.40
#> TCGA.22.5473.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.22.5482.11 5 0.0863 0.4038 0.00 0.00 0 0.00 0.96 0.0 0.04
#> TCGA.22.5489.11 5 0.3358 -0.4666 0.00 0.00 0 0.00 0.64 0.0 0.36
#> TCGA.44.2662.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.50.5930.11 2 0.3558 0.3572 0.00 0.52 0 0.48 0.00 0.0 0.00
#> TCGA.22.5474.11 4 0.3413 0.7956 0.00 0.00 0 0.62 0.00 0.0 0.38
#> TCGA.33.4583.11 5 0.2912 0.3821 0.14 0.00 0 0.00 0.82 0.0 0.04
#> TCGA.22.5491.11 5 0.1886 0.2452 0.00 0.00 0 0.00 0.88 0.0 0.12
#> TCGA.44.6146.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.43.6771.11 2 0.0000 0.8410 0.00 1.00 0 0.00 0.00 0.0 0.00
#> TCGA.39.5021.11 5 0.4214 0.1907 0.40 0.00 0 0.00 0.56 0.0 0.04
#> TCGA.39.5019.11 2 0.0000 0.8410 0.00 1.00 0 0.00 0.00 0.0 0.00
#> TCGA.56.8623.01 2 0.0000 0.8410 0.00 1.00 0 0.00 0.00 0.0 0.00
#> TCGA.44.2656.11 6 0.0000 1.0000 0.00 0.00 0 0.00 0.00 1.0 0.00
#> TCGA.44.6778.11 6 0.0000 1.0000 0.00 0.00 0 0.00 0.00 1.0 0.00
#> TCGA.33.4586.11 5 0.4244 0.1349 0.42 0.00 0 0.00 0.54 0.0 0.04
#> TCGA.39.5039.11 1 0.2016 0.8985 0.90 0.00 0 0.00 0.06 0.0 0.04
#> TCGA.38.4632.11 2 0.0000 0.8410 0.00 1.00 0 0.00 0.00 0.0 0.00
#> TCGA.33.4582.11 5 0.3294 -0.4070 0.00 0.00 0 0.00 0.66 0.0 0.34
#> TCGA.50.5939.11 5 0.0863 0.3765 0.00 0.00 0 0.00 0.96 0.0 0.04
#> TCGA.18.4721.11 1 0.2163 0.8673 0.88 0.00 0 0.00 0.10 0.0 0.02
#> TCGA.22.5477.11 6 0.0000 1.0000 0.00 0.00 0 0.00 0.00 1.0 0.00
#> TCGA.18.5595.11 4 0.0000 0.6966 0.00 0.00 0 1.00 0.00 0.0 0.00
#> TCGA.22.5478.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.49.6745.11 5 0.0863 0.3738 0.00 0.00 0 0.00 0.96 0.0 0.04
#> TCGA.49.AARR.01 2 0.0000 0.8410 0.00 1.00 0 0.00 0.00 0.0 0.00
#> TCGA.18.5592.11 7 0.3525 0.9797 0.00 0.00 0 0.00 0.44 0.0 0.56
#> TCGA.85.A4PA.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.0 0.00
#> TCGA.73.4676.11 6 0.0000 1.0000 0.00 0.00 0 0.00 0.00 1.0 0.00
#> TCGA.60.2697.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.0 0.00
#> TCGA.43.5668.11 1 0.0504 0.9658 0.98 0.00 0 0.00 0.00 0.0 0.02
#> TCGA.L4.A4E6.01 4 0.0000 0.6966 0.00 0.00 0 1.00 0.00 0.0 0.00
#> TCGA.43.3394.11 7 0.3546 0.9587 0.00 0.00 0 0.00 0.46 0.0 0.54
#> TCGA.39.5016.11 2 0.3139 0.5004 0.00 0.70 0 0.00 0.00 0.3 0.00
#> TCGA.90.6837.01 7 0.3525 0.9797 0.00 0.00 0 0.00 0.44 0.0 0.56
#> TCGA.44.6148.11 5 0.3294 -0.4070 0.00 0.00 0 0.00 0.66 0.0 0.34
#> TCGA.50.5933.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.98.A53D.01 4 0.3459 0.7931 0.00 0.00 0 0.60 0.00 0.0 0.40
#> TCGA.44.2668.11 2 0.3459 0.4970 0.00 0.60 0 0.40 0.00 0.0 0.00
#> TCGA.39.5036.11 1 0.0504 0.9652 0.98 0.00 0 0.00 0.00 0.0 0.02
#> TCGA.50.5936.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.22.5471.11 5 0.3358 -0.4666 0.00 0.00 0 0.00 0.64 0.0 0.36
#> TCGA.50.5932.11 5 0.4283 -0.0533 0.48 0.00 0 0.00 0.48 0.0 0.04
#> TCGA.77.A5FZ.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.0 0.00
#> TCGA.18.3417.11 6 0.0000 1.0000 0.00 0.00 0 0.00 0.00 1.0 0.00
#> TCGA.44.6144.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.39.5029.11 5 0.0504 0.3907 0.00 0.00 0 0.00 0.98 0.0 0.02
#> TCGA.22.5472.11 5 0.0863 0.3943 0.00 0.00 0 0.00 0.96 0.0 0.04
#> TCGA.44.5643.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.05.5420.11 1 0.0000 0.9770 1.00 0.00 0 0.00 0.00 0.0 0.00
#> TCGA.33.4566.11 6 0.0000 1.0000 0.00 0.00 0 0.00 0.00 1.0 0.00
#> TCGA.39.5037.11 2 0.0000 0.8410 0.00 1.00 0 0.00 0.00 0.0 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.43.3920.11 4 0.0000 0.9463 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5473.11 1 0.0471 0.9128 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.22.5482.11 5 0.0000 0.6943 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5489.11 7 0.2852 0.7686 0.00 0.00 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.44.2662.11 1 0.0000 0.9161 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5930.11 8 0.0471 0.9363 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.22.5474.11 4 0.1563 0.8860 0.00 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.33.4583.11 5 0.0000 0.6943 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5491.11 5 0.3272 -0.0443 0.00 0.00 0.00 0.00 0.58 0.00 0.42 0.00
#> TCGA.44.6146.11 1 0.0000 0.9161 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.6771.11 2 0.0941 0.9514 0.00 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.39.5021.11 5 0.1091 0.6723 0.06 0.00 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.39.5019.11 2 0.0471 0.9630 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.56.8623.01 2 0.0000 0.9646 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.2656.11 6 0.0000 0.9787 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.6778.11 6 0.0471 0.9765 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.33.4586.11 5 0.2114 0.6063 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.39.5039.11 1 0.3714 0.3298 0.54 0.00 0.00 0.00 0.44 0.00 0.00 0.02
#> TCGA.38.4632.11 2 0.0000 0.9646 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.4582.11 7 0.3142 0.6816 0.00 0.00 0.00 0.00 0.36 0.00 0.64 0.00
#> TCGA.50.5939.11 5 0.2650 0.5237 0.00 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.18.4721.11 1 0.2534 0.7452 0.78 0.00 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.22.5477.11 6 0.0471 0.9692 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.18.5595.11 8 0.0808 0.9328 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.22.5478.11 1 0.0471 0.9128 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.49.6745.11 5 0.2938 0.4011 0.00 0.00 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.49.AARR.01 2 0.0471 0.9630 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.18.5592.11 7 0.1091 0.7499 0.00 0.00 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.85.A4PA.01 3 0.0000 0.9928 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.11 6 0.0471 0.9765 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.60.2697.01 3 0.0471 0.9855 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.43.5668.11 1 0.1563 0.8683 0.90 0.00 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.L4.A4E6.01 8 0.0808 0.9328 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.43.3394.11 7 0.1341 0.7587 0.00 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.39.5016.11 2 0.1765 0.8488 0.00 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.90.6837.01 7 0.1091 0.7499 0.00 0.00 0.00 0.00 0.06 0.00 0.94 0.00
#> TCGA.44.6148.11 7 0.3083 0.7167 0.00 0.00 0.00 0.00 0.34 0.00 0.66 0.00
#> TCGA.50.5933.11 1 0.0471 0.9085 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.98.A53D.01 4 0.0000 0.9463 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.2668.11 8 0.1804 0.8792 0.00 0.08 0.00 0.00 0.00 0.00 0.02 0.90
#> TCGA.39.5036.11 1 0.2025 0.8569 0.88 0.00 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.50.5936.11 1 0.0000 0.9161 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5471.11 7 0.2938 0.7588 0.00 0.00 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.50.5932.11 5 0.3015 0.3967 0.32 0.00 0.00 0.00 0.68 0.00 0.00 0.00
#> TCGA.77.A5FZ.01 3 0.0000 0.9928 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.18.3417.11 6 0.0471 0.9757 0.00 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.44.6144.11 1 0.0000 0.9161 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5029.11 5 0.2406 0.5747 0.00 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.22.5472.11 5 0.0808 0.6846 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.44.5643.11 1 0.0000 0.9161 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.11 1 0.0000 0.9161 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.4566.11 6 0.0471 0.9757 0.00 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.39.5037.11 2 0.0000 0.9646 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: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node041 , Node042 , Node043 , Node051 , Node052 , Node061 , Node062-leaf , Node071 , Node072 , Node073 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["06"]
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 131 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 0.968 0.987 0.4624 0.546 0.546
#> 3 3 0.717 0.787 0.887 0.2420 0.891 0.804
#> 4 4 0.716 0.812 0.880 0.2068 0.817 0.612
#> 5 5 0.723 0.771 0.869 0.0856 0.888 0.651
#> 6 6 0.724 0.740 0.854 0.0300 0.988 0.947
#> 7 7 0.787 0.682 0.831 0.0315 0.989 0.950
#> 8 8 0.759 0.615 0.796 0.0121 0.976 0.892
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.43.7656.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.A4ZK.01 2 0.000 0.981 0.00 1.00
#> TCGA.63.A5MW.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.8479.01 2 0.000 0.981 0.00 1.00
#> TCGA.63.A5M9.01 2 0.000 0.981 0.00 1.00
#> TCGA.37.A5EM.01 2 0.000 0.981 0.00 1.00
#> TCGA.98.A53I.01 2 0.000 0.981 0.00 1.00
#> TCGA.98.8020.01 1 0.000 1.000 1.00 0.00
#> TCGA.39.5031.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.8622.01 1 0.000 1.000 1.00 0.00
#> TCGA.22.5471.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.7950.01 1 0.000 1.000 1.00 0.00
#> TCGA.22.5480.01 2 0.000 0.981 0.00 1.00
#> TCGA.58.8388.01 2 0.999 0.106 0.48 0.52
#> TCGA.85.7699.01 2 0.000 0.981 0.00 1.00
#> TCGA.33.AAS8.01 2 0.000 0.981 0.00 1.00
#> TCGA.50.5931.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.A5G8.01 2 0.000 0.981 0.00 1.00
#> TCGA.43.5670.01 2 0.000 0.981 0.00 1.00
#> TCGA.NC.A5HI.01 1 0.000 1.000 1.00 0.00
#> TCGA.NK.A5D1.01 2 0.000 0.981 0.00 1.00
#> TCGA.21.5783.01 2 0.000 0.981 0.00 1.00
#> TCGA.94.7557.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.6798.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.7696.01 2 0.000 0.981 0.00 1.00
#> TCGA.90.A4ED.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.6843.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.8130.01 1 0.000 1.000 1.00 0.00
#> TCGA.34.5928.01 2 0.000 0.981 0.00 1.00
#> TCGA.22.A5C4.01 2 0.000 0.981 0.00 1.00
#> TCGA.94.8035.01 1 0.000 1.000 1.00 0.00
#> TCGA.94.A5I4.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.8145.01 1 0.000 1.000 1.00 0.00
#> TCGA.O2.A52W.01 2 0.827 0.654 0.26 0.74
#> TCGA.77.8140.01 1 0.000 1.000 1.00 0.00
#> TCGA.22.5478.01 1 0.000 1.000 1.00 0.00
#> TCGA.90.7964.01 2 0.327 0.923 0.06 0.94
#> TCGA.68.8250.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.8504.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.8072.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.7337.01 1 0.000 1.000 1.00 0.00
#> TCGA.63.A5MI.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.A4CL.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.7698.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.8139.01 1 0.000 1.000 1.00 0.00
#> TCGA.39.5019.01 2 0.000 0.981 0.00 1.00
#> TCGA.22.4599.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.8052.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.7142.01 2 0.000 0.981 0.00 1.00
#> TCGA.96.A4JK.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.8305.01 2 0.000 0.981 0.00 1.00
#> TCGA.98.8022.01 1 0.000 1.000 1.00 0.00
#> TCGA.21.5786.01 2 0.000 0.981 0.00 1.00
#> TCGA.21.5782.01 1 0.000 1.000 1.00 0.00
#> TCGA.39.5016.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.A4CN.01 2 0.000 0.981 0.00 1.00
#> TCGA.O2.A52N.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.8664.01 2 0.000 0.981 0.00 1.00
#> TCGA.NC.A5HO.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.8133.01 2 0.000 0.981 0.00 1.00
#> TCGA.98.A53B.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.5898.01 2 0.000 0.981 0.00 1.00
#> TCGA.34.8455.01 1 0.000 1.000 1.00 0.00
#> TCGA.43.A56V.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.A4QQ.01 2 0.000 0.981 0.00 1.00
#> TCGA.37.A5EL.01 2 0.000 0.981 0.00 1.00
#> TCGA.39.5036.01 2 0.000 0.981 0.00 1.00
#> TCGA.22.5479.01 2 0.000 0.981 0.00 1.00
#> TCGA.58.A46K.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.A4BY.01 2 0.000 0.981 0.00 1.00
#> TCGA.18.3417.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.A4BW.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.8308.01 2 0.000 0.981 0.00 1.00
#> TCGA.63.7020.01 1 0.000 1.000 1.00 0.00
#> TCGA.NC.A5HQ.01 2 0.000 0.981 0.00 1.00
#> TCGA.LA.A446.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.A5GF.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.8304.01 1 0.000 1.000 1.00 0.00
#> TCGA.NC.A5HR.01 2 0.000 0.981 0.00 1.00
#> TCGA.39.5029.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.8629.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.7465.01 1 0.000 1.000 1.00 0.00
#> TCGA.43.7657.01 2 0.000 0.981 0.00 1.00
#> TCGA.33.4579.01 1 0.000 1.000 1.00 0.00
#> TCGA.94.A4VJ.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.A5DR.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.7844.01 2 0.000 0.981 0.00 1.00
#> TCGA.98.8021.01 2 0.242 0.943 0.04 0.96
#> TCGA.22.5472.01 1 0.000 1.000 1.00 0.00
#> TCGA.34.5239.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.7463.01 1 0.000 1.000 1.00 0.00
#> TCGA.44.5643.01 2 0.000 0.981 0.00 1.00
#> TCGA.33.4586.01 2 0.000 0.981 0.00 1.00
#> TCGA.52.7810.01 1 0.000 1.000 1.00 0.00
#> TCGA.90.7767.01 2 0.000 0.981 0.00 1.00
#> TCGA.33.4582.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.8288.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.7843.01 2 0.971 0.354 0.40 0.60
#> TCGA.56.7221.01 1 0.000 1.000 1.00 0.00
#> TCGA.98.A538.01 1 0.000 1.000 1.00 0.00
#> TCGA.98.A53J.01 2 0.000 0.981 0.00 1.00
#> TCGA.85.8277.01 2 0.000 0.981 0.00 1.00
#> TCGA.39.5035.01 1 0.000 1.000 1.00 0.00
#> TCGA.58.A46M.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.7338.01 2 0.000 0.981 0.00 1.00
#> TCGA.51.6867.01 2 0.000 0.981 0.00 1.00
#> TCGA.63.A5MJ.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.7822.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.A62T.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.A49D.01 1 0.000 1.000 1.00 0.00
#> TCGA.22.5474.01 2 0.000 0.981 0.00 1.00
#> TCGA.68.A59J.01 2 0.000 0.981 0.00 1.00
#> TCGA.22.5492.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.7141.01 2 0.000 0.981 0.00 1.00
#> TCGA.90.7766.01 1 0.000 1.000 1.00 0.00
#> TCGA.NC.A5HD.01 2 0.000 0.981 0.00 1.00
#> TCGA.NC.A5HM.01 2 0.971 0.354 0.40 0.60
#> TCGA.46.6025.01 2 0.000 0.981 0.00 1.00
#> TCGA.52.7809.01 2 0.000 0.981 0.00 1.00
#> TCGA.43.8116.01 1 0.000 1.000 1.00 0.00
#> TCGA.85.8350.01 2 0.000 0.981 0.00 1.00
#> TCGA.LA.A7SW.01 1 0.000 1.000 1.00 0.00
#> TCGA.96.7544.01 1 0.000 1.000 1.00 0.00
#> TCGA.77.A5G7.01 1 0.000 1.000 1.00 0.00
#> TCGA.56.8307.01 1 0.000 1.000 1.00 0.00
#> TCGA.98.A539.01 1 0.000 1.000 1.00 0.00
#> TCGA.O2.A52S.01 2 0.000 0.981 0.00 1.00
#> TCGA.58.A46L.01 2 0.000 0.981 0.00 1.00
#> TCGA.77.8144.01 2 0.000 0.981 0.00 1.00
#> TCGA.J1.A4AH.01 2 0.000 0.981 0.00 1.00
#> TCGA.56.7580.01 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.43.7656.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.56.A4ZK.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.63.A5MW.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.85.8479.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.63.A5M9.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.37.A5EM.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.98.A53I.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.98.8020.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.39.5031.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.56.8622.01 1 0.4002 0.6815 0.84 0.00 0.16
#> TCGA.22.5471.01 2 0.4555 0.7898 0.00 0.80 0.20
#> TCGA.85.7950.01 3 0.6192 0.5800 0.42 0.00 0.58
#> TCGA.22.5480.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.58.8388.01 3 0.6109 0.4639 0.08 0.14 0.78
#> TCGA.85.7699.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.33.AAS8.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.50.5931.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.77.A5G8.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.43.5670.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.NC.A5HI.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.NK.A5D1.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.21.5783.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.94.7557.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.85.6798.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.85.7696.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.90.A4ED.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.77.6843.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.8130.01 3 0.5706 0.7243 0.32 0.00 0.68
#> TCGA.34.5928.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.22.A5C4.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.94.8035.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.94.A5I4.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.8145.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.O2.A52W.01 1 0.6956 0.3633 0.66 0.04 0.30
#> TCGA.77.8140.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.22.5478.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.90.7964.01 2 0.4002 0.7496 0.16 0.84 0.00
#> TCGA.68.8250.01 2 0.9899 0.1701 0.28 0.40 0.32
#> TCGA.56.8504.01 2 0.5216 0.7504 0.00 0.74 0.26
#> TCGA.85.8072.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.7337.01 3 0.5706 0.7243 0.32 0.00 0.68
#> TCGA.63.A5MI.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.85.A4CL.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.85.7698.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.8139.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.39.5019.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.22.4599.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.85.8052.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.7142.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.96.A4JK.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.56.8305.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.98.8022.01 1 0.5016 0.5286 0.76 0.00 0.24
#> TCGA.21.5786.01 2 0.4555 0.7896 0.00 0.80 0.20
#> TCGA.21.5782.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.39.5016.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.85.A4CN.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.O2.A52N.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.85.8664.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.NC.A5HO.01 2 0.3340 0.8352 0.00 0.88 0.12
#> TCGA.77.8133.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.98.A53B.01 1 0.2537 0.7982 0.92 0.00 0.08
#> TCGA.56.5898.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.34.8455.01 3 0.5706 0.7243 0.32 0.00 0.68
#> TCGA.43.A56V.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.85.A4QQ.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.37.A5EL.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.39.5036.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.22.5479.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.58.A46K.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.56.A4BY.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.18.3417.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.56.A4BW.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.56.8308.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.63.7020.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.NC.A5HQ.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.LA.A446.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.A5GF.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.56.8304.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.NC.A5HR.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.39.5029.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.56.8629.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.7465.01 3 0.0892 0.6044 0.02 0.00 0.98
#> TCGA.43.7657.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.33.4579.01 3 0.6045 0.6475 0.38 0.00 0.62
#> TCGA.94.A4VJ.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.56.A5DR.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.85.7844.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.98.8021.01 3 0.5216 0.3075 0.00 0.26 0.74
#> TCGA.22.5472.01 3 0.5706 0.7243 0.32 0.00 0.68
#> TCGA.34.5239.01 3 0.4796 0.7307 0.22 0.00 0.78
#> TCGA.77.7463.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.44.5643.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.33.4586.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.52.7810.01 1 0.6192 -0.2046 0.58 0.00 0.42
#> TCGA.90.7767.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.33.4582.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.85.8288.01 3 0.4796 0.7307 0.22 0.00 0.78
#> TCGA.85.7843.01 3 0.0000 0.5901 0.00 0.00 1.00
#> TCGA.56.7221.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.98.A538.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.98.A53J.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.85.8277.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.39.5035.01 3 0.5706 0.7243 0.32 0.00 0.68
#> TCGA.58.A46M.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.77.7338.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.51.6867.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.63.A5MJ.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.56.7822.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.56.A62T.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.56.A49D.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.22.5474.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.68.A59J.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.22.5492.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.77.7141.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.90.7766.01 1 0.3686 0.7150 0.86 0.00 0.14
#> TCGA.NC.A5HD.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.NC.A5HM.01 1 0.9899 -0.0411 0.40 0.28 0.32
#> TCGA.46.6025.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.52.7809.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.43.8116.01 3 0.6192 0.5881 0.42 0.00 0.58
#> TCGA.85.8350.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.LA.A7SW.01 1 0.3686 0.6954 0.86 0.00 0.14
#> TCGA.96.7544.01 3 0.5016 0.7351 0.24 0.00 0.76
#> TCGA.77.A5G7.01 3 0.5560 0.7320 0.30 0.00 0.70
#> TCGA.56.8307.01 1 0.6126 -0.0837 0.60 0.00 0.40
#> TCGA.98.A539.01 1 0.0000 0.8768 1.00 0.00 0.00
#> TCGA.O2.A52S.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.58.A46L.01 2 0.5706 0.7078 0.00 0.68 0.32
#> TCGA.77.8144.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.J1.A4AH.01 2 0.0000 0.8955 0.00 1.00 0.00
#> TCGA.56.7580.01 1 0.2537 0.7898 0.92 0.00 0.08
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.43.7656.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.56.A4ZK.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.63.A5MW.01 4 0.0707 0.843 0.00 0.02 0.00 0.98
#> TCGA.85.8479.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.63.A5M9.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.37.A5EM.01 2 0.1637 0.757 0.00 0.94 0.06 0.00
#> TCGA.98.A53I.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.98.8020.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.39.5031.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.56.8622.01 1 0.3172 0.760 0.84 0.00 0.16 0.00
#> TCGA.22.5471.01 4 0.4624 0.307 0.00 0.34 0.00 0.66
#> TCGA.85.7950.01 3 0.5355 0.514 0.36 0.00 0.62 0.02
#> TCGA.22.5480.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.58.8388.01 4 0.2706 0.758 0.02 0.00 0.08 0.90
#> TCGA.85.7699.01 4 0.1211 0.830 0.00 0.04 0.00 0.96
#> TCGA.33.AAS8.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.50.5931.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.77.A5G8.01 2 0.3400 0.895 0.00 0.82 0.00 0.18
#> TCGA.43.5670.01 4 0.1411 0.840 0.00 0.02 0.02 0.96
#> TCGA.NC.A5HI.01 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> TCGA.NK.A5D1.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.21.5783.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.94.7557.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.85.6798.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.85.7696.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.90.A4ED.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.77.6843.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.77.8130.01 3 0.2011 0.901 0.08 0.00 0.92 0.00
#> TCGA.34.5928.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.22.A5C4.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.94.8035.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.94.A5I4.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.77.8145.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.O2.A52W.01 1 0.8480 0.227 0.48 0.16 0.06 0.30
#> TCGA.77.8140.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.22.5478.01 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> TCGA.90.7964.01 2 0.4778 0.621 0.06 0.82 0.08 0.04
#> TCGA.68.8250.01 4 0.5869 0.622 0.04 0.16 0.06 0.74
#> TCGA.56.8504.01 4 0.4994 -0.293 0.00 0.48 0.00 0.52
#> TCGA.85.8072.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.77.7337.01 3 0.2011 0.901 0.08 0.00 0.92 0.00
#> TCGA.63.A5MI.01 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> TCGA.85.A4CL.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.85.7698.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.77.8139.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.39.5019.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.22.4599.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.85.8052.01 2 0.3172 0.885 0.00 0.84 0.00 0.16
#> TCGA.77.7142.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.96.A4JK.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.56.8305.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.98.8022.01 4 0.5987 0.032 0.44 0.00 0.04 0.52
#> TCGA.21.5786.01 4 0.2345 0.782 0.00 0.10 0.00 0.90
#> TCGA.21.5782.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.39.5016.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.85.A4CN.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.O2.A52N.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.85.8664.01 4 0.2335 0.825 0.00 0.06 0.02 0.92
#> TCGA.NC.A5HO.01 2 0.4406 0.782 0.00 0.70 0.00 0.30
#> TCGA.77.8133.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.98.A53B.01 1 0.2345 0.829 0.90 0.00 0.10 0.00
#> TCGA.56.5898.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.34.8455.01 3 0.2011 0.901 0.08 0.00 0.92 0.00
#> TCGA.43.A56V.01 1 0.1211 0.884 0.96 0.00 0.04 0.00
#> TCGA.85.A4QQ.01 2 0.2335 0.742 0.00 0.92 0.06 0.02
#> TCGA.37.A5EL.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.39.5036.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.22.5479.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.58.A46K.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.56.A4BY.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.18.3417.01 4 0.2411 0.817 0.00 0.04 0.04 0.92
#> TCGA.56.A4BW.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.56.8308.01 2 0.1637 0.757 0.00 0.94 0.06 0.00
#> TCGA.63.7020.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HQ.01 2 0.4472 0.873 0.00 0.76 0.02 0.22
#> TCGA.LA.A446.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.77.A5GF.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.56.8304.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.NC.A5HR.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.39.5029.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.56.8629.01 2 0.3801 0.885 0.00 0.78 0.00 0.22
#> TCGA.77.7465.01 3 0.2011 0.858 0.00 0.00 0.92 0.08
#> TCGA.43.7657.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.33.4579.01 3 0.4553 0.805 0.18 0.00 0.78 0.04
#> TCGA.94.A4VJ.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.56.A5DR.01 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> TCGA.85.7844.01 2 0.2647 0.864 0.00 0.88 0.00 0.12
#> TCGA.98.8021.01 4 0.2011 0.778 0.00 0.00 0.08 0.92
#> TCGA.22.5472.01 3 0.2011 0.901 0.08 0.00 0.92 0.00
#> TCGA.34.5239.01 3 0.2335 0.880 0.02 0.00 0.92 0.06
#> TCGA.77.7463.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.44.5643.01 4 0.5355 0.569 0.00 0.36 0.02 0.62
#> TCGA.33.4586.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.52.7810.01 1 0.5535 0.119 0.56 0.00 0.42 0.02
#> TCGA.90.7767.01 4 0.0707 0.841 0.00 0.00 0.02 0.98
#> TCGA.33.4582.01 4 0.1411 0.830 0.02 0.02 0.00 0.96
#> TCGA.85.8288.01 3 0.2411 0.891 0.04 0.00 0.92 0.04
#> TCGA.85.7843.01 3 0.2011 0.858 0.00 0.00 0.92 0.08
#> TCGA.56.7221.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.98.A538.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.98.A53J.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.85.8277.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.39.5035.01 3 0.2011 0.901 0.08 0.00 0.92 0.00
#> TCGA.58.A46M.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.77.7338.01 2 0.1211 0.773 0.00 0.96 0.04 0.00
#> TCGA.51.6867.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.63.A5MJ.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.56.7822.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.56.A62T.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.56.A49D.01 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> TCGA.22.5474.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.68.A59J.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.22.5492.01 1 0.0707 0.899 0.98 0.00 0.02 0.00
#> TCGA.77.7141.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.90.7766.01 1 0.3610 0.702 0.80 0.00 0.20 0.00
#> TCGA.NC.A5HD.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.NC.A5HM.01 4 0.6922 0.572 0.08 0.16 0.08 0.68
#> TCGA.46.6025.01 2 0.3400 0.895 0.00 0.82 0.00 0.18
#> TCGA.52.7809.01 4 0.0000 0.852 0.00 0.00 0.00 1.00
#> TCGA.43.8116.01 3 0.4790 0.478 0.38 0.00 0.62 0.00
#> TCGA.85.8350.01 4 0.0707 0.841 0.00 0.00 0.02 0.98
#> TCGA.LA.A7SW.01 1 0.6220 0.558 0.68 0.04 0.04 0.24
#> TCGA.96.7544.01 3 0.2411 0.891 0.04 0.00 0.92 0.04
#> TCGA.77.A5G7.01 3 0.2011 0.901 0.08 0.00 0.92 0.00
#> TCGA.56.8307.01 1 0.5860 0.190 0.58 0.00 0.38 0.04
#> TCGA.98.A539.01 1 0.0000 0.907 1.00 0.00 0.00 0.00
#> TCGA.O2.A52S.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.58.A46L.01 4 0.4472 0.648 0.00 0.22 0.02 0.76
#> TCGA.77.8144.01 2 0.2335 0.772 0.00 0.92 0.06 0.02
#> TCGA.J1.A4AH.01 2 0.3610 0.903 0.00 0.80 0.00 0.20
#> TCGA.56.7580.01 1 0.3172 0.759 0.84 0.00 0.16 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.43.7656.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.A4ZK.01 5 0.3796 0.8031 0.00 0.30 0.00 0.00 0.70
#> TCGA.63.A5MW.01 4 0.3274 0.7413 0.00 0.22 0.00 0.78 0.00
#> TCGA.85.8479.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5M9.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.37.A5EM.01 5 0.3999 0.7760 0.00 0.24 0.00 0.02 0.74
#> TCGA.98.A53I.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.98.8020.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5031.01 4 0.1648 0.8279 0.00 0.04 0.00 0.94 0.02
#> TCGA.56.8622.01 1 0.2616 0.8235 0.88 0.00 0.10 0.02 0.00
#> TCGA.22.5471.01 2 0.3983 0.3931 0.00 0.66 0.00 0.34 0.00
#> TCGA.85.7950.01 3 0.7049 0.3193 0.32 0.00 0.50 0.12 0.06
#> TCGA.22.5480.01 4 0.1732 0.8355 0.00 0.08 0.00 0.92 0.00
#> TCGA.58.8388.01 4 0.2331 0.7926 0.00 0.02 0.00 0.90 0.08
#> TCGA.85.7699.01 4 0.4132 0.6842 0.00 0.26 0.00 0.72 0.02
#> TCGA.33.AAS8.01 5 0.3796 0.8031 0.00 0.30 0.00 0.00 0.70
#> TCGA.50.5931.01 4 0.1732 0.8355 0.00 0.08 0.00 0.92 0.00
#> TCGA.77.A5G8.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.43.5670.01 4 0.4263 0.7571 0.00 0.18 0.00 0.76 0.06
#> TCGA.NC.A5HI.01 1 0.3390 0.8367 0.84 0.00 0.00 0.06 0.10
#> TCGA.NK.A5D1.01 4 0.2020 0.8317 0.00 0.10 0.00 0.90 0.00
#> TCGA.21.5783.01 4 0.2516 0.8148 0.00 0.14 0.00 0.86 0.00
#> TCGA.94.7557.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.6798.01 5 0.3983 0.7732 0.00 0.34 0.00 0.00 0.66
#> TCGA.85.7696.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.90.A4ED.01 1 0.1648 0.8855 0.94 0.00 0.00 0.02 0.04
#> TCGA.77.6843.01 2 0.4302 -0.4349 0.00 0.52 0.00 0.00 0.48
#> TCGA.77.8130.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.34.5928.01 4 0.1043 0.8304 0.00 0.04 0.00 0.96 0.00
#> TCGA.22.A5C4.01 4 0.3731 0.7911 0.00 0.16 0.00 0.80 0.04
#> TCGA.94.8035.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.94.A5I4.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8145.01 1 0.1648 0.8845 0.94 0.00 0.00 0.02 0.04
#> TCGA.O2.A52W.01 5 0.5610 0.1378 0.18 0.00 0.00 0.18 0.64
#> TCGA.77.8140.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5478.01 1 0.2616 0.8626 0.88 0.00 0.00 0.02 0.10
#> TCGA.90.7964.01 5 0.3903 0.6824 0.02 0.16 0.00 0.02 0.80
#> TCGA.68.8250.01 5 0.4126 -0.1117 0.00 0.00 0.00 0.38 0.62
#> TCGA.56.8504.01 2 0.5828 0.0528 0.00 0.52 0.00 0.38 0.10
#> TCGA.85.8072.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7337.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.63.A5MI.01 1 0.2012 0.8766 0.92 0.00 0.00 0.02 0.06
#> TCGA.85.A4CL.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.7698.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8139.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5019.01 5 0.3895 0.7966 0.00 0.32 0.00 0.00 0.68
#> TCGA.22.4599.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8052.01 2 0.2020 0.7851 0.00 0.90 0.00 0.00 0.10
#> TCGA.77.7142.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.96.A4JK.01 2 0.0609 0.8990 0.00 0.98 0.00 0.02 0.00
#> TCGA.56.8305.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.98.8022.01 4 0.5727 0.2094 0.34 0.00 0.00 0.56 0.10
#> TCGA.21.5786.01 2 0.4287 -0.0265 0.00 0.54 0.00 0.46 0.00
#> TCGA.21.5782.01 1 0.0609 0.8953 0.98 0.00 0.00 0.00 0.02
#> TCGA.39.5016.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.A4CN.01 5 0.3983 0.7744 0.00 0.34 0.00 0.00 0.66
#> TCGA.O2.A52N.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8664.01 4 0.5788 0.5487 0.00 0.12 0.00 0.58 0.30
#> TCGA.NC.A5HO.01 2 0.2516 0.7477 0.00 0.86 0.00 0.14 0.00
#> TCGA.77.8133.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.98.A53B.01 1 0.3690 0.7380 0.78 0.00 0.20 0.00 0.02
#> TCGA.56.5898.01 5 0.3895 0.7966 0.00 0.32 0.00 0.00 0.68
#> TCGA.34.8455.01 3 0.2927 0.8180 0.08 0.00 0.88 0.02 0.02
#> TCGA.43.A56V.01 1 0.3641 0.8170 0.82 0.00 0.00 0.06 0.12
#> TCGA.85.A4QQ.01 5 0.3684 0.7516 0.00 0.28 0.00 0.00 0.72
#> TCGA.37.A5EL.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.39.5036.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5479.01 5 0.3895 0.7966 0.00 0.32 0.00 0.00 0.68
#> TCGA.58.A46K.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.A4BY.01 5 0.4307 0.4534 0.00 0.50 0.00 0.00 0.50
#> TCGA.18.3417.01 4 0.4398 0.6999 0.00 0.04 0.00 0.72 0.24
#> TCGA.56.A4BW.01 4 0.2754 0.8278 0.00 0.08 0.00 0.88 0.04
#> TCGA.56.8308.01 5 0.3796 0.8031 0.00 0.30 0.00 0.00 0.70
#> TCGA.63.7020.01 1 0.1820 0.8750 0.94 0.00 0.02 0.02 0.02
#> TCGA.NC.A5HQ.01 2 0.3291 0.7298 0.00 0.84 0.00 0.04 0.12
#> TCGA.LA.A446.01 5 0.3796 0.8031 0.00 0.30 0.00 0.00 0.70
#> TCGA.77.A5GF.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.8304.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HR.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.39.5029.01 1 0.0609 0.8953 0.98 0.00 0.00 0.00 0.02
#> TCGA.56.8629.01 2 0.1410 0.8547 0.00 0.94 0.00 0.06 0.00
#> TCGA.77.7465.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.43.7657.01 2 0.0609 0.8990 0.00 0.98 0.00 0.02 0.00
#> TCGA.33.4579.01 3 0.7655 0.3285 0.28 0.00 0.42 0.24 0.06
#> TCGA.94.A4VJ.01 4 0.3868 0.7916 0.00 0.14 0.00 0.80 0.06
#> TCGA.56.A5DR.01 1 0.1820 0.8865 0.94 0.00 0.02 0.02 0.02
#> TCGA.85.7844.01 2 0.2020 0.7799 0.00 0.90 0.00 0.00 0.10
#> TCGA.98.8021.01 4 0.1216 0.8130 0.00 0.02 0.00 0.96 0.02
#> TCGA.22.5472.01 3 0.2249 0.8437 0.04 0.00 0.92 0.02 0.02
#> TCGA.34.5239.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.77.7463.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.5643.01 4 0.5447 0.1498 0.00 0.06 0.00 0.50 0.44
#> TCGA.33.4586.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.52.7810.01 1 0.5589 0.5395 0.64 0.00 0.28 0.04 0.04
#> TCGA.90.7767.01 4 0.2331 0.8349 0.00 0.08 0.00 0.90 0.02
#> TCGA.33.4582.01 4 0.2012 0.8039 0.00 0.02 0.00 0.92 0.06
#> TCGA.85.8288.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.85.7843.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.56.7221.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.98.A538.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.98.A53J.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.85.8277.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.39.5035.01 3 0.0609 0.8659 0.00 0.00 0.98 0.02 0.00
#> TCGA.58.A46M.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7338.01 5 0.3895 0.7966 0.00 0.32 0.00 0.00 0.68
#> TCGA.51.6867.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5MJ.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.7822.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.A62T.01 2 0.0609 0.8987 0.00 0.98 0.00 0.02 0.00
#> TCGA.56.A49D.01 1 0.0000 0.8978 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5474.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.68.A59J.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5492.01 1 0.4096 0.7733 0.76 0.00 0.00 0.04 0.20
#> TCGA.77.7141.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.90.7766.01 1 0.3424 0.6766 0.76 0.00 0.24 0.00 0.00
#> TCGA.NC.A5HD.01 2 0.1410 0.8534 0.00 0.94 0.00 0.06 0.00
#> TCGA.NC.A5HM.01 5 0.4060 -0.0585 0.00 0.00 0.00 0.36 0.64
#> TCGA.46.6025.01 2 0.1043 0.8749 0.00 0.96 0.00 0.00 0.04
#> TCGA.52.7809.01 4 0.1043 0.8304 0.00 0.04 0.00 0.96 0.00
#> TCGA.43.8116.01 3 0.4990 0.3699 0.36 0.00 0.60 0.00 0.04
#> TCGA.85.8350.01 4 0.1043 0.8304 0.00 0.04 0.00 0.96 0.00
#> TCGA.LA.A7SW.01 1 0.6033 0.4894 0.58 0.00 0.00 0.20 0.22
#> TCGA.96.7544.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.77.A5G7.01 3 0.0000 0.8736 0.00 0.00 1.00 0.00 0.00
#> TCGA.56.8307.01 1 0.7318 0.3950 0.52 0.00 0.16 0.24 0.08
#> TCGA.98.A539.01 1 0.0609 0.8953 0.98 0.00 0.00 0.00 0.02
#> TCGA.O2.A52S.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.58.A46L.01 4 0.3521 0.7850 0.00 0.14 0.00 0.82 0.04
#> TCGA.77.8144.01 5 0.4060 0.7046 0.00 0.36 0.00 0.00 0.64
#> TCGA.J1.A4AH.01 2 0.0000 0.9175 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.7580.01 1 0.4225 0.8009 0.80 0.00 0.12 0.02 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.43.7656.01 1 0.0000 0.8566 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.A4ZK.01 5 0.2790 0.7593 0.00 0.14 0.00 0.02 0.84 0.00
#> TCGA.63.A5MW.01 4 0.3592 0.5607 0.00 0.24 0.00 0.74 0.00 0.02
#> TCGA.85.8479.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5M9.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.37.A5EM.01 5 0.3258 0.6774 0.00 0.10 0.00 0.02 0.84 0.04
#> TCGA.98.A53I.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.98.8020.01 1 0.0000 0.8566 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5031.01 4 0.2474 0.6224 0.00 0.00 0.00 0.88 0.08 0.04
#> TCGA.56.8622.01 1 0.3679 0.6980 0.76 0.00 0.20 0.00 0.00 0.04
#> TCGA.22.5471.01 2 0.4105 0.5698 0.00 0.72 0.00 0.24 0.02 0.02
#> TCGA.85.7950.01 3 0.7186 0.3532 0.20 0.00 0.48 0.08 0.02 0.22
#> TCGA.22.5480.01 4 0.2190 0.6872 0.00 0.06 0.00 0.90 0.00 0.04
#> TCGA.58.8388.01 4 0.2581 0.6119 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.85.7699.01 4 0.5012 0.4393 0.00 0.30 0.00 0.60 0.00 0.10
#> TCGA.33.AAS8.01 5 0.2790 0.7389 0.00 0.14 0.00 0.00 0.84 0.02
#> TCGA.50.5931.01 4 0.1865 0.6821 0.00 0.04 0.00 0.92 0.00 0.04
#> TCGA.77.A5G8.01 2 0.0547 0.9242 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.43.5670.01 4 0.5840 0.4641 0.00 0.16 0.00 0.56 0.02 0.26
#> TCGA.NC.A5HI.01 1 0.3688 0.7695 0.80 0.00 0.00 0.04 0.02 0.14
#> TCGA.NK.A5D1.01 4 0.1556 0.6866 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.21.5783.01 4 0.2350 0.6758 0.00 0.10 0.00 0.88 0.00 0.02
#> TCGA.94.7557.01 1 0.1267 0.8502 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.85.6798.01 5 0.3076 0.7027 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.85.7696.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.90.A4ED.01 1 0.2631 0.7971 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.77.6843.01 5 0.3828 0.5082 0.00 0.44 0.00 0.00 0.56 0.00
#> TCGA.77.8130.01 3 0.1267 0.8105 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.34.5928.01 4 0.1480 0.6852 0.00 0.04 0.00 0.94 0.00 0.02
#> TCGA.22.A5C4.01 4 0.5363 0.5375 0.00 0.20 0.00 0.64 0.02 0.14
#> TCGA.94.8035.01 1 0.0000 0.8566 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.A5I4.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8145.01 1 0.0937 0.8526 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.O2.A52W.01 6 0.6088 0.7925 0.10 0.00 0.00 0.08 0.24 0.58
#> TCGA.77.8140.01 1 0.0000 0.8566 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5478.01 1 0.3460 0.7263 0.76 0.00 0.00 0.00 0.02 0.22
#> TCGA.90.7964.01 5 0.5304 -0.0208 0.04 0.06 0.00 0.00 0.62 0.28
#> TCGA.68.8250.01 6 0.4926 0.8579 0.00 0.00 0.00 0.12 0.24 0.64
#> TCGA.56.8504.01 2 0.6649 0.0889 0.00 0.52 0.00 0.24 0.12 0.12
#> TCGA.85.8072.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7337.01 3 0.0000 0.8188 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.63.A5MI.01 1 0.2981 0.7903 0.82 0.00 0.00 0.00 0.02 0.16
#> TCGA.85.A4CL.01 2 0.0937 0.9099 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.85.7698.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8139.01 1 0.0547 0.8553 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.39.5019.01 5 0.2790 0.7593 0.00 0.14 0.00 0.02 0.84 0.00
#> TCGA.22.4599.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8052.01 2 0.0937 0.8996 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.77.7142.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.96.A4JK.01 2 0.0547 0.9255 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.56.8305.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.98.8022.01 4 0.5840 0.1166 0.16 0.00 0.00 0.56 0.02 0.26
#> TCGA.21.5786.01 2 0.4078 0.3726 0.00 0.64 0.00 0.34 0.00 0.02
#> TCGA.21.5782.01 1 0.0937 0.8529 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.39.5016.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4CN.01 5 0.2793 0.7335 0.00 0.20 0.00 0.00 0.80 0.00
#> TCGA.O2.A52N.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8664.01 4 0.6290 0.3807 0.00 0.14 0.00 0.54 0.06 0.26
#> TCGA.NC.A5HO.01 2 0.3111 0.7645 0.00 0.84 0.00 0.12 0.02 0.02
#> TCGA.77.8133.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.98.A53B.01 1 0.4121 0.6776 0.72 0.00 0.22 0.00 0.00 0.06
#> TCGA.56.5898.01 5 0.3270 0.7162 0.00 0.12 0.00 0.06 0.82 0.00
#> TCGA.34.8455.01 3 0.4213 0.7401 0.08 0.00 0.78 0.00 0.04 0.10
#> TCGA.43.A56V.01 1 0.3258 0.7958 0.84 0.00 0.00 0.02 0.04 0.10
#> TCGA.85.A4QQ.01 5 0.5840 0.4304 0.00 0.26 0.00 0.02 0.56 0.16
#> TCGA.37.A5EL.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5036.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5479.01 5 0.2790 0.7593 0.00 0.14 0.00 0.02 0.84 0.00
#> TCGA.58.A46K.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.A4BY.01 5 0.3828 0.5061 0.00 0.44 0.00 0.00 0.56 0.00
#> TCGA.18.3417.01 4 0.6057 0.1741 0.00 0.08 0.00 0.50 0.06 0.36
#> TCGA.56.A4BW.01 4 0.4678 0.5999 0.00 0.10 0.00 0.72 0.02 0.16
#> TCGA.56.8308.01 5 0.2581 0.7355 0.00 0.12 0.00 0.02 0.86 0.00
#> TCGA.63.7020.01 1 0.3103 0.8066 0.86 0.00 0.04 0.00 0.04 0.06
#> TCGA.NC.A5HQ.01 2 0.4838 0.5492 0.00 0.70 0.00 0.02 0.10 0.18
#> TCGA.LA.A446.01 5 0.2790 0.7593 0.00 0.14 0.00 0.02 0.84 0.00
#> TCGA.77.A5GF.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.8304.01 1 0.0547 0.8553 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.NC.A5HR.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5029.01 1 0.2190 0.8372 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.56.8629.01 2 0.1480 0.8876 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.77.7465.01 3 0.1865 0.7943 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.43.7657.01 2 0.0547 0.9255 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.33.4579.01 3 0.7428 0.2832 0.06 0.00 0.44 0.26 0.04 0.20
#> TCGA.94.A4VJ.01 4 0.5691 0.4689 0.00 0.14 0.00 0.58 0.02 0.26
#> TCGA.56.A5DR.01 1 0.2020 0.8427 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.85.7844.01 2 0.1267 0.8768 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.98.8021.01 4 0.2345 0.6372 0.00 0.00 0.02 0.90 0.02 0.06
#> TCGA.22.5472.01 3 0.4008 0.7548 0.06 0.00 0.80 0.00 0.06 0.08
#> TCGA.34.5239.01 3 0.0547 0.8168 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.77.7463.01 1 0.0000 0.8566 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.5643.01 4 0.6953 -0.1233 0.00 0.10 0.00 0.44 0.30 0.16
#> TCGA.33.4586.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.52.7810.01 1 0.6101 0.4620 0.58 0.00 0.22 0.06 0.00 0.14
#> TCGA.90.7767.01 4 0.2020 0.6674 0.00 0.02 0.00 0.92 0.02 0.04
#> TCGA.33.4582.01 4 0.3660 0.5463 0.00 0.00 0.00 0.78 0.06 0.16
#> TCGA.85.8288.01 3 0.0937 0.8120 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.85.7843.01 3 0.1480 0.7966 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.56.7221.01 1 0.0000 0.8566 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.A538.01 1 0.0547 0.8553 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.98.A53J.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.85.8277.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5035.01 3 0.2020 0.8053 0.04 0.00 0.92 0.00 0.02 0.02
#> TCGA.58.A46M.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7338.01 5 0.2790 0.7593 0.00 0.14 0.00 0.02 0.84 0.00
#> TCGA.51.6867.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MJ.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.7822.01 1 0.0547 0.8542 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.56.A62T.01 2 0.0547 0.9281 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.56.A49D.01 1 0.0000 0.8566 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5474.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.68.A59J.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5492.01 1 0.3679 0.7369 0.76 0.00 0.00 0.00 0.04 0.20
#> TCGA.77.7141.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.90.7766.01 1 0.3679 0.7094 0.76 0.00 0.20 0.00 0.00 0.04
#> TCGA.NC.A5HD.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HM.01 6 0.4680 0.8385 0.00 0.00 0.00 0.12 0.20 0.68
#> TCGA.46.6025.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.52.7809.01 4 0.1480 0.6712 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.43.8116.01 3 0.5289 0.4733 0.28 0.00 0.58 0.00 0.00 0.14
#> TCGA.85.8350.01 4 0.0937 0.6862 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.LA.A7SW.01 1 0.6481 0.4782 0.60 0.00 0.04 0.08 0.08 0.20
#> TCGA.96.7544.01 3 0.0547 0.8152 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.77.A5G7.01 3 0.0000 0.8188 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.8307.01 1 0.7999 -0.0721 0.34 0.00 0.20 0.22 0.02 0.22
#> TCGA.98.A539.01 1 0.0937 0.8532 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.O2.A52S.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.58.A46L.01 4 0.4995 0.5748 0.00 0.12 0.00 0.72 0.08 0.08
#> TCGA.77.8144.01 5 0.5992 0.4516 0.00 0.36 0.00 0.02 0.48 0.14
#> TCGA.J1.A4AH.01 2 0.0000 0.9443 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.7580.01 1 0.3351 0.7574 0.80 0.00 0.16 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.43.7656.01 1 0.1166 0.77283 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.56.A4ZK.01 5 0.1166 0.72682 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.63.A5MW.01 4 0.2376 0.61734 0.00 0.12 0.00 0.86 0.00 0.02 0.00
#> TCGA.85.8479.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5M9.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.37.A5EM.01 5 0.2509 0.68036 0.00 0.04 0.00 0.00 0.88 0.06 0.02
#> TCGA.98.A53I.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.8020.01 1 0.0863 0.77429 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.39.5031.01 4 0.3656 0.62975 0.00 0.00 0.00 0.80 0.08 0.04 0.08
#> TCGA.56.8622.01 1 0.4422 0.56451 0.72 0.00 0.16 0.00 0.00 0.04 0.08
#> TCGA.22.5471.01 2 0.2708 0.70459 0.00 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.85.7950.01 7 0.7133 0.50046 0.10 0.00 0.34 0.06 0.00 0.12 0.38
#> TCGA.22.5480.01 4 0.2652 0.67782 0.00 0.02 0.00 0.88 0.02 0.02 0.06
#> TCGA.58.8388.01 4 0.4610 0.48183 0.00 0.00 0.00 0.66 0.02 0.08 0.24
#> TCGA.85.7699.01 4 0.4030 0.52938 0.00 0.16 0.00 0.72 0.00 0.12 0.00
#> TCGA.33.AAS8.01 5 0.1664 0.72005 0.00 0.06 0.00 0.00 0.92 0.02 0.00
#> TCGA.50.5931.01 4 0.1664 0.68028 0.00 0.00 0.00 0.92 0.02 0.00 0.06
#> TCGA.77.A5G8.01 2 0.1166 0.89510 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.43.5670.01 4 0.4960 0.48772 0.00 0.04 0.00 0.60 0.00 0.30 0.06
#> TCGA.NC.A5HI.01 1 0.4422 0.62986 0.72 0.00 0.00 0.04 0.00 0.16 0.08
#> TCGA.NK.A5D1.01 4 0.1006 0.68795 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.21.5783.01 4 0.0504 0.68864 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.94.7557.01 1 0.2803 0.73273 0.84 0.00 0.00 0.00 0.00 0.10 0.06
#> TCGA.85.6798.01 5 0.1671 0.72127 0.00 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.85.7696.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.90.A4ED.01 1 0.5860 0.37055 0.54 0.00 0.00 0.02 0.02 0.18 0.24
#> TCGA.77.6843.01 5 0.3358 0.47535 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.77.8130.01 3 0.3370 0.66944 0.00 0.00 0.78 0.00 0.00 0.06 0.16
#> TCGA.34.5928.01 4 0.0504 0.68948 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.22.A5C4.01 4 0.4707 0.51426 0.00 0.10 0.00 0.66 0.00 0.22 0.02
#> TCGA.94.8035.01 1 0.0863 0.77272 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.94.A5I4.01 2 0.0863 0.91202 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.77.8145.01 1 0.2278 0.75698 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.O2.A52W.01 6 0.4767 0.86185 0.02 0.00 0.00 0.06 0.14 0.72 0.06
#> TCGA.77.8140.01 1 0.1166 0.77212 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.22.5478.01 1 0.4708 0.52746 0.64 0.00 0.00 0.00 0.02 0.26 0.08
#> TCGA.90.7964.01 5 0.4993 0.27289 0.04 0.02 0.00 0.00 0.64 0.26 0.04
#> TCGA.68.8250.01 6 0.4770 0.89519 0.02 0.00 0.00 0.10 0.12 0.72 0.04
#> TCGA.56.8504.01 2 0.6494 0.12037 0.00 0.48 0.00 0.24 0.06 0.20 0.02
#> TCGA.85.8072.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7337.01 3 0.2421 0.68950 0.02 0.00 0.88 0.00 0.00 0.02 0.08
#> TCGA.63.A5MI.01 1 0.4455 0.61580 0.70 0.00 0.02 0.00 0.00 0.18 0.10
#> TCGA.85.A4CL.01 2 0.0504 0.92605 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.85.7698.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8139.01 1 0.0504 0.77371 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.39.5019.01 5 0.1433 0.73755 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.22.4599.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8052.01 2 0.2081 0.79501 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.77.7142.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.96.A4JK.01 2 0.1433 0.87532 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.56.8305.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.8022.01 4 0.7070 -0.34524 0.26 0.00 0.00 0.30 0.00 0.24 0.20
#> TCGA.21.5786.01 2 0.3459 0.33230 0.00 0.60 0.00 0.40 0.00 0.00 0.00
#> TCGA.21.5782.01 1 0.1166 0.76613 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.39.5016.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4CN.01 5 0.1886 0.71190 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.O2.A52N.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8664.01 4 0.4974 0.39307 0.00 0.02 0.00 0.58 0.04 0.34 0.02
#> TCGA.NC.A5HO.01 2 0.3744 0.72413 0.00 0.78 0.00 0.12 0.02 0.08 0.00
#> TCGA.77.8133.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.A53B.01 1 0.5425 0.48527 0.64 0.00 0.12 0.04 0.00 0.02 0.18
#> TCGA.56.5898.01 5 0.1433 0.73755 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.34.8455.01 3 0.4964 0.56988 0.02 0.00 0.66 0.00 0.02 0.08 0.22
#> TCGA.43.A56V.01 1 0.4824 0.58715 0.68 0.00 0.00 0.00 0.04 0.16 0.12
#> TCGA.85.A4QQ.01 5 0.6132 0.18645 0.00 0.18 0.00 0.02 0.44 0.34 0.02
#> TCGA.37.A5EL.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5036.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5479.01 5 0.1433 0.73755 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.58.A46K.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.A4BY.01 5 0.3459 0.43255 0.00 0.40 0.00 0.00 0.60 0.00 0.00
#> TCGA.18.3417.01 4 0.5025 0.37515 0.00 0.02 0.00 0.56 0.02 0.36 0.04
#> TCGA.56.A4BW.01 4 0.4939 0.52977 0.00 0.02 0.02 0.64 0.00 0.26 0.06
#> TCGA.56.8308.01 5 0.1664 0.72464 0.00 0.06 0.02 0.00 0.92 0.00 0.00
#> TCGA.63.7020.01 1 0.3680 0.67252 0.78 0.00 0.02 0.00 0.00 0.06 0.14
#> TCGA.NC.A5HQ.01 2 0.5166 0.54448 0.00 0.66 0.00 0.08 0.04 0.20 0.02
#> TCGA.LA.A446.01 5 0.1363 0.70275 0.00 0.04 0.00 0.00 0.94 0.02 0.00
#> TCGA.77.A5GF.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8304.01 1 0.0000 0.77194 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HR.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5029.01 1 0.2163 0.74588 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.56.8629.01 2 0.1166 0.89269 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.77.7465.01 3 0.2081 0.64945 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.43.7657.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.4579.01 7 0.7134 0.33658 0.08 0.00 0.30 0.10 0.00 0.10 0.42
#> TCGA.94.A4VJ.01 4 0.4015 0.54201 0.00 0.00 0.00 0.68 0.00 0.26 0.06
#> TCGA.56.A5DR.01 1 0.2159 0.76468 0.90 0.00 0.02 0.00 0.00 0.02 0.06
#> TCGA.85.7844.01 2 0.0863 0.90930 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.98.8021.01 4 0.3086 0.62760 0.00 0.00 0.00 0.80 0.00 0.04 0.16
#> TCGA.22.5472.01 3 0.5051 0.57264 0.02 0.00 0.66 0.00 0.02 0.10 0.20
#> TCGA.34.5239.01 3 0.1671 0.69416 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.77.7463.01 1 0.0000 0.77194 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.5643.01 5 0.7469 -0.20780 0.00 0.04 0.02 0.28 0.40 0.16 0.10
#> TCGA.33.4586.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.52.7810.01 1 0.6642 -0.39018 0.36 0.00 0.28 0.02 0.00 0.04 0.30
#> TCGA.90.7767.01 4 0.2864 0.64917 0.00 0.00 0.00 0.84 0.02 0.02 0.12
#> TCGA.33.4582.01 4 0.5130 0.52051 0.00 0.00 0.00 0.64 0.04 0.14 0.18
#> TCGA.85.8288.01 3 0.1433 0.68892 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.85.7843.01 3 0.1860 0.67544 0.00 0.00 0.92 0.00 0.02 0.04 0.02
#> TCGA.56.7221.01 1 0.1166 0.77262 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.98.A538.01 1 0.0000 0.77194 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.A53J.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8277.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5035.01 3 0.3770 0.64828 0.00 0.00 0.74 0.00 0.00 0.08 0.18
#> TCGA.58.A46M.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7338.01 5 0.1433 0.73755 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.51.6867.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MJ.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7822.01 1 0.1671 0.76952 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.56.A62T.01 2 0.2016 0.85953 0.00 0.90 0.00 0.04 0.00 0.06 0.00
#> TCGA.56.A49D.01 1 0.0504 0.77500 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.22.5474.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.68.A59J.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5492.01 1 0.4681 0.42864 0.58 0.00 0.00 0.00 0.00 0.32 0.10
#> TCGA.77.7141.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.90.7766.01 1 0.2906 0.65436 0.80 0.00 0.18 0.00 0.00 0.00 0.02
#> TCGA.NC.A5HD.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HM.01 6 0.3541 0.85614 0.00 0.00 0.00 0.10 0.08 0.80 0.02
#> TCGA.46.6025.01 2 0.0504 0.92396 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.52.7809.01 4 0.0504 0.69086 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.43.8116.01 3 0.4783 -0.14737 0.36 0.00 0.54 0.00 0.00 0.00 0.10
#> TCGA.85.8350.01 4 0.1363 0.68750 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.LA.A7SW.01 1 0.7909 -0.00252 0.42 0.00 0.04 0.18 0.06 0.16 0.14
#> TCGA.96.7544.01 3 0.1006 0.70811 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.77.A5G7.01 3 0.0504 0.71159 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.56.8307.01 7 0.7184 0.54053 0.22 0.00 0.14 0.10 0.00 0.08 0.46
#> TCGA.98.A539.01 1 0.1664 0.76827 0.92 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.O2.A52S.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.58.A46L.01 4 0.6809 0.28317 0.00 0.08 0.00 0.48 0.18 0.04 0.22
#> TCGA.77.8144.01 5 0.5888 0.25405 0.00 0.36 0.00 0.00 0.40 0.22 0.02
#> TCGA.J1.A4AH.01 2 0.0000 0.93991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7580.01 1 0.5652 0.41021 0.60 0.00 0.18 0.00 0.00 0.10 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.43.7656.01 1 0.1947 0.7153 0.86 0.00 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.56.A4ZK.01 5 0.1408 0.7639 0.00 0.02 0.00 0.02 0.94 0.00 0.00 0.02
#> TCGA.63.A5MW.01 4 0.1563 0.5770 0.00 0.10 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.85.8479.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5M9.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.37.A5EM.01 5 0.2532 0.7437 0.00 0.02 0.00 0.02 0.88 0.04 0.00 0.04
#> TCGA.98.A53I.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.8020.01 1 0.0471 0.7381 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.39.5031.01 4 0.3771 0.4719 0.00 0.00 0.00 0.72 0.16 0.00 0.12 0.00
#> TCGA.56.8622.01 1 0.3934 0.5338 0.70 0.00 0.16 0.00 0.00 0.00 0.00 0.14
#> TCGA.22.5471.01 2 0.2267 0.7710 0.00 0.82 0.00 0.18 0.00 0.00 0.00 0.00
#> TCGA.85.7950.01 7 0.8013 0.0396 0.06 0.00 0.24 0.06 0.04 0.06 0.34 0.20
#> TCGA.22.5480.01 4 0.4522 0.5056 0.00 0.08 0.00 0.74 0.04 0.02 0.10 0.02
#> TCGA.58.8388.01 4 0.4581 0.3900 0.00 0.00 0.00 0.66 0.04 0.02 0.24 0.04
#> TCGA.85.7699.01 4 0.4647 0.4584 0.00 0.16 0.00 0.68 0.02 0.12 0.00 0.02
#> TCGA.33.AAS8.01 5 0.0941 0.7636 0.00 0.02 0.00 0.02 0.96 0.00 0.00 0.00
#> TCGA.50.5931.01 4 0.2265 0.5907 0.00 0.00 0.00 0.88 0.02 0.00 0.08 0.02
#> TCGA.77.A5G8.01 2 0.1341 0.8581 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.43.5670.01 4 0.4794 0.3596 0.00 0.08 0.00 0.48 0.00 0.42 0.00 0.02
#> TCGA.NC.A5HI.01 1 0.4004 0.4199 0.50 0.00 0.00 0.00 0.00 0.04 0.46 0.00
#> TCGA.NK.A5D1.01 4 0.0941 0.6149 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.21.5783.01 4 0.0941 0.6149 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.94.7557.01 1 0.2569 0.6982 0.82 0.00 0.00 0.00 0.00 0.00 0.16 0.02
#> TCGA.85.6798.01 5 0.3078 0.6710 0.00 0.06 0.00 0.00 0.82 0.10 0.00 0.02
#> TCGA.85.7696.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.90.A4ED.01 1 0.4370 0.2788 0.52 0.00 0.00 0.00 0.00 0.00 0.40 0.08
#> TCGA.77.6843.01 5 0.4415 0.3989 0.00 0.32 0.00 0.00 0.60 0.06 0.00 0.02
#> TCGA.77.8130.01 3 0.2114 0.6429 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.34.5928.01 4 0.0941 0.6126 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.22.A5C4.01 4 0.5158 0.4412 0.00 0.10 0.00 0.56 0.00 0.30 0.02 0.02
#> TCGA.94.8035.01 1 0.2132 0.7370 0.88 0.00 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.94.A5I4.01 2 0.1091 0.8741 0.00 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.77.8145.01 1 0.2981 0.6724 0.76 0.00 0.00 0.00 0.00 0.00 0.22 0.02
#> TCGA.O2.A52W.01 6 0.6101 0.5681 0.04 0.00 0.00 0.04 0.08 0.42 0.40 0.02
#> TCGA.77.8140.01 1 0.1765 0.7227 0.88 0.00 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.22.5478.01 1 0.4860 0.3734 0.50 0.00 0.00 0.00 0.00 0.06 0.40 0.04
#> TCGA.90.7964.01 5 0.7776 -0.3480 0.06 0.00 0.06 0.00 0.28 0.26 0.10 0.24
#> TCGA.68.8250.01 6 0.4968 0.5742 0.00 0.00 0.00 0.06 0.02 0.52 0.38 0.02
#> TCGA.56.8504.01 2 0.6383 0.3040 0.00 0.52 0.00 0.12 0.12 0.20 0.02 0.02
#> TCGA.85.8072.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7337.01 3 0.3986 0.6151 0.04 0.00 0.74 0.00 0.00 0.08 0.00 0.14
#> TCGA.63.A5MI.01 1 0.3843 0.6517 0.70 0.00 0.00 0.00 0.00 0.02 0.24 0.04
#> TCGA.85.A4CL.01 2 0.2407 0.8077 0.00 0.86 0.00 0.08 0.06 0.00 0.00 0.00
#> TCGA.85.7698.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8139.01 1 0.0000 0.7366 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5019.01 5 0.0941 0.7636 0.00 0.02 0.00 0.02 0.96 0.00 0.00 0.00
#> TCGA.22.4599.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8052.01 2 0.2756 0.6392 0.00 0.74 0.00 0.00 0.26 0.00 0.00 0.00
#> TCGA.77.7142.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.96.A4JK.01 2 0.2623 0.7911 0.00 0.84 0.00 0.06 0.10 0.00 0.00 0.00
#> TCGA.56.8305.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.8022.01 7 0.5125 -0.1885 0.08 0.00 0.00 0.26 0.02 0.00 0.60 0.04
#> TCGA.21.5786.01 2 0.2756 0.6434 0.00 0.74 0.00 0.26 0.00 0.00 0.00 0.00
#> TCGA.21.5782.01 1 0.2482 0.7286 0.88 0.00 0.02 0.00 0.00 0.02 0.06 0.02
#> TCGA.39.5016.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.A4CN.01 5 0.1275 0.7661 0.00 0.04 0.00 0.02 0.94 0.00 0.00 0.00
#> TCGA.O2.A52N.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8664.01 4 0.5843 0.3012 0.00 0.08 0.00 0.44 0.04 0.40 0.02 0.02
#> TCGA.NC.A5HO.01 2 0.3073 0.7578 0.00 0.80 0.00 0.10 0.00 0.10 0.00 0.00
#> TCGA.77.8133.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.A53B.01 1 0.6605 0.1331 0.50 0.00 0.24 0.02 0.00 0.08 0.08 0.08
#> TCGA.56.5898.01 5 0.2132 0.7315 0.00 0.08 0.00 0.04 0.88 0.00 0.00 0.00
#> TCGA.34.8455.01 3 0.5589 0.3133 0.10 0.00 0.46 0.00 0.00 0.02 0.04 0.38
#> TCGA.43.A56V.01 1 0.5125 0.5453 0.60 0.00 0.00 0.00 0.04 0.08 0.26 0.02
#> TCGA.85.A4QQ.01 2 0.6239 -0.3492 0.00 0.32 0.00 0.00 0.32 0.30 0.02 0.04
#> TCGA.37.A5EL.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5036.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5479.01 5 0.1741 0.7664 0.00 0.04 0.00 0.02 0.92 0.00 0.00 0.02
#> TCGA.58.A46K.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.A4BY.01 5 0.5322 0.2851 0.00 0.38 0.00 0.00 0.48 0.10 0.02 0.02
#> TCGA.18.3417.01 4 0.5677 0.2498 0.00 0.00 0.00 0.46 0.08 0.34 0.12 0.00
#> TCGA.56.A4BW.01 4 0.3449 0.5011 0.00 0.00 0.00 0.66 0.00 0.32 0.02 0.00
#> TCGA.56.8308.01 5 0.1874 0.7606 0.00 0.02 0.00 0.02 0.92 0.02 0.00 0.02
#> TCGA.63.7020.01 1 0.4747 0.5541 0.66 0.00 0.08 0.00 0.00 0.00 0.08 0.18
#> TCGA.NC.A5HQ.01 2 0.3991 0.6431 0.00 0.70 0.00 0.06 0.02 0.22 0.00 0.00
#> TCGA.LA.A446.01 5 0.1408 0.7639 0.00 0.02 0.00 0.02 0.94 0.00 0.00 0.02
#> TCGA.77.A5GF.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8304.01 1 0.0471 0.7365 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.NC.A5HR.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5029.01 1 0.3744 0.6329 0.74 0.00 0.02 0.00 0.00 0.06 0.18 0.00
#> TCGA.56.8629.01 2 0.2025 0.8292 0.00 0.88 0.00 0.10 0.00 0.02 0.00 0.00
#> TCGA.77.7465.01 3 0.3270 0.5695 0.00 0.00 0.80 0.02 0.00 0.00 0.06 0.12
#> TCGA.43.7657.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.4579.01 8 0.7168 0.0000 0.12 0.00 0.04 0.18 0.00 0.04 0.18 0.44
#> TCGA.94.A4VJ.01 4 0.4040 0.4445 0.00 0.02 0.00 0.58 0.00 0.38 0.00 0.02
#> TCGA.56.A5DR.01 1 0.4174 0.6569 0.70 0.00 0.02 0.00 0.02 0.00 0.22 0.04
#> TCGA.85.7844.01 2 0.1765 0.8186 0.00 0.88 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.98.8021.01 4 0.4492 0.4806 0.00 0.00 0.00 0.70 0.06 0.02 0.18 0.04
#> TCGA.22.5472.01 3 0.4216 0.3905 0.06 0.00 0.50 0.00 0.00 0.00 0.00 0.44
#> TCGA.34.5239.01 3 0.1887 0.6406 0.00 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.77.7463.01 1 0.0000 0.7366 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.5643.01 5 0.7440 0.1589 0.00 0.06 0.02 0.18 0.46 0.10 0.14 0.04
#> TCGA.33.4586.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.52.7810.01 7 0.7031 -0.0600 0.32 0.00 0.20 0.02 0.00 0.02 0.32 0.12
#> TCGA.90.7767.01 4 0.4075 0.5235 0.00 0.02 0.00 0.76 0.04 0.02 0.14 0.02
#> TCGA.33.4582.01 4 0.5957 0.3606 0.00 0.00 0.00 0.56 0.12 0.06 0.20 0.06
#> TCGA.85.8288.01 3 0.2407 0.6117 0.00 0.00 0.86 0.00 0.00 0.00 0.06 0.08
#> TCGA.85.7843.01 3 0.4031 0.5847 0.00 0.00 0.72 0.00 0.00 0.16 0.02 0.10
#> TCGA.56.7221.01 1 0.0471 0.7381 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.98.A538.01 1 0.0471 0.7365 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.98.A53J.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.85.8277.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5035.01 3 0.3991 0.5287 0.06 0.00 0.62 0.00 0.00 0.00 0.00 0.32
#> TCGA.58.A46M.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7338.01 5 0.2020 0.7573 0.00 0.06 0.00 0.02 0.90 0.00 0.00 0.02
#> TCGA.51.6867.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MJ.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7822.01 1 0.1557 0.7379 0.92 0.00 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.56.A62T.01 2 0.2624 0.8163 0.00 0.86 0.00 0.06 0.00 0.06 0.00 0.02
#> TCGA.56.A49D.01 1 0.1557 0.7358 0.92 0.00 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.22.5474.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.68.A59J.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5492.01 1 0.4954 0.3074 0.46 0.00 0.00 0.00 0.00 0.10 0.42 0.02
#> TCGA.77.7141.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.90.7766.01 1 0.3924 0.5713 0.72 0.00 0.20 0.00 0.00 0.00 0.04 0.04
#> TCGA.NC.A5HD.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HM.01 6 0.5292 0.5854 0.00 0.00 0.00 0.04 0.04 0.50 0.38 0.04
#> TCGA.46.6025.01 2 0.1563 0.8392 0.00 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.52.7809.01 4 0.1408 0.6150 0.00 0.00 0.00 0.94 0.02 0.02 0.02 0.00
#> TCGA.43.8116.01 3 0.5859 -0.0223 0.32 0.00 0.48 0.00 0.00 0.02 0.06 0.12
#> TCGA.85.8350.01 4 0.1275 0.6132 0.00 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.LA.A7SW.01 6 0.7981 -0.0111 0.30 0.00 0.08 0.02 0.06 0.32 0.12 0.10
#> TCGA.96.7544.01 3 0.3314 0.6370 0.00 0.00 0.80 0.00 0.00 0.08 0.02 0.10
#> TCGA.77.A5G7.01 3 0.1887 0.6579 0.00 0.00 0.90 0.00 0.00 0.04 0.00 0.06
#> TCGA.56.8307.01 7 0.8379 0.0556 0.12 0.00 0.16 0.12 0.02 0.08 0.34 0.16
#> TCGA.98.A539.01 1 0.2680 0.7200 0.84 0.00 0.00 0.00 0.02 0.00 0.12 0.02
#> TCGA.O2.A52S.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.58.A46L.01 4 0.6170 0.1952 0.00 0.04 0.00 0.48 0.32 0.04 0.10 0.02
#> TCGA.77.8144.01 2 0.6340 -0.1866 0.00 0.40 0.00 0.00 0.30 0.22 0.04 0.04
#> TCGA.J1.A4AH.01 2 0.0000 0.9090 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7580.01 1 0.5202 0.4782 0.58 0.00 0.12 0.00 0.00 0.00 0.24 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: Node06. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["061"]
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 45 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 0.4914 0.509 0.509
#> 3 3 1.000 0.986 0.994 0.3727 0.743 0.530
#> 4 4 0.908 0.924 0.949 0.0907 0.881 0.660
#> 5 5 0.889 0.853 0.904 0.0516 1.000 1.000
#> 6 6 0.823 0.677 0.841 0.0297 0.957 0.837
#> 7 7 0.789 0.631 0.784 0.0251 0.902 0.599
#> 8 8 0.791 0.631 0.814 0.0264 0.978 0.871
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.43.7656.01 2 0 1 0 1
#> TCGA.98.8020.01 2 0 1 0 1
#> TCGA.56.8622.01 2 0 1 0 1
#> TCGA.85.7950.01 1 0 1 1 0
#> TCGA.NC.A5HI.01 2 0 1 0 1
#> TCGA.94.7557.01 2 0 1 0 1
#> TCGA.90.A4ED.01 2 0 1 0 1
#> TCGA.77.8130.01 1 0 1 1 0
#> TCGA.94.8035.01 2 0 1 0 1
#> TCGA.77.8145.01 2 0 1 0 1
#> TCGA.77.8140.01 2 0 1 0 1
#> TCGA.22.5478.01 2 0 1 0 1
#> TCGA.77.7337.01 1 0 1 1 0
#> TCGA.63.A5MI.01 2 0 1 0 1
#> TCGA.77.8139.01 2 0 1 0 1
#> TCGA.98.8022.01 2 0 1 0 1
#> TCGA.21.5782.01 2 0 1 0 1
#> TCGA.98.A53B.01 1 0 1 1 0
#> TCGA.34.8455.01 1 0 1 1 0
#> TCGA.43.A56V.01 2 0 1 0 1
#> TCGA.63.7020.01 2 0 1 0 1
#> TCGA.56.8304.01 2 0 1 0 1
#> TCGA.39.5029.01 2 0 1 0 1
#> TCGA.77.7465.01 1 0 1 1 0
#> TCGA.33.4579.01 1 0 1 1 0
#> TCGA.56.A5DR.01 2 0 1 0 1
#> TCGA.22.5472.01 1 0 1 1 0
#> TCGA.34.5239.01 1 0 1 1 0
#> TCGA.77.7463.01 2 0 1 0 1
#> TCGA.52.7810.01 1 0 1 1 0
#> TCGA.85.8288.01 1 0 1 1 0
#> TCGA.56.7221.01 2 0 1 0 1
#> TCGA.98.A538.01 2 0 1 0 1
#> TCGA.39.5035.01 1 0 1 1 0
#> TCGA.56.7822.01 1 0 1 1 0
#> TCGA.56.A49D.01 2 0 1 0 1
#> TCGA.22.5492.01 2 0 1 0 1
#> TCGA.90.7766.01 2 0 1 0 1
#> TCGA.43.8116.01 1 0 1 1 0
#> TCGA.LA.A7SW.01 2 0 1 0 1
#> TCGA.96.7544.01 1 0 1 1 0
#> TCGA.77.A5G7.01 1 0 1 1 0
#> TCGA.56.8307.01 2 0 1 0 1
#> TCGA.98.A539.01 1 0 1 1 0
#> TCGA.56.7580.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.43.7656.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.98.8020.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.56.8622.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.85.7950.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.NC.A5HI.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.94.7557.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.90.A4ED.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.77.8130.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.94.8035.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.77.8145.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.77.8140.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.22.5478.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.77.7337.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.63.A5MI.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.77.8139.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.98.8022.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.21.5782.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.98.A53B.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.34.8455.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.43.A56V.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.63.7020.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.56.8304.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.39.5029.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.77.7465.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.33.4579.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.56.A5DR.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.22.5472.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.34.5239.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.77.7463.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.52.7810.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.85.8288.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.56.7221.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.98.A538.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.39.5035.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.56.7822.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.56.A49D.01 2 0.000 0.993 0 1.00 0.00
#> TCGA.22.5492.01 3 0.400 0.807 0 0.16 0.84
#> TCGA.90.7766.01 2 0.334 0.860 0 0.88 0.12
#> TCGA.43.8116.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.LA.A7SW.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.96.7544.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.77.A5G7.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.56.8307.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.98.A539.01 3 0.000 0.986 0 0.00 1.00
#> TCGA.56.7580.01 1 0.000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.43.7656.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.98.8020.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.56.8622.01 3 0.1211 0.943 0.00 0.00 0.96 0.04
#> TCGA.85.7950.01 4 0.3801 0.790 0.22 0.00 0.00 0.78
#> TCGA.NC.A5HI.01 2 0.0707 0.986 0.00 0.98 0.02 0.00
#> TCGA.94.7557.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.90.A4ED.01 3 0.2647 0.862 0.00 0.00 0.88 0.12
#> TCGA.77.8130.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.94.8035.01 2 0.0707 0.986 0.00 0.98 0.02 0.00
#> TCGA.77.8145.01 3 0.0000 0.936 0.00 0.00 1.00 0.00
#> TCGA.77.8140.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.22.5478.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.77.7337.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.63.A5MI.01 2 0.0707 0.986 0.00 0.98 0.02 0.00
#> TCGA.77.8139.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.98.8022.01 3 0.1211 0.943 0.00 0.00 0.96 0.04
#> TCGA.21.5782.01 3 0.0707 0.941 0.00 0.00 0.98 0.02
#> TCGA.98.A53B.01 4 0.2921 0.850 0.00 0.00 0.14 0.86
#> TCGA.34.8455.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.43.A56V.01 2 0.0707 0.986 0.00 0.98 0.02 0.00
#> TCGA.63.7020.01 3 0.1211 0.943 0.00 0.00 0.96 0.04
#> TCGA.56.8304.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.39.5029.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.77.7465.01 1 0.4713 0.304 0.64 0.00 0.00 0.36
#> TCGA.33.4579.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.56.A5DR.01 2 0.0707 0.986 0.00 0.98 0.02 0.00
#> TCGA.22.5472.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.34.5239.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.77.7463.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.52.7810.01 4 0.3400 0.834 0.18 0.00 0.00 0.82
#> TCGA.85.8288.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.56.7221.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.98.A538.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.39.5035.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.56.7822.01 4 0.2921 0.850 0.00 0.00 0.14 0.86
#> TCGA.56.A49D.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.22.5492.01 3 0.0707 0.926 0.00 0.02 0.98 0.00
#> TCGA.90.7766.01 3 0.2921 0.788 0.00 0.14 0.86 0.00
#> TCGA.43.8116.01 4 0.3400 0.834 0.18 0.00 0.00 0.82
#> TCGA.LA.A7SW.01 3 0.1211 0.943 0.00 0.00 0.96 0.04
#> TCGA.96.7544.01 1 0.0000 0.953 1.00 0.00 0.00 0.00
#> TCGA.77.A5G7.01 4 0.2921 0.850 0.00 0.00 0.14 0.86
#> TCGA.56.8307.01 3 0.1637 0.938 0.00 0.00 0.94 0.06
#> TCGA.98.A539.01 4 0.2921 0.850 0.00 0.00 0.14 0.86
#> TCGA.56.7580.01 4 0.3400 0.834 0.18 0.00 0.00 0.82
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.43.7656.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.98.8020.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.56.8622.01 3 0.0000 0.8754 0.00 0.00 1.00 0.00 0.00
#> TCGA.85.7950.01 4 0.4096 0.8498 0.04 0.00 0.00 0.76 0.20
#> TCGA.NC.A5HI.01 2 0.3561 0.7947 0.00 0.74 0.00 0.00 0.26
#> TCGA.94.7557.01 2 0.1043 0.8983 0.00 0.96 0.00 0.00 0.04
#> TCGA.90.A4ED.01 3 0.3796 0.7149 0.00 0.00 0.70 0.00 0.30
#> TCGA.77.8130.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.94.8035.01 2 0.5961 0.6018 0.00 0.58 0.16 0.00 0.26
#> TCGA.77.8145.01 3 0.0609 0.8737 0.00 0.00 0.98 0.00 0.02
#> TCGA.77.8140.01 2 0.1410 0.8939 0.00 0.94 0.00 0.00 0.06
#> TCGA.22.5478.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7337.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MI.01 2 0.3561 0.7947 0.00 0.74 0.00 0.00 0.26
#> TCGA.77.8139.01 2 0.1410 0.8939 0.00 0.94 0.00 0.00 0.06
#> TCGA.98.8022.01 3 0.2020 0.8604 0.00 0.00 0.90 0.00 0.10
#> TCGA.21.5782.01 3 0.0609 0.8737 0.00 0.00 0.98 0.00 0.02
#> TCGA.98.A53B.01 4 0.1648 0.8993 0.00 0.00 0.02 0.94 0.04
#> TCGA.34.8455.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.A56V.01 2 0.3561 0.7947 0.00 0.74 0.00 0.00 0.26
#> TCGA.63.7020.01 3 0.0609 0.8745 0.00 0.00 0.98 0.00 0.02
#> TCGA.56.8304.01 2 0.1043 0.8983 0.00 0.96 0.00 0.00 0.04
#> TCGA.39.5029.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.7465.01 1 0.6422 -0.0169 0.46 0.00 0.00 0.36 0.18
#> TCGA.33.4579.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.A5DR.01 2 0.5599 0.6637 0.00 0.62 0.12 0.00 0.26
#> TCGA.22.5472.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.34.5239.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7463.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.52.7810.01 4 0.2280 0.9183 0.00 0.00 0.00 0.88 0.12
#> TCGA.85.8288.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.7221.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.98.A538.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.39.5035.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.7822.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00 0.00
#> TCGA.56.A49D.01 2 0.0000 0.9017 0.00 1.00 0.00 0.00 0.00
#> TCGA.22.5492.01 3 0.3274 0.7767 0.00 0.00 0.78 0.00 0.22
#> TCGA.90.7766.01 3 0.3684 0.7270 0.00 0.00 0.72 0.00 0.28
#> TCGA.43.8116.01 4 0.2020 0.9218 0.00 0.00 0.00 0.90 0.10
#> TCGA.LA.A7SW.01 3 0.2020 0.8604 0.00 0.00 0.90 0.00 0.10
#> TCGA.96.7544.01 1 0.0000 0.9409 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5G7.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00 0.00
#> TCGA.56.8307.01 3 0.3424 0.7891 0.00 0.00 0.76 0.00 0.24
#> TCGA.98.A539.01 4 0.1648 0.8993 0.00 0.00 0.02 0.94 0.04
#> TCGA.56.7580.01 4 0.2280 0.9183 0.00 0.00 0.00 0.88 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.43.7656.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.98.8020.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.8622.01 3 0.1092 0.715 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.85.7950.01 5 0.3270 0.692 0.00 0.00 0.00 0.12 0.82 0.06
#> TCGA.NC.A5HI.01 2 0.3756 0.424 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.94.7557.01 2 0.1556 0.786 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.90.A4ED.01 3 0.5199 0.451 0.00 0.00 0.58 0.30 0.00 0.12
#> TCGA.77.8130.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.8035.01 2 0.5703 -0.195 0.00 0.42 0.16 0.00 0.00 0.42
#> TCGA.77.8145.01 3 0.1267 0.715 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.77.8140.01 2 0.2260 0.755 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.22.5478.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7337.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MI.01 2 0.4246 0.379 0.00 0.58 0.02 0.00 0.00 0.40
#> TCGA.77.8139.01 2 0.2260 0.756 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.98.8022.01 3 0.4200 0.610 0.00 0.00 0.74 0.14 0.00 0.12
#> TCGA.21.5782.01 3 0.1267 0.715 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.98.A53B.01 5 0.5071 0.595 0.00 0.00 0.08 0.40 0.52 0.00
#> TCGA.34.8455.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.A56V.01 2 0.3756 0.424 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.63.7020.01 3 0.2581 0.682 0.00 0.00 0.86 0.12 0.00 0.02
#> TCGA.56.8304.01 2 0.1814 0.776 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.39.5029.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.7465.01 5 0.5352 0.495 0.24 0.00 0.00 0.08 0.64 0.04
#> TCGA.33.4579.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.A5DR.01 6 0.5703 -0.418 0.00 0.42 0.16 0.00 0.00 0.42
#> TCGA.22.5472.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5239.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7463.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.52.7810.01 5 0.0000 0.770 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.85.8288.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7221.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.98.A538.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5035.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7822.01 5 0.3076 0.749 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.56.A49D.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5492.01 3 0.3076 0.580 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.90.7766.01 3 0.3647 0.410 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.43.8116.01 5 0.0547 0.772 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.LA.A7SW.01 3 0.3985 0.631 0.00 0.00 0.76 0.10 0.00 0.14
#> TCGA.96.7544.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.A5G7.01 5 0.3076 0.749 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.56.8307.01 6 0.6047 -0.398 0.00 0.00 0.26 0.34 0.00 0.40
#> TCGA.98.A539.01 5 0.4845 0.616 0.00 0.00 0.06 0.40 0.54 0.00
#> TCGA.56.7580.01 5 0.0000 0.770 0.00 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.43.7656.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.8020.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8622.01 3 0.1006 0.641 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.85.7950.01 5 0.0504 0.510 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.NC.A5HI.01 6 0.3459 0.629 0.00 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.94.7557.01 2 0.2572 0.685 0.00 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.90.A4ED.01 7 0.6816 -0.435 0.00 0.00 0.18 0.24 0.00 0.18 0.40
#> TCGA.77.8130.01 1 0.0000 0.985 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.8035.01 6 0.3745 0.727 0.00 0.26 0.04 0.00 0.00 0.70 0.00
#> TCGA.77.8145.01 3 0.3867 0.550 0.00 0.00 0.60 0.02 0.00 0.38 0.00
#> TCGA.77.8140.01 2 0.2832 0.614 0.00 0.76 0.00 0.00 0.00 0.24 0.00
#> TCGA.22.5478.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7337.01 1 0.0000 0.985 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MI.01 6 0.3294 0.701 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.77.8139.01 2 0.3221 0.411 0.00 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.98.8022.01 3 0.3833 0.497 0.00 0.00 0.78 0.12 0.00 0.06 0.04
#> TCGA.21.5782.01 3 0.3186 0.636 0.00 0.00 0.76 0.00 0.00 0.22 0.02
#> TCGA.98.A53B.01 7 0.4870 0.353 0.00 0.00 0.14 0.00 0.28 0.00 0.58
#> TCGA.34.8455.01 1 0.0000 0.985 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.A56V.01 6 0.3459 0.629 0.00 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.63.7020.01 3 0.0504 0.630 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.56.8304.01 2 0.2081 0.761 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.39.5029.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7465.01 5 0.2832 0.372 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.33.4579.01 1 0.1718 0.920 0.92 0.00 0.00 0.04 0.00 0.04 0.00
#> TCGA.56.A5DR.01 6 0.3745 0.727 0.00 0.26 0.04 0.00 0.00 0.70 0.00
#> TCGA.22.5472.01 1 0.0000 0.985 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5239.01 1 0.0000 0.985 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7463.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.52.7810.01 5 0.3780 0.590 0.00 0.00 0.00 0.02 0.72 0.02 0.24
#> TCGA.85.8288.01 1 0.0000 0.985 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7221.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.A538.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.39.5035.01 1 0.0000 0.985 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7822.01 7 0.3546 0.117 0.00 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.56.A49D.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5492.01 3 0.3459 0.526 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.90.7766.01 6 0.3496 -0.320 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.43.8116.01 5 0.3047 0.555 0.00 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.LA.A7SW.01 3 0.3630 0.427 0.00 0.00 0.80 0.10 0.00 0.06 0.04
#> TCGA.96.7544.01 1 0.0863 0.951 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.77.A5G7.01 7 0.3546 0.117 0.00 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.56.8307.01 4 0.3795 0.000 0.00 0.00 0.22 0.72 0.00 0.00 0.06
#> TCGA.98.A539.01 7 0.4787 0.353 0.00 0.00 0.12 0.00 0.30 0.00 0.58
#> TCGA.56.7580.01 5 0.2832 0.608 0.00 0.00 0.00 0.00 0.76 0.00 0.24
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.43.7656.01 2 0.0000 0.8505 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.8020.01 2 0.0000 0.8505 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.8622.01 3 0.2265 0.5910 0.00 0.00 0.88 0.00 0.08 0.02 0.00 0.02
#> TCGA.85.7950.01 5 0.4028 0.2001 0.00 0.00 0.00 0.00 0.66 0.02 0.28 0.04
#> TCGA.NC.A5HI.01 6 0.2267 0.7907 0.00 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.94.7557.01 2 0.2938 0.6056 0.00 0.70 0.00 0.00 0.00 0.30 0.00 0.00
#> TCGA.90.A4ED.01 8 0.2267 0.0000 0.00 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.77.8130.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.8035.01 6 0.2350 0.7896 0.00 0.10 0.00 0.00 0.04 0.86 0.00 0.00
#> TCGA.77.8145.01 3 0.3995 0.4053 0.00 0.00 0.60 0.02 0.00 0.36 0.00 0.02
#> TCGA.77.8140.01 2 0.3193 0.4673 0.00 0.62 0.00 0.00 0.00 0.38 0.00 0.00
#> TCGA.22.5478.01 2 0.0000 0.8505 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7337.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.63.A5MI.01 6 0.2725 0.8055 0.00 0.14 0.00 0.00 0.04 0.82 0.00 0.00
#> TCGA.77.8139.01 2 0.3237 0.4229 0.00 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.98.8022.01 3 0.4180 0.4633 0.00 0.00 0.70 0.20 0.06 0.04 0.00 0.00
#> TCGA.21.5782.01 3 0.1804 0.5922 0.00 0.00 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.98.A53B.01 7 0.5087 0.4695 0.00 0.00 0.08 0.02 0.10 0.06 0.70 0.04
#> TCGA.34.8455.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.A56V.01 6 0.2267 0.7907 0.00 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.63.7020.01 3 0.2807 0.5431 0.00 0.00 0.84 0.00 0.10 0.02 0.00 0.04
#> TCGA.56.8304.01 2 0.2756 0.6556 0.00 0.74 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.39.5029.01 2 0.0000 0.8505 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7465.01 5 0.5073 0.3729 0.32 0.00 0.00 0.00 0.46 0.00 0.22 0.00
#> TCGA.33.4579.01 1 0.2807 0.8154 0.84 0.00 0.00 0.10 0.00 0.02 0.00 0.04
#> TCGA.56.A5DR.01 6 0.1563 0.8019 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.22.5472.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.34.5239.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.7463.01 2 0.0000 0.8505 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.52.7810.01 7 0.3083 0.3162 0.00 0.00 0.00 0.00 0.34 0.00 0.66 0.00
#> TCGA.85.8288.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7221.01 2 0.0000 0.8505 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.98.A538.01 2 0.0471 0.8423 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.39.5035.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.7822.01 7 0.0471 0.5682 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.56.A49D.01 2 0.0000 0.8505 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5492.01 3 0.3426 0.5129 0.00 0.00 0.74 0.00 0.02 0.22 0.00 0.02
#> TCGA.90.7766.01 6 0.3714 -0.0992 0.00 0.00 0.44 0.00 0.00 0.54 0.00 0.02
#> TCGA.43.8116.01 7 0.2852 0.3884 0.00 0.00 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.LA.A7SW.01 3 0.6194 0.2525 0.00 0.00 0.50 0.20 0.20 0.04 0.00 0.06
#> TCGA.96.7544.01 1 0.1275 0.9136 0.94 0.00 0.00 0.00 0.04 0.00 0.02 0.00
#> TCGA.77.A5G7.01 7 0.0000 0.5679 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.56.8307.01 4 0.1563 0.0000 0.00 0.00 0.10 0.90 0.00 0.00 0.00 0.00
#> TCGA.98.A539.01 7 0.5087 0.4695 0.00 0.00 0.08 0.02 0.10 0.06 0.70 0.04
#> TCGA.56.7580.01 7 0.3083 0.3162 0.00 0.00 0.00 0.00 0.34 0.00 0.66 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: Node061. Child nodes: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0612"]
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 '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 0.4254 0.575 0.575
#> 3 3 0.739 0.969 0.942 0.4717 0.765 0.591
#> 4 4 0.791 0.882 0.883 0.1958 0.843 0.564
#> 5 5 0.778 0.837 0.870 0.0665 1.000 1.000
#> 6 6 0.778 0.507 0.733 0.0527 0.954 0.794
#> 7 7 0.791 0.721 0.802 0.0272 0.908 0.517
#> 8 8 0.791 0.552 0.772 0.0325 0.980 0.833
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.43.7656.01 2 0 1 0 1
#> TCGA.98.8020.01 1 0 1 1 0
#> TCGA.NC.A5HI.01 1 0 1 1 0
#> TCGA.94.7557.01 2 0 1 0 1
#> TCGA.94.8035.01 2 0 1 0 1
#> TCGA.77.8140.01 1 0 1 1 0
#> TCGA.22.5478.01 2 0 1 0 1
#> TCGA.63.A5MI.01 2 0 1 0 1
#> TCGA.77.8139.01 2 0 1 0 1
#> TCGA.43.A56V.01 2 0 1 0 1
#> TCGA.56.8304.01 1 0 1 1 0
#> TCGA.39.5029.01 2 0 1 0 1
#> TCGA.56.A5DR.01 2 0 1 0 1
#> TCGA.77.7463.01 2 0 1 0 1
#> TCGA.56.7221.01 2 0 1 0 1
#> TCGA.98.A538.01 2 0 1 0 1
#> TCGA.56.A49D.01 2 0 1 0 1
#> TCGA.90.7766.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.43.7656.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.98.8020.01 1 0.254 0.929 0.92 0.00 0.08
#> TCGA.NC.A5HI.01 1 0.254 0.929 0.92 0.00 0.08
#> TCGA.94.7557.01 3 0.502 0.895 0.00 0.24 0.76
#> TCGA.94.8035.01 3 0.400 0.967 0.00 0.16 0.84
#> TCGA.77.8140.01 1 0.254 0.929 0.92 0.00 0.08
#> TCGA.22.5478.01 3 0.400 0.967 0.00 0.16 0.84
#> TCGA.63.A5MI.01 3 0.400 0.967 0.00 0.16 0.84
#> TCGA.77.8139.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.43.A56V.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.56.8304.01 1 0.254 0.929 0.92 0.00 0.08
#> TCGA.39.5029.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.56.A5DR.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.77.7463.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.56.7221.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.98.A538.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.56.A49D.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.90.7766.01 1 0.000 0.938 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.43.7656.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.98.8020.01 1 0.5062 0.824 0.68 0.00 0.30 0.02
#> TCGA.NC.A5HI.01 1 0.0707 0.838 0.98 0.00 0.00 0.02
#> TCGA.94.7557.01 4 0.1211 0.390 0.00 0.04 0.00 0.96
#> TCGA.94.8035.01 3 0.4406 1.000 0.00 0.00 0.70 0.30
#> TCGA.77.8140.01 1 0.0707 0.838 0.98 0.00 0.00 0.02
#> TCGA.22.5478.01 3 0.4406 1.000 0.00 0.00 0.70 0.30
#> TCGA.63.A5MI.01 3 0.4406 1.000 0.00 0.00 0.70 0.30
#> TCGA.77.8139.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.43.A56V.01 4 0.4624 0.794 0.00 0.34 0.00 0.66
#> TCGA.56.8304.01 1 0.5062 0.824 0.68 0.00 0.30 0.02
#> TCGA.39.5029.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.56.A5DR.01 4 0.4624 0.794 0.00 0.34 0.00 0.66
#> TCGA.77.7463.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.56.7221.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.98.A538.01 4 0.4855 0.724 0.00 0.40 0.00 0.60
#> TCGA.56.A49D.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.90.7766.01 1 0.2647 0.855 0.88 0.00 0.12 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.43.7656.01 2 0.1043 0.905 0.00 0.96 0.00 0.04 0.00
#> TCGA.98.8020.01 1 0.4818 0.765 0.52 0.00 0.00 0.02 0.46
#> TCGA.NC.A5HI.01 1 0.0000 0.720 1.00 0.00 0.00 0.00 0.00
#> TCGA.94.7557.01 4 0.2675 0.811 0.00 0.04 0.02 0.90 0.04
#> TCGA.94.8035.01 3 0.0609 0.970 0.00 0.02 0.98 0.00 0.00
#> TCGA.77.8140.01 1 0.0000 0.720 1.00 0.00 0.00 0.00 0.00
#> TCGA.22.5478.01 3 0.1216 0.967 0.00 0.02 0.96 0.00 0.02
#> TCGA.63.A5MI.01 3 0.2012 0.951 0.00 0.02 0.92 0.00 0.06
#> TCGA.77.8139.01 2 0.1410 0.899 0.00 0.94 0.00 0.00 0.06
#> TCGA.43.A56V.01 4 0.1410 0.842 0.00 0.06 0.00 0.94 0.00
#> TCGA.56.8304.01 1 0.5157 0.767 0.52 0.00 0.00 0.04 0.44
#> TCGA.39.5029.01 2 0.1043 0.905 0.00 0.96 0.00 0.04 0.00
#> TCGA.56.A5DR.01 4 0.2020 0.833 0.00 0.10 0.00 0.90 0.00
#> TCGA.77.7463.01 2 0.2516 0.874 0.00 0.86 0.00 0.00 0.14
#> TCGA.56.7221.01 2 0.2732 0.863 0.00 0.84 0.00 0.00 0.16
#> TCGA.98.A538.01 4 0.6265 0.583 0.00 0.22 0.00 0.54 0.24
#> TCGA.56.A49D.01 2 0.1043 0.905 0.00 0.96 0.00 0.04 0.00
#> TCGA.90.7766.01 1 0.4540 0.784 0.64 0.00 0.02 0.00 0.34
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.43.7656.01 2 0.3864 0.735 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.98.8020.01 5 0.3797 0.000 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.NC.A5HI.01 1 0.0000 0.457 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.94.7557.01 4 0.0547 0.732 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.94.8035.01 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.77.8140.01 1 0.0000 0.457 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.22.5478.01 3 0.1807 0.927 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.63.A5MI.01 3 0.0547 0.954 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.77.8139.01 2 0.3409 0.711 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.43.A56V.01 4 0.2581 0.726 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.56.8304.01 1 0.5882 -0.676 0.42 0.00 0.00 0.00 0.38 0.20
#> TCGA.39.5029.01 2 0.3864 0.735 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.56.A5DR.01 4 0.2631 0.684 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.77.7463.01 2 0.0000 0.590 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.56.7221.01 2 0.0547 0.575 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.98.A538.01 6 0.5987 0.000 0.00 0.00 0.00 0.26 0.30 0.44
#> TCGA.56.A49D.01 2 0.3864 0.735 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.90.7766.01 1 0.3499 -0.177 0.68 0.00 0.00 0.00 0.32 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.43.7656.01 2 0.186 0.768 0.02 0.92 0.00 0.04 0.00 0.00 0.02
#> TCGA.98.8020.01 5 0.117 0.566 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.NC.A5HI.01 1 0.322 1.000 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.94.7557.01 4 0.251 0.714 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.94.8035.01 3 0.000 0.901 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.77.8140.01 1 0.322 1.000 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.22.5478.01 3 0.242 0.861 0.08 0.00 0.88 0.00 0.00 0.02 0.02
#> TCGA.63.A5MI.01 3 0.202 0.871 0.06 0.00 0.90 0.00 0.00 0.00 0.04
#> TCGA.77.8139.01 2 0.337 0.460 0.06 0.78 0.00 0.00 0.00 0.00 0.16
#> TCGA.43.A56V.01 4 0.193 0.765 0.00 0.02 0.00 0.90 0.00 0.08 0.00
#> TCGA.56.8304.01 5 0.398 0.546 0.00 0.00 0.00 0.00 0.72 0.10 0.18
#> TCGA.39.5029.01 2 0.000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.56.A5DR.01 4 0.208 0.734 0.00 0.14 0.00 0.86 0.00 0.00 0.00
#> TCGA.77.7463.01 7 0.350 0.886 0.00 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.56.7221.01 7 0.336 0.893 0.00 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.98.A538.01 6 0.345 0.000 0.00 0.08 0.00 0.14 0.00 0.78 0.00
#> TCGA.56.A49D.01 2 0.000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.90.7766.01 5 0.412 0.348 0.20 0.00 0.00 0.00 0.70 0.10 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.43.7656.01 2 0.2350 0.6424 0.04 0.86 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.98.8020.01 5 0.3169 0.6037 0.00 0.00 0.00 0.00 0.78 0.02 0.02 0.18
#> TCGA.NC.A5HI.01 1 0.2534 1.0000 0.78 0.00 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.94.7557.01 4 0.0000 0.1327 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.94.8035.01 3 0.0000 0.8258 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.77.8140.01 1 0.2534 1.0000 0.78 0.00 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.22.5478.01 3 0.2348 0.7996 0.04 0.00 0.88 0.00 0.00 0.02 0.00 0.06
#> TCGA.63.A5MI.01 3 0.2852 0.7160 0.00 0.00 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.77.8139.01 2 0.5315 0.0862 0.14 0.52 0.00 0.00 0.00 0.00 0.30 0.04
#> TCGA.43.A56V.01 6 0.3193 -0.2341 0.00 0.00 0.00 0.38 0.00 0.62 0.00 0.00
#> TCGA.56.8304.01 5 0.1887 0.5959 0.00 0.00 0.00 0.00 0.90 0.00 0.04 0.06
#> TCGA.39.5029.01 2 0.0471 0.7415 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.56.A5DR.01 4 0.6001 0.1037 0.00 0.30 0.00 0.38 0.00 0.26 0.00 0.06
#> TCGA.77.7463.01 7 0.2406 0.8099 0.00 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.56.7221.01 7 0.1804 0.8258 0.00 0.08 0.00 0.00 0.00 0.00 0.90 0.02
#> TCGA.98.A538.01 6 0.3975 0.2170 0.00 0.08 0.00 0.00 0.00 0.66 0.00 0.26
#> TCGA.56.A49D.01 2 0.0808 0.7386 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.90.7766.01 5 0.3941 0.3351 0.26 0.00 0.00 0.00 0.68 0.04 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node041 , Node042 , Node043 , Node051 , Node052 , Node061 , Node062-leaf , Node071 , Node072 , Node073 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["07"]
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 138 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4936 0.507 0.507
#> 3 3 1.000 0.967 0.987 0.3270 0.839 0.683
#> 4 4 0.737 0.906 0.917 0.1315 0.900 0.714
#> 5 5 0.947 0.930 0.958 0.0792 0.912 0.672
#> 6 6 0.859 0.846 0.892 0.0319 0.965 0.828
#> 7 7 0.801 0.773 0.837 0.0208 0.983 0.906
#> 8 8 0.793 0.753 0.816 0.0147 0.986 0.923
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.77.A5G1.01 2 0 1 0 1
#> TCGA.55.6975.01 2 0 1 0 1
#> TCGA.55.7910.01 1 0 1 1 0
#> TCGA.78.7539.01 1 0 1 1 0
#> TCGA.39.5040.01 2 0 1 0 1
#> TCGA.86.6851.01 1 0 1 1 0
#> TCGA.62.8398.01 2 0 1 0 1
#> TCGA.62.8394.01 1 0 1 1 0
#> TCGA.97.8176.01 2 0 1 0 1
#> TCGA.86.8281.01 2 0 1 0 1
#> TCGA.86.8358.01 2 0 1 0 1
#> TCGA.78.7149.01 2 0 1 0 1
#> TCGA.91.6831.01 2 0 1 0 1
#> TCGA.86.7954.01 1 0 1 1 0
#> TCGA.55.6642.01 2 0 1 0 1
#> TCGA.05.4415.01 2 0 1 0 1
#> TCGA.44.A479.01 1 0 1 1 0
#> TCGA.33.6737.01 2 0 1 0 1
#> TCGA.J2.8194.01 1 0 1 1 0
#> TCGA.55.6968.01 2 0 1 0 1
#> TCGA.55.A57B.01 1 0 1 1 0
#> TCGA.49.AAR0.01 2 0 1 0 1
#> TCGA.75.7027.01 2 0 1 0 1
#> TCGA.50.5072.01 2 0 1 0 1
#> TCGA.55.8512.01 2 0 1 0 1
#> TCGA.O2.A5IC.01 1 0 1 1 0
#> TCGA.86.8279.01 2 0 1 0 1
#> TCGA.55.8096.01 1 0 1 1 0
#> TCGA.44.3917.01 1 0 1 1 0
#> TCGA.53.7624.01 1 0 1 1 0
#> TCGA.55.7913.01 1 0 1 1 0
#> TCGA.33.4566.01 2 0 1 0 1
#> TCGA.78.8640.01 2 0 1 0 1
#> TCGA.44.7670.01 1 0 1 1 0
#> TCGA.L9.A5IP.01 1 0 1 1 0
#> TCGA.55.8615.01 2 0 1 0 1
#> TCGA.MP.A4TF.01 1 0 1 1 0
#> TCGA.62.A471.01 2 0 1 0 1
#> TCGA.49.4490.01 1 0 1 1 0
#> TCGA.NC.A5HK.01 1 0 1 1 0
#> TCGA.05.5425.01 2 0 1 0 1
#> TCGA.50.5066.02 2 0 1 0 1
#> TCGA.55.8092.01 2 0 1 0 1
#> TCGA.75.6207.01 2 0 1 0 1
#> TCGA.49.AARE.01 1 0 1 1 0
#> TCGA.43.5668.01 2 0 1 0 1
#> TCGA.69.7764.01 2 0 1 0 1
#> TCGA.91.6840.01 1 0 1 1 0
#> TCGA.95.7043.01 1 0 1 1 0
#> TCGA.73.4676.01 2 0 1 0 1
#> TCGA.55.8505.01 2 0 1 0 1
#> TCGA.78.7148.01 2 0 1 0 1
#> TCGA.55.8205.01 1 0 1 1 0
#> TCGA.91.6830.01 1 0 1 1 0
#> TCGA.MN.A4N4.01 2 0 1 0 1
#> TCGA.39.5022.01 2 0 1 0 1
#> TCGA.44.8120.01 2 0 1 0 1
#> TCGA.73.A9RS.01 2 0 1 0 1
#> TCGA.70.6722.01 2 0 1 0 1
#> TCGA.69.7979.01 1 0 1 1 0
#> TCGA.95.7039.01 1 0 1 1 0
#> TCGA.91.6848.01 2 0 1 0 1
#> TCGA.33.6738.01 2 0 1 0 1
#> TCGA.43.6773.01 2 0 1 0 1
#> TCGA.78.7146.01 1 0 1 1 0
#> TCGA.49.6743.01 1 0 1 1 0
#> TCGA.78.7161.01 1 0 1 1 0
#> TCGA.44.A4SU.01 1 0 1 1 0
#> TCGA.97.7937.01 2 0 1 0 1
#> TCGA.05.5428.01 2 0 1 0 1
#> TCGA.L9.A8F4.01 1 0 1 1 0
#> TCGA.91.A4BC.01 2 0 1 0 1
#> TCGA.J2.A4AD.01 1 0 1 1 0
#> TCGA.38.4631.01 1 0 1 1 0
#> TCGA.05.4390.01 1 0 1 1 0
#> TCGA.55.6972.01 2 0 1 0 1
#> TCGA.05.4433.01 2 0 1 0 1
#> TCGA.50.5932.01 2 0 1 0 1
#> TCGA.50.7109.01 2 0 1 0 1
#> TCGA.55.8508.01 1 0 1 1 0
#> TCGA.71.6725.01 1 0 1 1 0
#> TCGA.86.8075.01 1 0 1 1 0
#> TCGA.78.7633.01 2 0 1 0 1
#> TCGA.49.4514.01 1 0 1 1 0
#> TCGA.05.4396.01 2 0 1 0 1
#> TCGA.75.5147.01 1 0 1 1 0
#> TCGA.86.7711.01 2 0 1 0 1
#> TCGA.05.5420.01 2 0 1 0 1
#> TCGA.78.7154.01 2 0 1 0 1
#> TCGA.44.7667.01 1 0 1 1 0
#> TCGA.O1.A52J.01 1 0 1 1 0
#> TCGA.78.7167.01 2 0 1 0 1
#> TCGA.05.4427.01 1 0 1 1 0
#> TCGA.86.8585.01 2 0 1 0 1
#> TCGA.78.7147.01 1 0 1 1 0
#> TCGA.55.8085.01 2 0 1 0 1
#> TCGA.MP.A4TE.01 2 0 1 0 1
#> TCGA.78.7542.01 2 0 1 0 1
#> TCGA.49.AAR9.01 2 0 1 0 1
#> TCGA.95.A4VK.01 1 0 1 1 0
#> TCGA.49.4488.01 1 0 1 1 0
#> TCGA.55.7994.01 2 0 1 0 1
#> TCGA.MP.A5C7.01 1 0 1 1 0
#> TCGA.05.4424.01 2 0 1 0 1
#> TCGA.4B.A93V.01 1 0 1 1 0
#> TCGA.86.A4D0.01 2 0 1 0 1
#> TCGA.78.7159.01 1 0 1 1 0
#> TCGA.99.8032.01 2 0 1 0 1
#> TCGA.MP.A4TA.01 1 0 1 1 0
#> TCGA.75.5146.01 2 0 1 0 1
#> TCGA.64.5779.01 2 0 1 0 1
#> TCGA.50.6673.01 1 0 1 1 0
#> TCGA.95.7562.01 2 0 1 0 1
#> TCGA.50.5930.01 2 0 1 0 1
#> TCGA.55.7284.01 2 0 1 0 1
#> TCGA.91.6829.01 2 0 1 0 1
#> TCGA.86.8669.01 2 0 1 0 1
#> TCGA.64.1679.01 1 0 1 1 0
#> TCGA.55.8616.01 1 0 1 1 0
#> TCGA.50.5051.01 1 0 1 1 0
#> TCGA.64.1681.01 1 0 1 1 0
#> TCGA.86.8674.01 2 0 1 0 1
#> TCGA.78.7166.01 2 0 1 0 1
#> TCGA.86.7953.01 1 0 1 1 0
#> TCGA.MP.A4SV.01 2 0 1 0 1
#> TCGA.62.8402.01 1 0 1 1 0
#> TCGA.55.7995.01 1 0 1 1 0
#> TCGA.NJ.A55R.01 2 0 1 0 1
#> TCGA.86.8055.01 2 0 1 0 1
#> TCGA.33.AASB.01 2 0 1 0 1
#> TCGA.78.7156.01 2 0 1 0 1
#> TCGA.55.8506.01 1 0 1 1 0
#> TCGA.53.7813.01 1 0 1 1 0
#> TCGA.97.8179.01 2 0 1 0 1
#> TCGA.86.7713.01 2 0 1 0 1
#> TCGA.62.A46S.01 2 0 1 0 1
#> TCGA.95.7947.01 2 0 1 0 1
#> TCGA.J2.8192.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.77.A5G1.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.55.6975.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.55.7910.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.78.7539.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.39.5040.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.86.6851.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.62.8398.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.62.8394.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.97.8176.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.86.8281.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.86.8358.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.78.7149.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.91.6831.01 3 0.5835 0.4433 0 0.34 0.66
#> TCGA.86.7954.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.6642.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.05.4415.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.44.A479.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.33.6737.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.J2.8194.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.6968.01 2 0.4002 0.8058 0 0.84 0.16
#> TCGA.55.A57B.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.49.AAR0.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.75.7027.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.50.5072.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.55.8512.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.O2.A5IC.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.86.8279.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.55.8096.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.44.3917.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.53.7624.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.7913.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.33.4566.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.78.8640.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.44.7670.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.8615.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.MP.A4TF.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.62.A471.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.49.4490.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.NC.A5HK.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.05.5425.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.50.5066.02 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.55.8092.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.49.AARE.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.43.5668.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.69.7764.01 2 0.6309 0.0248 0 0.50 0.50
#> TCGA.91.6840.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.95.7043.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.73.4676.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.55.8505.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.78.7148.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.55.8205.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.91.6830.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.MN.A4N4.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.39.5022.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.44.8120.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.73.A9RS.01 2 0.1529 0.9328 0 0.96 0.04
#> TCGA.70.6722.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.69.7979.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.95.7039.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.91.6848.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.33.6738.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.43.6773.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.78.7146.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.49.6743.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.78.7161.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.44.A4SU.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.97.7937.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.05.5428.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.L9.A8F4.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.91.A4BC.01 2 0.5397 0.6319 0 0.72 0.28
#> TCGA.J2.A4AD.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.38.4631.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.05.4390.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.6972.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.05.4433.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.50.5932.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.50.7109.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.55.8508.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.71.6725.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.86.8075.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.78.7633.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.49.4514.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.05.4396.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.75.5147.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.86.7711.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.05.5420.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.78.7154.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.44.7667.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.O1.A52J.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.78.7167.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.05.4427.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.86.8585.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.78.7147.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.8085.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.MP.A4TE.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.78.7542.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.49.AAR9.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.95.A4VK.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.49.4488.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.7994.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.MP.A5C7.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.05.4424.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.4B.A93V.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.86.A4D0.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.78.7159.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.99.8032.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.MP.A4TA.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.75.5146.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.64.5779.01 2 0.5216 0.6662 0 0.74 0.26
#> TCGA.50.6673.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.95.7562.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.50.5930.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.55.7284.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.91.6829.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.86.8669.01 2 0.0892 0.9494 0 0.98 0.02
#> TCGA.64.1679.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.8616.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.50.5051.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.64.1681.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.86.8674.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.78.7166.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.86.7953.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.62.8402.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.55.7995.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.NJ.A55R.01 2 0.5216 0.6663 0 0.74 0.26
#> TCGA.86.8055.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.33.AASB.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.78.7156.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.55.8506.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.53.7813.01 1 0.0000 1.0000 1 0.00 0.00
#> TCGA.97.8179.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.86.7713.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.62.A46S.01 2 0.0000 0.9654 0 1.00 0.00
#> TCGA.95.7947.01 3 0.0000 0.9887 0 0.00 1.00
#> TCGA.J2.8192.01 1 0.0000 1.0000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.77.A5G1.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.55.6975.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.55.7910.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.78.7539.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.39.5040.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.86.6851.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.62.8398.01 3 0.5151 0.808 0.10 0.14 0.76 0.00
#> TCGA.62.8394.01 1 0.4624 0.651 0.66 0.00 0.00 0.34
#> TCGA.97.8176.01 3 0.4610 0.829 0.10 0.10 0.80 0.00
#> TCGA.86.8281.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.86.8358.01 2 0.2647 0.899 0.00 0.88 0.12 0.00
#> TCGA.78.7149.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.91.6831.01 3 0.5173 0.424 0.02 0.32 0.66 0.00
#> TCGA.86.7954.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.55.6642.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.05.4415.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.44.A479.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.33.6737.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.J2.8194.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.55.6968.01 2 0.3975 0.783 0.00 0.76 0.24 0.00
#> TCGA.55.A57B.01 4 0.2921 0.813 0.14 0.00 0.00 0.86
#> TCGA.49.AAR0.01 3 0.4610 0.829 0.10 0.10 0.80 0.00
#> TCGA.75.7027.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.50.5072.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.55.8512.01 3 0.4610 0.829 0.10 0.10 0.80 0.00
#> TCGA.O2.A5IC.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.86.8279.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.55.8096.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.44.3917.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.53.7624.01 1 0.2706 0.959 0.90 0.00 0.02 0.08
#> TCGA.55.7913.01 1 0.3172 0.925 0.84 0.00 0.00 0.16
#> TCGA.33.4566.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.78.8640.01 3 0.0707 0.894 0.00 0.02 0.98 0.00
#> TCGA.44.7670.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.L9.A5IP.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.55.8615.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.MP.A4TF.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.62.A471.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.49.4490.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.NC.A5HK.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.05.5425.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.50.5066.02 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.55.8092.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.75.6207.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.49.AARE.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.43.5668.01 3 0.0707 0.894 0.00 0.02 0.98 0.00
#> TCGA.69.7764.01 3 0.6831 0.302 0.10 0.42 0.48 0.00
#> TCGA.91.6840.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.95.7043.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.73.4676.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.55.8505.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.78.7148.01 3 0.4894 0.821 0.10 0.12 0.78 0.00
#> TCGA.55.8205.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.91.6830.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.MN.A4N4.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.39.5022.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.44.8120.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.73.A9RS.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.70.6722.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.69.7979.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.95.7039.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.91.6848.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.33.6738.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.43.6773.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.78.7146.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.49.6743.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.78.7161.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.44.A4SU.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.97.7937.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.05.5428.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.L9.A8F4.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.91.A4BC.01 2 0.4855 0.492 0.00 0.60 0.40 0.00
#> TCGA.J2.A4AD.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.38.4631.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.05.4390.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.55.6972.01 3 0.5151 0.808 0.10 0.14 0.76 0.00
#> TCGA.05.4433.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.50.5932.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.50.7109.01 2 0.0707 0.861 0.02 0.98 0.00 0.00
#> TCGA.55.8508.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.71.6725.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.86.8075.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.78.7633.01 2 0.3037 0.814 0.10 0.88 0.02 0.00
#> TCGA.49.4514.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.05.4396.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.75.5147.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.86.7711.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.05.5420.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.78.7154.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.44.7667.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.O1.A52J.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.78.7167.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.05.4427.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.86.8585.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.78.7147.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.55.8085.01 2 0.3037 0.814 0.10 0.88 0.02 0.00
#> TCGA.MP.A4TE.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.78.7542.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.49.AAR9.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.95.A4VK.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.49.4488.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.55.7994.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.MP.A5C7.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.05.4424.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.4B.A93V.01 1 0.2921 0.945 0.86 0.00 0.00 0.14
#> TCGA.86.A4D0.01 2 0.2647 0.899 0.00 0.88 0.12 0.00
#> TCGA.78.7159.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.99.8032.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.MP.A4TA.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.75.5146.01 3 0.5151 0.808 0.10 0.14 0.76 0.00
#> TCGA.64.5779.01 2 0.4624 0.621 0.00 0.66 0.34 0.00
#> TCGA.50.6673.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.95.7562.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.50.5930.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.55.7284.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.91.6829.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.86.8669.01 2 0.3935 0.782 0.10 0.84 0.06 0.00
#> TCGA.64.1679.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.55.8616.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.50.5051.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.64.1681.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.86.8674.01 3 0.4610 0.829 0.10 0.10 0.80 0.00
#> TCGA.78.7166.01 3 0.4894 0.821 0.10 0.12 0.78 0.00
#> TCGA.86.7953.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.MP.A4SV.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.62.8402.01 1 0.3801 0.852 0.78 0.00 0.00 0.22
#> TCGA.55.7995.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
#> TCGA.NJ.A55R.01 2 0.4277 0.727 0.00 0.72 0.28 0.00
#> TCGA.86.8055.01 3 0.0000 0.907 0.00 0.00 1.00 0.00
#> TCGA.33.AASB.01 2 0.2345 0.909 0.00 0.90 0.10 0.00
#> TCGA.78.7156.01 3 0.4610 0.829 0.10 0.10 0.80 0.00
#> TCGA.55.8506.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.53.7813.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.97.8179.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.86.7713.01 2 0.2345 0.828 0.10 0.90 0.00 0.00
#> TCGA.62.A46S.01 2 0.1637 0.846 0.06 0.94 0.00 0.00
#> TCGA.95.7947.01 3 0.1211 0.882 0.00 0.04 0.96 0.00
#> TCGA.J2.8192.01 1 0.2345 0.982 0.90 0.00 0.00 0.10
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.77.A5G1.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.6975.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7910.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.39.5040.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.6851.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.62.8398.01 5 0.0609 0.913 0.00 0.00 0.02 0.00 0.98
#> TCGA.62.8394.01 1 0.4360 0.559 0.68 0.00 0.00 0.30 0.02
#> TCGA.97.8176.01 5 0.1732 0.879 0.00 0.00 0.08 0.00 0.92
#> TCGA.86.8281.01 5 0.0609 0.915 0.00 0.02 0.00 0.00 0.98
#> TCGA.86.8358.01 2 0.2077 0.901 0.00 0.92 0.04 0.00 0.04
#> TCGA.78.7149.01 5 0.1732 0.888 0.00 0.08 0.00 0.00 0.92
#> TCGA.91.6831.01 5 0.6146 0.492 0.00 0.20 0.24 0.00 0.56
#> TCGA.86.7954.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6642.01 2 0.1410 0.908 0.00 0.94 0.00 0.00 0.06
#> TCGA.05.4415.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.A479.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.6737.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.J2.8194.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.55.6968.01 2 0.3291 0.833 0.00 0.84 0.12 0.00 0.04
#> TCGA.55.A57B.01 4 0.3513 0.789 0.18 0.00 0.00 0.80 0.02
#> TCGA.49.AAR0.01 5 0.1410 0.895 0.00 0.00 0.06 0.00 0.94
#> TCGA.75.7027.01 5 0.3424 0.703 0.00 0.24 0.00 0.00 0.76
#> TCGA.50.5072.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8512.01 5 0.1043 0.904 0.00 0.00 0.04 0.00 0.96
#> TCGA.O2.A5IC.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8279.01 5 0.1216 0.912 0.00 0.02 0.00 0.02 0.96
#> TCGA.55.8096.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.3917.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.53.7624.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.55.7913.01 1 0.1043 0.948 0.96 0.00 0.00 0.04 0.00
#> TCGA.33.4566.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.8640.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.7670.01 1 0.1648 0.941 0.94 0.00 0.00 0.04 0.02
#> TCGA.L9.A5IP.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8615.01 5 0.2516 0.838 0.00 0.14 0.00 0.00 0.86
#> TCGA.MP.A4TF.01 4 0.1216 0.978 0.02 0.00 0.00 0.96 0.02
#> TCGA.62.A471.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.49.4490.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.NC.A5HK.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.05.5425.01 2 0.2012 0.901 0.00 0.92 0.00 0.02 0.06
#> TCGA.50.5066.02 2 0.1216 0.922 0.00 0.96 0.00 0.02 0.02
#> TCGA.55.8092.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AARE.01 4 0.1216 0.978 0.02 0.00 0.00 0.96 0.02
#> TCGA.43.5668.01 3 0.0609 0.977 0.00 0.02 0.98 0.00 0.00
#> TCGA.69.7764.01 5 0.0609 0.913 0.00 0.00 0.02 0.00 0.98
#> TCGA.91.6840.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 4 0.1216 0.978 0.02 0.00 0.00 0.96 0.02
#> TCGA.73.4676.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8505.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7148.01 5 0.0609 0.913 0.00 0.00 0.02 0.00 0.98
#> TCGA.55.8205.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.91.6830.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 2 0.0609 0.932 0.00 0.98 0.00 0.02 0.00
#> TCGA.39.5022.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.44.8120.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.73.A9RS.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.70.6722.01 3 0.0609 0.981 0.00 0.00 0.98 0.02 0.00
#> TCGA.69.7979.01 4 0.1216 0.978 0.02 0.00 0.00 0.96 0.02
#> TCGA.95.7039.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.91.6848.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.33.6738.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.43.6773.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7146.01 4 0.1216 0.978 0.02 0.00 0.00 0.96 0.02
#> TCGA.49.6743.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7161.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.44.A4SU.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.97.7937.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 2 0.4456 0.571 0.00 0.66 0.32 0.00 0.02
#> TCGA.J2.A4AD.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.38.4631.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.05.4390.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.55.6972.01 5 0.0609 0.913 0.00 0.00 0.02 0.00 0.98
#> TCGA.05.4433.01 2 0.0609 0.932 0.00 0.98 0.00 0.02 0.00
#> TCGA.50.5932.01 5 0.0609 0.915 0.00 0.02 0.00 0.00 0.98
#> TCGA.50.7109.01 2 0.3895 0.520 0.00 0.68 0.00 0.00 0.32
#> TCGA.55.8508.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.71.6725.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.86.8075.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7633.01 5 0.0609 0.915 0.00 0.02 0.00 0.00 0.98
#> TCGA.49.4514.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4396.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.75.5147.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.86.7711.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.05.5420.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7154.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.7667.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.O1.A52J.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7167.01 5 0.2020 0.875 0.00 0.10 0.00 0.00 0.90
#> TCGA.05.4427.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.86.8585.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7147.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.55.8085.01 5 0.0609 0.915 0.00 0.02 0.00 0.00 0.98
#> TCGA.MP.A4TE.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7542.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.AAR9.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.A4VK.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.49.4488.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.55.7994.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.05.4424.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.4B.A93V.01 1 0.1410 0.929 0.94 0.00 0.00 0.06 0.00
#> TCGA.86.A4D0.01 2 0.1648 0.913 0.00 0.94 0.02 0.00 0.04
#> TCGA.78.7159.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.99.8032.01 2 0.1410 0.908 0.00 0.94 0.00 0.00 0.06
#> TCGA.MP.A4TA.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.5146.01 5 0.0609 0.913 0.00 0.00 0.02 0.00 0.98
#> TCGA.64.5779.01 2 0.5050 0.689 0.00 0.70 0.18 0.00 0.12
#> TCGA.50.6673.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.95.7562.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5930.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7284.01 2 0.2616 0.858 0.00 0.88 0.00 0.02 0.10
#> TCGA.91.6829.01 2 0.0609 0.932 0.00 0.98 0.00 0.02 0.00
#> TCGA.86.8669.01 5 0.1410 0.901 0.00 0.06 0.00 0.00 0.94
#> TCGA.64.1679.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.50.5051.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.64.1681.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8674.01 5 0.2280 0.843 0.00 0.00 0.12 0.00 0.88
#> TCGA.78.7166.01 5 0.1043 0.904 0.00 0.00 0.04 0.00 0.96
#> TCGA.86.7953.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.8402.01 1 0.2516 0.844 0.86 0.00 0.00 0.14 0.00
#> TCGA.55.7995.01 1 0.0609 0.969 0.98 0.00 0.00 0.00 0.02
#> TCGA.NJ.A55R.01 2 0.3922 0.769 0.00 0.78 0.18 0.00 0.04
#> TCGA.86.8055.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.33.AASB.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.78.7156.01 5 0.0609 0.913 0.00 0.00 0.02 0.00 0.98
#> TCGA.55.8506.01 4 0.0609 0.988 0.02 0.00 0.00 0.98 0.00
#> TCGA.53.7813.01 4 0.1410 0.952 0.06 0.00 0.00 0.94 0.00
#> TCGA.97.8179.01 5 0.2020 0.875 0.00 0.10 0.00 0.00 0.90
#> TCGA.86.7713.01 5 0.0609 0.915 0.00 0.02 0.00 0.00 0.98
#> TCGA.62.A46S.01 5 0.4287 0.165 0.00 0.46 0.00 0.00 0.54
#> TCGA.95.7947.01 3 0.1043 0.956 0.00 0.04 0.96 0.00 0.00
#> TCGA.J2.8192.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.77.A5G1.01 3 0.0937 0.9647 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.6975.01 3 0.0547 0.9658 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.55.7910.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 4 0.1267 0.9349 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.39.5040.01 3 0.0547 0.9550 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.86.6851.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.62.8398.01 5 0.2260 0.8425 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.62.8394.01 1 0.4246 0.3624 0.58 0.00 0.00 0.40 0.00 0.02
#> TCGA.97.8176.01 5 0.2794 0.8389 0.00 0.00 0.08 0.00 0.86 0.06
#> TCGA.86.8281.01 5 0.1814 0.8735 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.86.8358.01 6 0.5071 0.6265 0.00 0.40 0.08 0.00 0.00 0.52
#> TCGA.78.7149.01 5 0.2474 0.8564 0.00 0.04 0.00 0.00 0.88 0.08
#> TCGA.91.6831.01 6 0.6649 0.6424 0.00 0.24 0.12 0.00 0.12 0.52
#> TCGA.86.7954.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6642.01 6 0.3851 0.5309 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.05.4415.01 3 0.0000 0.9640 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.44.A479.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.6737.01 2 0.1480 0.8847 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.J2.8194.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.55.6968.01 6 0.5371 0.6433 0.00 0.36 0.12 0.00 0.00 0.52
#> TCGA.55.A57B.01 4 0.4503 0.5666 0.24 0.00 0.00 0.68 0.00 0.08
#> TCGA.49.AAR0.01 5 0.4004 0.7613 0.00 0.00 0.12 0.00 0.76 0.12
#> TCGA.75.7027.01 5 0.5490 0.3466 0.00 0.18 0.00 0.00 0.56 0.26
#> TCGA.50.5072.01 3 0.0000 0.9640 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8512.01 5 0.2190 0.8641 0.00 0.00 0.04 0.00 0.90 0.06
#> TCGA.O2.A5IC.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8279.01 5 0.1556 0.8697 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.55.8096.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.3917.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.53.7624.01 1 0.2048 0.8995 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.55.7913.01 1 0.2794 0.8544 0.86 0.00 0.00 0.08 0.00 0.06
#> TCGA.33.4566.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.8640.01 3 0.1807 0.8940 0.00 0.06 0.92 0.00 0.00 0.02
#> TCGA.44.7670.01 1 0.3163 0.8651 0.82 0.00 0.00 0.04 0.00 0.14
#> TCGA.L9.A5IP.01 1 0.0937 0.9246 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.55.8615.01 6 0.4902 -0.2309 0.00 0.06 0.00 0.00 0.46 0.48
#> TCGA.MP.A4TF.01 4 0.1814 0.8840 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.62.A471.01 3 0.0000 0.9640 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.49.4490.01 1 0.1556 0.9139 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.NC.A5HK.01 1 0.2260 0.8885 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.05.5425.01 2 0.4002 0.2274 0.00 0.66 0.00 0.00 0.02 0.32
#> TCGA.50.5066.02 2 0.1807 0.8620 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.55.8092.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARE.01 4 0.2048 0.8690 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.43.5668.01 3 0.1480 0.9232 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.69.7764.01 5 0.0937 0.8771 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.91.6840.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 4 0.1556 0.8965 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.73.4676.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8505.01 3 0.0547 0.9658 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.78.7148.01 5 0.1814 0.8636 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.55.8205.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.6830.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 2 0.1865 0.8606 0.00 0.92 0.04 0.00 0.00 0.04
#> TCGA.39.5022.01 3 0.0937 0.9647 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.44.8120.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.A9RS.01 2 0.1807 0.8479 0.00 0.92 0.06 0.00 0.00 0.02
#> TCGA.70.6722.01 3 0.1480 0.9532 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.69.7979.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.7039.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.6848.01 3 0.0000 0.9640 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.33.6738.01 3 0.0547 0.9550 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.43.6773.01 3 0.0937 0.9647 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.78.7146.01 4 0.0547 0.9307 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.49.6743.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7161.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.44.A4SU.01 1 0.0547 0.9293 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.97.7937.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 6 0.5736 0.5956 0.00 0.34 0.18 0.00 0.00 0.48
#> TCGA.J2.A4AD.01 1 0.2048 0.8993 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.38.4631.01 1 0.2260 0.8885 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.05.4390.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.55.6972.01 5 0.0547 0.8703 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.05.4433.01 2 0.2048 0.7913 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.50.5932.01 5 0.1814 0.8768 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.50.7109.01 6 0.5144 0.6261 0.00 0.34 0.00 0.00 0.10 0.56
#> TCGA.55.8508.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.71.6725.01 4 0.0547 0.9374 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.86.8075.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7633.01 5 0.1556 0.8721 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.49.4514.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4396.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.5147.01 1 0.2350 0.9007 0.88 0.00 0.00 0.02 0.00 0.10
#> TCGA.86.7711.01 3 0.0547 0.9638 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.05.5420.01 3 0.0937 0.9647 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.78.7154.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.7667.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.O1.A52J.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7167.01 5 0.2790 0.8565 0.00 0.02 0.00 0.00 0.84 0.14
#> TCGA.05.4427.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8585.01 3 0.0937 0.9647 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.78.7147.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8085.01 5 0.1556 0.8713 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.MP.A4TE.01 2 0.0547 0.9115 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.78.7542.01 2 0.0547 0.9127 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.49.AAR9.01 3 0.0547 0.9589 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.95.A4VK.01 4 0.1267 0.9349 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.49.4488.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.7994.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.05.4424.01 3 0.0937 0.9647 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.4B.A93V.01 1 0.2794 0.8342 0.86 0.00 0.00 0.08 0.00 0.06
#> TCGA.86.A4D0.01 6 0.4328 0.5400 0.00 0.46 0.02 0.00 0.00 0.52
#> TCGA.78.7159.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.99.8032.01 6 0.4310 0.5701 0.00 0.44 0.02 0.00 0.00 0.54
#> TCGA.MP.A4TA.01 1 0.1814 0.9068 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.75.5146.01 5 0.1556 0.8726 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.64.5779.01 6 0.5083 0.6638 0.00 0.32 0.10 0.00 0.00 0.58
#> TCGA.50.6673.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.95.7562.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.5930.01 3 0.0937 0.9647 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.7284.01 2 0.4462 0.2985 0.00 0.66 0.00 0.00 0.06 0.28
#> TCGA.91.6829.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8669.01 6 0.4246 0.0219 0.00 0.02 0.00 0.00 0.40 0.58
#> TCGA.64.1679.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.50.5051.01 4 0.1814 0.9273 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.64.1681.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8674.01 5 0.2956 0.7830 0.00 0.00 0.12 0.00 0.84 0.04
#> TCGA.78.7166.01 5 0.2350 0.8615 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.86.7953.01 1 0.0000 0.9333 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.62.8402.01 1 0.4121 0.6483 0.72 0.00 0.00 0.22 0.00 0.06
#> TCGA.55.7995.01 1 0.2048 0.8995 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.NJ.A55R.01 6 0.5523 0.6372 0.00 0.36 0.14 0.00 0.00 0.50
#> TCGA.86.8055.01 3 0.0547 0.9658 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.33.AASB.01 2 0.0000 0.9264 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7156.01 5 0.0547 0.8703 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.55.8506.01 4 0.0000 0.9376 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.53.7813.01 4 0.3321 0.8661 0.08 0.00 0.00 0.82 0.00 0.10
#> TCGA.97.8179.01 5 0.2956 0.8519 0.00 0.04 0.00 0.00 0.84 0.12
#> TCGA.86.7713.01 5 0.4144 0.5342 0.00 0.02 0.00 0.00 0.62 0.36
#> TCGA.62.A46S.01 6 0.5481 0.2543 0.00 0.14 0.00 0.00 0.34 0.52
#> TCGA.95.7947.01 3 0.2956 0.7987 0.00 0.04 0.84 0.00 0.00 0.12
#> TCGA.J2.8192.01 1 0.0000 0.9333 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.77.A5G1.01 3 0.3449 0.8524 0.00 0.00 0.78 0.00 0.00 0.14 0.08
#> TCGA.55.6975.01 3 0.0504 0.8945 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.7910.01 1 0.0504 0.8828 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.78.7539.01 4 0.1928 0.8656 0.00 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.39.5040.01 3 0.0000 0.8918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.6851.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.62.8398.01 5 0.4998 0.6089 0.00 0.00 0.00 0.00 0.54 0.14 0.32
#> TCGA.62.8394.01 4 0.3968 0.0650 0.44 0.00 0.00 0.54 0.00 0.02 0.00
#> TCGA.97.8176.01 5 0.5352 0.6876 0.00 0.00 0.06 0.00 0.62 0.12 0.20
#> TCGA.86.8281.01 5 0.2163 0.7556 0.00 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.86.8358.01 7 0.5597 0.6335 0.00 0.24 0.16 0.00 0.00 0.04 0.56
#> TCGA.78.7149.01 5 0.3061 0.7088 0.00 0.08 0.00 0.00 0.84 0.02 0.06
#> TCGA.91.6831.01 7 0.5308 0.5886 0.00 0.04 0.26 0.00 0.04 0.04 0.62
#> TCGA.86.7954.01 1 0.0863 0.8807 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.55.6642.01 7 0.4354 0.6279 0.00 0.26 0.02 0.00 0.02 0.02 0.68
#> TCGA.05.4415.01 3 0.0000 0.8918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A479.01 1 0.0504 0.8828 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.33.6737.01 2 0.4620 0.6590 0.00 0.72 0.08 0.00 0.00 0.10 0.10
#> TCGA.J2.8194.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.55.6968.01 7 0.5628 0.6461 0.00 0.18 0.22 0.00 0.00 0.04 0.56
#> TCGA.55.A57B.01 4 0.4873 0.4342 0.22 0.00 0.00 0.60 0.00 0.18 0.00
#> TCGA.49.AAR0.01 5 0.5795 0.5287 0.00 0.00 0.10 0.00 0.56 0.10 0.24
#> TCGA.75.7027.01 7 0.5945 0.2913 0.00 0.10 0.00 0.00 0.18 0.16 0.56
#> TCGA.50.5072.01 3 0.0863 0.8935 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.55.8512.01 5 0.5052 0.6561 0.00 0.00 0.02 0.00 0.62 0.14 0.22
#> TCGA.O2.A5IC.01 1 0.0863 0.8830 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.86.8279.01 5 0.2313 0.7400 0.00 0.00 0.00 0.00 0.88 0.06 0.06
#> TCGA.55.8096.01 1 0.0504 0.8842 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.44.3917.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.53.7624.01 1 0.3047 0.8009 0.72 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.55.7913.01 1 0.3835 0.7652 0.74 0.00 0.00 0.10 0.00 0.16 0.00
#> TCGA.33.4566.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.8640.01 3 0.1006 0.8690 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.44.7670.01 1 0.4191 0.7397 0.64 0.00 0.00 0.06 0.00 0.30 0.00
#> TCGA.L9.A5IP.01 1 0.1886 0.8656 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.55.8615.01 7 0.4963 0.3917 0.00 0.06 0.00 0.00 0.24 0.06 0.64
#> TCGA.MP.A4TF.01 4 0.2259 0.7878 0.00 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.62.A471.01 3 0.0000 0.8918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4490.01 1 0.2945 0.8229 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.NC.A5HK.01 1 0.3139 0.7850 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.05.5425.01 7 0.5480 0.4214 0.00 0.36 0.02 0.00 0.08 0.02 0.52
#> TCGA.50.5066.02 2 0.3680 0.7601 0.00 0.78 0.00 0.00 0.02 0.06 0.14
#> TCGA.55.8092.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.6207.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.AARE.01 4 0.2422 0.7747 0.00 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.43.5668.01 3 0.0504 0.8841 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.69.7764.01 5 0.1433 0.7569 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.91.6840.01 1 0.1166 0.8837 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.95.7043.01 4 0.2422 0.7747 0.00 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.73.4676.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8505.01 3 0.1433 0.8928 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.78.7148.01 5 0.4033 0.7119 0.00 0.00 0.00 0.00 0.70 0.08 0.22
#> TCGA.55.8205.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.6830.01 1 0.0504 0.8842 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.MN.A4N4.01 2 0.3149 0.7913 0.00 0.84 0.06 0.00 0.00 0.04 0.06
#> TCGA.39.5022.01 3 0.2722 0.8758 0.00 0.00 0.84 0.00 0.00 0.12 0.04
#> TCGA.44.8120.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.A9RS.01 2 0.3965 0.7039 0.00 0.76 0.12 0.00 0.00 0.02 0.10
#> TCGA.70.6722.01 3 0.4742 0.7056 0.00 0.00 0.62 0.00 0.00 0.22 0.16
#> TCGA.69.7979.01 4 0.0504 0.8709 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.95.7039.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.6848.01 3 0.0000 0.8918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.33.6738.01 3 0.0000 0.8918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.6773.01 3 0.3449 0.8524 0.00 0.00 0.78 0.00 0.00 0.14 0.08
#> TCGA.78.7146.01 4 0.0504 0.8709 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.49.6743.01 1 0.1433 0.8755 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.78.7161.01 4 0.2569 0.8524 0.00 0.00 0.00 0.84 0.00 0.14 0.02
#> TCGA.44.A4SU.01 1 0.1166 0.8846 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.97.7937.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5428.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.0000 0.8848 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 7 0.5635 0.4755 0.00 0.12 0.34 0.00 0.00 0.04 0.50
#> TCGA.J2.A4AD.01 1 0.2832 0.8211 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.38.4631.01 1 0.3139 0.7850 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.05.4390.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.55.6972.01 5 0.0000 0.7555 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.05.4433.01 2 0.3388 0.6858 0.00 0.76 0.00 0.00 0.00 0.04 0.20
#> TCGA.50.5932.01 5 0.3526 0.7232 0.00 0.00 0.00 0.00 0.76 0.06 0.18
#> TCGA.50.7109.01 7 0.4030 0.6172 0.00 0.16 0.00 0.00 0.12 0.00 0.72
#> TCGA.55.8508.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.71.6725.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8075.01 1 0.0863 0.8807 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.78.7633.01 5 0.1363 0.7506 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.49.4514.01 1 0.0000 0.8848 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4396.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.5147.01 1 0.2945 0.8103 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.86.7711.01 3 0.2512 0.8809 0.00 0.00 0.86 0.00 0.00 0.10 0.04
#> TCGA.05.5420.01 3 0.3370 0.8564 0.00 0.00 0.78 0.00 0.00 0.16 0.06
#> TCGA.78.7154.01 2 0.1860 0.8609 0.00 0.92 0.02 0.00 0.00 0.02 0.04
#> TCGA.44.7667.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.O1.A52J.01 1 0.0863 0.8807 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.78.7167.01 5 0.5276 0.5972 0.00 0.10 0.00 0.00 0.64 0.08 0.18
#> TCGA.05.4427.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.86.8585.01 3 0.3370 0.8564 0.00 0.00 0.78 0.00 0.00 0.16 0.06
#> TCGA.78.7147.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.8085.01 5 0.1718 0.7523 0.00 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.MP.A4TE.01 2 0.1363 0.8625 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.78.7542.01 2 0.1363 0.8733 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.49.AAR9.01 3 0.0863 0.8830 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.95.A4VK.01 4 0.1166 0.8737 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.49.4488.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7994.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.05.4424.01 3 0.3370 0.8523 0.00 0.00 0.78 0.00 0.00 0.16 0.06
#> TCGA.4B.A93V.01 1 0.3263 0.7501 0.80 0.00 0.00 0.08 0.00 0.12 0.00
#> TCGA.86.A4D0.01 7 0.5128 0.6480 0.00 0.24 0.10 0.00 0.00 0.04 0.62
#> TCGA.78.7159.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.99.8032.01 7 0.4211 0.6297 0.00 0.26 0.04 0.00 0.00 0.02 0.68
#> TCGA.MP.A4TA.01 1 0.2572 0.8388 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.75.5146.01 5 0.4248 0.6705 0.00 0.00 0.00 0.00 0.66 0.08 0.26
#> TCGA.64.5779.01 7 0.4708 0.6186 0.00 0.08 0.26 0.00 0.00 0.02 0.64
#> TCGA.50.6673.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.95.7562.01 2 0.0504 0.8918 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.50.5930.01 3 0.3370 0.8564 0.00 0.00 0.78 0.00 0.00 0.16 0.06
#> TCGA.55.7284.01 2 0.5751 -0.0189 0.00 0.48 0.00 0.00 0.10 0.06 0.36
#> TCGA.91.6829.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8669.01 7 0.3755 0.2647 0.00 0.02 0.00 0.00 0.34 0.00 0.64
#> TCGA.64.1679.01 1 0.0504 0.8842 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.55.8616.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.50.5051.01 4 0.2745 0.8470 0.00 0.00 0.00 0.82 0.00 0.16 0.02
#> TCGA.64.1681.01 1 0.0863 0.8807 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.86.8674.01 5 0.5977 0.5575 0.00 0.00 0.18 0.00 0.56 0.14 0.12
#> TCGA.78.7166.01 5 0.5498 0.6407 0.00 0.00 0.02 0.00 0.54 0.18 0.26
#> TCGA.86.7953.01 1 0.0504 0.8828 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.MP.A4SV.01 2 0.0000 0.8993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.62.8402.01 1 0.4204 0.6720 0.70 0.00 0.00 0.16 0.00 0.14 0.00
#> TCGA.55.7995.01 1 0.2832 0.8211 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.NJ.A55R.01 7 0.5218 0.6611 0.00 0.18 0.20 0.00 0.00 0.02 0.60
#> TCGA.86.8055.01 3 0.0863 0.8961 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.33.AASB.01 2 0.1006 0.8878 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.78.7156.01 5 0.0504 0.7582 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.55.8506.01 4 0.0000 0.8768 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.53.7813.01 4 0.4963 0.6922 0.16 0.00 0.00 0.64 0.00 0.18 0.02
#> TCGA.97.8179.01 5 0.4779 0.6380 0.00 0.10 0.00 0.00 0.68 0.04 0.18
#> TCGA.86.7713.01 7 0.4787 0.0792 0.00 0.00 0.00 0.00 0.30 0.12 0.58
#> TCGA.62.A46S.01 7 0.4478 0.5270 0.00 0.14 0.00 0.00 0.20 0.00 0.66
#> TCGA.95.7947.01 3 0.2563 0.7813 0.00 0.04 0.88 0.00 0.00 0.04 0.04
#> TCGA.J2.8192.01 1 0.0863 0.8807 0.96 0.00 0.00 0.00 0.00 0.04 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.77.A5G1.01 3 0.2534 0.8214 0.00 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6975.01 3 0.0808 0.8506 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.55.7910.01 1 0.1557 0.8151 0.92 0.06 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.78.7539.01 4 0.1341 0.8436 0.00 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.39.5040.01 3 0.1804 0.8299 0.00 0.02 0.90 0.00 0.00 0.08 0.00 0.00
#> TCGA.86.6851.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.62.8398.01 5 0.4041 0.7590 0.00 0.22 0.00 0.00 0.70 0.04 0.04 0.00
#> TCGA.62.8394.01 1 0.5618 -0.0512 0.38 0.02 0.00 0.30 0.00 0.00 0.30 0.00
#> TCGA.97.8176.01 5 0.3385 0.7690 0.00 0.16 0.08 0.00 0.76 0.00 0.00 0.00
#> TCGA.86.8281.01 5 0.1275 0.7993 0.00 0.02 0.00 0.00 0.94 0.04 0.00 0.00
#> TCGA.86.8358.01 6 0.3675 0.7259 0.00 0.00 0.08 0.00 0.00 0.76 0.02 0.14
#> TCGA.78.7149.01 5 0.4061 0.6902 0.00 0.14 0.00 0.00 0.72 0.00 0.02 0.12
#> TCGA.91.6831.01 6 0.3580 0.7170 0.00 0.02 0.10 0.00 0.04 0.80 0.00 0.04
#> TCGA.86.7954.01 1 0.0000 0.8303 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6642.01 6 0.4174 0.6646 0.00 0.02 0.00 0.00 0.04 0.70 0.02 0.22
#> TCGA.05.4415.01 3 0.0471 0.8538 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.44.A479.01 1 0.0808 0.8271 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.33.6737.01 8 0.4699 0.6829 0.00 0.12 0.10 0.00 0.00 0.10 0.00 0.68
#> TCGA.J2.8194.01 4 0.0941 0.8114 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.55.6968.01 6 0.3227 0.7330 0.00 0.00 0.08 0.00 0.00 0.78 0.00 0.14
#> TCGA.55.A57B.01 4 0.4199 0.6878 0.06 0.00 0.00 0.52 0.00 0.00 0.42 0.00
#> TCGA.49.AAR0.01 5 0.4627 0.6660 0.00 0.10 0.14 0.00 0.70 0.04 0.02 0.00
#> TCGA.75.7027.01 5 0.6574 0.2292 0.00 0.18 0.00 0.00 0.42 0.28 0.06 0.06
#> TCGA.50.5072.01 3 0.0941 0.8544 0.00 0.02 0.96 0.00 0.00 0.02 0.00 0.00
#> TCGA.55.8512.01 5 0.3483 0.7546 0.00 0.18 0.04 0.00 0.76 0.02 0.00 0.00
#> TCGA.O2.A5IC.01 1 0.1341 0.8279 0.92 0.00 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.86.8279.01 5 0.3913 0.7287 0.00 0.16 0.00 0.00 0.74 0.04 0.06 0.00
#> TCGA.55.8096.01 1 0.0000 0.8303 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.3917.01 4 0.0471 0.8188 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.53.7624.01 1 0.4672 0.7156 0.62 0.12 0.02 0.00 0.00 0.00 0.24 0.00
#> TCGA.55.7913.01 1 0.4799 0.5788 0.62 0.04 0.00 0.24 0.00 0.00 0.10 0.00
#> TCGA.33.4566.01 8 0.2020 0.8211 0.00 0.02 0.06 0.00 0.00 0.02 0.00 0.90
#> TCGA.78.8640.01 3 0.2132 0.8206 0.00 0.04 0.88 0.00 0.00 0.08 0.00 0.00
#> TCGA.44.7670.01 1 0.4340 0.6564 0.54 0.08 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.L9.A5IP.01 1 0.2350 0.8193 0.86 0.04 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.55.8615.01 6 0.5712 0.3074 0.00 0.10 0.00 0.00 0.28 0.50 0.12 0.00
#> TCGA.MP.A4TF.01 4 0.3272 0.7473 0.00 0.00 0.00 0.58 0.00 0.00 0.42 0.00
#> TCGA.62.A471.01 3 0.1275 0.8458 0.00 0.02 0.94 0.00 0.00 0.04 0.00 0.00
#> TCGA.49.4490.01 1 0.3036 0.7874 0.78 0.04 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.NC.A5HK.01 1 0.4302 0.6776 0.56 0.08 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.05.5425.01 8 0.6177 0.0660 0.00 0.10 0.02 0.00 0.06 0.36 0.02 0.44
#> TCGA.50.5066.02 8 0.4794 0.6931 0.00 0.16 0.02 0.00 0.04 0.06 0.02 0.70
#> TCGA.55.8092.01 8 0.0471 0.8463 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.75.6207.01 8 0.0000 0.8488 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.AARE.01 4 0.3690 0.7273 0.00 0.02 0.00 0.56 0.00 0.00 0.42 0.00
#> TCGA.43.5668.01 3 0.2020 0.8302 0.00 0.02 0.90 0.00 0.00 0.06 0.00 0.02
#> TCGA.69.7764.01 5 0.0000 0.7967 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.6840.01 1 0.2165 0.8226 0.88 0.06 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.95.7043.01 4 0.3658 0.7461 0.00 0.02 0.00 0.58 0.00 0.00 0.40 0.00
#> TCGA.73.4676.01 8 0.0000 0.8488 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.8505.01 3 0.0808 0.8536 0.00 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7148.01 5 0.2859 0.7944 0.00 0.14 0.00 0.00 0.82 0.02 0.02 0.00
#> TCGA.55.8205.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.91.6830.01 1 0.0000 0.8303 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 8 0.5241 0.6237 0.00 0.04 0.12 0.00 0.00 0.10 0.08 0.66
#> TCGA.39.5022.01 3 0.2534 0.8214 0.00 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.8120.01 8 0.0471 0.8431 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.73.A9RS.01 8 0.4664 0.6485 0.00 0.10 0.14 0.00 0.00 0.08 0.00 0.68
#> TCGA.70.6722.01 3 0.3808 0.7280 0.00 0.30 0.66 0.00 0.02 0.02 0.00 0.00
#> TCGA.69.7979.01 4 0.2938 0.8310 0.00 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.95.7039.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.91.6848.01 3 0.1557 0.8385 0.00 0.02 0.92 0.00 0.00 0.06 0.00 0.00
#> TCGA.33.6738.01 3 0.1557 0.8385 0.00 0.02 0.92 0.00 0.00 0.06 0.00 0.00
#> TCGA.43.6773.01 3 0.2534 0.8214 0.00 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7146.01 4 0.3083 0.8156 0.00 0.00 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.49.6743.01 1 0.2350 0.8181 0.86 0.04 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.78.7161.01 4 0.0000 0.8267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.44.A4SU.01 1 0.2132 0.8191 0.88 0.04 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.97.7937.01 8 0.0471 0.8463 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.05.5428.01 8 0.0000 0.8488 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.L9.A8F4.01 1 0.0471 0.8288 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 6 0.4503 0.6624 0.00 0.02 0.18 0.00 0.00 0.66 0.00 0.14
#> TCGA.J2.A4AD.01 1 0.3404 0.7624 0.72 0.04 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.38.4631.01 1 0.4302 0.6776 0.56 0.08 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.05.4390.01 4 0.0941 0.8114 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.55.6972.01 5 0.1887 0.7989 0.00 0.06 0.00 0.00 0.90 0.00 0.04 0.00
#> TCGA.05.4433.01 8 0.4211 0.5912 0.00 0.08 0.00 0.00 0.00 0.22 0.02 0.68
#> TCGA.50.5932.01 5 0.2484 0.7928 0.00 0.10 0.00 0.00 0.86 0.02 0.02 0.00
#> TCGA.50.7109.01 6 0.5103 0.6535 0.00 0.04 0.00 0.00 0.16 0.64 0.02 0.14
#> TCGA.55.8508.01 4 0.0808 0.8110 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.71.6725.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.86.8075.01 1 0.0808 0.8240 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7633.01 5 0.2350 0.7903 0.00 0.10 0.00 0.00 0.86 0.00 0.04 0.00
#> TCGA.49.4514.01 1 0.0000 0.8303 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4396.01 8 0.0000 0.8488 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.75.5147.01 1 0.3845 0.7335 0.66 0.06 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.86.7711.01 3 0.2267 0.8304 0.00 0.18 0.82 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.5420.01 3 0.2534 0.8214 0.00 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7154.01 8 0.2947 0.7987 0.00 0.06 0.04 0.00 0.00 0.06 0.00 0.84
#> TCGA.44.7667.01 4 0.1091 0.8051 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.O1.A52J.01 1 0.0471 0.8285 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7167.01 5 0.5818 0.5591 0.00 0.22 0.00 0.00 0.56 0.12 0.04 0.06
#> TCGA.05.4427.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.86.8585.01 3 0.2534 0.8214 0.00 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7147.01 4 0.2650 0.8534 0.00 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.55.8085.01 5 0.2407 0.7858 0.00 0.08 0.00 0.00 0.86 0.06 0.00 0.00
#> TCGA.MP.A4TE.01 8 0.1804 0.8104 0.00 0.02 0.00 0.00 0.00 0.08 0.00 0.90
#> TCGA.78.7542.01 8 0.1887 0.8255 0.00 0.04 0.00 0.00 0.00 0.06 0.00 0.90
#> TCGA.49.AAR9.01 3 0.2348 0.8405 0.00 0.06 0.88 0.00 0.00 0.04 0.02 0.00
#> TCGA.95.A4VK.01 4 0.2406 0.8523 0.00 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.49.4488.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.55.7994.01 8 0.0000 0.8488 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MP.A5C7.01 4 0.0941 0.8114 0.00 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.05.4424.01 3 0.3198 0.7876 0.00 0.26 0.72 0.00 0.00 0.02 0.00 0.00
#> TCGA.4B.A93V.01 1 0.4400 0.6322 0.68 0.04 0.00 0.20 0.00 0.00 0.08 0.00
#> TCGA.86.A4D0.01 6 0.3385 0.7224 0.00 0.00 0.08 0.00 0.00 0.76 0.00 0.16
#> TCGA.78.7159.01 4 0.0000 0.8267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.99.8032.01 6 0.3616 0.7048 0.00 0.02 0.00 0.00 0.02 0.76 0.02 0.18
#> TCGA.MP.A4TA.01 1 0.2981 0.7843 0.76 0.02 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.75.5146.01 5 0.3311 0.7802 0.00 0.14 0.02 0.00 0.80 0.02 0.02 0.00
#> TCGA.64.5779.01 6 0.3314 0.7422 0.00 0.00 0.10 0.00 0.00 0.80 0.02 0.08
#> TCGA.50.6673.01 4 0.2852 0.8379 0.00 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.95.7562.01 8 0.0000 0.8488 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.5930.01 3 0.2534 0.8214 0.00 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7284.01 8 0.6566 0.2570 0.00 0.10 0.04 0.00 0.06 0.28 0.04 0.48
#> TCGA.91.6829.01 8 0.0941 0.8443 0.00 0.00 0.02 0.00 0.00 0.00 0.02 0.96
#> TCGA.86.8669.01 6 0.4276 0.4892 0.00 0.02 0.00 0.00 0.28 0.64 0.06 0.00
#> TCGA.64.1679.01 1 0.0000 0.8303 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.50.5051.01 4 0.0000 0.8267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.64.1681.01 1 0.0471 0.8285 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8674.01 5 0.4471 0.7000 0.00 0.10 0.16 0.00 0.70 0.02 0.02 0.00
#> TCGA.78.7166.01 5 0.3178 0.7900 0.00 0.14 0.04 0.00 0.80 0.02 0.00 0.00
#> TCGA.86.7953.01 1 0.0000 0.8303 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 8 0.0000 0.8488 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.62.8402.01 1 0.4733 0.5532 0.62 0.06 0.00 0.26 0.00 0.00 0.06 0.00
#> TCGA.55.7995.01 1 0.4302 0.6828 0.56 0.08 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.NJ.A55R.01 6 0.3934 0.6924 0.00 0.00 0.14 0.00 0.00 0.70 0.00 0.16
#> TCGA.86.8055.01 3 0.1275 0.8494 0.00 0.02 0.94 0.00 0.00 0.04 0.00 0.00
#> TCGA.33.AASB.01 8 0.2348 0.8231 0.00 0.06 0.04 0.00 0.00 0.02 0.00 0.88
#> TCGA.78.7156.01 5 0.0471 0.7984 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.55.8506.01 4 0.2534 0.8574 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.53.7813.01 4 0.3178 0.6762 0.14 0.02 0.00 0.80 0.00 0.00 0.04 0.00
#> TCGA.97.8179.01 5 0.4053 0.7489 0.00 0.18 0.00 0.00 0.72 0.06 0.00 0.04
#> TCGA.86.7713.01 6 0.5983 0.0441 0.00 0.08 0.00 0.00 0.34 0.40 0.18 0.00
#> TCGA.62.A46S.01 6 0.6000 0.5531 0.00 0.08 0.00 0.00 0.20 0.56 0.06 0.10
#> TCGA.95.7947.01 3 0.3586 0.7187 0.00 0.06 0.78 0.00 0.00 0.12 0.00 0.04
#> TCGA.J2.8192.01 1 0.0000 0.8303 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node07. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["071"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 59 columns.
#> Top rows (1000) are extracted by '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 0.929 0.918 0.967 0.4812 0.534 0.534
#> 3 3 1.000 0.976 0.990 0.3295 0.774 0.597
#> 4 4 0.734 0.725 0.787 0.1113 0.960 0.889
#> 5 5 0.707 0.702 0.793 0.0630 0.845 0.547
#> 6 6 0.742 0.701 0.820 0.0510 0.943 0.745
#> 7 7 0.857 0.756 0.849 0.0350 0.981 0.898
#> 8 8 0.767 0.657 0.767 0.0113 0.956 0.775
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.55.7910.01 1 0.000 0.945 1.00 0.00
#> TCGA.78.7539.01 2 0.000 1.000 0.00 1.00
#> TCGA.86.6851.01 2 0.000 1.000 0.00 1.00
#> TCGA.62.8394.01 1 0.995 0.236 0.54 0.46
#> TCGA.86.7954.01 1 0.000 0.945 1.00 0.00
#> TCGA.44.A479.01 1 0.000 0.945 1.00 0.00
#> TCGA.J2.8194.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.A57B.01 1 0.000 0.945 1.00 0.00
#> TCGA.O2.A5IC.01 1 0.000 0.945 1.00 0.00
#> TCGA.55.8096.01 1 0.000 0.945 1.00 0.00
#> TCGA.44.3917.01 2 0.000 1.000 0.00 1.00
#> TCGA.53.7624.01 1 0.000 0.945 1.00 0.00
#> TCGA.55.7913.01 1 0.000 0.945 1.00 0.00
#> TCGA.44.7670.01 1 0.000 0.945 1.00 0.00
#> TCGA.L9.A5IP.01 1 0.000 0.945 1.00 0.00
#> TCGA.MP.A4TF.01 1 0.000 0.945 1.00 0.00
#> TCGA.49.4490.01 1 0.000 0.945 1.00 0.00
#> TCGA.NC.A5HK.01 1 0.000 0.945 1.00 0.00
#> TCGA.49.AARE.01 2 0.000 1.000 0.00 1.00
#> TCGA.91.6840.01 1 0.000 0.945 1.00 0.00
#> TCGA.95.7043.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.8205.01 2 0.000 1.000 0.00 1.00
#> TCGA.91.6830.01 1 0.000 0.945 1.00 0.00
#> TCGA.69.7979.01 2 0.000 1.000 0.00 1.00
#> TCGA.95.7039.01 2 0.000 1.000 0.00 1.00
#> TCGA.78.7146.01 2 0.000 1.000 0.00 1.00
#> TCGA.49.6743.01 1 0.000 0.945 1.00 0.00
#> TCGA.78.7161.01 2 0.000 1.000 0.00 1.00
#> TCGA.44.A4SU.01 1 0.000 0.945 1.00 0.00
#> TCGA.L9.A8F4.01 1 0.000 0.945 1.00 0.00
#> TCGA.J2.A4AD.01 1 0.000 0.945 1.00 0.00
#> TCGA.38.4631.01 1 0.000 0.945 1.00 0.00
#> TCGA.05.4390.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.8508.01 1 0.990 0.294 0.56 0.44
#> TCGA.71.6725.01 2 0.000 1.000 0.00 1.00
#> TCGA.86.8075.01 1 0.000 0.945 1.00 0.00
#> TCGA.49.4514.01 1 0.000 0.945 1.00 0.00
#> TCGA.75.5147.01 1 0.000 0.945 1.00 0.00
#> TCGA.44.7667.01 1 0.795 0.683 0.76 0.24
#> TCGA.O1.A52J.01 1 0.000 0.945 1.00 0.00
#> TCGA.05.4427.01 2 0.000 1.000 0.00 1.00
#> TCGA.78.7147.01 2 0.000 1.000 0.00 1.00
#> TCGA.95.A4VK.01 1 0.958 0.437 0.62 0.38
#> TCGA.49.4488.01 2 0.000 1.000 0.00 1.00
#> TCGA.MP.A5C7.01 2 0.000 1.000 0.00 1.00
#> TCGA.4B.A93V.01 1 0.000 0.945 1.00 0.00
#> TCGA.78.7159.01 2 0.000 1.000 0.00 1.00
#> TCGA.MP.A4TA.01 1 0.000 0.945 1.00 0.00
#> TCGA.50.6673.01 1 0.000 0.945 1.00 0.00
#> TCGA.64.1679.01 1 0.000 0.945 1.00 0.00
#> TCGA.55.8616.01 2 0.000 1.000 0.00 1.00
#> TCGA.50.5051.01 2 0.000 1.000 0.00 1.00
#> TCGA.64.1681.01 1 0.000 0.945 1.00 0.00
#> TCGA.86.7953.01 1 0.000 0.945 1.00 0.00
#> TCGA.62.8402.01 1 0.000 0.945 1.00 0.00
#> TCGA.55.7995.01 1 0.000 0.945 1.00 0.00
#> TCGA.55.8506.01 2 0.000 1.000 0.00 1.00
#> TCGA.53.7813.01 1 0.990 0.294 0.56 0.44
#> TCGA.J2.8192.01 1 0.000 0.945 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.55.7910.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.78.7539.01 2 0.522 0.663 0 0.74 0.26
#> TCGA.86.6851.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.62.8394.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.86.7954.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.44.A479.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.J2.8194.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.55.A57B.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.O2.A5IC.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.55.8096.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.44.3917.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.53.7624.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.55.7913.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.44.7670.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.MP.A4TF.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.49.4490.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.NC.A5HK.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.49.AARE.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.91.6840.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.95.7043.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.55.8205.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.91.6830.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.69.7979.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.95.7039.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.78.7146.01 2 0.583 0.517 0 0.66 0.34
#> TCGA.49.6743.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.78.7161.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.44.A4SU.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.J2.A4AD.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.38.4631.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.05.4390.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.55.8508.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.71.6725.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.86.8075.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.49.4514.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.75.5147.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.44.7667.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.O1.A52J.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.05.4427.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.78.7147.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.95.A4VK.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.49.4488.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.MP.A5C7.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.4B.A93V.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.78.7159.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.MP.A4TA.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.50.6673.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.64.1679.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.55.8616.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.50.5051.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.64.1681.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.86.7953.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.62.8402.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.55.7995.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.55.8506.01 2 0.000 0.959 0 1.00 0.00
#> TCGA.53.7813.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.J2.8192.01 1 0.000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.55.7910.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.78.7539.01 4 0.7382 0.634 0.00 0.26 0.22 0.52
#> TCGA.86.6851.01 4 0.5000 0.301 0.00 0.00 0.50 0.50
#> TCGA.62.8394.01 3 0.0707 0.718 0.00 0.00 0.98 0.02
#> TCGA.86.7954.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.44.A479.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.J2.8194.01 3 0.4994 -0.424 0.00 0.00 0.52 0.48
#> TCGA.55.A57B.01 3 0.2335 0.705 0.06 0.00 0.92 0.02
#> TCGA.O2.A5IC.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.55.8096.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.44.3917.01 2 0.0707 0.918 0.00 0.98 0.00 0.02
#> TCGA.53.7624.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.55.7913.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.44.7670.01 1 0.4790 0.796 0.62 0.00 0.00 0.38
#> TCGA.L9.A5IP.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.MP.A4TF.01 3 0.1637 0.710 0.06 0.00 0.94 0.00
#> TCGA.49.4490.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.NC.A5HK.01 1 0.3400 0.790 0.82 0.00 0.00 0.18
#> TCGA.49.AARE.01 3 0.4406 0.314 0.00 0.00 0.70 0.30
#> TCGA.91.6840.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.95.7043.01 3 0.4406 0.314 0.00 0.00 0.70 0.30
#> TCGA.55.8205.01 2 0.3975 0.704 0.00 0.76 0.00 0.24
#> TCGA.91.6830.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.69.7979.01 4 0.6766 0.406 0.00 0.38 0.10 0.52
#> TCGA.95.7039.01 2 0.0000 0.923 0.00 1.00 0.00 0.00
#> TCGA.78.7146.01 4 0.7285 0.630 0.00 0.18 0.30 0.52
#> TCGA.49.6743.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.78.7161.01 2 0.0000 0.923 0.00 1.00 0.00 0.00
#> TCGA.44.A4SU.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.J2.A4AD.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.38.4631.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.05.4390.01 2 0.0707 0.918 0.00 0.98 0.00 0.02
#> TCGA.55.8508.01 3 0.1637 0.709 0.00 0.00 0.94 0.06
#> TCGA.71.6725.01 2 0.3975 0.704 0.00 0.76 0.00 0.24
#> TCGA.86.8075.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.49.4514.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.75.5147.01 1 0.1637 0.799 0.94 0.00 0.00 0.06
#> TCGA.44.7667.01 3 0.2335 0.715 0.02 0.00 0.92 0.06
#> TCGA.O1.A52J.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.05.4427.01 2 0.0000 0.923 0.00 1.00 0.00 0.00
#> TCGA.78.7147.01 2 0.0000 0.923 0.00 1.00 0.00 0.00
#> TCGA.95.A4VK.01 3 0.0000 0.718 0.00 0.00 1.00 0.00
#> TCGA.49.4488.01 2 0.0000 0.923 0.00 1.00 0.00 0.00
#> TCGA.MP.A5C7.01 4 0.4977 0.366 0.00 0.00 0.46 0.54
#> TCGA.4B.A93V.01 1 0.4939 0.446 0.74 0.00 0.22 0.04
#> TCGA.78.7159.01 2 0.3801 0.722 0.00 0.78 0.00 0.22
#> TCGA.MP.A4TA.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.50.6673.01 3 0.2335 0.705 0.06 0.00 0.92 0.02
#> TCGA.64.1679.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
#> TCGA.55.8616.01 2 0.0000 0.923 0.00 1.00 0.00 0.00
#> TCGA.50.5051.01 2 0.0707 0.918 0.00 0.98 0.00 0.02
#> TCGA.64.1681.01 1 0.0707 0.791 0.98 0.00 0.00 0.02
#> TCGA.86.7953.01 1 0.0000 0.785 1.00 0.00 0.00 0.00
#> TCGA.62.8402.01 3 0.6074 0.332 0.34 0.00 0.60 0.06
#> TCGA.55.7995.01 1 0.3611 0.664 0.86 0.00 0.08 0.06
#> TCGA.55.8506.01 2 0.0000 0.923 0.00 1.00 0.00 0.00
#> TCGA.53.7813.01 3 0.1637 0.709 0.00 0.00 0.94 0.06
#> TCGA.J2.8192.01 1 0.4624 0.824 0.66 0.00 0.00 0.34
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.55.7910.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 4 0.4637 0.651 0.00 0.10 0.16 0.74 0.00
#> TCGA.86.6851.01 4 0.5157 0.453 0.00 0.00 0.44 0.52 0.04
#> TCGA.62.8394.01 3 0.1043 0.804 0.00 0.00 0.96 0.04 0.00
#> TCGA.86.7954.01 5 0.4262 0.791 0.44 0.00 0.00 0.00 0.56
#> TCGA.44.A479.01 5 0.4287 0.787 0.46 0.00 0.00 0.00 0.54
#> TCGA.J2.8194.01 4 0.5157 0.432 0.00 0.00 0.44 0.52 0.04
#> TCGA.55.A57B.01 3 0.2732 0.744 0.00 0.00 0.84 0.00 0.16
#> TCGA.O2.A5IC.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8096.01 5 0.4287 0.787 0.46 0.00 0.00 0.00 0.54
#> TCGA.44.3917.01 2 0.1043 0.868 0.00 0.96 0.00 0.04 0.00
#> TCGA.53.7624.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7913.01 5 0.4182 0.764 0.40 0.00 0.00 0.00 0.60
#> TCGA.44.7670.01 1 0.4818 0.527 0.72 0.00 0.00 0.18 0.10
#> TCGA.L9.A5IP.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TF.01 3 0.2280 0.759 0.00 0.00 0.88 0.00 0.12
#> TCGA.49.4490.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HK.01 1 0.6447 -0.254 0.44 0.00 0.00 0.18 0.38
#> TCGA.49.AARE.01 4 0.6064 0.369 0.00 0.00 0.42 0.46 0.12
#> TCGA.91.6840.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 4 0.6064 0.369 0.00 0.00 0.42 0.46 0.12
#> TCGA.55.8205.01 2 0.4527 0.642 0.00 0.70 0.00 0.26 0.04
#> TCGA.91.6830.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.69.7979.01 4 0.4588 0.527 0.00 0.22 0.06 0.72 0.00
#> TCGA.95.7039.01 2 0.2020 0.853 0.00 0.90 0.00 0.00 0.10
#> TCGA.78.7146.01 4 0.4558 0.656 0.00 0.08 0.18 0.74 0.00
#> TCGA.49.6743.01 5 0.4262 0.791 0.44 0.00 0.00 0.00 0.56
#> TCGA.78.7161.01 2 0.2020 0.853 0.00 0.90 0.00 0.00 0.10
#> TCGA.44.A4SU.01 5 0.4287 0.787 0.46 0.00 0.00 0.00 0.54
#> TCGA.L9.A8F4.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.J2.A4AD.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.38.4631.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.4390.01 2 0.1043 0.868 0.00 0.96 0.00 0.04 0.00
#> TCGA.55.8508.01 3 0.2280 0.777 0.00 0.00 0.88 0.12 0.00
#> TCGA.71.6725.01 2 0.4527 0.642 0.00 0.70 0.00 0.26 0.04
#> TCGA.86.8075.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.49.4514.01 5 0.4262 0.791 0.44 0.00 0.00 0.00 0.56
#> TCGA.75.5147.01 1 0.4302 -0.682 0.52 0.00 0.00 0.00 0.48
#> TCGA.44.7667.01 3 0.3110 0.768 0.00 0.00 0.86 0.08 0.06
#> TCGA.O1.A52J.01 5 0.4287 0.787 0.46 0.00 0.00 0.00 0.54
#> TCGA.05.4427.01 2 0.0609 0.870 0.00 0.98 0.00 0.00 0.02
#> TCGA.78.7147.01 2 0.0000 0.871 0.00 1.00 0.00 0.00 0.00
#> TCGA.95.A4VK.01 3 0.1043 0.804 0.00 0.00 0.96 0.04 0.00
#> TCGA.49.4488.01 2 0.0000 0.871 0.00 1.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 4 0.4456 0.594 0.00 0.00 0.32 0.66 0.02
#> TCGA.4B.A93V.01 5 0.5599 0.431 0.12 0.00 0.26 0.00 0.62
#> TCGA.78.7159.01 2 0.3684 0.656 0.00 0.72 0.00 0.28 0.00
#> TCGA.MP.A4TA.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.50.6673.01 3 0.2516 0.754 0.00 0.00 0.86 0.00 0.14
#> TCGA.64.1679.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 2 0.2020 0.853 0.00 0.90 0.00 0.00 0.10
#> TCGA.50.5051.01 2 0.1043 0.868 0.00 0.96 0.00 0.04 0.00
#> TCGA.64.1681.01 5 0.4287 0.787 0.46 0.00 0.00 0.00 0.54
#> TCGA.86.7953.01 5 0.4287 0.787 0.46 0.00 0.00 0.00 0.54
#> TCGA.62.8402.01 5 0.4798 -0.132 0.00 0.00 0.44 0.02 0.54
#> TCGA.55.7995.01 5 0.5548 0.582 0.22 0.00 0.06 0.04 0.68
#> TCGA.55.8506.01 2 0.2020 0.853 0.00 0.90 0.00 0.00 0.10
#> TCGA.53.7813.01 3 0.2280 0.777 0.00 0.00 0.88 0.12 0.00
#> TCGA.J2.8192.01 1 0.0000 0.878 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.55.7910.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 4 0.0547 0.626 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.86.6851.01 4 0.3834 0.538 0.00 0.00 0.20 0.76 0.02 0.02
#> TCGA.62.8394.01 3 0.1807 0.835 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.86.7954.01 5 0.3198 0.803 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.44.A479.01 5 0.3198 0.803 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.J2.8194.01 4 0.4613 0.465 0.00 0.00 0.26 0.66 0.00 0.08
#> TCGA.55.A57B.01 3 0.3679 0.771 0.00 0.00 0.76 0.00 0.20 0.04
#> TCGA.O2.A5IC.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8096.01 5 0.3198 0.803 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.44.3917.01 2 0.1556 0.877 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.53.7624.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7913.01 5 0.3076 0.784 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.44.7670.01 1 0.4993 -0.290 0.56 0.00 0.00 0.00 0.08 0.36
#> TCGA.L9.A5IP.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TF.01 3 0.3523 0.776 0.00 0.00 0.78 0.00 0.18 0.04
#> TCGA.49.4490.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HK.01 6 0.6103 0.000 0.30 0.00 0.00 0.00 0.32 0.38
#> TCGA.49.AARE.01 4 0.6554 -0.022 0.00 0.00 0.32 0.34 0.02 0.32
#> TCGA.91.6840.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 4 0.6554 -0.022 0.00 0.00 0.32 0.34 0.02 0.32
#> TCGA.55.8205.01 4 0.4764 0.246 0.00 0.42 0.00 0.54 0.02 0.02
#> TCGA.91.6830.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7979.01 4 0.0547 0.627 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.95.7039.01 2 0.2094 0.863 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.78.7146.01 4 0.0547 0.626 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.49.6743.01 5 0.3198 0.803 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.78.7161.01 2 0.2350 0.857 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.44.A4SU.01 5 0.3711 0.794 0.26 0.00 0.00 0.00 0.72 0.02
#> TCGA.L9.A8F4.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J2.A4AD.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4631.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.05.4390.01 2 0.2350 0.867 0.00 0.88 0.00 0.10 0.00 0.02
#> TCGA.55.8508.01 3 0.2725 0.829 0.00 0.00 0.88 0.06 0.04 0.02
#> TCGA.71.6725.01 4 0.4764 0.246 0.00 0.42 0.00 0.54 0.02 0.02
#> TCGA.86.8075.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4514.01 5 0.3198 0.803 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.75.5147.01 5 0.3578 0.638 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.44.7667.01 3 0.3688 0.768 0.00 0.00 0.80 0.04 0.02 0.14
#> TCGA.O1.A52J.01 5 0.3711 0.794 0.26 0.00 0.00 0.00 0.72 0.02
#> TCGA.05.4427.01 2 0.0000 0.880 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.78.7147.01 2 0.2260 0.833 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.95.A4VK.01 3 0.1807 0.835 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.49.4488.01 2 0.1556 0.877 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.MP.A5C7.01 4 0.3746 0.558 0.00 0.00 0.14 0.78 0.00 0.08
#> TCGA.4B.A93V.01 5 0.3318 0.421 0.02 0.00 0.14 0.00 0.82 0.02
#> TCGA.78.7159.01 4 0.4246 0.253 0.00 0.40 0.00 0.58 0.00 0.02
#> TCGA.MP.A4TA.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6673.01 3 0.3679 0.771 0.00 0.00 0.76 0.00 0.20 0.04
#> TCGA.64.1679.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 2 0.2094 0.863 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.50.5051.01 2 0.2350 0.867 0.00 0.88 0.00 0.10 0.00 0.02
#> TCGA.64.1681.01 5 0.3819 0.767 0.28 0.00 0.00 0.00 0.70 0.02
#> TCGA.86.7953.01 5 0.3198 0.803 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.62.8402.01 5 0.4282 -0.179 0.00 0.00 0.42 0.00 0.56 0.02
#> TCGA.55.7995.01 5 0.4361 0.251 0.04 0.00 0.06 0.00 0.76 0.14
#> TCGA.55.8506.01 2 0.2094 0.863 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.53.7813.01 3 0.2725 0.829 0.00 0.00 0.88 0.06 0.04 0.02
#> TCGA.J2.8192.01 1 0.0000 0.953 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.55.7910.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7539.01 4 0.1006 0.544 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.86.6851.01 4 0.3139 0.452 0.00 0.00 0.30 0.70 0.00 0.00 0.00
#> TCGA.62.8394.01 3 0.2572 0.698 0.00 0.00 0.86 0.08 0.00 0.00 0.06
#> TCGA.86.7954.01 5 0.1433 0.883 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.44.A479.01 5 0.1433 0.883 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.J2.8194.01 4 0.4244 0.235 0.00 0.00 0.42 0.54 0.00 0.00 0.04
#> TCGA.55.A57B.01 3 0.5680 0.555 0.00 0.00 0.60 0.00 0.10 0.16 0.14
#> TCGA.O2.A5IC.01 1 0.0504 0.980 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.8096.01 5 0.1433 0.883 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.44.3917.01 2 0.3055 0.791 0.00 0.82 0.00 0.14 0.00 0.02 0.02
#> TCGA.53.7624.01 1 0.0504 0.980 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.55.7913.01 5 0.0863 0.852 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.44.7670.01 6 0.4211 0.556 0.26 0.00 0.00 0.00 0.04 0.68 0.02
#> TCGA.L9.A5IP.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TF.01 3 0.5627 0.555 0.00 0.00 0.60 0.00 0.08 0.16 0.16
#> TCGA.49.4490.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NC.A5HK.01 6 0.4033 0.550 0.08 0.00 0.00 0.00 0.22 0.70 0.00
#> TCGA.49.AARE.01 7 0.4594 0.964 0.00 0.00 0.14 0.22 0.00 0.00 0.64
#> TCGA.91.6840.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.95.7043.01 7 0.4535 0.965 0.00 0.00 0.12 0.24 0.00 0.00 0.64
#> TCGA.55.8205.01 4 0.4356 0.352 0.00 0.40 0.02 0.56 0.00 0.02 0.00
#> TCGA.91.6830.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.69.7979.01 4 0.1006 0.544 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.95.7039.01 2 0.2509 0.807 0.00 0.88 0.00 0.00 0.04 0.06 0.02
#> TCGA.78.7146.01 4 0.1006 0.544 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.49.6743.01 5 0.1433 0.883 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.78.7161.01 2 0.2857 0.803 0.00 0.86 0.00 0.00 0.04 0.06 0.04
#> TCGA.44.A4SU.01 5 0.2421 0.868 0.08 0.00 0.00 0.00 0.88 0.02 0.02
#> TCGA.L9.A8F4.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J2.A4AD.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.38.4631.01 1 0.0504 0.980 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.05.4390.01 2 0.2569 0.802 0.00 0.84 0.00 0.14 0.00 0.00 0.02
#> TCGA.55.8508.01 3 0.1433 0.694 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.71.6725.01 4 0.4356 0.352 0.00 0.40 0.02 0.56 0.00 0.02 0.00
#> TCGA.86.8075.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.49.4514.01 5 0.1433 0.883 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.75.5147.01 5 0.1433 0.883 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.44.7667.01 3 0.2569 0.592 0.00 0.00 0.84 0.00 0.00 0.02 0.14
#> TCGA.O1.A52J.01 5 0.2421 0.868 0.08 0.00 0.00 0.00 0.88 0.02 0.02
#> TCGA.05.4427.01 2 0.0504 0.824 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.78.7147.01 2 0.2745 0.760 0.00 0.82 0.00 0.16 0.00 0.02 0.00
#> TCGA.95.A4VK.01 3 0.2572 0.698 0.00 0.00 0.86 0.08 0.00 0.00 0.06
#> TCGA.49.4488.01 2 0.2163 0.813 0.00 0.88 0.00 0.10 0.00 0.02 0.00
#> TCGA.MP.A5C7.01 4 0.3637 0.375 0.00 0.00 0.24 0.72 0.00 0.00 0.04
#> TCGA.4B.A93V.01 5 0.3485 0.711 0.00 0.00 0.04 0.02 0.82 0.02 0.10
#> TCGA.78.7159.01 4 0.4356 0.319 0.00 0.40 0.00 0.56 0.00 0.02 0.02
#> TCGA.MP.A4TA.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.6673.01 3 0.5680 0.555 0.00 0.00 0.60 0.00 0.10 0.16 0.14
#> TCGA.64.1679.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.8616.01 2 0.2509 0.807 0.00 0.88 0.00 0.00 0.04 0.06 0.02
#> TCGA.50.5051.01 2 0.2569 0.802 0.00 0.84 0.00 0.14 0.00 0.00 0.02
#> TCGA.64.1681.01 5 0.2421 0.868 0.08 0.00 0.00 0.00 0.88 0.02 0.02
#> TCGA.86.7953.01 5 0.1433 0.883 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.62.8402.01 5 0.5733 0.159 0.00 0.00 0.32 0.02 0.52 0.02 0.12
#> TCGA.55.7995.01 5 0.4964 0.401 0.00 0.00 0.02 0.02 0.66 0.22 0.08
#> TCGA.55.8506.01 2 0.2509 0.807 0.00 0.88 0.00 0.00 0.04 0.06 0.02
#> TCGA.53.7813.01 3 0.1433 0.694 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.J2.8192.01 1 0.0000 0.995 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.55.7910.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.78.7539.01 4 0.0000 0.7129 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.6851.01 4 0.5266 0.4095 0.08 0.02 0.30 0.56 0.00 0.00 0.04 0.00
#> TCGA.62.8394.01 3 0.0941 0.6323 0.00 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.86.7954.01 5 0.1947 0.8335 0.00 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.44.A479.01 5 0.1947 0.8335 0.00 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.J2.8194.01 3 0.6419 -0.3020 0.14 0.00 0.40 0.36 0.02 0.06 0.02 0.00
#> TCGA.55.A57B.01 7 0.4008 -0.0174 0.00 0.00 0.48 0.00 0.04 0.00 0.48 0.00
#> TCGA.O2.A5IC.01 8 0.0471 0.9743 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.55.8096.01 5 0.1947 0.8335 0.00 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.44.3917.01 2 0.1607 0.7307 0.04 0.92 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.53.7624.01 8 0.0471 0.9743 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.55.7913.01 5 0.2025 0.8213 0.02 0.00 0.00 0.00 0.88 0.00 0.00 0.10
#> TCGA.44.7670.01 6 0.3293 0.7630 0.00 0.00 0.00 0.00 0.04 0.74 0.00 0.22
#> TCGA.L9.A5IP.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MP.A4TF.01 3 0.4008 -0.2975 0.00 0.00 0.48 0.00 0.04 0.00 0.48 0.00
#> TCGA.49.4490.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.NC.A5HK.01 6 0.4367 0.7588 0.00 0.00 0.00 0.00 0.14 0.70 0.04 0.12
#> TCGA.49.AARE.01 7 0.6072 0.2472 0.08 0.00 0.02 0.24 0.00 0.16 0.50 0.00
#> TCGA.91.6840.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.95.7043.01 7 0.6265 0.2416 0.12 0.00 0.02 0.24 0.00 0.14 0.48 0.00
#> TCGA.55.8205.01 2 0.4906 0.2600 0.08 0.56 0.00 0.32 0.00 0.00 0.04 0.00
#> TCGA.91.6830.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.69.7979.01 4 0.0000 0.7129 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.95.7039.01 2 0.2938 0.6460 0.30 0.70 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7146.01 4 0.0471 0.7038 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.49.6743.01 5 0.1563 0.8281 0.00 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.78.7161.01 2 0.3015 0.6423 0.32 0.68 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.44.A4SU.01 5 0.2994 0.8245 0.06 0.00 0.00 0.00 0.80 0.00 0.00 0.14
#> TCGA.L9.A8F4.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.J2.A4AD.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.38.4631.01 8 0.0471 0.9743 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.05.4390.01 2 0.2071 0.7306 0.04 0.90 0.00 0.02 0.04 0.00 0.00 0.00
#> TCGA.55.8508.01 3 0.0471 0.6351 0.00 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.71.6725.01 2 0.4906 0.2600 0.08 0.56 0.00 0.32 0.00 0.00 0.04 0.00
#> TCGA.86.8075.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.49.4514.01 5 0.1563 0.8281 0.00 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.75.5147.01 5 0.2888 0.8039 0.04 0.00 0.00 0.00 0.80 0.00 0.00 0.16
#> TCGA.44.7667.01 3 0.5081 0.3957 0.20 0.00 0.64 0.00 0.02 0.08 0.06 0.00
#> TCGA.O1.A52J.01 5 0.3227 0.8164 0.08 0.00 0.00 0.00 0.78 0.00 0.00 0.14
#> TCGA.05.4427.01 2 0.0000 0.7354 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7147.01 2 0.1341 0.7170 0.00 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.95.A4VK.01 3 0.0941 0.6323 0.00 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.49.4488.01 2 0.0000 0.7354 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A5C7.01 4 0.6406 0.2872 0.16 0.00 0.28 0.46 0.02 0.06 0.02 0.00
#> TCGA.4B.A93V.01 5 0.3431 0.6000 0.20 0.00 0.06 0.00 0.74 0.00 0.00 0.00
#> TCGA.78.7159.01 2 0.5273 0.2652 0.12 0.50 0.00 0.34 0.04 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.50.6673.01 7 0.4008 -0.0174 0.00 0.00 0.48 0.00 0.04 0.00 0.48 0.00
#> TCGA.64.1679.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.55.8616.01 2 0.2938 0.6460 0.30 0.70 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.50.5051.01 2 0.2071 0.7306 0.04 0.90 0.00 0.02 0.04 0.00 0.00 0.00
#> TCGA.64.1681.01 5 0.3227 0.8164 0.08 0.00 0.00 0.00 0.78 0.00 0.00 0.14
#> TCGA.86.7953.01 5 0.2547 0.8319 0.04 0.00 0.00 0.00 0.84 0.00 0.00 0.12
#> TCGA.62.8402.01 5 0.5292 -0.0328 0.16 0.00 0.38 0.00 0.44 0.00 0.02 0.00
#> TCGA.55.7995.01 5 0.4948 0.4232 0.16 0.00 0.04 0.00 0.66 0.12 0.00 0.02
#> TCGA.55.8506.01 2 0.2938 0.6460 0.30 0.70 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.53.7813.01 3 0.0471 0.6351 0.00 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.J2.8192.01 8 0.0000 0.9931 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node071. Child nodes: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0711"]
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 29 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 0.3799 0.621 0.621
#> 3 3 0.532 0.784 0.891 0.6159 0.591 0.418
#> 4 4 0.840 0.947 0.946 0.1196 0.820 0.580
#> 5 5 0.877 0.838 0.929 0.0638 0.980 0.935
#> 6 6 0.775 0.515 0.853 0.0627 0.970 0.896
#> 7 7 0.707 0.386 0.743 0.0483 0.906 0.661
#> 8 8 0.712 0.567 0.806 0.0360 0.879 0.505
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.55.7910.01 1 0 1 1 0
#> TCGA.86.7954.01 1 0 1 1 0
#> TCGA.44.A479.01 1 0 1 1 0
#> TCGA.O2.A5IC.01 2 0 1 0 1
#> TCGA.55.8096.01 1 0 1 1 0
#> TCGA.53.7624.01 2 0 1 0 1
#> TCGA.55.7913.01 1 0 1 1 0
#> TCGA.44.7670.01 2 0 1 0 1
#> TCGA.L9.A5IP.01 1 0 1 1 0
#> TCGA.49.4490.01 1 0 1 1 0
#> TCGA.NC.A5HK.01 2 0 1 0 1
#> TCGA.91.6840.01 1 0 1 1 0
#> TCGA.91.6830.01 1 0 1 1 0
#> TCGA.49.6743.01 1 0 1 1 0
#> TCGA.44.A4SU.01 1 0 1 1 0
#> TCGA.L9.A8F4.01 1 0 1 1 0
#> TCGA.J2.A4AD.01 1 0 1 1 0
#> TCGA.38.4631.01 2 0 1 0 1
#> TCGA.86.8075.01 1 0 1 1 0
#> TCGA.49.4514.01 1 0 1 1 0
#> TCGA.75.5147.01 2 0 1 0 1
#> TCGA.O1.A52J.01 1 0 1 1 0
#> TCGA.4B.A93V.01 1 0 1 1 0
#> TCGA.MP.A4TA.01 1 0 1 1 0
#> TCGA.64.1679.01 1 0 1 1 0
#> TCGA.64.1681.01 1 0 1 1 0
#> TCGA.86.7953.01 1 0 1 1 0
#> TCGA.55.7995.01 2 0 1 0 1
#> TCGA.J2.8192.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.55.7910.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.86.7954.01 3 0.604 0.546 0.38 0.00 0.62
#> TCGA.44.A479.01 3 0.604 0.546 0.38 0.00 0.62
#> TCGA.O2.A5IC.01 3 0.429 0.592 0.00 0.18 0.82
#> TCGA.55.8096.01 1 0.429 0.717 0.82 0.00 0.18
#> TCGA.53.7624.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.55.7913.01 3 0.400 0.763 0.16 0.00 0.84
#> TCGA.44.7670.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.L9.A5IP.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.49.4490.01 3 0.000 0.737 0.00 0.00 1.00
#> TCGA.NC.A5HK.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.91.6840.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.91.6830.01 3 0.369 0.766 0.14 0.00 0.86
#> TCGA.49.6743.01 3 0.000 0.737 0.00 0.00 1.00
#> TCGA.44.A4SU.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.L9.A8F4.01 1 0.583 0.341 0.66 0.00 0.34
#> TCGA.J2.A4AD.01 3 0.400 0.763 0.16 0.00 0.84
#> TCGA.38.4631.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.86.8075.01 3 0.604 0.546 0.38 0.00 0.62
#> TCGA.49.4514.01 3 0.400 0.763 0.16 0.00 0.84
#> TCGA.75.5147.01 3 0.369 0.637 0.00 0.14 0.86
#> TCGA.O1.A52J.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.4B.A93V.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.MP.A4TA.01 3 0.000 0.737 0.00 0.00 1.00
#> TCGA.64.1679.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.64.1681.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.86.7953.01 3 0.604 0.546 0.38 0.00 0.62
#> TCGA.55.7995.01 3 0.429 0.592 0.00 0.18 0.82
#> TCGA.J2.8192.01 1 0.000 0.933 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.55.7910.01 1 0.2011 0.914 0.92 0.00 0.00 0.08
#> TCGA.86.7954.01 3 0.0707 0.953 0.02 0.00 0.98 0.00
#> TCGA.44.A479.01 3 0.1211 0.938 0.04 0.00 0.96 0.00
#> TCGA.O2.A5IC.01 4 0.5594 0.982 0.00 0.10 0.18 0.72
#> TCGA.55.8096.01 3 0.3172 0.788 0.16 0.00 0.84 0.00
#> TCGA.53.7624.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.55.7913.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.44.7670.01 2 0.0707 0.984 0.00 0.98 0.00 0.02
#> TCGA.L9.A5IP.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.49.4490.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.NC.A5HK.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.91.6840.01 1 0.4134 0.753 0.74 0.00 0.00 0.26
#> TCGA.91.6830.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.49.6743.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.44.A4SU.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 3 0.2345 0.872 0.10 0.00 0.90 0.00
#> TCGA.J2.A4AD.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.38.4631.01 2 0.0000 0.995 0.00 1.00 0.00 0.00
#> TCGA.86.8075.01 3 0.0707 0.953 0.02 0.00 0.98 0.00
#> TCGA.49.4514.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.75.5147.01 4 0.5486 0.964 0.00 0.08 0.20 0.72
#> TCGA.O1.A52J.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.4B.A93V.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.64.1679.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.64.1681.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.86.7953.01 3 0.0707 0.953 0.02 0.00 0.98 0.00
#> TCGA.55.7995.01 4 0.5594 0.982 0.00 0.10 0.18 0.72
#> TCGA.J2.8192.01 1 0.0000 0.963 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.55.7910.01 1 0.3895 -0.191 0.68 0.00 0.00 0.00 0.32
#> TCGA.86.7954.01 3 0.1410 0.950 0.00 0.00 0.94 0.00 0.06
#> TCGA.44.A479.01 3 0.1043 0.947 0.00 0.00 0.96 0.00 0.04
#> TCGA.O2.A5IC.01 4 0.2873 0.888 0.00 0.00 0.02 0.86 0.12
#> TCGA.55.8096.01 3 0.2012 0.938 0.02 0.00 0.92 0.00 0.06
#> TCGA.53.7624.01 2 0.0000 0.976 0.00 1.00 0.00 0.00 0.00
#> TCGA.55.7913.01 3 0.0609 0.951 0.00 0.00 0.98 0.00 0.02
#> TCGA.44.7670.01 2 0.0000 0.976 0.00 1.00 0.00 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.3513 0.581 0.80 0.00 0.00 0.02 0.18
#> TCGA.49.4490.01 3 0.2280 0.922 0.00 0.00 0.88 0.00 0.12
#> TCGA.NC.A5HK.01 2 0.0000 0.976 0.00 1.00 0.00 0.00 0.00
#> TCGA.91.6840.01 5 0.4227 0.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.91.6830.01 3 0.1410 0.943 0.00 0.00 0.94 0.00 0.06
#> TCGA.49.6743.01 3 0.1043 0.944 0.00 0.00 0.96 0.00 0.04
#> TCGA.44.A4SU.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 3 0.1648 0.938 0.02 0.00 0.94 0.00 0.04
#> TCGA.J2.A4AD.01 3 0.2020 0.934 0.00 0.00 0.90 0.00 0.10
#> TCGA.38.4631.01 2 0.1732 0.926 0.00 0.92 0.00 0.00 0.08
#> TCGA.86.8075.01 3 0.1410 0.950 0.00 0.00 0.94 0.00 0.06
#> TCGA.49.4514.01 3 0.0000 0.952 0.00 0.00 1.00 0.00 0.00
#> TCGA.75.5147.01 4 0.2012 0.914 0.00 0.00 0.02 0.92 0.06
#> TCGA.O1.A52J.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.4B.A93V.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 3 0.1732 0.927 0.00 0.00 0.92 0.00 0.08
#> TCGA.64.1679.01 1 0.1043 0.809 0.96 0.00 0.00 0.00 0.04
#> TCGA.64.1681.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.7953.01 3 0.1043 0.949 0.00 0.00 0.96 0.00 0.04
#> TCGA.55.7995.01 4 0.0609 0.927 0.00 0.00 0.02 0.98 0.00
#> TCGA.J2.8192.01 1 0.0000 0.853 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.55.7910.01 1 0.4360 0.2024 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.86.7954.01 3 0.1814 0.4806 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.44.A479.01 3 0.2094 0.5578 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.O2.A5IC.01 4 0.3660 0.7201 0.00 0.00 0.00 0.78 0.06 0.16
#> TCGA.55.8096.01 3 0.2725 0.5055 0.04 0.00 0.88 0.00 0.02 0.06
#> TCGA.53.7624.01 2 0.0000 0.9579 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.7913.01 3 0.0937 0.5494 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.44.7670.01 2 0.0547 0.9515 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.L9.A5IP.01 1 0.5007 0.3662 0.66 0.00 0.02 0.00 0.08 0.24
#> TCGA.49.4490.01 6 0.4337 0.0000 0.00 0.00 0.48 0.00 0.02 0.50
#> TCGA.NC.A5HK.01 2 0.0000 0.9579 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.91.6840.01 5 0.3409 0.0000 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.91.6830.01 3 0.3578 -0.1107 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.49.6743.01 3 0.3499 -0.0674 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.44.A4SU.01 1 0.0000 0.8189 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 3 0.2094 0.5578 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.J2.A4AD.01 3 0.3706 -0.1017 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.38.4631.01 2 0.2474 0.8841 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.86.8075.01 3 0.1814 0.4806 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.49.4514.01 3 0.1556 0.5418 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.75.5147.01 4 0.4004 0.7119 0.00 0.00 0.00 0.76 0.12 0.12
#> TCGA.O1.A52J.01 1 0.1092 0.8039 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.4B.A93V.01 1 0.1092 0.8039 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.MP.A4TA.01 3 0.3828 -0.3448 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.64.1679.01 1 0.2020 0.7490 0.92 0.00 0.02 0.00 0.02 0.04
#> TCGA.64.1681.01 1 0.0000 0.8189 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7953.01 3 0.0937 0.5414 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.55.7995.01 4 0.0000 0.7898 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J2.8192.01 1 0.0000 0.8189 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.55.7910.01 1 0.5276 0.34357 0.64 0.00 0.00 0.00 0.18 0.08 0.10
#> TCGA.86.7954.01 7 0.3294 0.78511 0.00 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.44.A479.01 3 0.5474 0.04366 0.00 0.00 0.58 0.00 0.06 0.10 0.26
#> TCGA.O2.A5IC.01 6 0.3496 0.00000 0.00 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.55.8096.01 3 0.5968 -0.19460 0.00 0.00 0.44 0.00 0.08 0.10 0.38
#> TCGA.53.7624.01 2 0.0000 0.93405 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7913.01 3 0.3985 -0.58740 0.00 0.00 0.52 0.00 0.00 0.02 0.46
#> TCGA.44.7670.01 2 0.0863 0.92303 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.L9.A5IP.01 1 0.6898 0.04662 0.38 0.00 0.02 0.00 0.08 0.30 0.22
#> TCGA.49.4490.01 3 0.4990 0.10991 0.00 0.00 0.58 0.22 0.00 0.00 0.20
#> TCGA.NC.A5HK.01 2 0.0000 0.93405 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6840.01 5 0.2912 0.00000 0.14 0.00 0.00 0.00 0.82 0.00 0.04
#> TCGA.91.6830.01 3 0.1433 0.38985 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.49.6743.01 3 0.0504 0.40680 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.44.A4SU.01 1 0.1664 0.73791 0.92 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.L9.A8F4.01 3 0.5474 0.04366 0.00 0.00 0.58 0.00 0.06 0.10 0.26
#> TCGA.J2.A4AD.01 3 0.2163 0.40163 0.00 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.38.4631.01 2 0.3289 0.82442 0.00 0.82 0.00 0.00 0.02 0.10 0.06
#> TCGA.86.8075.01 7 0.3755 0.77642 0.00 0.00 0.34 0.00 0.00 0.02 0.64
#> TCGA.49.4514.01 3 0.3417 0.00454 0.00 0.00 0.72 0.00 0.02 0.00 0.26
#> TCGA.75.5147.01 4 0.0000 0.22200 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.O1.A52J.01 1 0.0504 0.74683 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.4B.A93V.01 1 0.0504 0.74683 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.MP.A4TA.01 3 0.2376 0.37232 0.00 0.00 0.86 0.00 0.00 0.12 0.02
#> TCGA.64.1679.01 1 0.4878 0.55831 0.72 0.00 0.02 0.00 0.08 0.10 0.08
#> TCGA.64.1681.01 1 0.0000 0.74927 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.7953.01 7 0.3994 0.54401 0.00 0.00 0.48 0.00 0.00 0.02 0.50
#> TCGA.55.7995.01 4 0.3815 -0.41235 0.00 0.00 0.00 0.62 0.02 0.36 0.00
#> TCGA.J2.8192.01 1 0.1363 0.74332 0.94 0.00 0.00 0.00 0.02 0.00 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.55.7910.01 1 0.5512 0.286 0.52 0.00 0.02 0.02 0.16 0.00 0.00 0.28
#> TCGA.86.7954.01 7 0.1741 0.661 0.02 0.00 0.04 0.02 0.00 0.00 0.92 0.00
#> TCGA.44.A479.01 7 0.3975 0.620 0.00 0.00 0.26 0.00 0.00 0.00 0.66 0.08
#> TCGA.O2.A5IC.01 6 0.4155 0.635 0.00 0.00 0.10 0.12 0.02 0.74 0.00 0.02
#> TCGA.55.8096.01 7 0.5098 0.594 0.14 0.00 0.08 0.00 0.02 0.00 0.66 0.10
#> TCGA.53.7624.01 2 0.0000 0.890 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.7913.01 7 0.3710 0.619 0.00 0.00 0.12 0.10 0.00 0.00 0.76 0.02
#> TCGA.44.7670.01 2 0.1607 0.857 0.00 0.92 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.L9.A5IP.01 8 0.4491 0.000 0.40 0.00 0.02 0.02 0.00 0.00 0.02 0.54
#> TCGA.49.4490.01 3 0.4897 0.459 0.00 0.00 0.52 0.20 0.00 0.00 0.28 0.00
#> TCGA.NC.A5HK.01 2 0.0000 0.890 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.91.6840.01 5 0.0808 0.000 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.91.6830.01 3 0.2267 0.738 0.00 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.49.6743.01 3 0.2856 0.725 0.00 0.00 0.78 0.02 0.00 0.00 0.20 0.00
#> TCGA.44.A4SU.01 1 0.0941 0.624 0.96 0.00 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.L9.A8F4.01 7 0.3975 0.620 0.00 0.00 0.26 0.00 0.00 0.00 0.66 0.08
#> TCGA.J2.A4AD.01 3 0.3270 0.717 0.00 0.00 0.80 0.02 0.00 0.00 0.12 0.06
#> TCGA.38.4631.01 2 0.3895 0.715 0.00 0.74 0.00 0.12 0.02 0.00 0.00 0.12
#> TCGA.86.8075.01 7 0.3554 0.579 0.02 0.00 0.08 0.08 0.00 0.00 0.80 0.02
#> TCGA.49.4514.01 7 0.3291 0.571 0.00 0.00 0.28 0.02 0.00 0.00 0.70 0.00
#> TCGA.75.5147.01 4 0.3193 0.000 0.00 0.00 0.00 0.62 0.00 0.38 0.00 0.00
#> TCGA.O1.A52J.01 1 0.3169 0.601 0.78 0.00 0.00 0.02 0.02 0.00 0.00 0.18
#> TCGA.4B.A93V.01 1 0.3169 0.601 0.78 0.00 0.00 0.02 0.02 0.00 0.00 0.18
#> TCGA.MP.A4TA.01 3 0.2484 0.693 0.00 0.00 0.86 0.02 0.02 0.00 0.10 0.00
#> TCGA.64.1679.01 1 0.3763 0.233 0.78 0.00 0.02 0.00 0.02 0.00 0.08 0.10
#> TCGA.64.1681.01 1 0.1091 0.616 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.86.7953.01 7 0.1275 0.696 0.00 0.00 0.04 0.02 0.00 0.00 0.94 0.00
#> TCGA.55.7995.01 6 0.0000 0.571 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J2.8192.01 1 0.0941 0.624 0.96 0.00 0.00 0.00 0.02 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0711. Child nodes: Node071111-leaf , Node071112-leaf , Node071113-leaf , Node071114-leaf , Node071115-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["07111"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 22 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5200 0.481 0.481
#> 3 3 1.000 0.972 0.988 0.1579 0.710 0.504
#> 4 4 0.763 0.823 0.912 0.1529 0.619 0.302
#> 5 5 1.000 0.998 0.999 0.1545 0.792 0.422
#> 6 6 0.968 0.913 0.965 0.0165 0.991 0.957
#> 7 7 0.816 0.756 0.903 0.0308 0.987 0.932
#> 8 8 0.774 0.657 0.870 0.0374 0.926 0.605
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.55.7910.01 2 0 1 0 1
#> TCGA.86.7954.01 2 0 1 0 1
#> TCGA.44.A479.01 1 0 1 1 0
#> TCGA.55.8096.01 1 0 1 1 0
#> TCGA.55.7913.01 1 0 1 1 0
#> TCGA.L9.A5IP.01 1 0 1 1 0
#> TCGA.49.4490.01 2 0 1 0 1
#> TCGA.91.6840.01 2 0 1 0 1
#> TCGA.91.6830.01 1 0 1 1 0
#> TCGA.49.6743.01 1 0 1 1 0
#> TCGA.44.A4SU.01 2 0 1 0 1
#> TCGA.L9.A8F4.01 1 0 1 1 0
#> TCGA.J2.A4AD.01 1 0 1 1 0
#> TCGA.86.8075.01 2 0 1 0 1
#> TCGA.49.4514.01 1 0 1 1 0
#> TCGA.O1.A52J.01 2 0 1 0 1
#> TCGA.4B.A93V.01 2 0 1 0 1
#> TCGA.MP.A4TA.01 1 0 1 1 0
#> TCGA.64.1679.01 1 0 1 1 0
#> TCGA.64.1681.01 2 0 1 0 1
#> TCGA.86.7953.01 1 0 1 1 0
#> TCGA.J2.8192.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.55.7910.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.86.7954.01 2 0.0000 0.973 0.00 1.00 0
#> TCGA.44.A479.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.55.8096.01 2 0.0892 0.960 0.02 0.98 0
#> TCGA.55.7913.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.L9.A5IP.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.49.4490.01 2 0.0000 0.973 0.00 1.00 0
#> TCGA.91.6840.01 2 0.0000 0.973 0.00 1.00 0
#> TCGA.91.6830.01 2 0.2066 0.924 0.06 0.94 0
#> TCGA.49.6743.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.44.A4SU.01 2 0.0000 0.973 0.00 1.00 0
#> TCGA.L9.A8F4.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.J2.A4AD.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.86.8075.01 2 0.0000 0.973 0.00 1.00 0
#> TCGA.49.4514.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.O1.A52J.01 2 0.0000 0.973 0.00 1.00 0
#> TCGA.4B.A93V.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.MP.A4TA.01 1 0.0000 0.993 1.00 0.00 0
#> TCGA.64.1679.01 2 0.3686 0.830 0.14 0.86 0
#> TCGA.64.1681.01 2 0.0000 0.973 0.00 1.00 0
#> TCGA.86.7953.01 1 0.1529 0.945 0.96 0.04 0
#> TCGA.J2.8192.01 2 0.0000 0.973 0.00 1.00 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.55.7910.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.86.7954.01 2 0.317 0.839 0.00 0.84 0 0.16
#> TCGA.44.A479.01 2 0.000 0.833 0.00 1.00 0 0.00
#> TCGA.55.8096.01 2 0.317 0.839 0.00 0.84 0 0.16
#> TCGA.55.7913.01 2 0.121 0.816 0.04 0.96 0 0.00
#> TCGA.L9.A5IP.01 1 0.000 0.841 1.00 0.00 0 0.00
#> TCGA.49.4490.01 2 0.380 0.786 0.00 0.78 0 0.22
#> TCGA.91.6840.01 4 0.000 0.982 0.00 0.00 0 1.00
#> TCGA.91.6830.01 2 0.317 0.839 0.00 0.84 0 0.16
#> TCGA.49.6743.01 1 0.000 0.841 1.00 0.00 0 0.00
#> TCGA.44.A4SU.01 4 0.121 0.945 0.00 0.04 0 0.96
#> TCGA.L9.A8F4.01 2 0.121 0.816 0.04 0.96 0 0.00
#> TCGA.J2.A4AD.01 1 0.000 0.841 1.00 0.00 0 0.00
#> TCGA.86.8075.01 2 0.317 0.839 0.00 0.84 0 0.16
#> TCGA.49.4514.01 2 0.121 0.816 0.04 0.96 0 0.00
#> TCGA.O1.A52J.01 4 0.000 0.982 0.00 0.00 0 1.00
#> TCGA.4B.A93V.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.MP.A4TA.01 1 0.498 0.267 0.54 0.46 0 0.00
#> TCGA.64.1679.01 1 0.000 0.841 1.00 0.00 0 0.00
#> TCGA.64.1681.01 4 0.000 0.982 0.00 0.00 0 1.00
#> TCGA.86.7953.01 2 0.000 0.833 0.00 1.00 0 0.00
#> TCGA.J2.8192.01 2 0.498 0.328 0.00 0.54 0 0.46
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.55.7910.01 3 0.0000 1.000 0 0.00 1 0.00 0
#> TCGA.86.7954.01 2 0.0000 0.996 0 1.00 0 0.00 0
#> TCGA.44.A479.01 5 0.0000 1.000 0 0.00 0 0.00 1
#> TCGA.55.8096.01 2 0.0000 0.996 0 1.00 0 0.00 0
#> TCGA.55.7913.01 5 0.0000 1.000 0 0.00 0 0.00 1
#> TCGA.L9.A5IP.01 1 0.0000 1.000 1 0.00 0 0.00 0
#> TCGA.49.4490.01 2 0.0000 0.996 0 1.00 0 0.00 0
#> TCGA.91.6840.01 4 0.0000 1.000 0 0.00 0 1.00 0
#> TCGA.91.6830.01 2 0.0000 0.996 0 1.00 0 0.00 0
#> TCGA.49.6743.01 1 0.0000 1.000 1 0.00 0 0.00 0
#> TCGA.44.A4SU.01 2 0.0609 0.979 0 0.98 0 0.02 0
#> TCGA.L9.A8F4.01 5 0.0000 1.000 0 0.00 0 0.00 1
#> TCGA.J2.A4AD.01 1 0.0000 1.000 1 0.00 0 0.00 0
#> TCGA.86.8075.01 2 0.0000 0.996 0 1.00 0 0.00 0
#> TCGA.49.4514.01 5 0.0000 1.000 0 0.00 0 0.00 1
#> TCGA.O1.A52J.01 4 0.0000 1.000 0 0.00 0 1.00 0
#> TCGA.4B.A93V.01 3 0.0000 1.000 0 0.00 1 0.00 0
#> TCGA.MP.A4TA.01 5 0.0000 1.000 0 0.00 0 0.00 1
#> TCGA.64.1679.01 1 0.0000 1.000 1 0.00 0 0.00 0
#> TCGA.64.1681.01 4 0.0000 1.000 0 0.00 0 1.00 0
#> TCGA.86.7953.01 5 0.0000 1.000 0 0.00 0 0.00 1
#> TCGA.J2.8192.01 2 0.0000 0.996 0 1.00 0 0.00 0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.55.7910.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.86.7954.01 2 0.1865 0.920 0.00 0.92 0 0.04 0.00 0.04
#> TCGA.44.A479.01 5 0.0000 0.983 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.55.8096.01 2 0.0937 0.941 0.00 0.96 0 0.00 0.00 0.04
#> TCGA.55.7913.01 5 0.0000 0.983 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.L9.A5IP.01 1 0.1814 0.895 0.90 0.00 0 0.00 0.00 0.10
#> TCGA.49.4490.01 2 0.0000 0.951 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.91.6840.01 6 0.2631 0.000 0.00 0.00 0 0.18 0.00 0.82
#> TCGA.91.6830.01 2 0.1480 0.929 0.02 0.94 0 0.00 0.00 0.04
#> TCGA.49.6743.01 1 0.0000 0.946 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.44.A4SU.01 2 0.0547 0.945 0.00 0.98 0 0.02 0.00 0.00
#> TCGA.L9.A8F4.01 5 0.0000 0.983 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.J2.A4AD.01 1 0.0000 0.946 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.86.8075.01 2 0.1865 0.920 0.00 0.92 0 0.04 0.00 0.04
#> TCGA.49.4514.01 5 0.0000 0.983 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.O1.A52J.01 4 0.0937 1.000 0.00 0.04 0 0.96 0.00 0.00
#> TCGA.4B.A93V.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 5 0.0000 0.983 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.64.1679.01 1 0.1480 0.913 0.94 0.02 0 0.00 0.00 0.04
#> TCGA.64.1681.01 4 0.0937 1.000 0.00 0.04 0 0.96 0.00 0.00
#> TCGA.86.7953.01 5 0.1865 0.910 0.00 0.00 0 0.04 0.92 0.04
#> TCGA.J2.8192.01 2 0.0000 0.951 0.00 1.00 0 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.55.7910.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.86.7954.01 2 0.3228 0.775 0.00 0.80 0 0.02 0.00 0.02 0.16
#> TCGA.44.A479.01 5 0.1166 0.910 0.00 0.00 0 0.00 0.94 0.00 0.06
#> TCGA.55.8096.01 2 0.1433 0.827 0.00 0.92 0 0.00 0.00 0.00 0.08
#> TCGA.55.7913.01 5 0.1166 0.894 0.00 0.00 0 0.00 0.94 0.00 0.06
#> TCGA.L9.A5IP.01 7 0.3459 0.000 0.40 0.00 0 0.00 0.00 0.00 0.60
#> TCGA.49.4490.01 2 0.0504 0.845 0.00 0.98 0 0.00 0.00 0.00 0.02
#> TCGA.91.6840.01 6 0.0504 0.000 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.91.6830.01 2 0.3199 0.739 0.06 0.80 0 0.00 0.00 0.00 0.14
#> TCGA.49.6743.01 1 0.1363 0.633 0.94 0.00 0 0.00 0.02 0.00 0.04
#> TCGA.44.A4SU.01 2 0.2422 0.750 0.00 0.82 0 0.18 0.00 0.00 0.00
#> TCGA.L9.A8F4.01 5 0.1166 0.910 0.00 0.00 0 0.00 0.94 0.00 0.06
#> TCGA.J2.A4AD.01 1 0.0000 0.671 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.86.8075.01 2 0.3055 0.788 0.00 0.82 0 0.02 0.00 0.02 0.14
#> TCGA.49.4514.01 5 0.0000 0.911 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.O1.A52J.01 4 0.0504 1.000 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.4B.A93V.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TA.01 5 0.0000 0.911 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.64.1679.01 1 0.3867 0.508 0.74 0.12 0 0.00 0.00 0.00 0.14
#> TCGA.64.1681.01 4 0.0504 1.000 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.86.7953.01 5 0.3887 0.715 0.00 0.00 0 0.02 0.70 0.02 0.26
#> TCGA.J2.8192.01 2 0.0504 0.845 0.00 0.98 0 0.02 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.55.7910.01 3 0.0000 1.000 0.00 0.00 1 0.0 0.00 0 0.00 0.00
#> TCGA.86.7954.01 8 0.0000 0.496 0.00 0.00 0 0.0 0.00 0 0.00 1.00
#> TCGA.44.A479.01 5 0.0471 0.906 0.00 0.02 0 0.0 0.98 0 0.00 0.00
#> TCGA.55.8096.01 2 0.3690 0.774 0.00 0.56 0 0.0 0.00 0 0.02 0.42
#> TCGA.55.7913.01 5 0.2818 0.773 0.00 0.12 0 0.0 0.82 0 0.06 0.00
#> TCGA.L9.A5IP.01 7 0.2114 0.000 0.16 0.00 0 0.0 0.00 0 0.84 0.00
#> TCGA.49.4490.01 2 0.3318 0.776 0.00 0.54 0 0.0 0.00 0 0.00 0.46
#> TCGA.91.6840.01 6 0.0000 0.000 0.00 0.00 0 0.0 0.00 1 0.00 0.00
#> TCGA.91.6830.01 2 0.5171 0.694 0.06 0.54 0 0.0 0.02 0 0.04 0.34
#> TCGA.49.6743.01 1 0.5124 0.302 0.62 0.10 0 0.0 0.18 0 0.10 0.00
#> TCGA.44.A4SU.01 2 0.5622 0.536 0.00 0.46 0 0.2 0.00 0 0.04 0.30
#> TCGA.L9.A8F4.01 5 0.0471 0.906 0.00 0.02 0 0.0 0.98 0 0.00 0.00
#> TCGA.J2.A4AD.01 1 0.0000 0.584 1.00 0.00 0 0.0 0.00 0 0.00 0.00
#> TCGA.86.8075.01 8 0.0471 0.469 0.00 0.02 0 0.0 0.00 0 0.00 0.98
#> TCGA.49.4514.01 5 0.0808 0.897 0.00 0.04 0 0.0 0.96 0 0.00 0.00
#> TCGA.O1.A52J.01 4 0.0000 1.000 0.00 0.00 0 1.0 0.00 0 0.00 0.00
#> TCGA.4B.A93V.01 3 0.0000 1.000 0.00 0.00 1 0.0 0.00 0 0.00 0.00
#> TCGA.MP.A4TA.01 5 0.1563 0.857 0.00 0.10 0 0.0 0.90 0 0.00 0.00
#> TCGA.64.1679.01 1 0.2994 0.543 0.80 0.14 0 0.0 0.00 0 0.06 0.00
#> TCGA.64.1681.01 4 0.0000 1.000 0.00 0.00 0 1.0 0.00 0 0.00 0.00
#> TCGA.86.7953.01 8 0.5674 0.175 0.00 0.20 0 0.0 0.24 0 0.06 0.50
#> TCGA.J2.8192.01 2 0.3971 0.763 0.00 0.54 0 0.0 0.00 0 0.04 0.42
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: Node07. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["072"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 46 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.983 0.992 0.4547 0.551 0.551
#> 3 3 0.751 0.933 0.955 0.4692 0.748 0.552
#> 4 4 0.890 0.906 0.933 0.0855 0.933 0.799
#> 5 5 0.733 0.636 0.837 0.0642 0.952 0.829
#> 6 6 0.757 0.497 0.774 0.0388 0.967 0.868
#> 7 7 0.806 0.549 0.723 0.0298 0.926 0.687
#> 8 8 0.792 0.635 0.788 0.0165 0.938 0.689
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.86.8281.01 1 0.000 0.988 1.00 0.00
#> TCGA.86.8358.01 1 0.000 0.988 1.00 0.00
#> TCGA.78.7149.01 1 0.000 0.988 1.00 0.00
#> TCGA.55.6642.01 1 0.000 0.988 1.00 0.00
#> TCGA.33.6737.01 1 0.327 0.934 0.94 0.06
#> TCGA.55.6968.01 1 0.000 0.988 1.00 0.00
#> TCGA.75.7027.01 1 0.000 0.988 1.00 0.00
#> TCGA.86.8279.01 1 0.000 0.988 1.00 0.00
#> TCGA.33.4566.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.8615.01 1 0.000 0.988 1.00 0.00
#> TCGA.05.5425.01 1 0.000 0.988 1.00 0.00
#> TCGA.50.5066.02 1 0.000 0.988 1.00 0.00
#> TCGA.55.8092.01 2 0.000 1.000 0.00 1.00
#> TCGA.75.6207.01 2 0.000 1.000 0.00 1.00
#> TCGA.69.7764.01 1 0.000 0.988 1.00 0.00
#> TCGA.73.4676.01 2 0.000 1.000 0.00 1.00
#> TCGA.MN.A4N4.01 1 0.795 0.694 0.76 0.24
#> TCGA.44.8120.01 2 0.000 1.000 0.00 1.00
#> TCGA.73.A9RS.01 2 0.000 1.000 0.00 1.00
#> TCGA.97.7937.01 2 0.000 1.000 0.00 1.00
#> TCGA.05.5428.01 2 0.000 1.000 0.00 1.00
#> TCGA.91.A4BC.01 1 0.000 0.988 1.00 0.00
#> TCGA.05.4433.01 1 0.327 0.934 0.94 0.06
#> TCGA.50.5932.01 1 0.000 0.988 1.00 0.00
#> TCGA.50.7109.01 1 0.000 0.988 1.00 0.00
#> TCGA.78.7633.01 1 0.000 0.988 1.00 0.00
#> TCGA.05.4396.01 2 0.000 1.000 0.00 1.00
#> TCGA.78.7154.01 2 0.000 1.000 0.00 1.00
#> TCGA.78.7167.01 1 0.000 0.988 1.00 0.00
#> TCGA.55.8085.01 1 0.000 0.988 1.00 0.00
#> TCGA.MP.A4TE.01 1 0.000 0.988 1.00 0.00
#> TCGA.78.7542.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.7994.01 2 0.000 1.000 0.00 1.00
#> TCGA.86.A4D0.01 1 0.000 0.988 1.00 0.00
#> TCGA.99.8032.01 1 0.000 0.988 1.00 0.00
#> TCGA.64.5779.01 1 0.000 0.988 1.00 0.00
#> TCGA.95.7562.01 2 0.000 1.000 0.00 1.00
#> TCGA.55.7284.01 1 0.000 0.988 1.00 0.00
#> TCGA.91.6829.01 2 0.000 1.000 0.00 1.00
#> TCGA.86.8669.01 1 0.000 0.988 1.00 0.00
#> TCGA.MP.A4SV.01 2 0.000 1.000 0.00 1.00
#> TCGA.NJ.A55R.01 1 0.000 0.988 1.00 0.00
#> TCGA.33.AASB.01 1 0.000 0.988 1.00 0.00
#> TCGA.97.8179.01 1 0.000 0.988 1.00 0.00
#> TCGA.86.7713.01 1 0.000 0.988 1.00 0.00
#> TCGA.62.A46S.01 1 0.000 0.988 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.86.8281.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.86.8358.01 3 0.334 0.899 0.12 0.00 0.88
#> TCGA.78.7149.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.55.6642.01 3 0.334 0.899 0.12 0.00 0.88
#> TCGA.33.6737.01 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.55.6968.01 3 0.334 0.899 0.12 0.00 0.88
#> TCGA.75.7027.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.86.8279.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.33.4566.01 2 0.000 0.912 0.00 1.00 0.00
#> TCGA.55.8615.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.05.5425.01 3 0.334 0.899 0.12 0.00 0.88
#> TCGA.50.5066.02 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.55.8092.01 2 0.369 0.901 0.00 0.86 0.14
#> TCGA.75.6207.01 2 0.000 0.912 0.00 1.00 0.00
#> TCGA.69.7764.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.73.4676.01 2 0.000 0.912 0.00 1.00 0.00
#> TCGA.MN.A4N4.01 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.44.8120.01 2 0.369 0.901 0.00 0.86 0.14
#> TCGA.73.A9RS.01 2 0.540 0.758 0.00 0.72 0.28
#> TCGA.97.7937.01 2 0.369 0.901 0.00 0.86 0.14
#> TCGA.05.5428.01 2 0.000 0.912 0.00 1.00 0.00
#> TCGA.91.A4BC.01 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.05.4433.01 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.50.5932.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.50.7109.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.78.7633.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.05.4396.01 2 0.000 0.912 0.00 1.00 0.00
#> TCGA.78.7154.01 2 0.000 0.912 0.00 1.00 0.00
#> TCGA.78.7167.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.55.8085.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.MP.A4TE.01 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.78.7542.01 2 0.369 0.901 0.00 0.86 0.14
#> TCGA.55.7994.01 2 0.000 0.912 0.00 1.00 0.00
#> TCGA.86.A4D0.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.99.8032.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.64.5779.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.95.7562.01 2 0.502 0.810 0.00 0.76 0.24
#> TCGA.55.7284.01 3 0.369 0.878 0.14 0.00 0.86
#> TCGA.91.6829.01 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.86.8669.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.369 0.901 0.00 0.86 0.14
#> TCGA.NJ.A55R.01 3 0.334 0.899 0.12 0.00 0.88
#> TCGA.33.AASB.01 3 0.000 0.922 0.00 0.00 1.00
#> TCGA.97.8179.01 1 0.334 0.851 0.88 0.00 0.12
#> TCGA.86.7713.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.62.A46S.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.86.8281.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.86.8358.01 3 0.3037 0.905 0.02 0.00 0.88 0.10
#> TCGA.78.7149.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.55.6642.01 3 0.0707 0.949 0.02 0.00 0.98 0.00
#> TCGA.33.6737.01 3 0.1211 0.927 0.00 0.04 0.96 0.00
#> TCGA.55.6968.01 3 0.0707 0.949 0.02 0.00 0.98 0.00
#> TCGA.75.7027.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.86.8279.01 1 0.0707 0.956 0.98 0.00 0.00 0.02
#> TCGA.33.4566.01 4 0.2921 0.958 0.00 0.14 0.00 0.86
#> TCGA.55.8615.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.05.5425.01 3 0.0707 0.949 0.02 0.00 0.98 0.00
#> TCGA.50.5066.02 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.55.8092.01 2 0.0707 0.881 0.00 0.98 0.02 0.00
#> TCGA.75.6207.01 4 0.2921 0.958 0.00 0.14 0.00 0.86
#> TCGA.69.7764.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.73.4676.01 4 0.2921 0.958 0.00 0.14 0.00 0.86
#> TCGA.MN.A4N4.01 3 0.2345 0.870 0.00 0.10 0.90 0.00
#> TCGA.44.8120.01 2 0.0707 0.881 0.00 0.98 0.02 0.00
#> TCGA.73.A9RS.01 2 0.2345 0.832 0.00 0.90 0.10 0.00
#> TCGA.97.7937.01 2 0.0707 0.881 0.00 0.98 0.02 0.00
#> TCGA.05.5428.01 4 0.2921 0.958 0.00 0.14 0.00 0.86
#> TCGA.91.A4BC.01 3 0.0000 0.947 0.00 0.00 1.00 0.00
#> TCGA.05.4433.01 3 0.1913 0.926 0.00 0.04 0.94 0.02
#> TCGA.50.5932.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.50.7109.01 1 0.2335 0.923 0.92 0.00 0.06 0.02
#> TCGA.78.7633.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.05.4396.01 2 0.2345 0.744 0.00 0.90 0.00 0.10
#> TCGA.78.7154.01 4 0.4522 0.747 0.00 0.32 0.00 0.68
#> TCGA.78.7167.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.55.8085.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 3 0.2647 0.899 0.00 0.00 0.88 0.12
#> TCGA.78.7542.01 2 0.0707 0.881 0.00 0.98 0.02 0.00
#> TCGA.55.7994.01 4 0.2921 0.958 0.00 0.14 0.00 0.86
#> TCGA.86.A4D0.01 1 0.3611 0.882 0.86 0.00 0.06 0.08
#> TCGA.99.8032.01 1 0.1913 0.936 0.94 0.00 0.04 0.02
#> TCGA.64.5779.01 1 0.0707 0.956 0.98 0.00 0.00 0.02
#> TCGA.95.7562.01 2 0.2011 0.850 0.00 0.92 0.08 0.00
#> TCGA.55.7284.01 3 0.1913 0.934 0.02 0.00 0.94 0.04
#> TCGA.91.6829.01 2 0.5487 0.349 0.00 0.58 0.40 0.02
#> TCGA.86.8669.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.0707 0.881 0.00 0.98 0.02 0.00
#> TCGA.NJ.A55R.01 3 0.0707 0.949 0.02 0.00 0.98 0.00
#> TCGA.33.AASB.01 3 0.1211 0.941 0.00 0.00 0.96 0.04
#> TCGA.97.8179.01 1 0.4939 0.717 0.74 0.00 0.22 0.04
#> TCGA.86.7713.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.62.A46S.01 1 0.2335 0.923 0.92 0.00 0.06 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.86.8281.01 1 0.0000 0.8277 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8358.01 3 0.4126 -0.2362 0.00 0.00 0.62 0.00 0.38
#> TCGA.78.7149.01 1 0.0000 0.8277 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.6642.01 3 0.0609 0.5684 0.00 0.00 0.98 0.00 0.02
#> TCGA.33.6737.01 3 0.4527 0.1875 0.00 0.04 0.70 0.00 0.26
#> TCGA.55.6968.01 3 0.1410 0.5564 0.00 0.00 0.94 0.00 0.06
#> TCGA.75.7027.01 1 0.0000 0.8277 1.00 0.00 0.00 0.00 0.00
#> TCGA.86.8279.01 1 0.5263 0.6408 0.66 0.00 0.24 0.00 0.10
#> TCGA.33.4566.01 4 0.1043 0.9544 0.00 0.04 0.00 0.96 0.00
#> TCGA.55.8615.01 1 0.0609 0.8269 0.98 0.00 0.00 0.02 0.00
#> TCGA.05.5425.01 3 0.0609 0.5736 0.00 0.00 0.98 0.00 0.02
#> TCGA.50.5066.02 3 0.2732 0.4495 0.00 0.00 0.84 0.00 0.16
#> TCGA.55.8092.01 2 0.0609 0.8498 0.00 0.98 0.00 0.02 0.00
#> TCGA.75.6207.01 4 0.1043 0.9544 0.00 0.04 0.00 0.96 0.00
#> TCGA.69.7764.01 1 0.0000 0.8277 1.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.01 4 0.1043 0.9544 0.00 0.04 0.00 0.96 0.00
#> TCGA.MN.A4N4.01 3 0.5599 0.0273 0.00 0.12 0.62 0.00 0.26
#> TCGA.44.8120.01 2 0.2012 0.8469 0.00 0.92 0.00 0.02 0.06
#> TCGA.73.A9RS.01 2 0.4613 0.5772 0.00 0.62 0.02 0.00 0.36
#> TCGA.97.7937.01 2 0.0609 0.8498 0.00 0.98 0.00 0.02 0.00
#> TCGA.05.5428.01 4 0.1043 0.9544 0.00 0.04 0.00 0.96 0.00
#> TCGA.91.A4BC.01 3 0.1410 0.5571 0.00 0.00 0.94 0.00 0.06
#> TCGA.05.4433.01 3 0.5305 -0.1103 0.00 0.04 0.64 0.02 0.30
#> TCGA.50.5932.01 1 0.0609 0.8269 0.98 0.00 0.00 0.02 0.00
#> TCGA.50.7109.01 1 0.5864 0.5311 0.56 0.00 0.32 0.00 0.12
#> TCGA.78.7633.01 1 0.0609 0.8269 0.98 0.00 0.00 0.02 0.00
#> TCGA.05.4396.01 2 0.2754 0.7749 0.00 0.88 0.00 0.08 0.04
#> TCGA.78.7154.01 4 0.5083 0.7370 0.00 0.14 0.00 0.70 0.16
#> TCGA.78.7167.01 1 0.0609 0.8269 0.98 0.00 0.00 0.02 0.00
#> TCGA.55.8085.01 1 0.0000 0.8277 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 5 0.4798 0.4908 0.00 0.02 0.44 0.00 0.54
#> TCGA.78.7542.01 2 0.1648 0.8494 0.00 0.94 0.00 0.02 0.04
#> TCGA.55.7994.01 4 0.1043 0.9544 0.00 0.04 0.00 0.96 0.00
#> TCGA.86.A4D0.01 1 0.6530 0.3448 0.44 0.00 0.36 0.00 0.20
#> TCGA.99.8032.01 1 0.5864 0.5311 0.56 0.00 0.32 0.00 0.12
#> TCGA.64.5779.01 1 0.4818 0.6907 0.72 0.00 0.18 0.00 0.10
#> TCGA.95.7562.01 2 0.1732 0.8332 0.00 0.92 0.00 0.00 0.08
#> TCGA.55.7284.01 3 0.2616 0.4774 0.00 0.00 0.88 0.02 0.10
#> TCGA.91.6829.01 2 0.6422 0.1325 0.00 0.46 0.18 0.00 0.36
#> TCGA.86.8669.01 1 0.0000 0.8277 1.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.0609 0.8498 0.00 0.98 0.00 0.02 0.00
#> TCGA.NJ.A55R.01 3 0.0609 0.5684 0.00 0.00 0.98 0.00 0.02
#> TCGA.33.AASB.01 5 0.4126 0.5139 0.00 0.00 0.38 0.00 0.62
#> TCGA.97.8179.01 3 0.5934 0.1908 0.26 0.00 0.62 0.02 0.10
#> TCGA.86.7713.01 1 0.0609 0.8269 0.98 0.00 0.00 0.02 0.00
#> TCGA.62.A46S.01 1 0.5864 0.5311 0.56 0.00 0.32 0.00 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.86.8281.01 1 0.0000 0.7074 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8358.01 3 0.5963 -0.0852 0.00 0.00 0.44 0.00 0.32 0.24
#> TCGA.78.7149.01 1 0.0000 0.7074 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6642.01 3 0.0547 0.6048 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.33.6737.01 3 0.5331 0.3870 0.00 0.04 0.66 0.00 0.20 0.10
#> TCGA.55.6968.01 3 0.2790 0.5422 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.75.7027.01 1 0.1480 0.7074 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.86.8279.01 1 0.5867 -0.2936 0.48 0.00 0.28 0.00 0.00 0.24
#> TCGA.33.4566.01 4 0.0000 0.9080 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8615.01 1 0.1480 0.7074 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.05.5425.01 3 0.1807 0.6277 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.50.5066.02 3 0.2190 0.6331 0.00 0.00 0.90 0.00 0.04 0.06
#> TCGA.55.8092.01 2 0.0000 0.9111 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.75.6207.01 4 0.0000 0.9080 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.69.7764.01 1 0.0000 0.7074 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.73.4676.01 4 0.0000 0.9080 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MN.A4N4.01 3 0.6012 0.2601 0.00 0.14 0.62 0.00 0.14 0.10
#> TCGA.44.8120.01 2 0.1865 0.8837 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.73.A9RS.01 5 0.6540 0.1173 0.00 0.32 0.02 0.00 0.36 0.30
#> TCGA.97.7937.01 2 0.0000 0.9111 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.05.5428.01 4 0.0000 0.9080 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.91.A4BC.01 3 0.0547 0.6238 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.05.4433.01 3 0.5106 0.0249 0.00 0.02 0.50 0.00 0.44 0.04
#> TCGA.50.5932.01 1 0.1480 0.7074 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.50.7109.01 1 0.5682 -0.3950 0.46 0.00 0.38 0.00 0.00 0.16
#> TCGA.78.7633.01 1 0.1480 0.7074 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.05.4396.01 2 0.2474 0.8132 0.00 0.88 0.00 0.04 0.00 0.08
#> TCGA.78.7154.01 4 0.6188 0.3742 0.00 0.08 0.00 0.52 0.08 0.32
#> TCGA.78.7167.01 1 0.1480 0.7074 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.55.8085.01 1 0.0000 0.7074 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 5 0.4723 0.3236 0.00 0.00 0.14 0.00 0.68 0.18
#> TCGA.78.7542.01 2 0.0937 0.9011 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.7994.01 4 0.0000 0.9080 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.A4D0.01 6 0.7265 0.0000 0.24 0.00 0.30 0.00 0.10 0.36
#> TCGA.99.8032.01 1 0.5682 -0.3950 0.46 0.00 0.38 0.00 0.00 0.16
#> TCGA.64.5779.01 1 0.5102 0.0580 0.62 0.00 0.24 0.00 0.00 0.14
#> TCGA.95.7562.01 2 0.3746 0.7348 0.00 0.78 0.00 0.00 0.08 0.14
#> TCGA.55.7284.01 3 0.3950 0.4350 0.00 0.00 0.72 0.00 0.04 0.24
#> TCGA.91.6829.01 5 0.7208 0.4342 0.00 0.22 0.20 0.00 0.44 0.14
#> TCGA.86.8669.01 1 0.0000 0.7074 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.0000 0.9111 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 3 0.0547 0.6048 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.33.AASB.01 5 0.3409 0.2832 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.97.8179.01 3 0.6471 -0.3128 0.20 0.00 0.48 0.00 0.04 0.28
#> TCGA.86.7713.01 1 0.1480 0.7074 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.62.A46S.01 1 0.5682 -0.3950 0.46 0.00 0.38 0.00 0.00 0.16
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.86.8281.01 1 0.1166 0.8905 0.94 0.00 0.00 0.0 0.00 0.06 0.00
#> TCGA.86.8358.01 3 0.5982 -0.0791 0.00 0.00 0.36 0.0 0.02 0.36 0.26
#> TCGA.78.7149.01 1 0.1166 0.8905 0.94 0.00 0.00 0.0 0.00 0.06 0.00
#> TCGA.55.6642.01 3 0.2832 0.2219 0.00 0.00 0.76 0.0 0.00 0.24 0.00
#> TCGA.33.6737.01 3 0.5655 -0.2298 0.00 0.00 0.44 0.0 0.38 0.16 0.02
#> TCGA.55.6968.01 3 0.3294 0.2663 0.00 0.00 0.66 0.0 0.00 0.34 0.00
#> TCGA.75.7027.01 1 0.0000 0.8974 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.86.8279.01 3 0.5596 -0.6351 0.30 0.00 0.40 0.0 0.00 0.30 0.00
#> TCGA.33.4566.01 4 0.0000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.55.8615.01 1 0.0000 0.8974 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.05.5425.01 3 0.0000 0.4270 0.00 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.50.5066.02 3 0.3199 0.3722 0.00 0.00 0.80 0.0 0.06 0.14 0.00
#> TCGA.55.8092.01 2 0.0000 0.8835 0.00 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.75.6207.01 4 0.0000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.69.7764.01 1 0.1166 0.8905 0.94 0.00 0.00 0.0 0.00 0.06 0.00
#> TCGA.73.4676.01 4 0.0000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 3 0.5293 0.0210 0.00 0.00 0.58 0.0 0.24 0.16 0.02
#> TCGA.44.8120.01 2 0.2512 0.8340 0.00 0.86 0.00 0.0 0.10 0.04 0.00
#> TCGA.73.A9RS.01 5 0.1166 0.3393 0.00 0.06 0.00 0.0 0.94 0.00 0.00
#> TCGA.97.7937.01 2 0.0000 0.8835 0.00 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.05.5428.01 4 0.0000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.91.A4BC.01 3 0.1886 0.3754 0.00 0.00 0.88 0.0 0.00 0.12 0.00
#> TCGA.05.4433.01 3 0.6149 0.0324 0.00 0.00 0.52 0.0 0.16 0.10 0.22
#> TCGA.50.5932.01 1 0.0000 0.8974 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.50.7109.01 6 0.5735 0.8801 0.18 0.00 0.36 0.0 0.00 0.44 0.02
#> TCGA.78.7633.01 1 0.0000 0.8974 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.05.4396.01 2 0.3734 0.7270 0.00 0.78 0.00 0.0 0.04 0.14 0.04
#> TCGA.78.7154.01 5 0.5234 0.0351 0.00 0.00 0.00 0.3 0.56 0.12 0.02
#> TCGA.78.7167.01 1 0.0000 0.8974 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.55.8085.01 1 0.1166 0.8905 0.94 0.00 0.00 0.0 0.00 0.06 0.00
#> TCGA.MP.A4TE.01 7 0.0863 0.0000 0.00 0.00 0.04 0.0 0.00 0.00 0.96
#> TCGA.78.7542.01 2 0.1006 0.8764 0.00 0.96 0.00 0.0 0.02 0.02 0.00
#> TCGA.55.7994.01 4 0.0000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.86.A4D0.01 6 0.5577 0.6642 0.08 0.00 0.28 0.0 0.00 0.56 0.08
#> TCGA.99.8032.01 6 0.5798 0.8623 0.20 0.00 0.34 0.0 0.00 0.44 0.02
#> TCGA.64.5779.01 1 0.5589 -0.5855 0.40 0.00 0.28 0.0 0.00 0.32 0.00
#> TCGA.95.7562.01 2 0.3637 0.6864 0.00 0.72 0.00 0.0 0.24 0.04 0.00
#> TCGA.55.7284.01 3 0.3199 0.3203 0.00 0.00 0.80 0.0 0.00 0.14 0.06
#> TCGA.91.6829.01 5 0.5482 0.3767 0.00 0.04 0.10 0.0 0.62 0.22 0.02
#> TCGA.86.8669.01 1 0.1166 0.8905 0.94 0.00 0.00 0.0 0.00 0.06 0.00
#> TCGA.MP.A4SV.01 2 0.0000 0.8835 0.00 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 3 0.2832 0.2219 0.00 0.00 0.76 0.0 0.00 0.24 0.00
#> TCGA.33.AASB.01 5 0.6930 0.0989 0.00 0.00 0.20 0.0 0.36 0.18 0.26
#> TCGA.97.8179.01 3 0.4772 -0.2305 0.04 0.00 0.60 0.0 0.00 0.32 0.04
#> TCGA.86.7713.01 1 0.0000 0.8974 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.62.A46S.01 6 0.5735 0.8801 0.18 0.00 0.36 0.0 0.00 0.44 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.86.8281.01 1 0.109 0.9501 0.94 0.00 0.00 0.0 0.00 0.06 0.00 0.00
#> TCGA.86.8358.01 6 0.526 -0.1922 0.00 0.00 0.18 0.0 0.00 0.50 0.02 0.30
#> TCGA.78.7149.01 1 0.109 0.9501 0.94 0.00 0.00 0.0 0.00 0.06 0.00 0.00
#> TCGA.55.6642.01 3 0.438 0.4061 0.00 0.00 0.52 0.0 0.00 0.42 0.02 0.04
#> TCGA.33.6737.01 3 0.432 -0.2351 0.00 0.00 0.60 0.0 0.10 0.00 0.00 0.30
#> TCGA.55.6968.01 3 0.525 0.2959 0.00 0.00 0.38 0.0 0.00 0.34 0.00 0.28
#> TCGA.75.7027.01 1 0.000 0.9595 1.00 0.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.86.8279.01 6 0.556 0.5111 0.36 0.00 0.14 0.0 0.02 0.46 0.00 0.02
#> TCGA.33.4566.01 4 0.000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.55.8615.01 1 0.000 0.9595 1.00 0.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.05.5425.01 3 0.227 0.5489 0.00 0.00 0.82 0.0 0.00 0.18 0.00 0.00
#> TCGA.50.5066.02 3 0.000 0.4370 0.00 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.55.8092.01 2 0.000 0.8585 0.00 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.75.6207.01 4 0.000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.69.7764.01 1 0.109 0.9501 0.94 0.00 0.00 0.0 0.00 0.06 0.00 0.00
#> TCGA.73.4676.01 4 0.000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 3 0.213 0.3389 0.00 0.00 0.88 0.0 0.08 0.00 0.00 0.04
#> TCGA.44.8120.01 2 0.227 0.7995 0.00 0.88 0.00 0.0 0.08 0.00 0.02 0.02
#> TCGA.73.A9RS.01 5 0.257 0.5579 0.00 0.02 0.00 0.0 0.82 0.00 0.00 0.16
#> TCGA.97.7937.01 2 0.000 0.8585 0.00 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.05.5428.01 4 0.000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.91.A4BC.01 3 0.329 0.5240 0.00 0.00 0.74 0.0 0.00 0.22 0.00 0.04
#> TCGA.05.4433.01 3 0.414 0.2539 0.00 0.00 0.66 0.0 0.00 0.00 0.22 0.12
#> TCGA.50.5932.01 1 0.000 0.9595 1.00 0.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.50.7109.01 6 0.276 0.6477 0.26 0.00 0.00 0.0 0.00 0.74 0.00 0.00
#> TCGA.78.7633.01 1 0.000 0.9595 1.00 0.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.05.4396.01 2 0.520 0.5690 0.00 0.66 0.00 0.0 0.12 0.06 0.04 0.12
#> TCGA.78.7154.01 5 0.294 0.6280 0.00 0.02 0.00 0.1 0.84 0.00 0.02 0.02
#> TCGA.78.7167.01 1 0.000 0.9595 1.00 0.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.55.8085.01 1 0.109 0.9501 0.94 0.00 0.00 0.0 0.00 0.06 0.00 0.00
#> TCGA.MP.A4TE.01 7 0.161 0.0000 0.00 0.00 0.04 0.0 0.00 0.04 0.92 0.00
#> TCGA.78.7542.01 2 0.000 0.8585 0.00 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.55.7994.01 4 0.000 1.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.86.A4D0.01 6 0.180 0.4838 0.08 0.00 0.00 0.0 0.00 0.90 0.00 0.02
#> TCGA.99.8032.01 6 0.276 0.6477 0.26 0.00 0.00 0.0 0.00 0.74 0.00 0.00
#> TCGA.64.5779.01 6 0.330 0.4194 0.44 0.00 0.00 0.0 0.00 0.56 0.00 0.00
#> TCGA.95.7562.01 2 0.467 0.5033 0.00 0.64 0.02 0.0 0.26 0.00 0.04 0.04
#> TCGA.55.7284.01 3 0.582 0.2610 0.00 0.00 0.50 0.0 0.02 0.30 0.06 0.12
#> TCGA.91.6829.01 8 0.676 0.4476 0.00 0.00 0.26 0.0 0.30 0.02 0.12 0.30
#> TCGA.86.8669.01 1 0.109 0.9501 0.94 0.00 0.00 0.0 0.00 0.06 0.00 0.00
#> TCGA.MP.A4SV.01 2 0.000 0.8585 0.00 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 3 0.438 0.4061 0.00 0.00 0.52 0.0 0.00 0.42 0.02 0.04
#> TCGA.33.AASB.01 8 0.638 0.4069 0.00 0.00 0.26 0.0 0.06 0.02 0.30 0.36
#> TCGA.97.8179.01 6 0.629 -0.0514 0.02 0.00 0.34 0.0 0.02 0.44 0.06 0.12
#> TCGA.86.7713.01 1 0.000 0.9595 1.00 0.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.62.A46S.01 6 0.309 0.6404 0.24 0.00 0.00 0.0 0.00 0.74 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node072. Child nodes: Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02341-leaf , Node02342-leaf , Node02343-leaf , Node02344-leaf , Node02345-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node06121-leaf , Node06122-leaf , Node06123-leaf , Node07111 , Node07112-leaf , Node07211-leaf , Node07212-leaf , Node07213-leaf , Node07214-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0721"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.985 0.994 0.4315 0.574 0.574
#> 3 3 1.000 0.999 0.999 0.5904 0.740 0.547
#> 4 4 0.975 0.960 0.972 0.0802 0.948 0.836
#> 5 5 0.818 0.839 0.885 0.0424 1.000 1.000
#> 6 6 0.788 0.737 0.775 0.0267 1.000 1.000
#> 7 7 0.751 0.424 0.745 0.0330 0.942 0.779
#> 8 8 0.729 0.513 0.721 0.0245 0.875 0.477
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.86.8281.01 1 0.000 1.00 1.0 0.0
#> TCGA.86.8358.01 2 0.000 0.99 0.0 1.0
#> TCGA.78.7149.01 1 0.000 1.00 1.0 0.0
#> TCGA.55.6642.01 2 0.000 0.99 0.0 1.0
#> TCGA.33.6737.01 2 0.000 0.99 0.0 1.0
#> TCGA.55.6968.01 2 0.000 0.99 0.0 1.0
#> TCGA.75.7027.01 2 0.000 0.99 0.0 1.0
#> TCGA.86.8279.01 1 0.000 1.00 1.0 0.0
#> TCGA.55.8615.01 2 0.000 0.99 0.0 1.0
#> TCGA.05.5425.01 2 0.000 0.99 0.0 1.0
#> TCGA.50.5066.02 2 0.722 0.75 0.2 0.8
#> TCGA.69.7764.01 1 0.000 1.00 1.0 0.0
#> TCGA.MN.A4N4.01 2 0.000 0.99 0.0 1.0
#> TCGA.91.A4BC.01 2 0.000 0.99 0.0 1.0
#> TCGA.05.4433.01 2 0.000 0.99 0.0 1.0
#> TCGA.50.5932.01 1 0.000 1.00 1.0 0.0
#> TCGA.50.7109.01 2 0.000 0.99 0.0 1.0
#> TCGA.78.7633.01 1 0.000 1.00 1.0 0.0
#> TCGA.78.7167.01 1 0.000 1.00 1.0 0.0
#> TCGA.55.8085.01 1 0.000 1.00 1.0 0.0
#> TCGA.MP.A4TE.01 2 0.000 0.99 0.0 1.0
#> TCGA.86.A4D0.01 2 0.000 0.99 0.0 1.0
#> TCGA.99.8032.01 2 0.000 0.99 0.0 1.0
#> TCGA.64.5779.01 2 0.000 0.99 0.0 1.0
#> TCGA.55.7284.01 2 0.000 0.99 0.0 1.0
#> TCGA.86.8669.01 2 0.000 0.99 0.0 1.0
#> TCGA.NJ.A55R.01 2 0.000 0.99 0.0 1.0
#> TCGA.33.AASB.01 2 0.000 0.99 0.0 1.0
#> TCGA.97.8179.01 1 0.000 1.00 1.0 0.0
#> TCGA.86.7713.01 2 0.000 0.99 0.0 1.0
#> TCGA.62.A46S.01 2 0.000 0.99 0.0 1.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.86.8281.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.86.8358.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.78.7149.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.6642.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.33.6737.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.55.6968.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.75.7027.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.86.8279.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.8615.01 3 0.0892 0.979 0 0.02 0.98
#> TCGA.05.5425.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.50.5066.02 3 0.0000 0.998 0 0.00 1.00
#> TCGA.69.7764.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.MN.A4N4.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.91.A4BC.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.05.4433.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.50.5932.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.50.7109.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.78.7633.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.78.7167.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.55.8085.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.86.A4D0.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.99.8032.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.64.5779.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.55.7284.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.86.8669.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.NJ.A55R.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.33.AASB.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.97.8179.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.86.7713.01 3 0.0000 0.998 0 0.00 1.00
#> TCGA.62.A46S.01 3 0.0000 0.998 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.86.8281.01 1 0.0707 0.986 0.98 0.00 0.00 0.02
#> TCGA.86.8358.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.78.7149.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.55.6642.01 2 0.2011 0.921 0.00 0.92 0.00 0.08
#> TCGA.33.6737.01 3 0.0000 0.927 0.00 0.00 1.00 0.00
#> TCGA.55.6968.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.75.7027.01 3 0.0000 0.927 0.00 0.00 1.00 0.00
#> TCGA.86.8279.01 1 0.0707 0.986 0.98 0.00 0.00 0.02
#> TCGA.55.8615.01 4 0.1913 0.961 0.00 0.02 0.04 0.94
#> TCGA.05.5425.01 3 0.1637 0.926 0.00 0.00 0.94 0.06
#> TCGA.50.5066.02 3 0.2647 0.891 0.00 0.00 0.88 0.12
#> TCGA.69.7764.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.MN.A4N4.01 3 0.1211 0.928 0.00 0.00 0.96 0.04
#> TCGA.91.A4BC.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.05.4433.01 3 0.2921 0.880 0.00 0.00 0.86 0.14
#> TCGA.50.5932.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.50.7109.01 2 0.2011 0.921 0.00 0.92 0.00 0.08
#> TCGA.78.7633.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.78.7167.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.55.8085.01 1 0.0707 0.986 0.98 0.00 0.00 0.02
#> TCGA.MP.A4TE.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.86.A4D0.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.99.8032.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.64.5779.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.55.7284.01 3 0.3400 0.840 0.00 0.00 0.82 0.18
#> TCGA.86.8669.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.NJ.A55R.01 2 0.0000 0.983 0.00 1.00 0.00 0.00
#> TCGA.33.AASB.01 3 0.0000 0.927 0.00 0.00 1.00 0.00
#> TCGA.97.8179.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.86.7713.01 4 0.0707 0.970 0.00 0.00 0.02 0.98
#> TCGA.62.A46S.01 4 0.1211 0.967 0.00 0.00 0.04 0.96
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.86.8281.01 5 0.2280 0.858 0.12 0.00 0.00 0.00 0.88
#> TCGA.86.8358.01 2 0.1410 0.906 0.06 0.94 0.00 0.00 0.00
#> TCGA.78.7149.01 5 0.2929 0.848 0.18 0.00 0.00 0.00 0.82
#> TCGA.55.6642.01 2 0.4170 0.770 0.08 0.78 0.00 0.14 0.00
#> TCGA.33.6737.01 3 0.2929 0.798 0.18 0.00 0.82 0.00 0.00
#> TCGA.55.6968.01 2 0.1410 0.906 0.06 0.94 0.00 0.00 0.00
#> TCGA.75.7027.01 3 0.2516 0.796 0.14 0.00 0.86 0.00 0.00
#> TCGA.86.8279.01 5 0.1732 0.875 0.08 0.00 0.00 0.00 0.92
#> TCGA.55.8615.01 4 0.3999 0.763 0.24 0.02 0.00 0.74 0.00
#> TCGA.05.5425.01 3 0.0609 0.837 0.00 0.00 0.98 0.02 0.00
#> TCGA.50.5066.02 3 0.6721 0.495 0.24 0.00 0.58 0.12 0.06
#> TCGA.69.7764.01 5 0.1043 0.886 0.04 0.00 0.00 0.00 0.96
#> TCGA.MN.A4N4.01 3 0.1410 0.836 0.06 0.00 0.94 0.00 0.00
#> TCGA.91.A4BC.01 2 0.0609 0.903 0.00 0.98 0.00 0.02 0.00
#> TCGA.05.4433.01 3 0.2616 0.805 0.02 0.00 0.88 0.10 0.00
#> TCGA.50.5932.01 5 0.1043 0.888 0.04 0.00 0.00 0.00 0.96
#> TCGA.50.7109.01 2 0.4373 0.745 0.08 0.76 0.00 0.16 0.00
#> TCGA.78.7633.01 5 0.2929 0.848 0.18 0.00 0.00 0.00 0.82
#> TCGA.78.7167.01 5 0.2929 0.848 0.18 0.00 0.00 0.00 0.82
#> TCGA.55.8085.01 5 0.2280 0.858 0.12 0.00 0.00 0.00 0.88
#> TCGA.MP.A4TE.01 2 0.1410 0.906 0.06 0.94 0.00 0.00 0.00
#> TCGA.86.A4D0.01 2 0.1410 0.906 0.06 0.94 0.00 0.00 0.00
#> TCGA.99.8032.01 2 0.1410 0.906 0.06 0.94 0.00 0.00 0.00
#> TCGA.64.5779.01 2 0.2012 0.885 0.06 0.92 0.00 0.02 0.00
#> TCGA.55.7284.01 3 0.2616 0.810 0.02 0.00 0.88 0.10 0.00
#> TCGA.86.8669.01 2 0.2012 0.885 0.06 0.92 0.00 0.02 0.00
#> TCGA.NJ.A55R.01 2 0.0609 0.903 0.00 0.98 0.00 0.02 0.00
#> TCGA.33.AASB.01 3 0.2516 0.815 0.14 0.00 0.86 0.00 0.00
#> TCGA.97.8179.01 5 0.0609 0.890 0.02 0.00 0.00 0.00 0.98
#> TCGA.86.7713.01 4 0.2077 0.829 0.04 0.00 0.04 0.92 0.00
#> TCGA.62.A46S.01 4 0.2331 0.810 0.02 0.00 0.08 0.90 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.86.8281.01 5 0.3483 0.812 0.12 0.00 0.04 0.02 0.82 0.00
#> TCGA.86.8358.01 2 0.1480 0.895 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.78.7149.01 5 0.2793 0.794 0.00 0.00 0.20 0.00 0.80 0.00
#> TCGA.55.6642.01 2 0.4345 0.714 0.02 0.74 0.18 0.06 0.00 0.00
#> TCGA.33.6737.01 6 0.3864 0.524 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.55.6968.01 2 0.1480 0.895 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.75.7027.01 6 0.4806 0.486 0.38 0.00 0.06 0.00 0.00 0.56
#> TCGA.86.8279.01 5 0.3572 0.814 0.10 0.00 0.06 0.02 0.82 0.00
#> TCGA.55.8615.01 4 0.4337 0.551 0.02 0.00 0.48 0.50 0.00 0.00
#> TCGA.05.5425.01 6 0.0547 0.673 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.50.5066.02 6 0.7015 0.312 0.36 0.00 0.06 0.10 0.04 0.44
#> TCGA.69.7764.01 5 0.2190 0.849 0.06 0.00 0.04 0.00 0.90 0.00
#> TCGA.MN.A4N4.01 6 0.0547 0.671 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.91.A4BC.01 2 0.0547 0.889 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.05.4433.01 6 0.2629 0.635 0.08 0.00 0.02 0.02 0.00 0.88
#> TCGA.50.5932.01 5 0.0547 0.851 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.50.7109.01 2 0.5684 0.579 0.02 0.64 0.20 0.12 0.00 0.02
#> TCGA.78.7633.01 5 0.2793 0.794 0.00 0.00 0.20 0.00 0.80 0.00
#> TCGA.78.7167.01 5 0.2793 0.794 0.00 0.00 0.20 0.00 0.80 0.00
#> TCGA.55.8085.01 5 0.3572 0.823 0.10 0.00 0.06 0.02 0.82 0.00
#> TCGA.MP.A4TE.01 2 0.1480 0.895 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.86.A4D0.01 2 0.1480 0.895 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.99.8032.01 2 0.1480 0.895 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.64.5779.01 2 0.1480 0.876 0.02 0.94 0.04 0.00 0.00 0.00
#> TCGA.55.7284.01 6 0.2350 0.641 0.10 0.00 0.02 0.00 0.00 0.88
#> TCGA.86.8669.01 2 0.1814 0.855 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.NJ.A55R.01 2 0.0547 0.889 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.33.AASB.01 6 0.4282 0.557 0.42 0.00 0.02 0.00 0.00 0.56
#> TCGA.97.8179.01 5 0.0547 0.853 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.86.7713.01 4 0.0937 0.640 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.62.A46S.01 4 0.5636 0.507 0.06 0.00 0.08 0.62 0.00 0.24
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.86.8281.01 3 0.3413 0.8490 0.00 0.00 0.62 0.00 0.38 0.00 0.00
#> TCGA.86.8358.01 2 0.0504 0.7789 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.78.7149.01 5 0.0504 0.6181 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.55.6642.01 2 0.7417 0.4898 0.10 0.48 0.10 0.10 0.00 0.02 0.20
#> TCGA.33.6737.01 1 0.3459 0.0000 0.60 0.00 0.00 0.00 0.00 0.40 0.00
#> TCGA.55.6968.01 2 0.0504 0.7789 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.75.7027.01 6 0.6226 -0.0749 0.38 0.00 0.08 0.14 0.00 0.40 0.00
#> TCGA.86.8279.01 3 0.3546 0.7601 0.00 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.55.8615.01 7 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.05.5425.01 6 0.1433 0.3361 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.50.5066.02 6 0.6920 -0.2637 0.28 0.00 0.26 0.14 0.00 0.32 0.00
#> TCGA.69.7764.01 5 0.3943 -0.4689 0.02 0.00 0.42 0.00 0.56 0.00 0.00
#> TCGA.MN.A4N4.01 6 0.1671 0.3152 0.10 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.91.A4BC.01 2 0.4507 0.7517 0.08 0.76 0.06 0.06 0.00 0.00 0.04
#> TCGA.05.4433.01 6 0.1860 0.3727 0.02 0.00 0.02 0.04 0.00 0.92 0.00
#> TCGA.50.5932.01 5 0.3186 0.4111 0.02 0.00 0.22 0.00 0.76 0.00 0.00
#> TCGA.50.7109.01 2 0.7987 0.3868 0.10 0.42 0.12 0.12 0.00 0.04 0.20
#> TCGA.78.7633.01 5 0.0000 0.6227 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.78.7167.01 5 0.0000 0.6227 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.55.8085.01 3 0.3496 0.8449 0.00 0.00 0.58 0.00 0.42 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.0504 0.7789 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.86.A4D0.01 2 0.0504 0.7789 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.99.8032.01 2 0.0000 0.7814 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.64.5779.01 2 0.5158 0.7263 0.06 0.70 0.12 0.08 0.00 0.00 0.04
#> TCGA.55.7284.01 6 0.1363 0.3784 0.00 0.00 0.02 0.04 0.00 0.94 0.00
#> TCGA.86.8669.01 2 0.5401 0.6944 0.02 0.66 0.14 0.12 0.00 0.00 0.06
#> TCGA.NJ.A55R.01 2 0.3346 0.7720 0.04 0.84 0.06 0.04 0.00 0.00 0.02
#> TCGA.33.AASB.01 6 0.4421 -0.7068 0.46 0.00 0.02 0.02 0.00 0.50 0.00
#> TCGA.97.8179.01 5 0.3294 -0.0377 0.00 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.86.7713.01 4 0.4305 0.3981 0.00 0.00 0.02 0.66 0.00 0.04 0.28
#> TCGA.62.A46S.01 4 0.7085 0.4366 0.02 0.00 0.12 0.38 0.00 0.20 0.28
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.86.8281.01 3 0.0000 0.6788 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8358.01 2 0.0000 0.7583 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.78.7149.01 5 0.3015 0.9166 0.00 0.00 0.32 0.00 0.68 0.00 0.00 0.00
#> TCGA.55.6642.01 4 0.4848 0.7932 0.00 0.34 0.00 0.54 0.00 0.10 0.02 0.00
#> TCGA.33.6737.01 1 0.4921 0.2677 0.52 0.00 0.00 0.00 0.00 0.26 0.00 0.22
#> TCGA.55.6968.01 2 0.0000 0.7583 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.75.7027.01 8 0.3095 0.0000 0.02 0.00 0.00 0.00 0.00 0.24 0.00 0.74
#> TCGA.86.8279.01 3 0.1804 0.6765 0.02 0.00 0.90 0.00 0.08 0.00 0.00 0.00
#> TCGA.55.8615.01 7 0.2224 0.2420 0.00 0.00 0.00 0.12 0.00 0.02 0.86 0.00
#> TCGA.05.5425.01 6 0.3227 0.5343 0.14 0.00 0.00 0.00 0.00 0.78 0.00 0.08
#> TCGA.50.5066.02 1 0.6377 0.1657 0.50 0.00 0.20 0.04 0.04 0.20 0.02 0.00
#> TCGA.69.7764.01 3 0.3078 0.6502 0.02 0.00 0.82 0.00 0.10 0.00 0.00 0.06
#> TCGA.MN.A4N4.01 6 0.3227 0.5180 0.14 0.00 0.00 0.00 0.00 0.78 0.00 0.08
#> TCGA.91.A4BC.01 2 0.2938 0.3820 0.00 0.70 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.05.4433.01 6 0.1408 0.5734 0.02 0.00 0.00 0.02 0.00 0.94 0.00 0.02
#> TCGA.50.5932.01 3 0.4607 -0.0446 0.02 0.00 0.50 0.00 0.42 0.00 0.00 0.06
#> TCGA.50.7109.01 4 0.4672 0.8189 0.00 0.24 0.00 0.62 0.00 0.12 0.02 0.00
#> TCGA.78.7633.01 5 0.2852 0.9595 0.00 0.00 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.78.7167.01 5 0.2852 0.9595 0.00 0.00 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.55.8085.01 3 0.0808 0.6888 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.MP.A4TE.01 2 0.0000 0.7583 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.A4D0.01 2 0.0000 0.7583 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.99.8032.01 2 0.0808 0.7458 0.00 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.64.5779.01 2 0.3193 0.2293 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.55.7284.01 6 0.0000 0.5949 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.86.8669.01 2 0.4586 -0.0389 0.00 0.52 0.00 0.40 0.02 0.00 0.00 0.06
#> TCGA.NJ.A55R.01 2 0.1947 0.6705 0.00 0.86 0.00 0.14 0.00 0.00 0.00 0.00
#> TCGA.33.AASB.01 1 0.5674 0.2919 0.50 0.00 0.00 0.00 0.06 0.24 0.00 0.20
#> TCGA.97.8179.01 3 0.3675 0.4137 0.00 0.00 0.66 0.00 0.30 0.00 0.00 0.04
#> TCGA.86.7713.01 7 0.7832 0.2489 0.16 0.00 0.00 0.26 0.16 0.08 0.30 0.04
#> TCGA.62.A46S.01 6 0.7304 -0.0819 0.10 0.00 0.00 0.22 0.08 0.40 0.18 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node07. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0214-leaf , Node0221 , Node0222-leaf , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0234 , Node0235-leaf , Node0241-leaf , Node0242 , Node0411-leaf , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0511-leaf , Node0512-leaf , Node0513-leaf , Node0514-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf , Node0525-leaf , Node0611-leaf , Node0612 , Node0613-leaf , Node0711 , Node0712-leaf , Node0713-leaf , Node0721 , Node0722-leaf , Node0731-leaf , Node0732-leaf , Node0733-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["073"]
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 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.995 0.998 0.4379 0.564 0.564
#> 3 3 1.000 0.972 0.979 0.5256 0.761 0.577
#> 4 4 0.744 0.704 0.863 0.0906 0.975 0.924
#> 5 5 0.690 0.630 0.795 0.0399 0.936 0.790
#> 6 6 0.649 0.612 0.764 0.0367 0.970 0.881
#> 7 7 0.634 0.474 0.693 0.0336 0.972 0.884
#> 8 8 0.680 0.455 0.716 0.0261 0.949 0.791
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.77.A5G1.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6975.01 2 0.000 0.996 0.00 1.00
#> TCGA.39.5040.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.8398.01 1 0.000 1.000 1.00 0.00
#> TCGA.97.8176.01 1 0.000 1.000 1.00 0.00
#> TCGA.91.6831.01 2 0.242 0.960 0.04 0.96
#> TCGA.05.4415.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.AAR0.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5072.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8512.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.8640.01 2 0.000 0.996 0.00 1.00
#> TCGA.62.A471.01 2 0.000 0.996 0.00 1.00
#> TCGA.43.5668.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.8505.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7148.01 1 0.000 1.000 1.00 0.00
#> TCGA.39.5022.01 2 0.000 0.996 0.00 1.00
#> TCGA.70.6722.01 2 0.000 0.996 0.00 1.00
#> TCGA.91.6848.01 2 0.000 0.996 0.00 1.00
#> TCGA.33.6738.01 2 0.000 0.996 0.00 1.00
#> TCGA.43.6773.01 2 0.000 0.996 0.00 1.00
#> TCGA.55.6972.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.7711.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.5420.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8585.01 2 0.000 0.996 0.00 1.00
#> TCGA.49.AAR9.01 2 0.000 0.996 0.00 1.00
#> TCGA.05.4424.01 2 0.242 0.960 0.04 0.96
#> TCGA.75.5146.01 1 0.000 1.000 1.00 0.00
#> TCGA.50.5930.01 2 0.000 0.996 0.00 1.00
#> TCGA.86.8674.01 1 0.000 1.000 1.00 0.00
#> TCGA.78.7166.01 1 0.000 1.000 1.00 0.00
#> TCGA.86.8055.01 2 0.000 0.996 0.00 1.00
#> TCGA.78.7156.01 1 0.000 1.000 1.00 0.00
#> TCGA.95.7947.01 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.77.A5G1.01 3 0.0892 0.965 0.00 0.02 0.98
#> TCGA.55.6975.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.39.5040.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.62.8398.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.97.8176.01 1 0.0892 0.985 0.98 0.00 0.02
#> TCGA.91.6831.01 2 0.1529 0.955 0.04 0.96 0.00
#> TCGA.05.4415.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.49.AAR0.01 1 0.0892 0.985 0.98 0.00 0.02
#> TCGA.50.5072.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.55.8512.01 1 0.0892 0.985 0.98 0.00 0.02
#> TCGA.78.8640.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.62.A471.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.43.5668.01 2 0.0892 0.977 0.00 0.98 0.02
#> TCGA.55.8505.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.78.7148.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.39.5022.01 3 0.1529 0.953 0.00 0.04 0.96
#> TCGA.70.6722.01 3 0.0892 0.965 0.00 0.02 0.98
#> TCGA.91.6848.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.33.6738.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.43.6773.01 3 0.0892 0.965 0.00 0.02 0.98
#> TCGA.55.6972.01 1 0.0892 0.981 0.98 0.00 0.02
#> TCGA.86.7711.01 3 0.1529 0.951 0.00 0.04 0.96
#> TCGA.05.5420.01 3 0.0892 0.965 0.00 0.02 0.98
#> TCGA.86.8585.01 3 0.0892 0.965 0.00 0.02 0.98
#> TCGA.49.AAR9.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.05.4424.01 3 0.6495 0.733 0.06 0.20 0.74
#> TCGA.75.5146.01 1 0.0892 0.985 0.98 0.00 0.02
#> TCGA.50.5930.01 3 0.0892 0.965 0.00 0.02 0.98
#> TCGA.86.8674.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.78.7166.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.86.8055.01 2 0.1529 0.958 0.00 0.96 0.04
#> TCGA.78.7156.01 1 0.0892 0.981 0.98 0.00 0.02
#> TCGA.95.7947.01 2 0.0000 0.992 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.77.A5G1.01 3 0.0000 0.8832 0.00 0.00 1.00 0.00
#> TCGA.55.6975.01 2 0.0707 0.8509 0.00 0.98 0.00 0.02
#> TCGA.39.5040.01 2 0.0000 0.8567 0.00 1.00 0.00 0.00
#> TCGA.62.8398.01 1 0.2011 0.7871 0.92 0.00 0.00 0.08
#> TCGA.97.8176.01 1 0.2345 0.7906 0.90 0.00 0.00 0.10
#> TCGA.91.6831.01 4 0.6838 0.0000 0.08 0.30 0.02 0.60
#> TCGA.05.4415.01 2 0.1211 0.8467 0.00 0.96 0.00 0.04
#> TCGA.49.AAR0.01 1 0.6831 0.5148 0.48 0.00 0.10 0.42
#> TCGA.50.5072.01 2 0.0707 0.8509 0.00 0.98 0.00 0.02
#> TCGA.55.8512.01 1 0.5062 0.7167 0.68 0.00 0.02 0.30
#> TCGA.78.8640.01 2 0.0000 0.8567 0.00 1.00 0.00 0.00
#> TCGA.62.A471.01 2 0.0000 0.8567 0.00 1.00 0.00 0.00
#> TCGA.43.5668.01 2 0.4949 0.5087 0.00 0.76 0.18 0.06
#> TCGA.55.8505.01 2 0.1913 0.8162 0.00 0.94 0.04 0.02
#> TCGA.78.7148.01 1 0.2345 0.7962 0.90 0.00 0.00 0.10
#> TCGA.39.5022.01 3 0.1211 0.8560 0.00 0.04 0.96 0.00
#> TCGA.70.6722.01 3 0.0707 0.8688 0.02 0.00 0.98 0.00
#> TCGA.91.6848.01 2 0.0000 0.8567 0.00 1.00 0.00 0.00
#> TCGA.33.6738.01 2 0.0000 0.8567 0.00 1.00 0.00 0.00
#> TCGA.43.6773.01 3 0.0000 0.8832 0.00 0.00 1.00 0.00
#> TCGA.55.6972.01 1 0.4406 0.7314 0.70 0.00 0.00 0.30
#> TCGA.86.7711.01 3 0.3400 0.6734 0.00 0.18 0.82 0.00
#> TCGA.05.5420.01 3 0.0000 0.8832 0.00 0.00 1.00 0.00
#> TCGA.86.8585.01 3 0.0000 0.8832 0.00 0.00 1.00 0.00
#> TCGA.49.AAR9.01 2 0.2345 0.8035 0.00 0.90 0.00 0.10
#> TCGA.05.4424.01 3 0.8172 -0.1956 0.04 0.14 0.44 0.38
#> TCGA.75.5146.01 1 0.4277 0.7006 0.72 0.00 0.00 0.28
#> TCGA.50.5930.01 3 0.0000 0.8832 0.00 0.00 1.00 0.00
#> TCGA.86.8674.01 1 0.2921 0.7886 0.86 0.00 0.00 0.14
#> TCGA.78.7166.01 1 0.1637 0.7833 0.94 0.00 0.00 0.06
#> TCGA.86.8055.01 2 0.6261 0.0795 0.02 0.62 0.04 0.32
#> TCGA.78.7156.01 1 0.4277 0.7326 0.72 0.00 0.00 0.28
#> TCGA.95.7947.01 2 0.5392 0.2471 0.04 0.68 0.00 0.28
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.77.A5G1.01 3 0.0609 0.8843 0.00 0.02 0.98 0.00 0.00
#> TCGA.55.6975.01 2 0.1216 0.8483 0.00 0.96 0.00 0.02 0.02
#> TCGA.39.5040.01 2 0.1648 0.8491 0.00 0.94 0.00 0.04 0.02
#> TCGA.62.8398.01 1 0.3946 0.4986 0.80 0.00 0.00 0.12 0.08
#> TCGA.97.8176.01 1 0.5013 0.4423 0.68 0.00 0.00 0.24 0.08
#> TCGA.91.6831.01 4 0.4254 0.2118 0.00 0.22 0.00 0.74 0.04
#> TCGA.05.4415.01 2 0.1820 0.8397 0.02 0.94 0.02 0.00 0.02
#> TCGA.49.AAR0.01 4 0.7976 -0.3100 0.32 0.00 0.08 0.34 0.26
#> TCGA.50.5072.01 2 0.1648 0.8493 0.00 0.94 0.00 0.02 0.04
#> TCGA.55.8512.01 1 0.6671 0.2669 0.48 0.00 0.02 0.36 0.14
#> TCGA.78.8640.01 2 0.1043 0.8466 0.00 0.96 0.00 0.00 0.04
#> TCGA.62.A471.01 2 0.0609 0.8511 0.00 0.98 0.00 0.00 0.02
#> TCGA.43.5668.01 2 0.4837 0.6553 0.00 0.74 0.18 0.02 0.06
#> TCGA.55.8505.01 2 0.2675 0.8326 0.00 0.90 0.04 0.02 0.04
#> TCGA.78.7148.01 1 0.4458 0.4430 0.76 0.00 0.00 0.12 0.12
#> TCGA.39.5022.01 3 0.1410 0.8649 0.00 0.06 0.94 0.00 0.00
#> TCGA.70.6722.01 3 0.2848 0.8350 0.02 0.02 0.90 0.02 0.04
#> TCGA.91.6848.01 2 0.0000 0.8506 0.00 1.00 0.00 0.00 0.00
#> TCGA.33.6738.01 2 0.0609 0.8498 0.00 0.98 0.00 0.00 0.02
#> TCGA.43.6773.01 3 0.1043 0.8810 0.00 0.04 0.96 0.00 0.00
#> TCGA.55.6972.01 5 0.4840 0.9012 0.32 0.00 0.00 0.04 0.64
#> TCGA.86.7711.01 3 0.5705 0.3552 0.00 0.32 0.60 0.02 0.06
#> TCGA.05.5420.01 3 0.0609 0.8843 0.00 0.02 0.98 0.00 0.00
#> TCGA.86.8585.01 3 0.1216 0.8795 0.00 0.02 0.96 0.02 0.00
#> TCGA.49.AAR9.01 2 0.4449 0.7426 0.00 0.78 0.02 0.06 0.14
#> TCGA.05.4424.01 4 0.5925 0.0866 0.02 0.00 0.40 0.52 0.06
#> TCGA.75.5146.01 1 0.6070 0.2973 0.44 0.00 0.00 0.44 0.12
#> TCGA.50.5930.01 3 0.1216 0.8800 0.00 0.02 0.96 0.00 0.02
#> TCGA.86.8674.01 1 0.4008 0.4162 0.82 0.00 0.02 0.08 0.08
#> TCGA.78.7166.01 1 0.2927 0.4574 0.88 0.00 0.02 0.08 0.02
#> TCGA.86.8055.01 2 0.7747 0.4081 0.04 0.56 0.12 0.18 0.10
#> TCGA.78.7156.01 5 0.4540 0.9008 0.34 0.00 0.00 0.02 0.64
#> TCGA.95.7947.01 2 0.5990 0.2976 0.00 0.52 0.04 0.40 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.77.A5G1.01 3 0.0547 0.845 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.55.6975.01 2 0.0000 0.833 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.39.5040.01 2 0.1267 0.831 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.62.8398.01 1 0.5996 0.457 0.62 0.00 0.00 0.12 0.10 0.16
#> TCGA.97.8176.01 1 0.7048 0.248 0.44 0.00 0.02 0.34 0.08 0.12
#> TCGA.91.6831.01 6 0.4806 0.000 0.02 0.02 0.00 0.48 0.00 0.48
#> TCGA.05.4415.01 2 0.0937 0.830 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.49.AAR0.01 4 0.4066 0.435 0.12 0.00 0.08 0.78 0.02 0.00
#> TCGA.50.5072.01 2 0.0000 0.833 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.55.8512.01 4 0.5210 0.411 0.26 0.00 0.06 0.64 0.04 0.00
#> TCGA.78.8640.01 2 0.0937 0.833 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.62.A471.01 2 0.0000 0.833 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.43.5668.01 2 0.4179 0.726 0.00 0.76 0.06 0.00 0.02 0.16
#> TCGA.55.8505.01 2 0.2048 0.753 0.00 0.88 0.12 0.00 0.00 0.00
#> TCGA.78.7148.01 1 0.4334 0.438 0.72 0.00 0.00 0.22 0.04 0.02
#> TCGA.39.5022.01 3 0.3045 0.793 0.00 0.06 0.86 0.02 0.00 0.06
#> TCGA.70.6722.01 3 0.4221 0.749 0.04 0.00 0.80 0.08 0.02 0.06
#> TCGA.91.6848.01 2 0.1267 0.831 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.33.6738.01 2 0.0937 0.833 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.43.6773.01 3 0.1092 0.847 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.55.6972.01 5 0.5259 0.813 0.16 0.00 0.00 0.24 0.60 0.00
#> TCGA.86.7711.01 3 0.4887 0.586 0.00 0.22 0.68 0.00 0.02 0.08
#> TCGA.05.5420.01 3 0.0547 0.847 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.86.8585.01 3 0.2882 0.828 0.00 0.02 0.86 0.02 0.00 0.10
#> TCGA.49.AAR9.01 2 0.5150 0.490 0.00 0.62 0.00 0.00 0.22 0.16
#> TCGA.05.4424.01 4 0.8196 -0.291 0.06 0.04 0.22 0.40 0.04 0.24
#> TCGA.75.5146.01 4 0.2941 0.396 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.50.5930.01 3 0.3162 0.826 0.02 0.02 0.86 0.02 0.00 0.08
#> TCGA.86.8674.01 1 0.4279 0.540 0.78 0.00 0.00 0.08 0.06 0.08
#> TCGA.78.7166.01 1 0.2350 0.571 0.88 0.00 0.00 0.10 0.02 0.00
#> TCGA.86.8055.01 2 0.7545 0.108 0.00 0.46 0.10 0.16 0.04 0.24
#> TCGA.78.7156.01 5 0.5840 0.807 0.16 0.00 0.00 0.26 0.56 0.02
#> TCGA.95.7947.01 2 0.6086 0.321 0.02 0.52 0.00 0.20 0.00 0.26
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.77.A5G1.01 3 0.1006 0.6858 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.55.6975.01 2 0.4418 0.7175 0.06 0.76 0.02 0.00 0.00 0.08 0.08
#> TCGA.39.5040.01 2 0.1363 0.7517 0.02 0.94 0.00 0.00 0.00 0.04 0.00
#> TCGA.62.8398.01 4 0.7040 -0.1159 0.36 0.00 0.00 0.36 0.14 0.10 0.04
#> TCGA.97.8176.01 1 0.6846 0.3061 0.42 0.00 0.00 0.34 0.06 0.08 0.10
#> TCGA.91.6831.01 6 0.3284 0.0000 0.00 0.10 0.00 0.10 0.00 0.80 0.00
#> TCGA.05.4415.01 2 0.5395 0.6466 0.08 0.66 0.02 0.00 0.00 0.16 0.08
#> TCGA.49.AAR0.01 4 0.4029 0.4326 0.06 0.00 0.02 0.80 0.02 0.08 0.02
#> TCGA.50.5072.01 2 0.2509 0.7445 0.06 0.88 0.00 0.00 0.00 0.04 0.02
#> TCGA.55.8512.01 4 0.1664 0.4674 0.00 0.00 0.02 0.92 0.06 0.00 0.00
#> TCGA.78.8640.01 2 0.1363 0.7509 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.62.A471.01 2 0.0863 0.7528 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.43.5668.01 2 0.3600 0.6876 0.02 0.82 0.04 0.00 0.00 0.04 0.08
#> TCGA.55.8505.01 2 0.3346 0.7281 0.04 0.84 0.04 0.00 0.00 0.02 0.06
#> TCGA.78.7148.01 4 0.6067 0.0740 0.34 0.00 0.00 0.48 0.04 0.12 0.02
#> TCGA.39.5022.01 3 0.3965 0.5574 0.00 0.10 0.76 0.00 0.00 0.02 0.12
#> TCGA.70.6722.01 3 0.4158 0.4977 0.06 0.02 0.76 0.00 0.00 0.02 0.14
#> TCGA.91.6848.01 2 0.0504 0.7522 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.33.6738.01 2 0.0504 0.7517 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.43.6773.01 3 0.0863 0.6862 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.55.6972.01 5 0.4388 0.7037 0.02 0.00 0.00 0.30 0.64 0.00 0.04
#> TCGA.86.7711.01 3 0.5377 0.2721 0.00 0.26 0.56 0.00 0.00 0.02 0.16
#> TCGA.05.5420.01 3 0.1860 0.6764 0.02 0.00 0.92 0.00 0.02 0.00 0.04
#> TCGA.86.8585.01 3 0.3208 0.6412 0.04 0.00 0.82 0.00 0.02 0.00 0.12
#> TCGA.49.AAR9.01 2 0.6956 0.1201 0.02 0.40 0.00 0.00 0.16 0.12 0.30
#> TCGA.05.4424.01 7 0.8365 0.0000 0.06 0.12 0.24 0.08 0.00 0.16 0.34
#> TCGA.75.5146.01 4 0.3542 0.4397 0.04 0.00 0.02 0.84 0.02 0.04 0.04
#> TCGA.50.5930.01 3 0.5565 0.3839 0.10 0.04 0.66 0.00 0.02 0.02 0.16
#> TCGA.86.8674.01 1 0.5951 0.4677 0.58 0.00 0.00 0.24 0.06 0.08 0.04
#> TCGA.78.7166.01 1 0.3606 0.5285 0.68 0.00 0.00 0.30 0.00 0.00 0.02
#> TCGA.86.8055.01 2 0.7081 -0.0897 0.06 0.46 0.04 0.02 0.02 0.08 0.32
#> TCGA.78.7156.01 5 0.4451 0.6995 0.10 0.00 0.00 0.26 0.64 0.00 0.00
#> TCGA.95.7947.01 2 0.7476 -0.0689 0.02 0.46 0.02 0.12 0.02 0.22 0.14
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.77.A5G1.01 3 0.0471 0.786 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6975.01 2 0.2864 0.634 0.06 0.84 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.39.5040.01 2 0.2132 0.632 0.00 0.88 0.00 0.00 0.00 0.04 0.00 0.08
#> TCGA.62.8398.01 7 0.6688 0.233 0.02 0.00 0.00 0.32 0.22 0.02 0.36 0.06
#> TCGA.97.8176.01 7 0.5796 0.387 0.12 0.00 0.00 0.18 0.04 0.02 0.60 0.04
#> TCGA.91.6831.01 6 0.2071 0.000 0.00 0.00 0.04 0.02 0.00 0.90 0.04 0.00
#> TCGA.05.4415.01 2 0.3601 0.576 0.16 0.76 0.02 0.00 0.00 0.00 0.00 0.06
#> TCGA.49.AAR0.01 4 0.5144 0.359 0.08 0.00 0.06 0.70 0.08 0.06 0.02 0.00
#> TCGA.50.5072.01 2 0.1804 0.651 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.55.8512.01 4 0.4396 0.360 0.00 0.00 0.12 0.74 0.08 0.02 0.02 0.02
#> TCGA.78.8640.01 2 0.2407 0.657 0.08 0.86 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.62.A471.01 2 0.2680 0.651 0.12 0.84 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.43.5668.01 2 0.5943 0.385 0.20 0.56 0.04 0.00 0.00 0.10 0.00 0.10
#> TCGA.55.8505.01 2 0.2991 0.619 0.04 0.86 0.04 0.00 0.00 0.02 0.02 0.02
#> TCGA.78.7148.01 7 0.5216 0.214 0.00 0.00 0.00 0.42 0.10 0.00 0.44 0.04
#> TCGA.39.5022.01 3 0.1275 0.781 0.04 0.02 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.70.6722.01 3 0.5963 0.536 0.14 0.00 0.62 0.06 0.00 0.06 0.04 0.08
#> TCGA.91.6848.01 2 0.0808 0.653 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.33.6738.01 2 0.3078 0.630 0.06 0.82 0.00 0.00 0.00 0.02 0.00 0.10
#> TCGA.43.6773.01 3 0.1091 0.783 0.06 0.00 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.55.6972.01 5 0.3337 0.527 0.02 0.00 0.00 0.16 0.78 0.00 0.04 0.00
#> TCGA.86.7711.01 3 0.5081 0.545 0.08 0.20 0.64 0.00 0.00 0.06 0.02 0.00
#> TCGA.05.5420.01 3 0.1275 0.788 0.04 0.02 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.86.8585.01 3 0.3651 0.732 0.16 0.04 0.76 0.00 0.00 0.00 0.04 0.00
#> TCGA.49.AAR9.01 8 0.2852 0.000 0.00 0.28 0.00 0.00 0.00 0.00 0.00 0.72
#> TCGA.05.4424.01 4 0.8659 -0.167 0.14 0.06 0.20 0.24 0.00 0.22 0.04 0.10
#> TCGA.75.5146.01 4 0.3688 0.305 0.00 0.00 0.04 0.80 0.04 0.04 0.08 0.00
#> TCGA.50.5930.01 3 0.4750 0.692 0.20 0.06 0.68 0.00 0.00 0.02 0.02 0.02
#> TCGA.86.8674.01 7 0.6664 0.240 0.18 0.00 0.00 0.22 0.10 0.02 0.46 0.02
#> TCGA.78.7166.01 7 0.2940 0.435 0.02 0.00 0.00 0.10 0.02 0.00 0.84 0.02
#> TCGA.86.8055.01 2 0.8835 -0.271 0.16 0.28 0.06 0.10 0.00 0.16 0.08 0.16
#> TCGA.78.7156.01 5 0.5612 0.555 0.10 0.00 0.00 0.14 0.64 0.02 0.04 0.06
#> TCGA.95.7947.01 2 0.7391 0.118 0.20 0.40 0.04 0.02 0.00 0.22 0.02 0.10
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6