Date: 2021-07-22 18:25:56 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 375959 rows and 429 columns.
#> Performed in total 102200 partitions.
#> There are 48 groups under the following parameters:
#> - min_samples: 6
#> - mean_silhouette_cutoff: 0.9
#> - min_n_signatures: 1000 (signatures are selected based on:)
#> - fdr_cutoff: 0.05
#> - group_diff: 0.25
#>
#> Hierarchy of the partition:
#> 0, 429 cols
#> |-- 01, 87 cols, 16461 signatures
#> | |-- 011, 36 cols, 5965 signatures
#> | | |-- 0111, 19 cols, 690 signatures (c)
#> | | |-- 0112, 10 cols (b)
#> | | `-- 0113, 7 cols (b)
#> | |-- 012, 25 cols, 1312 signatures
#> | | |-- 0121, 8 cols (b)
#> | | |-- 0122, 6 cols (b)
#> | | |-- 0123, 6 cols (b)
#> | | `-- 0124, 5 cols (b)
#> | `-- 013, 26 cols, 2409 signatures
#> | |-- 0131, 8 cols (b)
#> | |-- 0132, 11 cols (b)
#> | `-- 0133, 7 cols (b)
#> |-- 02, 200 cols, 27985 signatures
#> | |-- 021, 41 cols, 1728 signatures
#> | | |-- 0211, 18 cols, 1 signatures (c)
#> | | |-- 0212, 15 cols, 21933 signatures
#> | | | |-- 02121, 13 cols, 1442 signatures
#> | | | | |-- 021211, 11 cols (b)
#> | | | | `-- 021212, 2 cols (b)
#> | | | `-- 02122, 2 cols (b)
#> | | `-- 0213, 8 cols (b)
#> | |-- 022, 61 cols, 12535 signatures
#> | | |-- 0221, 22 cols, 15935 signatures
#> | | | |-- 02211, 5 cols (b)
#> | | | |-- 02212, 10 cols (b)
#> | | | `-- 02213, 7 cols (b)
#> | | |-- 0222, 26 cols, 2132 signatures
#> | | | |-- 02221, 18 cols, 1271 signatures
#> | | | | |-- 022211, 3 cols (b)
#> | | | | |-- 022212, 12 cols, 329 signatures (c)
#> | | | | `-- 022213, 3 cols (b)
#> | | | `-- 02222, 8 cols (b)
#> | | `-- 0223, 13 cols, 15 signatures (c)
#> | |-- 023, 29 cols, 21451 signatures
#> | | |-- 0231, 24 cols, 1739 signatures
#> | | | |-- 02311, 9 cols (b)
#> | | | |-- 02312, 4 cols (b)
#> | | | |-- 02313, 4 cols (b)
#> | | | `-- 02314, 7 cols (b)
#> | | |-- 0232, 3 cols (b)
#> | | `-- 0233, 2 cols (b)
#> | |-- 024, 40 cols, 9569 signatures
#> | | |-- 0241, 16 cols, 2066 signatures
#> | | | |-- 02411, 11 cols (b)
#> | | | `-- 02412, 5 cols (b)
#> | | |-- 0242, 12 cols, 1180 signatures
#> | | | |-- 02421, 2 cols (b)
#> | | | `-- 02422, 10 cols (b)
#> | | `-- 0243, 12 cols, 4836 signatures
#> | | |-- 02431, 4 cols (b)
#> | | |-- 02432, 2 cols (b)
#> | | `-- 02433, 6 cols (b)
#> | `-- 025, 29 cols, 1622 signatures
#> | |-- 0251, 10 cols (b)
#> | `-- 0252, 19 cols, 442 signatures (c)
#> |-- 03, 34 cols, 6112 signatures
#> | |-- 031, 11 cols (b)
#> | `-- 032, 23 cols, 4332 signatures
#> | |-- 0321, 11 cols (b)
#> | `-- 0322, 12 cols, 336 signatures (c)
#> `-- 04, 108 cols, 1235 signatures
#> |-- 041, 41 cols, 8815 signatures
#> | |-- 0411, 15 cols, 335 signatures (c)
#> | |-- 0412, 21 cols, 62 signatures (c)
#> | `-- 0413, 5 cols (b)
#> `-- 042, 67 cols, 10598 signatures
#> |-- 0421, 16 cols, 429 signatures (c)
#> |-- 0422, 17 cols, 930 signatures (c)
#> |-- 0423, 19 cols, 960 signatures (c)
#> `-- 0424, 15 cols, 70 signatures (c)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375959 429
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" "012" "0121" "0122" "0123"
#> [11] "0124" "013" "0131" "0132" "0133" "02" "021" "0211" "0212" "02121"
#> [21] "021211" "021212" "02122" "0213" "022" "0221" "02211" "02212" "02213" "0222"
#> [31] "02221" "022211" "022212" "022213" "02222" "0223" "023" "0231" "02311" "02312"
#> [41] "02313" "02314" "0232" "0233" "024" "0241" "02411" "02412" "0242" "02421"
#> [51] "02422" "0243" "02431" "02432" "02433" "025" "0251" "0252" "03" "031"
#> [61] "032" "0321" "0322" "04" "041" "0411" "0412" "0413" "042" "0421"
#> [71] "0422" "0423" "0424"
all_leaves(res_rh)
#> [1] "0111" "0112" "0113" "0121" "0122" "0123" "0124" "0131" "0132" "0133"
#> [11] "0211" "021211" "021212" "02122" "0213" "02211" "02212" "02213" "022211" "022212"
#> [21] "022213" "02222" "0223" "02311" "02312" "02313" "02314" "0232" "0233" "02411"
#> [31] "02412" "02421" "02422" "02431" "02432" "02433" "0251" "0252" "031" "0321"
#> [41] "0322" "0411" "0412" "0413" "0421" "0422" "0423" "0424"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 4 429 74620 1.98e-01 FALSE
#> 2 01 ATC:kmeans 2 3 87 16461 4.38e-02 FALSE
#> 3 011 ATC:skmeans 3 3 36 5965 1.59e-02 FALSE
#> 4 0111 ATC:kmeans 4 2 19 690 1.84e-03 TRUE
#> 5 0112 not applied 4 NA 10 NA NA TRUE
#> 6 0113 not applied 4 NA 7 NA NA TRUE
#> 7 012 ATC:kmeans 3 4 25 1312 3.49e-03 FALSE
#> 8 0121 not applied 4 NA 8 NA NA TRUE
#> 9 0122 not applied 4 NA 6 NA NA TRUE
#> 10 0123 not applied 4 NA 6 NA NA TRUE
#> 11 0124 not applied 4 NA 5 NA NA TRUE
#> 12 013 ATC:skmeans 3 3 26 2409 6.41e-03 FALSE
#> 13 0131 not applied 4 NA 8 NA NA TRUE
#> 14 0132 not applied 4 NA 11 NA NA TRUE
#> 15 0133 not applied 4 NA 7 NA NA TRUE
#> 16 02 SD:skmeans 2 5 200 27985 7.44e-02 FALSE
#> 17 021 SD:skmeans 3 3 41 1728 4.60e-03 FALSE
#> 18 0211 ATC:skmeans 4 3 18 1 2.66e-06 TRUE
#> 19 0212 ATC:kmeans 4 2 15 21933 5.83e-02 FALSE
#> 20 02121 ATC:kmeans 5 2 13 1442 3.84e-03 FALSE
#> 21 021211 not applied 6 NA 11 NA NA TRUE
#> 22 021212 not applied 6 NA 2 NA NA TRUE
#> 23 02122 not applied 5 NA 2 NA NA TRUE
#> 24 0213 not applied 4 NA 8 NA NA TRUE
#> 25 022 ATC:skmeans 3 3 61 12535 3.33e-02 FALSE
#> 26 0221 SD:kmeans 4 3 22 15935 4.24e-02 FALSE
#> 27 02211 not applied 5 NA 5 NA NA TRUE
#> 28 02212 not applied 5 NA 10 NA NA TRUE
#> 29 02213 not applied 5 NA 7 NA NA TRUE
#> 30 0222 ATC:skmeans 4 2 26 2132 5.67e-03 FALSE
#> 31 02221 ATC:skmeans 5 3 18 1271 3.38e-03 FALSE
#> 32 022211 not applied 6 NA 3 NA NA TRUE
#> 33 022212 ATC:kmeans 6 3 12 329 8.75e-04 TRUE
#> 34 022213 not applied 6 NA 3 NA NA TRUE
#> 35 02222 not applied 5 NA 8 NA NA TRUE
#> 36 0223 ATC:skmeans 4 2 13 15 3.99e-05 TRUE
#> 37 023 ATC:skmeans 3 3 29 21451 5.71e-02 FALSE
#> 38 0231 ATC:skmeans 4 4 24 1739 4.63e-03 FALSE
#> 39 02311 not applied 5 NA 9 NA NA TRUE
#> 40 02312 not applied 5 NA 4 NA NA TRUE
#> 41 02313 not applied 5 NA 4 NA NA TRUE
#> 42 02314 not applied 5 NA 7 NA NA TRUE
#> 43 0232 not applied 4 NA 3 NA NA TRUE
#> 44 0233 not applied 4 NA 2 NA NA TRUE
#> 45 024 ATC:kmeans 3 3 40 9569 2.55e-02 FALSE
#> 46 0241 SD:skmeans 4 2 16 2066 5.50e-03 FALSE
#> 47 02411 not applied 5 NA 11 NA NA TRUE
#> 48 02412 not applied 5 NA 5 NA NA TRUE
#> 49 0242 ATC:kmeans 4 2 12 1180 3.14e-03 FALSE
#> 50 02421 not applied 5 NA 2 NA NA TRUE
#> 51 02422 not applied 5 NA 10 NA NA TRUE
#> 52 0243 ATC:kmeans 4 3 12 4836 1.29e-02 FALSE
#> 53 02431 not applied 5 NA 4 NA NA TRUE
#> 54 02432 not applied 5 NA 2 NA NA TRUE
#> 55 02433 not applied 5 NA 6 NA NA TRUE
#> 56 025 ATC:kmeans 3 2 29 1622 4.31e-03 FALSE
#> 57 0251 not applied 4 NA 10 NA NA TRUE
#> 58 0252 ATC:skmeans 4 2 19 442 1.18e-03 TRUE
#> 59 03 ATC:skmeans 2 2 34 6112 1.63e-02 FALSE
#> 60 031 not applied 3 NA 11 NA NA TRUE
#> 61 032 ATC:kmeans 3 2 23 4332 1.15e-02 FALSE
#> 62 0321 not applied 4 NA 11 NA NA TRUE
#> 63 0322 ATC:skmeans 4 3 12 336 8.94e-04 TRUE
#> 64 04 ATC:kmeans 2 2 108 1235 3.28e-03 FALSE
#> 65 041 ATC:skmeans 3 3 41 8815 2.34e-02 FALSE
#> 66 0411 ATC:kmeans 4 2 15 335 8.91e-04 TRUE
#> 67 0412 SD:kmeans 4 2 21 62 1.65e-04 TRUE
#> 68 0413 not applied 4 NA 5 NA NA TRUE
#> 69 042 ATC:skmeans 3 4 67 10598 2.82e-02 FALSE
#> 70 0421 ATC:kmeans 4 3 16 429 1.14e-03 TRUE
#> 71 0422 SD:kmeans 4 2 17 930 2.47e-03 TRUE
#> 72 0423 ATC:kmeans 4 2 19 960 2.55e-03 TRUE
#> 73 0424 ATC:kmeans 4 2 15 70 1.86e-04 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 | 7 | 0.90 | 0.85 | 0.92 | 429 | * | |
| Node01 | ATC:kmeans | 3 | 1.00 | 0.99 | 1.00 | 87 | ** | |
| Node011 | ATC:skmeans | 3 | 0.99 | 0.97 | 0.98 | 36 | ** | |
| Node0111-leaf | ATC:kmeans | ✓ (c) | 3 | 0.91 | 0.92 | 0.97 | 19 | * |
| Node0112-leaf | not applied | ✓ (b) | 10 | |||||
| Node0113-leaf | not applied | ✓ (b) | 7 | |||||
| Node012 | ATC:kmeans | 5 | 0.91 | 0.92 | 0.89 | 25 | * | |
| Node0121-leaf | not applied | ✓ (b) | 8 | |||||
| Node0122-leaf | not applied | ✓ (b) | 6 | |||||
| Node0123-leaf | not applied | ✓ (b) | 6 | |||||
| Node0124-leaf | not applied | ✓ (b) | 5 | |||||
| Node013 | ATC:skmeans | 3 | 0.95 | 0.95 | 0.98 | 26 | ** | |
| Node0131-leaf | not applied | ✓ (b) | 8 | |||||
| Node0132-leaf | not applied | ✓ (b) | 11 | |||||
| Node0133-leaf | not applied | ✓ (b) | 7 | |||||
| Node02 | SD:skmeans | 6 | 0.91 | 0.81 | 0.92 | 200 | * | |
| Node021 | SD:skmeans | 3 | 1.00 | 0.99 | 1.00 | 41 | ** | |
| Node0211-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.94 | 1.00 | 18 | ** |
| Node0212 | ATC:kmeans | 7 | 0.99 | 0.77 | 0.96 | 15 | ** | |
| Node02121 | ATC:kmeans | 4 | 0.95 | 0.90 | 0.97 | 13 | * | |
| Node021211-leaf | not applied | ✓ (b) | 11 | |||||
| Node021212-leaf | not applied | ✓ (b) | 2 | |||||
| Node02122-leaf | not applied | ✓ (b) | 2 | |||||
| Node0213-leaf | not applied | ✓ (b) | 8 | |||||
| Node022 | ATC:skmeans | 4 | 0.98 | 0.94 | 0.96 | 61 | ** | |
| Node0221 | SD:kmeans | 3 | 1.00 | 1.00 | 0.99 | 22 | ** | |
| Node02211-leaf | not applied | ✓ (b) | 5 | |||||
| Node02212-leaf | not applied | ✓ (b) | 10 | |||||
| Node02213-leaf | not applied | ✓ (b) | 7 | |||||
| Node0222 | ATC:skmeans | 4 | 0.95 | 0.92 | 0.96 | 26 | * | |
| Node02221 | ATC:skmeans | 3 | 0.99 | 0.99 | 0.99 | 18 | ** | |
| Node022211-leaf | not applied | ✓ (b) | 3 | |||||
| Node022212-leaf | ATC:kmeans | ✓ (c) | 8 | 0.91 | 0.52 | 0.81 | 12 | * |
| Node022213-leaf | not applied | ✓ (b) | 3 | |||||
| Node02222-leaf | not applied | ✓ (b) | 8 | |||||
| Node0223-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 13 | ** |
| Node023 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 29 | ** | |
| Node0231 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 24 | ** | |
| Node02311-leaf | not applied | ✓ (b) | 9 | |||||
| Node02312-leaf | not applied | ✓ (b) | 4 | |||||
| Node02313-leaf | not applied | ✓ (b) | 4 | |||||
| Node02314-leaf | not applied | ✓ (b) | 7 | |||||
| Node0232-leaf | not applied | ✓ (b) | 3 | |||||
| Node0233-leaf | not applied | ✓ (b) | 2 | |||||
| Node024 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 40 | ** | |
| Node0241 | SD:skmeans | 2 | 1.00 | 0.98 | 0.98 | 16 | ** | |
| Node02411-leaf | not applied | ✓ (b) | 11 | |||||
| Node02412-leaf | not applied | ✓ (b) | 5 | |||||
| Node0242 | ATC:kmeans | 4 | 0.91 | 0.88 | 0.97 | 12 | * | |
| Node02421-leaf | not applied | ✓ (b) | 2 | |||||
| Node02422-leaf | not applied | ✓ (b) | 10 | |||||
| Node0243 | ATC:kmeans | 4 | 1.00 | 0.97 | 0.97 | 12 | ** | |
| Node02431-leaf | not applied | ✓ (b) | 4 | |||||
| Node02432-leaf | not applied | ✓ (b) | 2 | |||||
| Node02433-leaf | not applied | ✓ (b) | 6 | |||||
| Node025 | ATC:kmeans | 2 | 0.81 | 0.97 | 0.98 | 29 | ||
| Node0251-leaf | not applied | ✓ (b) | 10 | |||||
| Node0252-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 19 | ** |
| Node03 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 34 | ** | |
| Node031-leaf | not applied | ✓ (b) | 11 | |||||
| Node032 | ATC:kmeans | 8 | 0.94 | 0.83 | 0.91 | 23 | * | |
| Node0321-leaf | not applied | ✓ (b) | 11 | |||||
| Node0322-leaf | ATC:skmeans | ✓ (c) | 8 | 0.92 | 0.43 | 0.93 | 12 | * |
| Node04 | ATC:kmeans | 2 | 0.96 | 0.96 | 0.98 | 108 | ** | |
| Node041 | ATC:skmeans | 3 | 1.00 | 0.99 | 1.00 | 41 | ** | |
| Node0411-leaf | ATC:kmeans | ✓ (c) | 3 | 0.91 | 0.50 | 0.83 | 15 | * |
| Node0412-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 21 | ** |
| Node0413-leaf | not applied | ✓ (b) | 5 | |||||
| Node042 | ATC:skmeans | 4 | 0.98 | 0.96 | 0.98 | 67 | ** | |
| Node0421-leaf | ATC:kmeans | ✓ (c) | 6 | 0.91 | 0.75 | 0.89 | 16 | * |
| Node0422-leaf | SD:kmeans | ✓ (c) | 2 | 0.88 | 0.96 | 0.98 | 17 | |
| Node0423-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 19 | ** |
| Node0424-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 15 | ** |
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 = 1180))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1235))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1271))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1312))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1442))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1622))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1728))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1739))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2066))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2132))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2409))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4332))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4836))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5965))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6112))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8815))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9569))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10598))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12535))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15935))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 16461))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21451))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21933))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 27985))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 74620))
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 = 1180))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "0411" "0322" "0121" "0412" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "02422" "02213" "0424" "0424" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022212" "0111" "0422" "0422" "0411" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "0423" "022212" "0422" "0121" "0252" "0252"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "0412" "0411" "0223" "031" "0421"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "0211" "0422"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "0124" "0124" "022212" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "0211" "02311" "0121" "0321" "0412" "0123"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "0211" "0411" "0322" "0111" "0424" "0422"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "0123" "0112" "0423" "02412" "0424" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "0422" "0412" "0132" "0123" "0411"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "0423" "0213" "02422" "0412"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "0252" "031" "0111" "0421" "0421" "021212"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021211" "02213" "0423" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022212" "0421" "0422" "0233" "031" "0252"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "0122" "0424" "0112" "0251" "0424" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "0252" "0421" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "0122" "0213" "0111" "0421" "0251" "0252"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "02422" "0412" "0122" "02412" "02411" "021211"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "0211" "02222" "0423" "0251" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "0252" "021212" "022212" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "0423" "02313" "0223" "0211"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "0251" "0321" "0223" "0111" "0252"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "0252" "02411" "02433" "02421"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "0422" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "0252" "0424" "022211" "0412" "0211" "0423"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "0411" "02212" "02212" "0113" "0423"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "0252"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "0411" "02412" "0211" "02222" "0213"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "0213" "0251" "0122" "0211" "022213" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "0252" "0131" "0123" "0421" "0412" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "0424" "021211" "0412" "0412" "02433" "0252"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "0412" "031" "02422" "0223" "0111" "0213"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "0213" "02311" "0111" "0111" "022212" "021211"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "0412" "02122" "02311" "0422"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "0412" "02314" "0423"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "0121" "0423" "0121" "0412" "0411" "0252"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "0124" "02433" "0251" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "0412" "02433" "0112" "0422" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "0423" "02431" "022212" "0121" "0232" "0211"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "0124" "0421" "02311" "02212" "022211"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "022212" "0251" "0131" "0423"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "0422" "02311" "0211" "022212" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "0251" "02314" "02311" "0113" "0412" "022213"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "0423" "021211" "0421" "0122" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022212" "02411" "0124" "0423" "021211" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "02422" "0133" "0411" "0112" "022212" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "0252" "02314" "031" "02422" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "0123" "0424" "0423" "0421" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "0422" "0111" "031" "02212" "0421" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "0423" "0131" "0132" "0412" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "0412" "0424" "02433" "0424" "02213" "0422"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "0412" "02312" "02313" "0424" "0413" "02421"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "0413" "0252" "031" "022212" "02422" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "022213" "0123" "0422" "0132" "0252"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "02422" "0223" "0223" "021211" "0411" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "0421" "0213" "0421" "0113" "0121" "0411"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "0423" "0322" "0211" "0411" "0423"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "0251" "0111" "0421"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "0211" "0411" "02213" "02422" "0422" "0211"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "0121" "021211" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02122" "02432" "02431" "0413" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "0211" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "0424" "0421" "0321" "02222" "02222" "021211"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "02422" "0111" "0423" "0223" "0211" "0412"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021211" "0252" "021211" "0211" "0251" "0411"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "0411" "0413" "0113" "022211" "02212" "0211"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "0424" "0424" "0131" "0211"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "0422" "0112" "02411" "0422" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "0122" "0213" "0252"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "0421" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "0412" "0111" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1235))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "0411" "0322" "0121" "0412" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "0424" "0424" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022212" "0111" "0422" "0422" "0411" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "0423" "022212" "0422" "0121" "0252" "0252"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "0412" "0411" "0223" "031" "0421"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "0211" "0422"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "0124" "0124" "022212" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "0211" "02311" "0121" "0321" "0412" "0123"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "0211" "0411" "0322" "0111" "0424" "0422"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "0123" "0112" "0423" "02412" "0424" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "0422" "0412" "0132" "0123" "0411"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "0423" "0213" "0242" "0412"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "0252" "031" "0111" "0421" "0421" "021212"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021211" "02213" "0423" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022212" "0421" "0422" "0233" "031" "0252"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "0122" "0424" "0112" "0251" "0424" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "0252" "0421" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "0122" "0213" "0111" "0421" "0251" "0252"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "0412" "0122" "02412" "02411" "021211"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "0211" "02222" "0423" "0251" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "0252" "021212" "022212" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "0423" "02313" "0223" "0211"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "0251" "0321" "0223" "0111" "0252"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "0252" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "0422" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "0252" "0424" "022211" "0412" "0211" "0423"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "0411" "02212" "02212" "0113" "0423"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "0252"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "0411" "02412" "0211" "02222" "0213"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "0213" "0251" "0122" "0211" "022213" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "0252" "0131" "0123" "0421" "0412" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "0424" "021211" "0412" "0412" "02433" "0252"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "0412" "031" "0242" "0223" "0111" "0213"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "0213" "02311" "0111" "0111" "022212" "021211"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "0412" "02122" "02311" "0422"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "0412" "02314" "0423"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "0121" "0423" "0121" "0412" "0411" "0252"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "0124" "02433" "0251" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "0412" "02433" "0112" "0422" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "0423" "02431" "022212" "0121" "0232" "0211"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "0124" "0421" "02311" "02212" "022211"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "022212" "0251" "0131" "0423"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "0422" "02311" "0211" "022212" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "0251" "02314" "02311" "0113" "0412" "022213"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "0423" "021211" "0421" "0122" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022212" "02411" "0124" "0423" "021211" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "0411" "0112" "022212" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "0252" "02314" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "0123" "0424" "0423" "0421" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "0422" "0111" "031" "02212" "0421" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "0423" "0131" "0132" "0412" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "0412" "0424" "02433" "0424" "02213" "0422"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "0412" "02312" "02313" "0424" "0413" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "0413" "0252" "031" "022212" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "022213" "0123" "0422" "0132" "0252"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021211" "0411" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "0421" "0213" "0421" "0113" "0121" "0411"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "0423" "0322" "0211" "0411" "0423"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "0251" "0111" "0421"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "0211" "0411" "02213" "0242" "0422" "0211"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "0121" "021211" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02122" "02432" "02431" "0413" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "0211" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "0424" "0421" "0321" "02222" "02222" "021211"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "0423" "0223" "0211" "0412"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021211" "0252" "021211" "0211" "0251" "0411"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "0411" "0413" "0113" "022211" "02212" "0211"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "0424" "0424" "0131" "0211"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "0422" "0112" "02411" "0422" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "0122" "0213" "0252"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "0421" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "0412" "0111" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1271))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "0121" "04" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022212" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "022212" "04" "0121" "0252" "0252"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "0211" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "0124" "0124" "022212" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "0211" "02311" "0121" "0321" "04" "0123"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "0211" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "0123" "0112" "04" "02412" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "0123" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "0213" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "0252" "031" "0111" "04" "04" "021212"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021211" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022212" "04" "04" "0233" "031" "0252"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "0122" "04" "0112" "0251" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "0252" "04" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "0122" "0213" "0111" "04" "0251" "0252"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "0122" "02412" "02411" "021211"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "0211" "02222" "04" "0251" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "0252" "021212" "022212" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "02313" "0223" "0211"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "0251" "0321" "0223" "0111" "0252"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "0252" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "0252" "04" "022211" "04" "0211" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "0252"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "02412" "0211" "02222" "0213"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "0213" "0251" "0122" "0211" "022213" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "0252" "0131" "0123" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021211" "04" "04" "02433" "0252"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "0213"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "0213" "02311" "0111" "0111" "022212" "021211"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "02122" "02311" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "04" "02314" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "0121" "04" "0121" "04" "04" "0252"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "0124" "02433" "0251" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "022212" "0121" "0232" "0211"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "0124" "04" "02311" "02212" "022211"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "022212" "0251" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "04" "02311" "0211" "022212" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "0251" "02314" "02311" "0113" "04" "022213"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021211" "04" "0122" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022212" "02411" "0124" "04" "021211" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "022212" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "0252" "02314" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "0123" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "02312" "02313" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "0252" "031" "022212" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "022213" "0123" "04" "0132" "0252"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021211" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "0213" "04" "0113" "0121" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "04" "0322" "0211" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "0251" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "0211" "04" "02213" "0242" "04" "0211"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "0121" "021211" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02122" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "0211" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "021211"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "0211" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021211" "0252" "021211" "0211" "0251" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "022211" "02212" "0211"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "04" "04" "0131" "0211"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "02411" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "0122" "0213" "0252"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "04" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1312))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "0121" "04" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02221" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02221" "04" "0121" "0252" "0252"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "0211" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "0124" "0124" "02221" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "0211" "02311" "0121" "0321" "04" "0123"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "0211" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "0123" "0112" "04" "02412" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "0123" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "0213" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "0252" "031" "0111" "04" "04" "021212"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021211" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02221" "04" "04" "0233" "031" "0252"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "0122" "04" "0112" "0251" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "0252" "04" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "0122" "0213" "0111" "04" "0251" "0252"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "0122" "02412" "02411" "021211"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "0211" "02222" "04" "0251" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "0252" "021212" "02221" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "02313" "0223" "0211"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "0251" "0321" "0223" "0111" "0252"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "0252" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "0252" "04" "02221" "04" "0211" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "0252"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "02412" "0211" "02222" "0213"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "0213" "0251" "0122" "0211" "02221" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "0252" "0131" "0123" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021211" "04" "04" "02433" "0252"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "0213"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "0213" "02311" "0111" "0111" "02221" "021211"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "02122" "02311" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "04" "02314" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "0121" "04" "0121" "04" "04" "0252"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "0124" "02433" "0251" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "02221" "0121" "0232" "0211"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "0124" "04" "02311" "02212" "02221"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "02221" "0251" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "04" "02311" "0211" "02221" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "0251" "02314" "02311" "0113" "04" "02221"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021211" "04" "0122" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02221" "02411" "0124" "04" "021211" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "02221" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "0252" "02314" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "0123" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "02312" "02313" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "0252" "031" "02221" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "02221" "0123" "04" "0132" "0252"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021211" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "0213" "04" "0113" "0121" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "04" "0322" "0211" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "0251" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "0211" "04" "02213" "0242" "04" "0211"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "0121" "021211" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02122" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "0211" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "021211"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "0211" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021211" "0252" "021211" "0211" "0251" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "02221" "02212" "0211"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "04" "04" "0131" "0211"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "02411" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "0122" "0213" "0252"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "04" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1442))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02221" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02221" "04" "012" "0252" "0252"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "0211" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "02221" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "0211" "02311" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "0211" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "02412" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "0213" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "0252" "031" "0111" "04" "04" "021212"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021211" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02221" "04" "04" "0233" "031" "0252"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "0251" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "0252" "04" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "0213" "0111" "04" "0251" "0252"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "02412" "02411" "021211"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "0211" "02222" "04" "0251" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "0252" "021212" "02221" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "02313" "0223" "0211"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "0251" "0321" "0223" "0111" "0252"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "0252" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "0252" "04" "02221" "04" "0211" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "0252"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "02412" "0211" "02222" "0213"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "0213" "0251" "012" "0211" "02221" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "0252" "0131" "012" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021211" "04" "04" "02433" "0252"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "0213"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "0213" "02311" "0111" "0111" "02221" "021211"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "02122" "02311" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "04" "02314" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "0252"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "0251" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "02221" "012" "0232" "0211"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "02311" "02212" "02221"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "02221" "0251" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "04" "02311" "0211" "02221" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "0251" "02314" "02311" "0113" "04" "02221"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021211" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02221" "02411" "012" "04" "021211" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "02221" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "0252" "02314" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "02312" "02313" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "0252" "031" "02221" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "02221" "012" "04" "0132" "0252"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021211" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "0213" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "04" "0322" "0211" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "0251" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "0211" "04" "02213" "0242" "04" "0211"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "012" "021211" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02122" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "0211" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "021211"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "0211" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021211" "0252" "021211" "0211" "0251" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "02221" "02212" "0211"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "04" "04" "0131" "0211"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "02411" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "012" "0213" "0252"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "04" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1622))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02221" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02221" "04" "012" "0252" "0252"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "0211" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "02221" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "0211" "02311" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "0211" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "02412" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "0213" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "0252" "031" "0111" "04" "04" "02121"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "02121" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02221" "04" "04" "0233" "031" "0252"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "0251" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "0252" "04" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "0213" "0111" "04" "0251" "0252"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "02412" "02411" "02121"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "0211" "02222" "04" "0251" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "0252" "02121" "02221" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "02313" "0223" "0211"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "0251" "0321" "0223" "0111" "0252"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "0252" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "0252" "04" "02221" "04" "0211" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "0252"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "02412" "0211" "02222" "0213"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "0213" "0251" "012" "0211" "02221" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "0252" "0131" "012" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "02121" "04" "04" "02433" "0252"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "0213"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "0213" "02311" "0111" "0111" "02221" "02121"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "02122" "02311" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "04" "02314" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "0252"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "0251" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "02221" "012" "0232" "0211"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "02311" "02212" "02221"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "02221" "0251" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "04" "02311" "0211" "02221" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "0251" "02314" "02311" "0113" "04" "02221"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "02121" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02221" "02411" "012" "04" "02121" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "02221" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "0252" "02314" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "02312" "02313" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "0252" "031" "02221" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "02221" "012" "04" "0132" "0252"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "02121" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "0213" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "04" "0322" "0211" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "0251" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "0211" "04" "02213" "0242" "04" "0211"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "012" "02121" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02122" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "0211" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "02121"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "0211" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "02121" "0252" "02121" "0211" "0251" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "02221" "02212" "0211"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "04" "04" "0131" "0211"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "02411" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "012" "0213" "0252"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "04" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1728))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02221" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02221" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "0211" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "02221" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "0211" "02311" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "0211" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "02412" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "0213" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "02121"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "02121" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02221" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "025" "04" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "0213" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "02412" "02411" "02121"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "0211" "02222" "04" "025" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "02121" "02221" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "02313" "0223" "0211"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "0321" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "025" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "02221" "04" "0211" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "02412" "0211" "02222" "0213"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "0213" "025" "012" "0211" "02221" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "0131" "012" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "02121" "04" "04" "02433" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "0213"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "0213" "02311" "0111" "0111" "02221" "02121"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "02122" "02311" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "04" "02314" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "025" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "02221" "012" "0232" "0211"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "02311" "02212" "02221"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "02221" "025" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "04" "02311" "0211" "02221" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "02314" "02311" "0113" "04" "02221"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "02121" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02221" "02411" "012" "04" "02121" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "02221" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "02314" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "02312" "02313" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "02221" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "02221" "012" "04" "0132" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "02121" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "0213" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "04" "0322" "0211" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "0211" "04" "02213" "0242" "04" "0211"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "012" "02121" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02122" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "0211" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "02121"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "0211" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "02121" "025" "02121" "0211" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "02221" "02212" "0211"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "04" "04" "0131" "0211"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "02411" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "012" "0213" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "04" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1739))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02221" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02221" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02314" "02411" "0133" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "02221" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "02311" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "02412" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02221" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "025" "04" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "02412" "02411" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "02222" "04" "025" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "02221" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "02313" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "0321" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "025" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "02221" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "02412" "021" "02222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "02221" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "0131" "012" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "02433" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "02311" "0111" "0111" "02221" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "021" "02311" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "02312" "031" "04" "02314" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "025" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "02221" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "02311" "02212" "02221"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "02312" "02221" "025" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02313" "04" "02311" "021" "02221" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "02314" "02311" "0113" "04" "02221"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02221" "02411" "012" "04" "021" "02314"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "02221" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "02314" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "02312" "02313" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "02221" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "02221" "012" "04" "0132" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02311" "04" "0322" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02313" "0131" "02311" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02314" "012" "021" "0132" "02314" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "02221" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02312" "0223" "04" "04" "0131" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "02411" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "04" "02311"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2066))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "02411" "02411"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02412" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02221" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02221" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "02411" "0133" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "02221" "02213" "02411"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "02412" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02221" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "025" "04" "02411"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "02412" "02411" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "02222" "04" "025" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "02221" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "0321" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "025" "02411" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "02411" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "02221" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "02412" "021" "02222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "02221" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "0131" "012" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "02433" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "0111" "0111" "02221" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "031" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "025" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "02221" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "0231" "02212" "02221"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "0231" "02221" "025" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "02221" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "0113" "04" "02221"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02221" "02411" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "02221" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "02411"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "02221" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "02221" "012" "04" "0132" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "0322" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "0131" "0231" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "0132" "0231" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "02221" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "0131" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "02411" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "02412" "02213" "0322" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2132))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02221" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02221" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "0133" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "02221" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "0241" "04" "02222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02221" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "02222" "0131" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "02222" "04" "025" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "02221" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "0321" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "025" "0241" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "0241" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "02221" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "0241" "021" "02222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "02221" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "0131" "012" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "02433" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "0111" "0111" "02221" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "031" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "025" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "02221" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "0231" "02212" "02221"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "0231" "02221" "025" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "02221" "02222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "0113" "04" "02221"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02221" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "02221" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "02221" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "02221" "012" "04" "0132" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "0322" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "0131" "0231" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "0132" "0231" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "02222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "02222" "02222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "02221" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "0131" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "0241" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "0322" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2409))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "0132"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "0133" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "0222" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "0241" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "0132" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "0133"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "0222" "0131" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "0132"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "0321" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "025" "0241" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "0132" "02211" "0133" "04" "0241" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "0133" "0131" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "0241" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "0131" "012" "04" "04" "0131"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "02433" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "0111" "0111" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "0133" "0321" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "031" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "025" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "0231" "0222" "025" "0131" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "0113" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "0133" "04" "0112" "0222" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "0133"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "0131" "0132" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "0222" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "0132" "0222" "012" "04" "0132" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "0322" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "0131" "0231" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "0132" "0231" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "0132" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "0131" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "0241" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "0132" "0132" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "0322" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4332))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "0322" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "0322" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "0321" "012" "012" "0222" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "0321" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "0322" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "0241" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "0322" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "0322" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "0222" "013" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "0321" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "0321" "0322" "025" "0241" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "0241" "0322"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "0241" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "02433" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "0111" "0111" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "0321" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "031" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "025" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "0321" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "0113" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "0321"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "013" "04" "0112" "0222" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "031" "0242" "0321" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "0321" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "0222" "0242" "0322"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "0322" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "0321"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "0112" "0322"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "0321" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "0241" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "0322" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "0322" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4836))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "032" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "0111" "04" "04" "04" "02431"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "032" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "032" "012" "012" "0222" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "032" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "032" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "0241" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "032" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "032" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "0222" "013" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "0113" "0111" "02433"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "032" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "032" "032" "025" "0241" "02433" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "0241" "032"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "0241" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "02433" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "0111" "0111" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "032" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "031" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "02433" "025" "0111" "0111" "02431"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "02433" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02431" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "032" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "0113" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "032"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "013" "04" "0112" "0222" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "031" "0242" "032" "02432"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "032" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02433" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "0222" "0242" "032"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "032" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "032"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "02432" "02431" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "0112" "032"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "032" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "0241" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "032" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "032" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5965))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "032" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "0111" "04" "04" "04" "0243"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "032" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "032" "012" "012" "0222" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "032" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "032" "0111" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "0112" "04" "0241" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "0111" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "0112" "032" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "0111" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "0112" "032" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "0112" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "0111" "0222" "013" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "0111" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "0113" "0111" "0243"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "0112" "025" "032" "0223" "0111" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "032" "032" "025" "0241" "0243" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "0241" "032"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "0113" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "0113" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "0112" "04" "0241" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "0243" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "0111" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "0111" "0111" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "032" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "031" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "0243" "025" "0111" "0111" "0243"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "0243" "0112" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "0243" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "032" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "0113" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "032"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "013" "04" "0112" "0222" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "031" "0242" "032" "0243"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "0111" "031" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "032" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "0243" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "0222" "0242" "032"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "0111"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "0113" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "032" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "0111" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "032"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "0243" "0243" "04" "0113" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "0112" "032"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "032" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "0111" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "0113" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "0112" "0241" "04" "0111"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "032" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "032" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "0111" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6112))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "032" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "011" "04" "04" "04" "0243"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "032" "04" "04" "0223" "031" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "032" "012" "012" "0222" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "032" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "032" "011" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "011" "04" "0241" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "011" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "011" "032" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "031" "011" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "011" "032" "021" "02213" "04" "031"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "031" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "011" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "011" "0222" "013" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "011" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "011" "011" "0243"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "011" "025" "032" "0223" "011" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "032" "032" "025" "0241" "0243" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "0241" "032"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "011" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "011" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "011" "04" "0241" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "0243" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "031" "0242" "0223" "011" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "011" "011" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "032" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "031" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "0243" "025" "011" "011" "0243"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "0243" "011" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "0243" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "031" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "032" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "011" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "032"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "013" "04" "011" "0222" "031"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "031" "0242" "032" "0243"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "011" "031" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "032" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "0243" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "031" "0222" "0242" "032"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "011"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "011" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "032" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "011" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "032"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "0243" "0243" "04" "011" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "011" "032"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "032" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "011" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "011" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "011" "0241" "04" "011"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "032" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "032" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "011" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8815))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "011" "04" "04" "04" "0243"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "0223" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "012" "012" "0222" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "03" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "011" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "011" "04" "0241" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "011" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "011" "03" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "011" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "011" "03" "021" "02213" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "011" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "011" "0222" "013" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "011" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "011" "011" "0243"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "011" "025" "03" "0223" "011" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "0241" "0243" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "0241" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "011" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "011" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "011" "04" "0241" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "0243" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "0242" "0223" "011" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "011" "011" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "03" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "03" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "0243" "025" "011" "011" "0243"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "0243" "011" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "0243" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "011" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "013" "04" "011" "0222" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "03" "0242" "03" "0243"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "011" "03" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "0243" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "0222" "0242" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "011"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "011" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "011" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "0243" "0243" "04" "011" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "011" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "011" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "011" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "011" "0241" "04" "011"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "03" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "011" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9569))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "012" "04" "0241" "0241"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "0241" "0242" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "011" "04" "04" "04" "0243"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "0223" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "0241" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "012" "012" "0222" "02213" "0241"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "03" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "011" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "011" "04" "0241" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "011" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "011" "03" "04" "021" "0242" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "011" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "011" "03" "021" "02213" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "011" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "011" "0222" "013" "025" "04" "0241"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "011" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "0242" "04" "012" "0241" "0241" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "011" "011" "0243"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "011" "025" "03" "0223" "011" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "0241" "0243" "0242"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "0241" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "011" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "011" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "011" "04" "0241" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "0243" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "0242" "0223" "011" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "011" "011" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "03" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "03" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "0243" "025" "011" "011" "0243"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "0243" "011" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "0243" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "011" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "0241" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "0242" "013" "04" "011" "0222" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "03" "0242" "03" "0243"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "011" "03" "02212" "04" "0241"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "0243" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "0242"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "0222" "0242" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "0242" "0223" "0223" "021" "04" "011"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "011" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "011" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "0242" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "0243" "0243" "04" "011" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "011" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "0242" "011" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "011" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "011" "0241" "04" "011"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "0241" "02213" "03" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "011" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10598))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "012" "04" "024" "024"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "024" "024" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "011" "04" "04" "04" "024"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "0223" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "024" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "012" "012" "0222" "02213" "024"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "03" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "011" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "011" "04" "024" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "011" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "011" "03" "04" "021" "024" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "011" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "011" "03" "021" "02213" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "011" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "011" "0222" "013" "025" "04" "024"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "011" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "024" "04" "012" "024" "024" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "011" "011" "024"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "011" "025" "03" "0223" "011" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "024" "024" "024"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "024" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "011" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "011" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "011" "04" "024" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "024" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "024" "0223" "011" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "011" "011" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "03" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "03" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "024" "025" "011" "011" "024"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "024" "011" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "024" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "011" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "024" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "024" "013" "04" "011" "0222" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "03" "024" "03" "024"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "011" "03" "02212" "04" "024"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "024" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "024"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "0222" "024" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "024" "0223" "0223" "021" "04" "011"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "011" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "011" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "024" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "024" "024" "04" "011" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "011" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "024" "011" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "011" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "011" "024" "04" "011"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "024" "02213" "03" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "011" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12535))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "012" "04" "024" "024"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "024" "024" "02213" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "0222" "011" "04" "04" "04" "024"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "0222" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "0223" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "024" "013" "02211" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "012" "012" "0222" "02213" "024"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "03" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "011" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "011" "04" "024" "04" "0222"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "011" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "011" "03" "04" "021" "024" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "011" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "011" "03" "021" "02213" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "0222" "04" "04" "0233" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "011" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "011" "0222" "013" "025" "04" "024"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "011" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "024" "04" "012" "024" "024" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02213" "021" "0222" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "0222" "011" "011" "024"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "0223" "02212" "04" "0231" "0223" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "011" "025" "03" "0223" "011" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "024" "024" "024"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "02211" "013" "04" "024" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "0222" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "02212" "02212" "011" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02212" "013" "013" "0232" "011" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "011" "04" "024" "021" "0222" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "0222" "0223"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "024" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "024" "0223" "011" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "011" "011" "0222" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "03" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "03" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "024" "025" "011" "011" "024"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02212" "04" "024" "011" "04" "02212"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "024" "0222" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "012" "04" "0231" "02212" "0222"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "0231" "0222" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "0222" "0222"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "011" "04" "0222"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "0223" "04" "021" "04" "012" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "0222" "024" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "024" "013" "04" "011" "0222" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "03" "024" "03" "024"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "02212" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "011" "03" "02212" "04" "024"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "013" "013" "04" "02211"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "024" "04" "02213" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "024"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "0222" "024" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "0222" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "024" "0223" "0223" "021" "04" "011"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "011" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "011" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "02213" "024" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "024" "024" "04" "011" "0223"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "0223" "0222" "013" "011" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "0222" "0222" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "024" "011" "04" "0223" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "011" "0222" "02212" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "0223" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02211" "04" "011" "024" "04" "011"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02211" "024" "02213" "03" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "011" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15935))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "012" "04" "024" "024"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "024" "024" "022" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022" "011" "04" "04" "04" "024"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "022" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "022" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "024" "013" "022" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "012" "012" "022" "022" "024"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "03" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "011" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "011" "04" "024" "04" "022"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "011" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "011" "03" "04" "021" "024" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "011" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "011" "03" "021" "022" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022" "04" "04" "0233" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "011" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "011" "022" "013" "025" "04" "024"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "011" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "024" "04" "012" "024" "024" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "022" "021" "022" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "022" "011" "011" "024"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "022" "022" "04" "0231" "022" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "011" "025" "03" "022" "011" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "024" "024" "024"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "022" "013" "04" "024" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "022" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "022" "022" "011" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "022" "013" "013" "0232" "011" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "011" "04" "024" "021" "022" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "022" "022"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "024" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "024" "022" "011" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "011" "011" "022" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "03" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "03" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "024" "025" "011" "011" "024"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "022" "04" "024" "011" "04" "022"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "024" "022" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "012" "04" "0231" "022" "022"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "0231" "022" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "022" "022"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "011" "04" "022"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "022" "04" "021" "04" "012" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022" "024" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "024" "013" "04" "011" "022" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "03" "024" "03" "024"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "022" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "011" "03" "022" "04" "024"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "013" "013" "04" "022"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "024" "04" "022" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "024"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "022" "024" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "022" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "024" "022" "022" "021" "04" "011"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "011" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "011" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "022" "024" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "024" "024" "04" "011" "022"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "022" "022" "013" "011" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "022" "022" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "024" "011" "04" "022" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "011" "022" "022" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "022" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "022" "04" "011" "024" "04" "011"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "022" "024" "022" "03" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "011" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 16461))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "012" "04" "024" "024"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "024" "024" "022" "04" "04" "013"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022" "011" "04" "04" "04" "024"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "022" "04" "012" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "022" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "024" "013" "022" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "012" "012" "022" "022" "024"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "012" "03" "04" "012"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "011" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "012" "011" "04" "024" "04" "022"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "011" "04" "04" "013" "012" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "011" "03" "04" "021" "024" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "011" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "011" "03" "021" "022" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022" "04" "04" "0233" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "012" "04" "011" "025" "04" "013"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "011" "022" "013" "025" "04" "024"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "012" "021" "011" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "024" "04" "012" "024" "024" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "022" "021" "022" "04" "025" "013"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "022" "011" "011" "024"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "022" "022" "04" "0231" "022" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "011" "025" "03" "022" "011" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "024" "024" "024"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "013" "022" "013" "04" "024" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "022" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "022" "022" "011" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "022" "013" "013" "0232" "011" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "011" "04" "024" "021" "022" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "012" "021" "022" "022"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "013" "012" "04" "04" "013"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "024" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "024" "022" "011" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "011" "011" "022" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "013" "03" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "03" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "012" "04" "012" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "012" "024" "025" "011" "011" "024"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "022" "04" "024" "011" "04" "022"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "024" "022" "012" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "012" "04" "0231" "022" "022"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "0231" "022" "025" "013" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "022" "022"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "011" "04" "022"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "022" "04" "021" "04" "012" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022" "024" "012" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "024" "013" "04" "011" "022" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "03" "024" "03" "024"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "012" "04" "04" "04" "022" "013"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "011" "03" "022" "04" "024"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "013" "013" "04" "022"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "024" "04" "022" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "024"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "022" "024" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "013" "022" "012" "04" "013" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "024" "022" "022" "021" "04" "011"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "011" "012" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "013" "0231" "025" "011" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "022" "024" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "012" "021" "013" "0231" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "024" "024" "04" "011" "022"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "022" "022" "013" "011" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "022" "022" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "024" "011" "04" "022" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "011" "022" "022" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "022" "04" "04" "013" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "022" "04" "011" "024" "04" "011"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "013" "013" "012" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "022" "024" "022" "03" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "011" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21451))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "01" "04" "024" "024"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "024" "024" "022" "04" "04" "01"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022" "01" "04" "04" "04" "024"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "022" "04" "01" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "022" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "0231" "024" "01" "022" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "01" "01" "022" "022" "024"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "0231" "01" "03" "04" "01"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "01" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "01" "01" "04" "024" "04" "022"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "01" "04" "04" "01" "01" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "01" "03" "04" "021" "024" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "01" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "01" "03" "021" "022" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022" "04" "04" "0233" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "01" "04" "01" "025" "04" "01"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "01" "022" "01" "025" "04" "024"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "01" "021" "01" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "024" "04" "01" "024" "024" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "022" "021" "022" "04" "025" "01"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "022" "01" "01" "024"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "022" "022" "04" "0231" "022" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "01" "025" "03" "022" "01" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "024" "024" "024"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "01" "022" "01" "04" "024" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "022" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "0233" "04" "022" "022" "01" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "022" "01" "01" "0232" "01" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "01" "04" "024" "021" "022" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "01" "021" "022" "022"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "01" "01" "04" "04" "01"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "024" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "024" "022" "01" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "0231" "01" "01" "022" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "01" "03" "04" "021" "0231" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "0232" "0231" "03" "04" "0231" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "01" "04" "01" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "01" "024" "025" "01" "01" "024"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "022" "04" "024" "01" "04" "022"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "024" "022" "01" "0232" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "01" "04" "0231" "022" "022"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "0231" "022" "025" "01" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "0231" "04" "0231" "021" "022" "022"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "0231" "0231" "01" "04" "022"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "022" "04" "021" "04" "01" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022" "024" "01" "04" "021" "0231"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "024" "01" "04" "01" "022" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "0231" "03" "024" "03" "024"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "01" "04" "04" "04" "022" "01"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "01" "03" "022" "04" "024"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "01" "01" "04" "022"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "024" "04" "022" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "0231" "0231" "04" "04" "024"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "022" "024" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "01" "022" "01" "04" "01" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "024" "022" "022" "021" "04" "01"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "01" "01" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "0231" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "0231" "01" "0231" "025" "01" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "022" "024" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "0231" "01" "021" "01" "0231" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "024" "024" "04" "01" "022"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "022" "022" "01" "01" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "022" "022" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "024" "01" "04" "022" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "01" "022" "022" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "0231" "022" "04" "04" "01" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "022" "04" "01" "024" "04" "01"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "01" "01" "01" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "022" "024" "022" "03" "04" "0231"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "01" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21933))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "01" "04" "024" "024"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "024" "024" "022" "04" "04" "01"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022" "01" "04" "04" "04" "024"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "022" "04" "01" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "022" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "023" "024" "01" "022" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "01" "01" "022" "022" "024"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "023" "01" "03" "04" "01"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "01" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "01" "01" "04" "024" "04" "022"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "01" "04" "04" "01" "01" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "01" "03" "04" "021" "024" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "01" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "01" "03" "021" "022" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022" "04" "04" "023" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "01" "04" "01" "025" "04" "01"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "01" "022" "01" "025" "04" "024"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "01" "021" "01" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "024" "04" "01" "024" "024" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "022" "021" "022" "04" "025" "01"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "022" "01" "01" "024"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "022" "022" "04" "023" "022" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "01" "025" "03" "022" "01" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "024" "024" "024"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "01" "022" "01" "04" "024" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "022" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "023" "04" "022" "022" "01" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "022" "01" "01" "023" "01" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "01" "04" "024" "021" "022" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "01" "021" "022" "022"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "01" "01" "04" "04" "01"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "024" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "024" "022" "01" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "023" "01" "01" "022" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "01" "03" "04" "021" "023" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "023" "023" "03" "04" "023" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "01" "04" "01" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "01" "024" "025" "01" "01" "024"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "022" "04" "024" "01" "04" "022"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "024" "022" "01" "023" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "01" "04" "023" "022" "022"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "023" "022" "025" "01" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "023" "04" "023" "021" "022" "022"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "023" "023" "01" "04" "022"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "022" "04" "021" "04" "01" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022" "024" "01" "04" "021" "023"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "024" "01" "04" "01" "022" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "023" "03" "024" "03" "024"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "01" "04" "04" "04" "022" "01"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "01" "03" "022" "04" "024"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "01" "01" "04" "022"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "024" "04" "022" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "023" "023" "04" "04" "024"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "022" "024" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "01" "022" "01" "04" "01" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "024" "022" "022" "021" "04" "01"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "01" "01" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "023" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "023" "01" "023" "025" "01" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "022" "024" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "023" "01" "021" "01" "023" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "024" "024" "04" "01" "022"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "022" "022" "01" "01" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "022" "022" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "024" "01" "04" "022" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "01" "022" "022" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "023" "022" "04" "04" "01" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "022" "04" "01" "024" "04" "01"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "01" "01" "01" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "022" "024" "022" "03" "04" "023"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "01" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 27985))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "01" "04" "024" "024"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "024" "024" "022" "04" "04" "01"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "022" "01" "04" "04" "04" "024"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "022" "04" "01" "025" "025"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "022" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "023" "024" "01" "022" "021" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "01" "01" "022" "022" "024"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "021" "023" "01" "03" "04" "01"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "021" "04" "03" "01" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "01" "01" "04" "024" "04" "022"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "01" "04" "04" "01" "01" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "01" "03" "04" "021" "024" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "025" "03" "01" "04" "04" "021"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "01" "03" "021" "022" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "022" "04" "04" "023" "03" "025"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "01" "04" "01" "025" "04" "01"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "01" "022" "01" "025" "04" "024"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "01" "021" "01" "04" "025" "025"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "024" "04" "01" "024" "024" "021"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "022" "021" "022" "04" "025" "01"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "025" "021" "022" "01" "01" "024"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "022" "022" "04" "023" "022" "021"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "01" "025" "03" "022" "01" "025"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "025" "024" "024" "024"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "01" "022" "01" "04" "024" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "025" "04" "022" "04" "021" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "023" "04" "022" "022" "01" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "022" "01" "01" "023" "01" "025"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "01" "04" "024" "021" "022" "021"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "021" "025" "01" "021" "022" "022"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "025" "01" "01" "04" "04" "01"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "021" "04" "04" "024" "025"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "024" "022" "01" "021"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "021" "023" "01" "01" "022" "021"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "01" "03" "04" "021" "023" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "023" "023" "03" "04" "023" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "01" "04" "01" "04" "04" "025"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "01" "024" "025" "01" "01" "024"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "022" "04" "024" "01" "04" "022"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "024" "022" "01" "023" "021"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "01" "04" "023" "022" "022"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "023" "022" "025" "01" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "023" "04" "023" "021" "022" "022"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "025" "023" "023" "01" "04" "022"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "022" "04" "021" "04" "01" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "022" "024" "01" "04" "021" "023"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "024" "01" "04" "01" "022" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "025" "023" "03" "024" "03" "024"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "01" "04" "04" "04" "022" "01"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "01" "03" "022" "04" "024"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "01" "01" "04" "022"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "024" "04" "022" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "023" "023" "04" "04" "024"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "025" "03" "022" "024" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "01" "022" "01" "04" "01" "025"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "024" "022" "022" "021" "04" "01"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "021" "04" "01" "01" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "023" "04" "03" "021" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "023" "01" "023" "025" "01" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "021" "04" "022" "024" "04" "021"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "023" "01" "021" "01" "023" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "021" "024" "024" "04" "01" "022"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "021" "022" "022" "01" "01" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "022" "022" "021"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "024" "01" "04" "022" "021" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "021" "025" "021" "021" "025" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "01" "022" "022" "021"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "023" "022" "04" "04" "01" "021"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "022" "04" "01" "024" "04" "01"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "01" "01" "01" "021" "025"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "022" "024" "022" "03" "04" "023"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "01" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 74620))
#> TCGA.FV.A495.01 TCGA.KR.A7K7.01 TCGA.BC.A3KF.01 TCGA.DD.A4NV.01 TCGA.DD.A4NQ.01 TCGA.CC.A1HT.01
#> "04" "03" "01" "04" "02" "02"
#> TCGA.BD.A3EP.01 TCGA.ES.A2HT.01 TCGA.CC.A3MA.01 TCGA.ZP.A9CV.01 TCGA.DD.AACY.01 TCGA.XR.A8TG.01
#> "02" "02" "02" "04" "04" "01"
#> TCGA.DD.AADW.01 TCGA.BC.A10Y.01 TCGA.CC.A3MB.01 TCGA.ED.A459.01 TCGA.PD.A5DF.01 TCGA.ED.A5KG.01
#> "02" "01" "04" "04" "04" "02"
#> TCGA.DD.AAVX.01 TCGA.ED.A7PY.01 TCGA.DD.A3A0.01 TCGA.RC.A7SF.01 TCGA.DD.AAW0.01 TCGA.ED.A66X.01
#> "04" "02" "04" "01" "02" "02"
#> TCGA.DD.AAC8.01 TCGA.DD.AACM.01 TCGA.FV.A3I1.01 TCGA.RC.A7S9.01 TCGA.ZP.A9D2.01 TCGA.G3.A5SL.01
#> "03" "04" "04" "02" "03" "04"
#> TCGA.DD.A3A2.11 TCGA.CC.A3M9.01 TCGA.BC.A216.01 TCGA.ED.A82E.01 TCGA.BC.A10T.11 TCGA.DD.A11A.01
#> "02" "02" "01" "02" "02" "04"
#> TCGA.DD.A73B.01 TCGA.DD.AACA.02 TCGA.DD.AACA.01 TCGA.DD.A1EH.01 TCGA.DD.AA3A.01 TCGA.RG.A7D4.01
#> "03" "01" "01" "02" "02" "02"
#> TCGA.FV.A2QR.11 TCGA.G3.A25W.11 TCGA.2Y.A9H4.01 TCGA.K7.AAU7.01 TCGA.DD.A3A2.01 TCGA.EP.A26S.01
#> "02" "02" "01" "03" "04" "01"
#> TCGA.DD.A1EG.11 TCGA.FV.A2QQ.01 TCGA.3K.AAZ8.01 TCGA.BC.A217.01 TCGA.DD.AADP.01 TCGA.CC.5259.01
#> "02" "04" "03" "01" "04" "04"
#> TCGA.DD.A1EA.01 TCGA.CC.A8HU.01 TCGA.ES.A2HS.01 TCGA.G3.A25W.01 TCGA.2V.A95S.01 TCGA.2Y.A9GU.01
#> "01" "01" "04" "02" "04" "02"
#> TCGA.RC.A7SB.01 TCGA.FV.A4ZP.01 TCGA.DD.AAD3.01 TCGA.2Y.A9H9.01 TCGA.DD.AAW2.01 TCGA.DD.A39V.01
#> "01" "04" "04" "01" "01" "04"
#> TCGA.DD.AADD.01 TCGA.CC.A9FW.01 TCGA.DD.AACS.01 TCGA.CC.A9FV.01 TCGA.G3.A7M7.01 TCGA.DD.A4NK.01
#> "01" "03" "04" "02" "02" "04"
#> TCGA.ED.A97K.01 TCGA.T1.A6J8.01 TCGA.DD.AACV.01 TCGA.DD.A4NF.01 TCGA.DD.A3A8.01 TCGA.WX.AA46.01
#> "02" "03" "01" "04" "04" "02"
#> TCGA.DD.A1EL.01 TCGA.DD.AACH.01 TCGA.DD.A119.11 TCGA.WQ.A9G7.01 TCGA.DD.A4NO.01 TCGA.G3.A7M9.01
#> "01" "03" "02" "02" "04" "03"
#> TCGA.CC.5261.01 TCGA.ZS.A9CG.01 TCGA.CC.A123.01 TCGA.5R.AA1D.01 TCGA.BC.A69H.01 TCGA.DD.AAVZ.01
#> "02" "04" "04" "02" "03" "02"
#> TCGA.DD.AAD0.01 TCGA.EP.A2KA.01 TCGA.2Y.A9HA.01 TCGA.DD.AACD.01 TCGA.DD.AAE7.01 TCGA.BC.A8YO.01
#> "01" "04" "01" "02" "04" "01"
#> TCGA.DD.AAE2.01 TCGA.DD.AAEG.01 TCGA.XR.A8TF.01 TCGA.CC.A5UC.01 TCGA.KR.A7K0.01 TCGA.K7.A5RG.01
#> "01" "02" "01" "02" "04" "02"
#> TCGA.G3.AAV4.01 TCGA.ED.A627.01 TCGA.2Y.A9GZ.01 TCGA.DD.AACX.01 TCGA.DD.AAVR.01 TCGA.2Y.A9H3.01
#> "01" "02" "01" "04" "02" "02"
#> TCGA.MR.A8JO.01 TCGA.DD.AAEK.01 TCGA.DD.A1EE.01 TCGA.DD.AACL.01 TCGA.KR.A7K8.01 TCGA.DD.A115.11
#> "02" "04" "01" "02" "02" "02"
#> TCGA.FV.A3I0.01 TCGA.DD.A11B.11 TCGA.DD.AADA.01 TCGA.G3.A5SM.01 TCGA.G3.A3CH.01 TCGA.G3.AAUZ.01
#> "02" "02" "02" "04" "02" "01"
#> TCGA.DD.AAVV.01 TCGA.DD.A4NP.01 TCGA.ED.A66Y.01 TCGA.LG.A6GG.01 TCGA.DD.AAE4.01 TCGA.HP.A5MZ.01
#> "02" "02" "02" "01" "01" "02"
#> TCGA.G3.A5SI.01 TCGA.BC.A112.01 TCGA.G3.AAV1.01 TCGA.DD.A1EF.11 TCGA.DD.A113.01 TCGA.BC.A10Y.11
#> "02" "02" "04" "02" "02" "02"
#> TCGA.DD.AACB.01 TCGA.CC.A9FS.01 TCGA.BC.A5W4.01 TCGA.2Y.A9H5.01 TCGA.BW.A5NO.01 TCGA.CC.A7IE.01
#> "01" "02" "03" "02" "01" "02"
#> TCGA.KR.A7K2.01 TCGA.DD.AADM.01 TCGA.CC.5258.01 TCGA.BW.A5NQ.01 TCGA.2Y.A9GX.01 TCGA.LG.A9QC.01
#> "03" "03" "02" "02" "02" "02"
#> TCGA.DD.A11C.01 TCGA.BC.A10Q.01 TCGA.4R.AA8I.01 TCGA.FV.A4ZQ.01 TCGA.BC.4073.01 TCGA.DD.AADQ.01
#> "01" "02" "01" "04" "02" "03"
#> TCGA.DD.AAD2.01 TCGA.WQ.AB4B.01 TCGA.RC.A7SH.01 TCGA.BC.A10T.01 TCGA.DD.A11A.11 TCGA.DD.A39W.01
#> "02" "04" "02" "04" "02" "04"
#> TCGA.RC.A6M5.01 TCGA.UB.A7MD.01 TCGA.WX.AA44.01 TCGA.5C.A9VG.01 TCGA.CC.5264.01 TCGA.DD.AADE.01
#> "02" "04" "02" "02" "01" "04"
#> TCGA.DD.AAD1.01 TCGA.QA.A7B7.01 TCGA.DD.AAEB.01 TCGA.DD.A3A6.01 TCGA.CC.5263.01 TCGA.DD.AACW.01
#> "02" "01" "01" "02" "01" "02"
#> TCGA.G3.A7M6.01 TCGA.GJ.A6C0.01 TCGA.BC.4072.01 TCGA.DD.A116.11 TCGA.2Y.A9H6.01 TCGA.MR.A520.01
#> "01" "04" "02" "02" "02" "02"
#> TCGA.EP.A12J.11 TCGA.DD.AADK.01 TCGA.DD.A73D.01 TCGA.ES.A2HS.11 TCGA.DD.A4NN.01 TCGA.ZP.A9CZ.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.CC.A8HS.01 TCGA.G3.A6UC.01 TCGA.CC.A7IH.01 TCGA.BC.A69I.01 TCGA.K7.A6G5.01 TCGA.BC.A10U.01
#> "02" "01" "01" "04" "04" "01"
#> TCGA.DD.A4NG.01 TCGA.BD.A2L6.11 TCGA.UB.A7MC.01 TCGA.UB.AA0U.01 TCGA.DD.A4NB.01 TCGA.ED.A8O6.01
#> "04" "02" "04" "04" "02" "02"
#> TCGA.DD.AACQ.01 TCGA.G3.AAV6.01 TCGA.DD.A3A4.01 TCGA.UB.A7MF.01 TCGA.DD.A1EK.01 TCGA.DD.A114.11
#> "04" "03" "02" "02" "01" "02"
#> TCGA.ES.A2HT.11 TCGA.DD.A39Z.11 TCGA.BC.A10Z.01 TCGA.WJ.A86L.01 TCGA.G3.A25Y.01 TCGA.DD.A1EI.11
#> "02" "02" "01" "01" "02" "02"
#> TCGA.DD.AACU.01 TCGA.MI.A75C.01 TCGA.DD.A4NJ.01 TCGA.G3.A25V.01 TCGA.BC.A10X.11 TCGA.FV.A496.01
#> "01" "03" "04" "02" "02" "04"
#> TCGA.DD.A4ND.01 TCGA.DD.A11D.11 TCGA.DD.AAD5.01 TCGA.DD.AAE8.01 TCGA.DD.A118.11 TCGA.DD.AAEH.01
#> "02" "02" "03" "04" "02" "04"
#> TCGA.G3.A25U.01 TCGA.2Y.A9GW.01 TCGA.ZS.A9CE.01 TCGA.NI.A4U2.01 TCGA.5C.AAPD.01 TCGA.DD.AAVW.01
#> "01" "04" "01" "04" "04" "02"
#> TCGA.EP.A2KC.01 TCGA.MI.A75E.01 TCGA.DD.A116.01 TCGA.GJ.A9DB.01 TCGA.CC.A7IL.01 TCGA.DD.AACC.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.FV.A3R3.01 TCGA.HP.A5N0.01 TCGA.K7.A5RF.01 TCGA.ED.A7PZ.01 TCGA.YA.A8S7.01 TCGA.DD.A39X.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.DD.AACF.01 TCGA.DD.A1EC.01 TCGA.DD.AAE0.01 TCGA.G3.AAV0.01 TCGA.XR.A8TD.01 TCGA.DD.A1EE.11
#> "04" "02" "02" "01" "02" "02"
#> TCGA.CC.A5UE.01 TCGA.DD.AACJ.01 TCGA.G3.AAV5.01 TCGA.DD.A1EB.11 TCGA.CC.A7IJ.01 TCGA.DD.AAVS.01
#> "03" "01" "04" "02" "02" "02"
#> TCGA.DD.A11B.01 TCGA.DD.A4NS.01 TCGA.ED.A8O5.01 TCGA.DD.A3A3.01 TCGA.DD.AAW3.01 TCGA.G3.A5SK.01
#> "03" "02" "02" "02" "01" "04"
#> TCGA.BC.A110.01 TCGA.DD.A3A7.01 TCGA.BC.A10R.11 TCGA.BC.A112.11 TCGA.DD.AACN.01 TCGA.DD.A1EF.01
#> "02" "04" "02" "02" "02" "02"
#> TCGA.CC.A3MC.01 TCGA.DD.A113.11 TCGA.DD.A1EJ.11 TCGA.G3.A25S.01 TCGA.DD.A73A.01 TCGA.DD.AADI.01
#> "02" "02" "02" "01" "04" "02"
#> TCGA.CC.A7IG.01 TCGA.G3.AAV3.01 TCGA.DD.A1ED.11 TCGA.MI.A75H.01 TCGA.DD.A73E.01 TCGA.2Y.A9H7.01
#> "02" "04" "02" "04" "01" "03"
#> TCGA.CC.A8HV.01 TCGA.DD.A1E9.01 TCGA.DD.AAD6.01 TCGA.BC.A10S.01 TCGA.DD.A11C.11 TCGA.BC.A10Q.11
#> "02" "02" "01" "04" "02" "02"
#> TCGA.LG.A9QD.01 TCGA.DD.A3A1.01 TCGA.DD.A73F.01 TCGA.CC.A7IK.01 TCGA.DD.AADO.01 TCGA.CC.A7II.01
#> "02" "01" "04" "01" "02" "03"
#> TCGA.RC.A6M3.01 TCGA.DD.A39W.11 TCGA.BC.A10W.01 TCGA.NI.A8LF.01 TCGA.FV.A23B.01 TCGA.DD.AADC.01
#> "02" "02" "03" "02" "03" "02"
#> TCGA.G3.A3CJ.01 TCGA.ZP.A9D1.01 TCGA.DD.A73C.01 TCGA.DD.AADU.01 TCGA.G3.A25X.01 TCGA.DD.AACP.01
#> "01" "04" "04" "04" "02" "01"
#> TCGA.UB.A7MB.01 TCGA.DD.AADG.01 TCGA.RC.A6M6.01 TCGA.DD.A4NH.01 TCGA.EP.A12J.01 TCGA.CC.5262.01
#> "04" "01" "03" "02" "04" "02"
#> TCGA.DD.AADJ.01 TCGA.ZS.A9CD.01 TCGA.DD.AAE9.01 TCGA.BD.A2L6.01 TCGA.DD.AAEI.01 TCGA.G3.A25T.01
#> "03" "04" "01" "01" "04" "02"
#> TCGA.2Y.A9GV.01 TCGA.DD.AADS.01 TCGA.DD.A114.01 TCGA.DD.A39Z.01 TCGA.UB.A7MA.01 TCGA.EP.A2KB.01
#> "04" "04" "02" "04" "02" "04"
#> TCGA.DD.AAEA.01 TCGA.UB.AA0V.01 TCGA.BD.A3EP.11 TCGA.FV.A3R2.01 TCGA.2Y.A9GY.01 TCGA.XR.A8TE.01
#> "04" "02" "02" "04" "04" "02"
#> TCGA.DD.AACZ.01 TCGA.ED.A4XI.01 TCGA.DD.AACG.01 TCGA.BW.A5NP.01 TCGA.DD.AAC9.01 TCGA.DD.AAE1.01
#> "04" "02" "03" "02" "02" "03"
#> TCGA.DD.A11D.01 TCGA.DD.AADY.01 TCGA.ZP.A9D4.01 TCGA.DD.AAED.01 TCGA.DD.AACK.01 TCGA.DD.AAVQ.01
#> "01" "02" "01" "04" "01" "02"
#> TCGA.DD.A1EI.01 TCGA.DD.A118.01 TCGA.DD.AACO.01 TCGA.DD.A4NL.01 TCGA.EP.A3JL.01 TCGA.DD.AAD8.01
#> "02" "02" "02" "02" "04" "01"
#> TCGA.5R.AA1C.01 TCGA.G3.A3CI.01 TCGA.G3.A3CK.01 TCGA.2Y.A9H0.01 TCGA.MI.A75G.01 TCGA.G3.A5SJ.01
#> "04" "02" "04" "01" "01" "04"
#> TCGA.BC.A216.11 TCGA.5R.AAAM.01 TCGA.BC.A3KG.01 TCGA.DD.A1EH.11 TCGA.2Y.A9GS.01 TCGA.BD.A3ER.01
#> "02" "04" "03" "02" "04" "04"
#> TCGA.BC.A10X.01 TCGA.FV.A2QR.01 TCGA.DD.A1EC.11 TCGA.CC.A7IF.01 TCGA.DD.AACE.01 TCGA.DD.AAVY.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.EP.A26S.11 TCGA.DD.A1EG.01 TCGA.ED.A7PX.01 TCGA.DD.A1EB.01 TCGA.DD.AADN.01 TCGA.DD.A3A3.11
#> "02" "04" "02" "02" "04" "02"
#> TCGA.DD.A39X.11 TCGA.G3.A25Z.01 TCGA.BC.A10U.11 TCGA.DD.A3A5.01 TCGA.BC.A110.11 TCGA.BC.A10R.01
#> "02" "01" "02" "01" "02" "03"
#> TCGA.ED.A7XO.01 TCGA.G3.AAV7.01 TCGA.GJ.A3OU.01 TCGA.DD.AADB.01 TCGA.RC.A7SK.01 TCGA.DD.A4NE.01
#> "02" "02" "02" "04" "01" "02"
#> TCGA.DD.A39V.11 TCGA.DD.AACT.01 TCGA.ZP.A9D0.01 TCGA.DD.AADF.01 TCGA.DD.A1EJ.01 TCGA.DD.AAVU.01
#> "02" "02" "02" "01" "01" "03"
#> TCGA.G3.A3CG.01 TCGA.DD.AAW1.01 TCGA.O8.A75V.01 TCGA.DD.A3A9.01 TCGA.DD.A73G.01 TCGA.DD.A1ED.01
#> "04" "04" "03" "02" "02" "02"
#> TCGA.WX.AA47.01 TCGA.G3.A7M5.01 TCGA.DD.A4NI.01 TCGA.2Y.A9H8.01 TCGA.DD.A1E9.11 TCGA.2Y.A9GT.01
#> "02" "01" "04" "02" "02" "04"
#> TCGA.BC.A10S.11 TCGA.UB.A7ME.01 TCGA.DD.A1EL.11 TCGA.DD.A3A1.11 TCGA.DD.A119.01 TCGA.MI.A75I.01
#> "02" "02" "02" "02" "02" "04"
#> TCGA.2Y.A9H1.01 TCGA.CC.A8HT.01 TCGA.DD.AADL.01 TCGA.XR.A8TC.01 TCGA.ED.A7XP.01 TCGA.BC.A10W.11
#> "04" "04" "01" "02" "02" "02"
#> TCGA.FV.A23B.11 TCGA.5C.A9VH.01 TCGA.DD.AADR.01 TCGA.2Y.A9HB.01 TCGA.DD.AAE3.01 TCGA.G3.A25X.11
#> "02" "02" "04" "04" "01" "02"
#> TCGA.DD.A4NA.01 TCGA.DD.AACI.01 TCGA.CC.A9FU.01 TCGA.EP.A3RK.01 TCGA.CC.A5UD.01 TCGA.DD.AADV.01
#> "02" "04" "01" "02" "04" "01"
#> TCGA.DD.AAEE.01 TCGA.ZS.A9CF.02 TCGA.ZS.A9CF.01 TCGA.RC.A6M4.01 TCGA.G3.A7M8.01 TCGA.DD.AAVP.01
#> "03" "01" "01" "01" "02" "02"
#> TCGA.CC.5260.01 TCGA.DD.A4NR.01 TCGA.2Y.A9H2.01 TCGA.DD.AAE6.01 TCGA.G3.AAV2.01 TCGA.BC.A10Z.11
#> "02" "02" "02" "03" "04" "02"
#> TCGA.ZP.A9CY.01 TCGA.DD.A115.01 TCGA.DD.A39Y.01
#> "04" "01" "04"
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
#> Error in h(simpleError(msg, call)) :
#> error in evaluating the argument 'object' in selecting a method for function 'draw': no applicable method for 'height' applied to an object of class "list"
Top rows on each node:
top_rows_overlap(res_rh, method = "upset")
UMAP plot which shows how samples are separated.
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1180),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1180),
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 = 1235),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1235),
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 = 1271),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1271),
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 = 1312),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1312),
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 = 1442),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1442),
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 = 1622),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1622),
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 = 1728),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1728),
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 = 1739),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1739),
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 = 2066),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2066),
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 = 2132),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2132),
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 = 2409),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2409),
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 = 4332),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4332),
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 = 4836),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4836),
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 = 5965),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5965),
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 = 6112),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6112),
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 = 8815),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8815),
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 = 9569),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9569),
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 = 10598),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10598),
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 = 12535),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12535),
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 = 15935),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 15935),
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 = 16461),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 16461),
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 = 21451),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 21451),
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 = 21933),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 21933),
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 = 27985),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 27985),
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 = 74620),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 74620),
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 = 1180))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1235))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1271))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1312))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1442))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1622))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1728))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1739))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2066))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2132))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2409))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4332))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4836))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5965))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6112))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8815))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9569))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10598))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 12535))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 15935))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 16461))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 21451))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 21933))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 27985))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 74620))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 , Node04 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 429 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 7.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.972 0.989 0.4675 0.532 0.532
#> 3 3 0.991 0.959 0.983 0.1688 0.892 0.802
#> 4 4 0.991 0.952 0.981 0.2345 0.784 0.565
#> 5 5 0.910 0.876 0.947 0.0768 0.905 0.728
#> 6 6 0.941 0.889 0.953 0.0304 0.952 0.834
#> 7 7 0.904 0.847 0.925 0.0236 0.957 0.837
#> 8 8 0.880 0.778 0.879 0.0117 0.993 0.968
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 7
#> attr(,"optional")
#> [1] 2 3 4 5 6
There is also optional best \(k\) = 2 3 4 5 6 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.FV.A495.01 2 0.000 0.992 0.00 1.00
#> TCGA.KR.A7K7.01 1 0.000 0.984 1.00 0.00
#> TCGA.BC.A3KF.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A4NV.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A4NQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.CC.A1HT.01 2 0.000 0.992 0.00 1.00
#> TCGA.BD.A3EP.01 2 0.000 0.992 0.00 1.00
#> TCGA.ES.A2HT.01 2 0.000 0.992 0.00 1.00
#> TCGA.CC.A3MA.01 2 0.000 0.992 0.00 1.00
#> TCGA.ZP.A9CV.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AACY.01 1 0.000 0.984 1.00 0.00
#> TCGA.XR.A8TG.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AADW.01 2 0.000 0.992 0.00 1.00
#> TCGA.BC.A10Y.01 1 0.000 0.984 1.00 0.00
#> TCGA.CC.A3MB.01 2 0.000 0.992 0.00 1.00
#> TCGA.ED.A459.01 2 0.000 0.992 0.00 1.00
#> TCGA.PD.A5DF.01 1 0.000 0.984 1.00 0.00
#> TCGA.ED.A5KG.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AAVX.01 2 0.000 0.992 0.00 1.00
#> TCGA.ED.A7PY.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A3A0.01 2 0.000 0.992 0.00 1.00
#> TCGA.RC.A7SF.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AAW0.01 2 0.000 0.992 0.00 1.00
#> TCGA.ED.A66X.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AAC8.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AACM.01 2 0.000 0.992 0.00 1.00
#> TCGA.FV.A3I1.01 2 0.000 0.992 0.00 1.00
#> TCGA.RC.A7S9.01 2 0.000 0.992 0.00 1.00
#> TCGA.ZP.A9D2.01 2 0.242 0.951 0.04 0.96
#> TCGA.G3.A5SL.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A3A2.11 2 0.000 0.992 0.00 1.00
#> TCGA.CC.A3M9.01 2 0.000 0.992 0.00 1.00
#> TCGA.BC.A216.01 1 0.000 0.984 1.00 0.00
#> TCGA.ED.A82E.01 2 0.000 0.992 0.00 1.00
#> TCGA.BC.A10T.11 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A11A.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A73B.01 1 0.634 0.806 0.84 0.16
#> TCGA.DD.AACA.02 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AACA.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A1EH.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AA3A.01 2 0.000 0.992 0.00 1.00
#> TCGA.RG.A7D4.01 2 0.000 0.992 0.00 1.00
#> TCGA.FV.A2QR.11 2 0.000 0.992 0.00 1.00
#> TCGA.G3.A25W.11 2 0.000 0.992 0.00 1.00
#> TCGA.2Y.A9H4.01 1 0.000 0.984 1.00 0.00
#> TCGA.K7.AAU7.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A3A2.01 1 0.000 0.984 1.00 0.00
#> TCGA.EP.A26S.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A1EG.11 2 0.000 0.992 0.00 1.00
#> TCGA.FV.A2QQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.3K.AAZ8.01 1 0.000 0.984 1.00 0.00
#> TCGA.BC.A217.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AADP.01 1 0.000 0.984 1.00 0.00
#> TCGA.CC.5259.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A1EA.01 1 0.000 0.984 1.00 0.00
#> TCGA.CC.A8HU.01 1 0.000 0.984 1.00 0.00
#> TCGA.ES.A2HS.01 2 0.000 0.992 0.00 1.00
#> TCGA.G3.A25W.01 2 0.000 0.992 0.00 1.00
#> TCGA.2V.A95S.01 2 0.000 0.992 0.00 1.00
#> TCGA.2Y.A9GU.01 2 0.000 0.992 0.00 1.00
#> TCGA.RC.A7SB.01 1 0.000 0.984 1.00 0.00
#> TCGA.FV.A4ZP.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AAD3.01 1 0.981 0.284 0.58 0.42
#> TCGA.2Y.A9H9.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AAW2.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A39V.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AADD.01 1 0.000 0.984 1.00 0.00
#> TCGA.CC.A9FW.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AACS.01 2 0.000 0.992 0.00 1.00
#> TCGA.CC.A9FV.01 2 0.000 0.992 0.00 1.00
#> TCGA.G3.A7M7.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A4NK.01 1 0.000 0.984 1.00 0.00
#> TCGA.ED.A97K.01 2 0.000 0.992 0.00 1.00
#> TCGA.T1.A6J8.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AACV.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A4NF.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A3A8.01 1 0.990 0.224 0.56 0.44
#> TCGA.WX.AA46.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A1EL.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AACH.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A119.11 2 0.000 0.992 0.00 1.00
#> TCGA.WQ.A9G7.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A4NO.01 2 0.000 0.992 0.00 1.00
#> TCGA.G3.A7M9.01 2 0.000 0.992 0.00 1.00
#> TCGA.CC.5261.01 2 0.000 0.992 0.00 1.00
#> TCGA.ZS.A9CG.01 1 0.634 0.805 0.84 0.16
#> TCGA.CC.A123.01 2 0.000 0.992 0.00 1.00
#> TCGA.5R.AA1D.01 2 0.000 0.992 0.00 1.00
#> TCGA.BC.A69H.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AAVZ.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AAD0.01 1 0.000 0.984 1.00 0.00
#> TCGA.EP.A2KA.01 2 0.000 0.992 0.00 1.00
#> TCGA.2Y.A9HA.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AACD.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AAE7.01 2 0.981 0.266 0.42 0.58
#> TCGA.BC.A8YO.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AAE2.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AAEG.01 2 0.000 0.992 0.00 1.00
#> TCGA.XR.A8TF.01 1 0.000 0.984 1.00 0.00
#> TCGA.CC.A5UC.01 2 0.000 0.992 0.00 1.00
#> TCGA.KR.A7K0.01 2 0.000 0.992 0.00 1.00
#> TCGA.K7.A5RG.01 2 0.000 0.992 0.00 1.00
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#> TCGA.ED.A627.01 2 0.000 0.992 0.00 1.00
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#> TCGA.DD.A73D.01 1 0.000 0.984 1.00 0.00
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#> TCGA.ZP.A9CZ.01 2 0.000 0.992 0.00 1.00
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#> TCGA.DD.A4NG.01 1 0.141 0.965 0.98 0.02
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#> TCGA.UB.AA0U.01 2 0.925 0.479 0.34 0.66
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#> TCGA.MI.A75C.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A4NJ.01 2 0.000 0.992 0.00 1.00
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#> TCGA.DD.A118.11 2 0.000 0.992 0.00 1.00
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#> TCGA.ZP.A9D1.01 1 0.995 0.157 0.54 0.46
#> TCGA.DD.A73C.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AADU.01 2 0.000 0.992 0.00 1.00
#> TCGA.G3.A25X.01 2 0.000 0.992 0.00 1.00
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#> TCGA.CC.5262.01 2 0.000 0.992 0.00 1.00
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#> TCGA.DD.AAE9.01 1 0.000 0.984 1.00 0.00
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#> TCGA.XR.A8TE.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AACZ.01 2 0.795 0.680 0.24 0.76
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#> TCGA.DD.AACG.01 1 0.000 0.984 1.00 0.00
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#> TCGA.DD.AAE1.01 1 0.000 0.984 1.00 0.00
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#> TCGA.DD.A119.01 2 0.000 0.992 0.00 1.00
#> TCGA.MI.A75I.01 1 0.000 0.984 1.00 0.00
#> TCGA.2Y.A9H1.01 1 0.000 0.984 1.00 0.00
#> TCGA.CC.A8HT.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AADL.01 1 0.000 0.984 1.00 0.00
#> TCGA.XR.A8TC.01 2 0.000 0.992 0.00 1.00
#> TCGA.ED.A7XP.01 2 0.000 0.992 0.00 1.00
#> TCGA.BC.A10W.11 2 0.000 0.992 0.00 1.00
#> TCGA.FV.A23B.11 2 0.000 0.992 0.00 1.00
#> TCGA.5C.A9VH.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AADR.01 1 0.000 0.984 1.00 0.00
#> TCGA.2Y.A9HB.01 2 0.584 0.833 0.14 0.86
#> TCGA.DD.AAE3.01 1 0.000 0.984 1.00 0.00
#> TCGA.G3.A25X.11 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A4NA.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AACI.01 2 0.000 0.992 0.00 1.00
#> TCGA.CC.A9FU.01 1 0.000 0.984 1.00 0.00
#> TCGA.EP.A3RK.01 2 0.000 0.992 0.00 1.00
#> TCGA.CC.A5UD.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AADV.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.AAEE.01 1 0.000 0.984 1.00 0.00
#> TCGA.ZS.A9CF.02 1 0.000 0.984 1.00 0.00
#> TCGA.ZS.A9CF.01 1 0.000 0.984 1.00 0.00
#> TCGA.RC.A6M4.01 1 0.000 0.984 1.00 0.00
#> TCGA.G3.A7M8.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AAVP.01 2 0.000 0.992 0.00 1.00
#> TCGA.CC.5260.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.A4NR.01 2 0.000 0.992 0.00 1.00
#> TCGA.2Y.A9H2.01 2 0.000 0.992 0.00 1.00
#> TCGA.DD.AAE6.01 1 0.000 0.984 1.00 0.00
#> TCGA.G3.AAV2.01 1 0.242 0.946 0.96 0.04
#> TCGA.BC.A10Z.11 2 0.000 0.992 0.00 1.00
#> TCGA.ZP.A9CY.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A115.01 1 0.000 0.984 1.00 0.00
#> TCGA.DD.A39Y.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.FV.A495.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.KR.A7K7.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.BC.A3KF.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A4NV.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NQ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A1HT.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BD.A3EP.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ES.A2HT.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A3MA.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZP.A9CV.01 3 0.2947 0.8671 0.02 0.06 0.92
#> TCGA.DD.AACY.01 3 0.0892 0.8937 0.02 0.00 0.98
#> TCGA.XR.A8TG.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10Y.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A3MB.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A459.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.PD.A5DF.01 1 0.0892 0.9540 0.98 0.02 0.00
#> TCGA.ED.A5KG.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAVX.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A7PY.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A3A0.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.RC.A7SF.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAW0.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A66X.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAC8.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AACM.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A3I1.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.RC.A7S9.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZP.A9D2.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.G3.A5SL.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A3A2.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A3M9.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A216.01 1 0.4555 0.7403 0.80 0.00 0.20
#> TCGA.ED.A82E.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10T.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A11A.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A73B.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AACA.02 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AACA.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.RG.A7D4.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A2QR.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A25W.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9H4.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.K7.AAU7.01 3 0.0892 0.8966 0.00 0.02 0.98
#> TCGA.DD.A3A2.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.EP.A26S.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A1EG.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A2QQ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.3K.AAZ8.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.BC.A217.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AADP.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.5259.01 3 0.0892 0.8966 0.00 0.02 0.98
#> TCGA.DD.A1EA.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A8HU.01 1 0.6280 0.1332 0.54 0.00 0.46
#> TCGA.ES.A2HS.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A25W.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2V.A95S.01 3 0.5706 0.5698 0.00 0.32 0.68
#> TCGA.2Y.A9GU.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.RC.A7SB.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.FV.A4ZP.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAD3.01 2 0.5560 0.5456 0.30 0.70 0.00
#> TCGA.2Y.A9H9.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAW2.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A39V.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AADD.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A9FW.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AACS.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A9FV.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A7M7.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NK.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.ED.A97K.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.T1.A6J8.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AACV.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A4NF.01 3 0.5216 0.6379 0.26 0.00 0.74
#> TCGA.DD.A3A8.01 3 0.2066 0.8714 0.00 0.06 0.94
#> TCGA.WX.AA46.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EL.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AACH.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.A119.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.WQ.A9G7.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NO.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A7M9.01 3 0.0892 0.8966 0.00 0.02 0.98
#> TCGA.CC.5261.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZS.A9CG.01 3 0.2537 0.8550 0.00 0.08 0.92
#> TCGA.CC.A123.01 3 0.3340 0.8155 0.00 0.12 0.88
#> TCGA.5R.AA1D.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A69H.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AAVZ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAD0.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.EP.A2KA.01 2 0.0892 0.9740 0.00 0.98 0.02
#> TCGA.2Y.A9HA.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AACD.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAE7.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A8YO.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAE2.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.XR.A8TF.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.KR.A7K0.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.K7.A5RG.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.AAV4.01 3 0.4796 0.6928 0.22 0.00 0.78
#> TCGA.ED.A627.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AACX.01 3 0.5016 0.6631 0.24 0.00 0.76
#> TCGA.DD.AAVR.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9H3.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.MR.A8JO.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAEK.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EE.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AACL.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.KR.A7K8.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A115.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A3I0.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A11B.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A5SM.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A3CH.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.AAUZ.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAVV.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NP.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.LG.A6GG.01 1 0.5397 0.6064 0.72 0.00 0.28
#> TCGA.DD.AAE4.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.HP.A5MZ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A5SI.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.AAV1.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EF.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10Y.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACB.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A9FS.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A5W4.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.2Y.A9H5.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BW.A5NO.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.KR.A7K2.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AADM.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.CC.5258.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BW.A5NQ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9GX.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.LG.A9QC.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A11C.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BC.A10Q.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.4R.AA8I.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.FV.A4ZQ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.4073.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADQ.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AAD2.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.WQ.AB4B.01 3 0.7515 0.6451 0.22 0.10 0.68
#> TCGA.RC.A7SH.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10T.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A11A.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A39W.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.RC.A6M5.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.UB.A7MD.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.WX.AA44.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.5264.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AADE.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.QA.A7B7.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A3A6.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.5263.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AACW.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A7M6.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.GJ.A6C0.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BC.4072.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A116.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.MR.A520.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.EP.A12J.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADK.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A73D.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.ES.A2HS.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A8HS.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A6UC.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A7IH.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BC.A69I.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.K7.A6G5.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10U.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A4NG.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BD.A2L6.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.UB.A7MC.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.UB.AA0U.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NB.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A8O6.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACQ.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.AAV6.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.A3A4.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.UB.A7MF.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EK.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A114.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ES.A2HT.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A39Z.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10Z.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EI.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACU.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.MI.A75C.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.A4NJ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A25V.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10X.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A496.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4ND.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A11D.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAD5.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AAE8.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A118.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAEH.01 1 0.2959 0.8279 0.90 0.10 0.00
#> TCGA.G3.A25U.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.2Y.A9GW.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZS.A9CE.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.NI.A4U2.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.5C.AAPD.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAVW.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.EP.A2KC.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.MI.A75E.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A116.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.GJ.A9DB.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AACC.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A3R3.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.HP.A5N0.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.K7.A5RF.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.YA.A8S7.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACF.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EC.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAE0.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.AAV0.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.XR.A8TD.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EE.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A5UE.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AACJ.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.AAV5.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A1EB.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A7IJ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAVS.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A11B.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.A4NS.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A3A3.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAW3.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.A5SK.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A110.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A3A7.01 3 0.2959 0.8371 0.00 0.10 0.90
#> TCGA.BC.A10R.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A112.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACN.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EF.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A3MC.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A113.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EJ.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A25S.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A73A.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A7IG.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.AAV3.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1ED.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.MI.A75H.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A73E.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.2Y.A9H7.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.CC.A8HV.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1E9.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAD6.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BC.A10S.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A11C.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10Q.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.LG.A9QD.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A3A1.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A73F.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A7IK.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AADO.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A7II.01 3 0.0892 0.8966 0.00 0.02 0.98
#> TCGA.RC.A6M3.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A39W.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10W.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.NI.A8LF.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A23B.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.AADC.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A3CJ.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.ZP.A9D1.01 2 0.5835 0.4396 0.00 0.66 0.34
#> TCGA.DD.A73C.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADU.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A25X.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACP.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.UB.A7MB.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADG.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.RC.A6M6.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.A4NH.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.EP.A12J.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.CC.5262.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADJ.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.ZS.A9CD.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAE9.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BD.A2L6.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAEI.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.A25T.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9GV.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADS.01 1 0.2066 0.9224 0.94 0.00 0.06
#> TCGA.DD.A114.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A39Z.01 3 0.2959 0.8345 0.10 0.00 0.90
#> TCGA.UB.A7MA.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.EP.A2KB.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAEA.01 1 0.3340 0.8511 0.88 0.00 0.12
#> TCGA.UB.AA0V.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BD.A3EP.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A3R2.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.2Y.A9GY.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.XR.A8TE.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACZ.01 3 0.6045 0.4428 0.00 0.38 0.62
#> TCGA.ED.A4XI.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACG.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.BW.A5NP.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAC9.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAE1.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.A11D.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AADY.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZP.A9D4.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAED.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACK.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAVQ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EI.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A118.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACO.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NL.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.EP.A3JL.01 2 0.4796 0.6952 0.00 0.78 0.22
#> TCGA.DD.AAD8.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.5R.AA1C.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.A3CI.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A3CK.01 1 0.5216 0.5296 0.74 0.26 0.00
#> TCGA.2Y.A9H0.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.MI.A75G.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.A5SJ.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A216.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.5R.AAAM.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A3KG.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.DD.A1EH.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9GS.01 1 0.2537 0.8610 0.92 0.08 0.00
#> TCGA.BD.A3ER.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10X.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A2QR.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A1EC.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A7IF.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACE.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAVY.01 2 0.4796 0.6881 0.22 0.78 0.00
#> TCGA.EP.A26S.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EG.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A7PX.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EB.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADN.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A3A3.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A39X.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A25Z.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BC.A10U.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A3A5.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.BC.A110.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10R.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.ED.A7XO.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.AAV7.01 3 0.6192 0.3408 0.00 0.42 0.58
#> TCGA.GJ.A3OU.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADB.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.RC.A7SK.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A4NE.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A39V.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AACT.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZP.A9D0.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADF.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A1EJ.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAVU.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.G3.A3CG.01 3 0.2066 0.8714 0.00 0.06 0.94
#> TCGA.DD.AAW1.01 1 0.0892 0.9644 0.98 0.00 0.02
#> TCGA.O8.A75V.01 3 0.1529 0.8849 0.00 0.04 0.96
#> TCGA.DD.A3A9.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1ED.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.WX.AA47.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A4NI.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9H8.01 3 0.2537 0.8554 0.00 0.08 0.92
#> TCGA.DD.A1E9.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9GT.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10S.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.UB.A7ME.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A1EL.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A3A1.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A119.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.MI.A75I.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.2Y.A9H1.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.CC.A8HT.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADL.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.XR.A8TC.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ED.A7XP.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.BC.A10W.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.FV.A23B.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADR.01 3 0.1529 0.8825 0.04 0.00 0.96
#> TCGA.2Y.A9HB.01 2 0.0892 0.9740 0.00 0.98 0.02
#> TCGA.DD.AAE3.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.G3.A25X.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.A4NA.01 3 0.2959 0.8371 0.00 0.10 0.90
#> TCGA.DD.AACI.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A9FU.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.EP.A3RK.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.A5UD.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.AAEE.01 3 0.0892 0.8941 0.02 0.00 0.98
#> TCGA.ZS.A9CF.02 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.ZS.A9CF.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.RC.A6M4.01 3 0.5706 0.5225 0.32 0.00 0.68
#> TCGA.G3.A7M8.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAVP.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.CC.5260.01 3 0.6309 0.0791 0.00 0.50 0.50
#> TCGA.DD.A4NR.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.2Y.A9H2.01 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.DD.AAE6.01 3 0.0000 0.9037 0.00 0.00 1.00
#> TCGA.G3.AAV2.01 3 0.9684 0.3890 0.26 0.28 0.46
#> TCGA.BC.A10Z.11 2 0.0000 0.9952 0.00 1.00 0.00
#> TCGA.ZP.A9CY.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.0000 0.9831 1.00 0.00 0.00
#> TCGA.DD.A39Y.01 1 0.0000 0.9831 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.FV.A495.01 4 0.1211 0.912 0.00 0.04 0.00 0.96
#> TCGA.KR.A7K7.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.BC.A3KF.01 1 0.2011 0.888 0.92 0.00 0.00 0.08
#> TCGA.DD.A4NV.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.A4NQ.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.A1HT.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BD.A3EP.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ES.A2HT.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.A3MA.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9CV.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AACY.01 4 0.2345 0.860 0.00 0.00 0.10 0.90
#> TCGA.XR.A8TG.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A10Y.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.CC.A3MB.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.ED.A459.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.PD.A5DF.01 4 0.1211 0.917 0.04 0.00 0.00 0.96
#> TCGA.ED.A5KG.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVX.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.ED.A7PY.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A0.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.RC.A7SF.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AAW0.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ED.A66X.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AAC8.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.DD.AACM.01 4 0.1211 0.912 0.00 0.04 0.00 0.96
#> TCGA.FV.A3I1.01 4 0.1211 0.912 0.00 0.04 0.00 0.96
#> TCGA.RC.A7S9.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9D2.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.G3.A5SL.01 4 0.0707 0.933 0.02 0.00 0.00 0.98
#> TCGA.DD.A3A2.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.A3M9.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A216.01 1 0.1913 0.927 0.94 0.00 0.04 0.02
#> TCGA.ED.A82E.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A10T.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A11A.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.A73B.01 3 0.0707 0.961 0.00 0.00 0.98 0.02
#> TCGA.DD.AACA.02 1 0.4790 0.387 0.62 0.00 0.00 0.38
#> TCGA.DD.AACA.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.RG.A7D4.01 2 0.0707 0.971 0.00 0.98 0.00 0.02
#> TCGA.FV.A2QR.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.G3.A25W.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H4.01 1 0.4277 0.598 0.72 0.00 0.00 0.28
#> TCGA.K7.AAU7.01 3 0.1637 0.901 0.00 0.06 0.94 0.00
#> TCGA.DD.A3A2.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.EP.A26S.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.FV.A2QQ.01 4 0.2647 0.801 0.00 0.12 0.00 0.88
#> TCGA.3K.AAZ8.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.BC.A217.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
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#> TCGA.2Y.A9GZ.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
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#> TCGA.DD.A1EE.01 1 0.0707 0.957 0.98 0.00 0.00 0.02
#> TCGA.DD.AACL.01 2 0.0707 0.971 0.00 0.98 0.00 0.02
#> TCGA.KR.A7K8.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.DD.A4NP.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.LG.A6GG.01 1 0.1637 0.923 0.94 0.00 0.06 0.00
#> TCGA.DD.AAE4.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.G3.A5SI.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.G3.AAV1.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EF.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.DD.AACB.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.CC.A9FS.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A5W4.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
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#> TCGA.KR.A7K2.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
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#> TCGA.CC.5258.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BW.A5NQ.01 2 0.3400 0.764 0.00 0.82 0.00 0.18
#> TCGA.2Y.A9GX.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.DD.A11C.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.4R.AA8I.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.FV.A4ZQ.01 4 0.2921 0.764 0.00 0.14 0.00 0.86
#> TCGA.BC.4073.01 2 0.0707 0.971 0.00 0.98 0.00 0.02
#> TCGA.DD.AADQ.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD2.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.RC.A7SH.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A10T.01 4 0.3801 0.704 0.22 0.00 0.00 0.78
#> TCGA.DD.A11A.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A39W.01 4 0.0707 0.930 0.00 0.02 0.00 0.98
#> TCGA.RC.A6M5.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.UB.A7MD.01 4 0.1211 0.912 0.00 0.04 0.00 0.96
#> TCGA.WX.AA44.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.G3.A7M6.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.GJ.A6C0.01 4 0.4134 0.648 0.26 0.00 0.00 0.74
#> TCGA.BC.4072.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A116.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.DD.AADK.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A73D.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
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#> TCGA.ZP.A9CZ.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.A8HS.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
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#> TCGA.BC.A69I.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.K7.A6G5.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
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#> TCGA.UB.A7MC.01 4 0.0707 0.933 0.02 0.00 0.00 0.98
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#> TCGA.DD.AACQ.01 4 0.0707 0.933 0.02 0.00 0.00 0.98
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#> TCGA.DD.A1EK.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
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#> TCGA.DD.AACU.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.MI.A75C.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.DD.A4NJ.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.G3.A25V.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A10X.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.FV.A496.01 4 0.1637 0.884 0.00 0.06 0.00 0.94
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#> TCGA.DD.AAD5.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
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#> TCGA.FV.A3R3.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.HP.A5N0.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
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#> TCGA.DD.A1EC.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.DD.A1EE.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.A5UE.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
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#> TCGA.CC.A7IJ.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.DD.A3A7.01 4 0.2921 0.815 0.00 0.00 0.14 0.86
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#> TCGA.RC.A6M3.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A39W.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
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#> TCGA.FV.A23B.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.DD.AADC.01 2 0.4855 0.316 0.00 0.60 0.00 0.40
#> TCGA.G3.A3CJ.01 1 0.2647 0.839 0.88 0.00 0.00 0.12
#> TCGA.ZP.A9D1.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.A73C.01 4 0.1211 0.909 0.00 0.04 0.00 0.96
#> TCGA.DD.AADU.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.G3.A25X.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AACP.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.UB.A7MB.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AADG.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.EP.A12J.01 4 0.2647 0.838 0.00 0.00 0.12 0.88
#> TCGA.CC.5262.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AADJ.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.ZS.A9CD.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AAE9.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.BD.A2L6.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEI.01 4 0.4948 0.234 0.44 0.00 0.00 0.56
#> TCGA.G3.A25T.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9GV.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AADS.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.A114.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A39Z.01 4 0.3037 0.844 0.02 0.00 0.10 0.88
#> TCGA.UB.A7MA.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.EP.A2KB.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AAEA.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.UB.AA0V.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BD.A3EP.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.FV.A3R2.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9GY.01 4 0.1211 0.912 0.00 0.04 0.00 0.96
#> TCGA.XR.A8TE.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AACZ.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.ED.A4XI.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AACG.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.BW.A5NP.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AAC9.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE1.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.DD.A11D.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AADY.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9D4.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AAED.01 4 0.1637 0.885 0.00 0.06 0.00 0.94
#> TCGA.DD.AACK.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EI.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A118.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NL.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.EP.A3JL.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AAD8.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.5R.AA1C.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.G3.A3CI.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.G3.A3CK.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9H0.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.MI.A75G.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.G3.A5SJ.01 4 0.1211 0.912 0.00 0.04 0.00 0.96
#> TCGA.BC.A216.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.5R.AAAM.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.BC.A3KG.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EH.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9GS.01 4 0.1211 0.917 0.04 0.00 0.00 0.96
#> TCGA.BD.A3ER.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.BC.A10X.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.FV.A2QR.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IF.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AACE.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVY.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.EP.A26S.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EG.01 4 0.1211 0.912 0.00 0.04 0.00 0.96
#> TCGA.ED.A7PX.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EB.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AADN.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A3.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A39X.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.G3.A25Z.01 1 0.0707 0.957 0.98 0.00 0.00 0.02
#> TCGA.BC.A10U.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A5.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A10R.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.ED.A7XO.01 2 0.1211 0.949 0.00 0.96 0.00 0.04
#> TCGA.G3.AAV7.01 2 0.2011 0.909 0.00 0.92 0.08 0.00
#> TCGA.GJ.A3OU.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AADB.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.RC.A7SK.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NE.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A39V.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AACT.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9D0.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AADF.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVU.01 3 0.5062 0.561 0.02 0.00 0.68 0.30
#> TCGA.G3.A3CG.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AAW1.01 4 0.4994 0.071 0.48 0.00 0.00 0.52
#> TCGA.O8.A75V.01 3 0.3801 0.714 0.00 0.00 0.78 0.22
#> TCGA.DD.A3A9.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A1ED.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.WX.AA47.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9H8.01 2 0.4790 0.393 0.00 0.62 0.38 0.00
#> TCGA.DD.A1E9.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9GT.01 4 0.2011 0.860 0.00 0.08 0.00 0.92
#> TCGA.BC.A10S.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EL.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A1.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A119.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.MI.A75I.01 4 0.4522 0.545 0.32 0.00 0.00 0.68
#> TCGA.2Y.A9H1.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.CC.A8HT.01 4 0.4713 0.396 0.00 0.36 0.00 0.64
#> TCGA.DD.AADL.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TC.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ED.A7XP.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.BC.A10W.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.FV.A23B.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AADR.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9HB.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AAE3.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.G3.A25X.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NA.01 2 0.3975 0.686 0.00 0.76 0.24 0.00
#> TCGA.DD.AACI.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.CC.A9FU.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.EP.A3RK.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.A5UD.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.AADV.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 3 0.0707 0.961 0.02 0.00 0.98 0.00
#> TCGA.ZS.A9CF.02 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.RC.A6M4.01 1 0.3400 0.778 0.82 0.00 0.18 0.00
#> TCGA.G3.A7M8.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVP.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.CC.5260.01 2 0.1211 0.953 0.00 0.96 0.04 0.00
#> TCGA.DD.A4NR.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H2.01 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE6.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.G3.AAV2.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Z.11 2 0.0000 0.992 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9CY.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
#> TCGA.DD.A115.01 1 0.0000 0.977 1.00 0.00 0.00 0.00
#> TCGA.DD.A39Y.01 4 0.0000 0.948 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FV.A495.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.KR.A7K7.01 3 0.0609 0.96260 0.00 0.00 0.98 0.02 0.00
#> TCGA.BC.A3KF.01 1 0.3037 0.84400 0.86 0.00 0.00 0.04 0.10
#> TCGA.DD.A4NV.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A4NQ.01 4 0.3109 0.62408 0.00 0.20 0.00 0.80 0.00
#> TCGA.CC.A1HT.01 4 0.4182 0.31715 0.00 0.40 0.00 0.60 0.00
#> TCGA.BD.A3EP.01 4 0.2929 0.65044 0.00 0.18 0.00 0.82 0.00
#> TCGA.ES.A2HT.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A3MA.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9CV.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACY.01 4 0.6133 0.29196 0.00 0.00 0.16 0.54 0.30
#> TCGA.XR.A8TG.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MB.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.ED.A459.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.PD.A5DF.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A5KG.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.ED.A7PY.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A0.01 5 0.1648 0.83984 0.00 0.02 0.00 0.04 0.94
#> TCGA.RC.A7SF.01 1 0.4262 0.20122 0.56 0.00 0.00 0.44 0.00
#> TCGA.DD.AAW0.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A66X.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAC8.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACM.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.FV.A3I1.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.RC.A7S9.01 2 0.1410 0.91257 0.00 0.94 0.00 0.00 0.06
#> TCGA.ZP.A9D2.01 3 0.0609 0.96260 0.00 0.00 0.98 0.02 0.00
#> TCGA.G3.A5SL.01 1 0.6555 0.16636 0.46 0.00 0.00 0.32 0.22
#> TCGA.DD.A3A2.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 2 0.3796 0.56778 0.00 0.70 0.00 0.30 0.00
#> TCGA.BC.A216.01 4 0.1732 0.82273 0.08 0.00 0.00 0.92 0.00
#> TCGA.ED.A82E.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10T.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.A73B.01 3 0.1732 0.89552 0.00 0.00 0.92 0.08 0.00
#> TCGA.DD.AACA.02 5 0.2929 0.67185 0.18 0.00 0.00 0.00 0.82
#> TCGA.DD.AACA.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.RG.A7D4.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.FV.A2QR.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H4.01 4 0.3109 0.68842 0.20 0.00 0.00 0.80 0.00
#> TCGA.K7.AAU7.01 4 0.2280 0.79940 0.00 0.00 0.12 0.88 0.00
#> TCGA.DD.A3A2.01 5 0.4126 0.39222 0.00 0.00 0.00 0.38 0.62
#> TCGA.EP.A26S.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A2QQ.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.3K.AAZ8.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A217.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADP.01 5 0.3109 0.71421 0.00 0.00 0.00 0.20 0.80
#> TCGA.CC.5259.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.A1EA.01 1 0.2280 0.83296 0.88 0.00 0.00 0.12 0.00
#> TCGA.CC.A8HU.01 1 0.2516 0.82227 0.86 0.00 0.14 0.00 0.00
#> TCGA.ES.A2HS.01 5 0.0609 0.84265 0.00 0.00 0.00 0.02 0.98
#> TCGA.G3.A25W.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.2V.A95S.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9GU.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SB.01 4 0.4307 -0.00998 0.50 0.00 0.00 0.50 0.00
#> TCGA.FV.A4ZP.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.AAD3.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9H9.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW2.01 1 0.2020 0.87552 0.90 0.00 0.00 0.00 0.10
#> TCGA.DD.A39V.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADD.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FW.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACS.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.CC.A9FV.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 2 0.4287 0.15479 0.00 0.54 0.00 0.46 0.00
#> TCGA.DD.A4NK.01 5 0.6133 0.40510 0.16 0.00 0.00 0.30 0.54
#> TCGA.ED.A97K.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.T1.A6J8.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACV.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NF.01 4 0.3983 0.46941 0.00 0.00 0.00 0.66 0.34
#> TCGA.DD.A3A8.01 4 0.2280 0.79904 0.00 0.00 0.00 0.88 0.12
#> TCGA.WX.AA46.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 1 0.2280 0.83555 0.88 0.00 0.00 0.12 0.00
#> TCGA.DD.AACH.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A119.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NO.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.G3.A7M9.01 3 0.2732 0.78442 0.00 0.00 0.84 0.16 0.00
#> TCGA.CC.5261.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZS.A9CG.01 4 0.3796 0.55413 0.00 0.00 0.00 0.70 0.30
#> TCGA.CC.A123.01 5 0.3424 0.70063 0.00 0.00 0.00 0.24 0.76
#> TCGA.5R.AA1D.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVZ.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAD0.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KA.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9HA.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACD.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAE7.01 4 0.1043 0.85903 0.00 0.00 0.00 0.96 0.04
#> TCGA.BC.A8YO.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE2.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.KR.A7K0.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.K7.A5RG.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV4.01 1 0.5382 0.53329 0.64 0.00 0.26 0.00 0.10
#> TCGA.ED.A627.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACX.01 5 0.7672 0.26991 0.32 0.00 0.12 0.12 0.44
#> TCGA.DD.AAVR.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H3.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.MR.A8JO.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EE.01 1 0.2020 0.87552 0.90 0.00 0.00 0.00 0.10
#> TCGA.DD.AACL.01 4 0.1043 0.84485 0.00 0.04 0.00 0.96 0.00
#> TCGA.KR.A7K8.01 4 0.3983 0.41188 0.00 0.34 0.00 0.66 0.00
#> TCGA.DD.A115.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11B.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 4 0.2020 0.80742 0.00 0.00 0.00 0.90 0.10
#> TCGA.G3.A3CH.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAUZ.01 1 0.3109 0.73149 0.80 0.00 0.00 0.20 0.00
#> TCGA.DD.AAVV.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NP.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 1 0.1043 0.92242 0.96 0.00 0.04 0.00 0.00
#> TCGA.DD.AAE4.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A5SI.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV1.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.A1EF.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FS.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A5W4.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H5.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BW.A5NO.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADM.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.5258.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BW.A5NQ.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9GX.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.LG.A9QC.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11C.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.4R.AA8I.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A4ZQ.01 5 0.2077 0.82235 0.00 0.04 0.00 0.04 0.92
#> TCGA.BC.4073.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADQ.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD2.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.RC.A7SH.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10T.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A11A.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39W.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.RC.A6M5.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.UB.A7MD.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.WX.AA44.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.5264.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADE.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.AAD1.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.QA.A7B7.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A6.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.5263.01 4 0.2020 0.80395 0.10 0.00 0.00 0.90 0.00
#> TCGA.DD.AACW.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A7M6.01 4 0.2929 0.71365 0.18 0.00 0.00 0.82 0.00
#> TCGA.GJ.A6C0.01 4 0.0609 0.86965 0.02 0.00 0.00 0.98 0.00
#> TCGA.BC.4072.01 4 0.2280 0.74113 0.00 0.12 0.00 0.88 0.00
#> TCGA.DD.A116.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.MR.A520.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A12J.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADK.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HS.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A8HS.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IH.01 1 0.1043 0.92608 0.96 0.00 0.00 0.00 0.04
#> TCGA.BC.A69I.01 5 0.0000 0.82961 0.00 0.00 0.00 0.00 1.00
#> TCGA.K7.A6G5.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.A10U.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.BD.A2L6.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.UB.A7MC.01 5 0.0000 0.82961 0.00 0.00 0.00 0.00 1.00
#> TCGA.UB.AA0U.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A4NB.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A8O6.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACQ.01 5 0.0609 0.84199 0.00 0.00 0.00 0.02 0.98
#> TCGA.G3.AAV6.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A4.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.UB.A7MF.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EK.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75C.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NJ.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.G3.A25V.01 2 0.3274 0.70818 0.00 0.78 0.00 0.22 0.00
#> TCGA.BC.A10X.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A496.01 5 0.2077 0.82235 0.00 0.04 0.00 0.04 0.92
#> TCGA.DD.A4ND.01 4 0.3684 0.49661 0.00 0.28 0.00 0.72 0.00
#> TCGA.DD.A11D.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAD5.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE8.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A118.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEH.01 5 0.4227 0.32365 0.00 0.00 0.00 0.42 0.58
#> TCGA.G3.A25U.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GW.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZS.A9CE.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.NI.A4U2.01 4 0.0609 0.87099 0.00 0.00 0.00 0.98 0.02
#> TCGA.5C.AAPD.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAVW.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A2KC.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75E.01 2 0.2280 0.84114 0.00 0.88 0.00 0.12 0.00
#> TCGA.DD.A116.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.GJ.A9DB.01 4 0.4126 0.37490 0.38 0.00 0.00 0.62 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACC.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.HP.A5N0.01 5 0.3684 0.65411 0.00 0.00 0.00 0.28 0.72
#> TCGA.K7.A5RF.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.YA.A8S7.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACF.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.A1EC.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 1 0.1732 0.89365 0.92 0.00 0.00 0.00 0.08
#> TCGA.XR.A8TD.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EE.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A5UE.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACJ.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV5.01 5 0.0000 0.82961 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EB.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11B.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NS.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAW3.01 1 0.1043 0.92621 0.96 0.00 0.00 0.00 0.04
#> TCGA.G3.A5SK.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.A110.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A7.01 4 0.3641 0.74496 0.00 0.00 0.12 0.82 0.06
#> TCGA.BC.A10R.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A112.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A113.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A25S.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IG.01 2 0.1043 0.93296 0.00 0.96 0.00 0.04 0.00
#> TCGA.G3.AAV3.01 5 0.3291 0.72260 0.00 0.12 0.00 0.04 0.84
#> TCGA.DD.A1ED.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.MI.A75H.01 4 0.0609 0.87099 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.A73E.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A8HV.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD6.01 1 0.0609 0.93976 0.98 0.00 0.00 0.00 0.02
#> TCGA.BC.A10S.01 5 0.0609 0.84265 0.00 0.00 0.00 0.02 0.98
#> TCGA.DD.A11C.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.LG.A9QD.01 2 0.3983 0.48503 0.00 0.66 0.00 0.34 0.00
#> TCGA.DD.A3A1.01 4 0.4302 0.07074 0.48 0.00 0.00 0.52 0.00
#> TCGA.DD.A73F.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.CC.A7IK.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADO.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7II.01 3 0.2516 0.80867 0.00 0.00 0.86 0.14 0.00
#> TCGA.RC.A6M3.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39W.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.NI.A8LF.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A23B.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADC.01 5 0.4254 0.56933 0.00 0.22 0.00 0.04 0.74
#> TCGA.G3.A3CJ.01 1 0.3561 0.66890 0.74 0.00 0.00 0.00 0.26
#> TCGA.ZP.A9D1.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A73C.01 5 0.4527 0.52321 0.00 0.26 0.00 0.04 0.70
#> TCGA.DD.AADU.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.G3.A25X.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACP.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MB.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.AADG.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 3 0.0609 0.96260 0.00 0.00 0.98 0.02 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A12J.01 4 0.6200 0.23261 0.00 0.00 0.16 0.52 0.32
#> TCGA.CC.5262.01 4 0.3109 0.62408 0.00 0.20 0.00 0.80 0.00
#> TCGA.DD.AADJ.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZS.A9CD.01 5 0.3796 0.61634 0.00 0.00 0.00 0.30 0.70
#> TCGA.DD.AAE9.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A2L6.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEI.01 4 0.2020 0.80121 0.10 0.00 0.00 0.90 0.00
#> TCGA.G3.A25T.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9GV.01 5 0.3561 0.68256 0.00 0.00 0.00 0.26 0.74
#> TCGA.DD.AADS.01 4 0.2280 0.80531 0.00 0.00 0.00 0.88 0.12
#> TCGA.DD.A114.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.01 5 0.7125 0.13259 0.02 0.00 0.22 0.38 0.38
#> TCGA.UB.A7MA.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A2KB.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.AAEA.01 4 0.3424 0.61832 0.00 0.00 0.00 0.76 0.24
#> TCGA.UB.AA0V.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BD.A3EP.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A3R2.01 4 0.1732 0.83553 0.00 0.00 0.00 0.92 0.08
#> TCGA.2Y.A9GY.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.XR.A8TE.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACZ.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A4XI.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACG.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.BW.A5NP.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAC9.01 2 0.1043 0.93376 0.00 0.96 0.00 0.00 0.04
#> TCGA.DD.AAE1.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A11D.01 1 0.1410 0.89988 0.94 0.00 0.00 0.06 0.00
#> TCGA.DD.AADY.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9D4.01 1 0.2020 0.87552 0.90 0.00 0.00 0.00 0.10
#> TCGA.DD.AAED.01 5 0.2077 0.82235 0.00 0.04 0.00 0.04 0.92
#> TCGA.DD.AACK.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A118.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A3JL.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD8.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1C.01 5 0.2331 0.79731 0.02 0.00 0.00 0.08 0.90
#> TCGA.G3.A3CI.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 4 0.4060 0.39343 0.00 0.00 0.00 0.64 0.36
#> TCGA.2Y.A9H0.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75G.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SJ.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.A216.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 4 0.1732 0.82406 0.00 0.00 0.00 0.92 0.08
#> TCGA.BC.A3KG.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EH.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9GS.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.BD.A3ER.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.BC.A10X.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A2QR.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IF.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACE.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVY.01 5 0.0000 0.82961 0.00 0.00 0.00 0.00 1.00
#> TCGA.EP.A26S.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A7PX.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADN.01 4 0.0609 0.87135 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.A3A3.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A25Z.01 4 0.3895 0.50979 0.32 0.00 0.00 0.68 0.00
#> TCGA.BC.A10U.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A5.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10R.01 3 0.0609 0.96260 0.00 0.00 0.98 0.02 0.00
#> TCGA.ED.A7XO.01 4 0.1043 0.84485 0.00 0.04 0.00 0.96 0.00
#> TCGA.G3.AAV7.01 2 0.5173 0.05326 0.00 0.50 0.04 0.46 0.00
#> TCGA.GJ.A3OU.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADB.01 5 0.1732 0.82970 0.00 0.00 0.00 0.08 0.92
#> TCGA.RC.A7SK.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NE.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39V.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACT.01 2 0.3895 0.52871 0.00 0.68 0.00 0.32 0.00
#> TCGA.ZP.A9D0.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADF.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVU.01 5 0.4227 0.23313 0.00 0.00 0.42 0.00 0.58
#> TCGA.G3.A3CG.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAW1.01 1 0.5579 0.43212 0.60 0.00 0.00 0.10 0.30
#> TCGA.O8.A75V.01 4 0.0609 0.87225 0.00 0.00 0.02 0.98 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 5 0.2020 0.82425 0.00 0.00 0.00 0.10 0.90
#> TCGA.2Y.A9H8.01 2 0.5700 0.41478 0.00 0.60 0.12 0.28 0.00
#> TCGA.DD.A1E9.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9GT.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.A10S.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A119.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.MI.A75I.01 4 0.0609 0.86965 0.02 0.00 0.00 0.98 0.00
#> TCGA.2Y.A9H1.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.CC.A8HT.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADL.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TC.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A7XP.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10W.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADR.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9HB.01 4 0.1410 0.84345 0.00 0.00 0.00 0.94 0.06
#> TCGA.DD.AAE3.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25X.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NA.01 2 0.5861 0.10816 0.00 0.50 0.10 0.40 0.00
#> TCGA.DD.AACI.01 4 0.3796 0.49924 0.00 0.00 0.00 0.70 0.30
#> TCGA.CC.A9FU.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A3RK.01 2 0.4126 0.39315 0.00 0.62 0.00 0.38 0.00
#> TCGA.CC.A5UD.01 5 0.1043 0.85196 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.AADV.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 3 0.1043 0.93415 0.04 0.00 0.96 0.00 0.00
#> TCGA.ZS.A9CF.02 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M4.01 1 0.4558 0.69563 0.74 0.00 0.18 0.00 0.08
#> TCGA.G3.A7M8.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 2 0.5394 0.20587 0.00 0.54 0.06 0.40 0.00
#> TCGA.DD.A4NR.01 2 0.4182 0.33428 0.00 0.60 0.00 0.40 0.00
#> TCGA.2Y.A9H2.01 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAE6.01 3 0.0000 0.97777 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.AAV2.01 5 0.0000 0.82961 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Z.11 2 0.0000 0.97296 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 4 0.0000 0.88231 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A115.01 1 0.0000 0.95269 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Y.01 4 0.0609 0.87128 0.00 0.00 0.00 0.98 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FV.A495.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.KR.A7K7.01 3 0.0547 0.9288 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BC.A3KF.01 6 0.1267 0.8503 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.DD.A4NV.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.DD.A4NQ.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CC.A1HT.01 4 0.0937 0.8708 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.BD.A3EP.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.ES.A2HT.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MA.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CV.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AACY.01 6 0.0000 0.8568 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.XR.A8TG.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MB.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A459.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.PD.A5DF.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A5KG.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A7PY.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A0.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.RC.A7SF.01 1 0.3409 0.5785 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.DD.AAW0.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66X.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC8.01 3 0.0937 0.9248 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DD.AACM.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FV.A3I1.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A7S9.01 2 0.3198 0.6407 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.ZP.A9D2.01 3 0.1480 0.9131 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.G3.A5SL.01 6 0.2728 0.8170 0.10 0.00 0.00 0.04 0.00 0.86
#> TCGA.DD.A3A2.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 4 0.3756 0.3449 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.BC.A216.01 4 0.2631 0.7056 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.ED.A82E.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10T.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A73B.01 3 0.4282 0.4122 0.00 0.00 0.56 0.02 0.00 0.42
#> TCGA.DD.AACA.02 5 0.5120 0.3271 0.12 0.00 0.00 0.00 0.60 0.28
#> TCGA.DD.AACA.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RG.A7D4.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.FV.A2QR.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H4.01 4 0.3916 0.4964 0.30 0.00 0.00 0.68 0.00 0.02
#> TCGA.K7.AAU7.01 4 0.1092 0.8866 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.DD.A3A2.01 6 0.3523 0.7655 0.00 0.00 0.00 0.04 0.18 0.78
#> TCGA.EP.A26S.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A2QQ.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.3K.AAZ8.01 3 0.2260 0.8595 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.BC.A217.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADP.01 6 0.2793 0.7587 0.00 0.00 0.00 0.00 0.20 0.80
#> TCGA.CC.5259.01 5 0.0547 0.8660 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.A1EA.01 1 0.3045 0.8240 0.84 0.00 0.00 0.06 0.00 0.10
#> TCGA.CC.A8HU.01 1 0.3660 0.7297 0.78 0.00 0.06 0.00 0.00 0.16
#> TCGA.ES.A2HS.01 5 0.2631 0.7065 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.G3.A25W.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.2V.A95S.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.2Y.A9GU.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SB.01 1 0.2941 0.7036 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.FV.A4ZP.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD3.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H9.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW2.01 6 0.0937 0.8552 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.DD.A39V.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADD.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FW.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACS.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CC.A9FV.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 4 0.4002 0.4525 0.00 0.32 0.00 0.66 0.00 0.02
#> TCGA.DD.A4NK.01 6 0.3324 0.8291 0.08 0.00 0.00 0.02 0.06 0.84
#> TCGA.ED.A97K.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.T1.A6J8.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACV.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NF.01 6 0.0000 0.8568 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A8.01 6 0.2454 0.7128 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.WX.AA46.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AACH.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NO.01 5 0.0937 0.8506 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.G3.A7M9.01 3 0.2350 0.8205 0.00 0.00 0.88 0.10 0.00 0.02
#> TCGA.CC.5261.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CG.01 6 0.0000 0.8568 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A123.01 5 0.3156 0.6792 0.00 0.00 0.00 0.18 0.80 0.02
#> TCGA.5R.AA1D.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVZ.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD0.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KA.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.2Y.A9HA.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AACD.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE7.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BC.A8YO.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE2.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KR.A7K0.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.K7.A5RG.01 2 0.1267 0.9162 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.G3.AAV4.01 6 0.0547 0.8566 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.ED.A627.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACX.01 6 0.0000 0.8568 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAVR.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H3.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A8JO.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.DD.A1EE.01 6 0.2260 0.8035 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.DD.AACL.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.KR.A7K8.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DD.A115.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11B.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 4 0.1556 0.8514 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.G3.A3CH.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAUZ.01 1 0.1556 0.8896 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.DD.AAVV.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NP.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 1 0.0937 0.9241 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.DD.AAE4.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HP.A5MZ.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SI.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV1.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EF.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CC.A9FS.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A5W4.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H5.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BW.A5NO.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 3 0.1865 0.8949 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.CC.5258.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BW.A5NQ.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9GX.01 2 0.2260 0.8154 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.LG.A9QC.01 2 0.0937 0.9429 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DD.A11C.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4R.AA8I.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FV.A4ZQ.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.4073.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DD.AADQ.01 3 0.2260 0.8692 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.DD.AAD2.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.RC.A7SH.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10T.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A11A.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.RC.A6M5.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MD.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WX.AA44.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5264.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADE.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QA.A7B7.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A6.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5263.01 4 0.3198 0.5849 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.DD.AACW.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M6.01 4 0.3706 0.3414 0.38 0.00 0.00 0.62 0.00 0.00
#> TCGA.GJ.A6C0.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.4072.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.A116.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A520.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A12J.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADK.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HS.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HS.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IH.01 1 0.3756 0.2828 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.BC.A69I.01 6 0.3309 0.6611 0.00 0.00 0.00 0.00 0.28 0.72
#> TCGA.K7.A6G5.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BC.A10U.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BD.A2L6.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MC.01 5 0.0547 0.8658 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.UB.AA0U.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NB.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A8O6.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACQ.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G3.AAV6.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A4.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MF.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EK.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A114.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.MI.A75C.01 3 0.2260 0.8690 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.DD.A4NJ.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A25V.01 4 0.3647 0.4057 0.00 0.36 0.00 0.64 0.00 0.00
#> TCGA.BC.A10X.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A496.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A4ND.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DD.A11D.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD5.01 3 0.0547 0.9288 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.AAE8.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A118.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEH.01 6 0.4165 0.7343 0.00 0.00 0.00 0.10 0.16 0.74
#> TCGA.G3.A25U.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GW.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZS.A9CE.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NI.A4U2.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.5C.AAPD.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVW.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KC.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.MI.A75E.01 2 0.3797 0.2351 0.00 0.58 0.00 0.42 0.00 0.00
#> TCGA.DD.A116.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GJ.A9DB.01 1 0.3409 0.5786 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACC.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5N0.01 5 0.3499 0.5177 0.00 0.00 0.00 0.32 0.68 0.00
#> TCGA.K7.A5RF.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YA.A8S7.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACF.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EC.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 6 0.2793 0.7424 0.20 0.00 0.00 0.00 0.00 0.80
#> TCGA.XR.A8TD.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DD.A1EE.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UE.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACJ.01 1 0.0937 0.9238 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.G3.AAV5.01 6 0.3198 0.6917 0.00 0.00 0.00 0.00 0.26 0.74
#> TCGA.DD.A1EB.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11B.01 3 0.2260 0.8595 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.DD.A4NS.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW3.01 1 0.3706 0.3388 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.G3.A5SK.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BC.A110.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A7.01 4 0.1267 0.8737 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.BC.A10R.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25S.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A73A.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IG.01 2 0.0547 0.9612 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.G3.AAV3.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1ED.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75H.01 4 0.3198 0.5905 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.DD.A73E.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A8HV.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AAD6.01 1 0.1556 0.8850 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.BC.A10S.01 5 0.1814 0.8020 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.DD.A11C.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A9QD.01 2 0.4337 -0.0392 0.00 0.50 0.00 0.48 0.00 0.02
#> TCGA.DD.A3A1.01 1 0.2793 0.7333 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.DD.A73F.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IK.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADO.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7II.01 3 0.1556 0.8560 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.RC.A6M3.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NI.A8LF.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADC.01 5 0.0547 0.8548 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.G3.A3CJ.01 6 0.2454 0.7851 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.ZP.A9D1.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.A73C.01 5 0.3499 0.3579 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.DD.AADU.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G3.A25X.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACP.01 1 0.2094 0.8672 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.UB.A7MB.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADG.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 3 0.0547 0.9288 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.A4NH.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A12J.01 6 0.0000 0.8568 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.5262.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DD.AADJ.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 5 0.3797 0.3087 0.00 0.00 0.00 0.42 0.58 0.00
#> TCGA.DD.AAE9.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BD.A2L6.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEI.01 4 0.2094 0.8135 0.08 0.00 0.00 0.90 0.00 0.02
#> TCGA.G3.A25T.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GV.01 5 0.3578 0.4915 0.00 0.00 0.00 0.34 0.66 0.00
#> TCGA.DD.AADS.01 6 0.3076 0.6516 0.00 0.00 0.00 0.24 0.00 0.76
#> TCGA.DD.A114.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.01 6 0.0000 0.8568 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.UB.A7MA.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KB.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAEA.01 4 0.1267 0.8677 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.UB.AA0V.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A3EP.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3R2.01 4 0.3828 0.1293 0.00 0.00 0.00 0.56 0.00 0.44
#> TCGA.2Y.A9GY.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TE.01 2 0.1267 0.9218 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.DD.AACZ.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ED.A4XI.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACG.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BW.A5NP.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC9.01 2 0.3499 0.5186 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.DD.AAE1.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11D.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AADY.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9D4.01 6 0.1814 0.8319 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.DD.AAED.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACK.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAVQ.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A118.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A3JL.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AAD8.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1C.01 6 0.1556 0.8427 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.G3.A3CI.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 6 0.3544 0.7740 0.00 0.00 0.00 0.12 0.08 0.80
#> TCGA.2Y.A9H0.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.MI.A75G.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.G3.A5SJ.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A216.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 4 0.0547 0.8943 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BC.A3KG.01 3 0.0000 0.9345 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GS.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BD.A3ER.01 5 0.2260 0.7500 0.00 0.00 0.00 0.14 0.86 0.00
#> TCGA.BC.A10X.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A2QR.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A1EC.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IF.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACE.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVY.01 5 0.3409 0.4903 0.00 0.00 0.00 0.00 0.70 0.30
#> TCGA.EP.A26S.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A7PX.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADN.01 4 0.1556 0.8520 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.DD.A3A3.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Z.01 4 0.3851 0.0803 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.BC.A10U.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A5.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BC.A110.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10R.01 3 0.1267 0.9173 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.ED.A7XO.01 4 0.0547 0.8909 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.G3.AAV7.01 4 0.3678 0.6551 0.00 0.18 0.02 0.78 0.00 0.02
#> TCGA.GJ.A3OU.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADB.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.RC.A7SK.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A4NE.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39V.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACT.01 2 0.4328 0.0409 0.00 0.52 0.00 0.46 0.00 0.02
#> TCGA.ZP.A9D0.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADF.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAVU.01 6 0.0937 0.8431 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.G3.A3CG.01 4 0.1556 0.8598 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.DD.AAW1.01 6 0.0000 0.8568 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.O8.A75V.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.A3A9.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A4NI.01 5 0.2048 0.7724 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.2Y.A9H8.01 2 0.5835 0.1502 0.00 0.52 0.06 0.36 0.00 0.06
#> TCGA.DD.A1E9.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GT.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A10S.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75I.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H1.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A8HT.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADL.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.XR.A8TC.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7XP.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADR.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.2Y.A9HB.01 4 0.0547 0.8960 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AAE3.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25X.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NA.01 4 0.4222 0.5315 0.00 0.26 0.02 0.70 0.00 0.02
#> TCGA.DD.AACI.01 4 0.2793 0.7055 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.CC.A9FU.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A3RK.01 4 0.3198 0.5600 0.00 0.26 0.00 0.74 0.00 0.00
#> TCGA.CC.A5UD.01 5 0.0000 0.8795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 3 0.3851 0.3007 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.ZS.A9CF.02 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M4.01 6 0.0547 0.8566 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.G3.A7M8.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 4 0.4222 0.5315 0.00 0.26 0.02 0.70 0.00 0.02
#> TCGA.DD.A4NR.01 4 0.3819 0.5154 0.00 0.28 0.00 0.70 0.00 0.02
#> TCGA.2Y.A9H2.01 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE6.01 3 0.0937 0.9222 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.G3.AAV2.01 6 0.3198 0.6813 0.00 0.00 0.00 0.00 0.26 0.74
#> TCGA.BC.A10Z.11 2 0.0000 0.9826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 4 0.0000 0.8986 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.0547 0.9492 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A39Y.01 4 0.2581 0.7977 0.02 0.00 0.00 0.86 0.12 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FV.A495.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KR.A7K7.01 7 0.2376 0.6146 0.00 0.00 0.12 0.02 0.00 0.00 0.86
#> TCGA.BC.A3KF.01 6 0.1166 0.7130 0.06 0.00 0.00 0.00 0.00 0.94 0.00
#> TCGA.DD.A4NV.01 4 0.0504 0.8742 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DD.A4NQ.01 4 0.1166 0.8219 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CC.A1HT.01 4 0.3546 0.0774 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.BD.A3EP.01 4 0.0504 0.8660 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.ES.A2HT.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MA.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CV.01 4 0.1664 0.8480 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.DD.AACY.01 6 0.2163 0.6959 0.00 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.XR.A8TG.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AADW.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.01 1 0.0504 0.9348 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CC.A3MB.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A459.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.PD.A5DF.01 4 0.1363 0.8614 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.ED.A5KG.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A7PY.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A0.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A7SF.01 4 0.3086 0.7364 0.16 0.00 0.00 0.80 0.00 0.00 0.04
#> TCGA.DD.AAW0.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66X.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC8.01 7 0.3815 0.1980 0.00 0.00 0.36 0.00 0.00 0.02 0.62
#> TCGA.DD.AACM.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A3I1.01 4 0.0504 0.8756 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.RC.A7S9.01 2 0.3496 0.2821 0.00 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.ZP.A9D2.01 7 0.2569 0.6098 0.00 0.00 0.14 0.02 0.00 0.00 0.84
#> TCGA.G3.A5SL.01 6 0.3680 0.6682 0.06 0.00 0.00 0.14 0.00 0.78 0.02
#> TCGA.DD.A3A2.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 7 0.5241 0.3738 0.00 0.32 0.00 0.18 0.00 0.00 0.50
#> TCGA.BC.A216.01 4 0.4033 0.6503 0.08 0.00 0.00 0.70 0.00 0.00 0.22
#> TCGA.ED.A82E.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10T.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A73B.01 7 0.2906 0.5677 0.00 0.00 0.02 0.00 0.00 0.18 0.80
#> TCGA.DD.AACA.02 6 0.5930 0.2286 0.16 0.00 0.00 0.00 0.38 0.42 0.04
#> TCGA.DD.AACA.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RG.A7D4.01 7 0.2259 0.6530 0.00 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.FV.A2QR.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H4.01 4 0.3208 0.7738 0.12 0.00 0.00 0.82 0.00 0.02 0.04
#> TCGA.K7.AAU7.01 7 0.2259 0.6530 0.00 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.DD.A3A2.01 6 0.4795 0.5495 0.00 0.00 0.00 0.28 0.08 0.62 0.02
#> TCGA.EP.A26S.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A1EG.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A2QQ.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.3K.AAZ8.01 3 0.3388 0.7083 0.00 0.00 0.76 0.00 0.00 0.20 0.04
#> TCGA.BC.A217.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.AADP.01 6 0.3244 0.6796 0.00 0.00 0.00 0.04 0.18 0.78 0.00
#> TCGA.CC.5259.01 5 0.0863 0.8763 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DD.A1EA.01 4 0.5802 0.1483 0.36 0.00 0.00 0.46 0.00 0.14 0.04
#> TCGA.CC.A8HU.01 1 0.4824 0.6125 0.68 0.00 0.12 0.00 0.00 0.16 0.04
#> TCGA.ES.A2HS.01 5 0.2832 0.6334 0.00 0.00 0.00 0.00 0.76 0.24 0.00
#> TCGA.G3.A25W.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2V.A95S.01 4 0.3221 0.4669 0.00 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.2Y.A9GU.01 2 0.0863 0.9440 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.RC.A7SB.01 4 0.3519 0.6526 0.22 0.00 0.00 0.74 0.00 0.00 0.04
#> TCGA.FV.A4ZP.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD3.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H9.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.AAW2.01 6 0.0504 0.7179 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.A39V.01 4 0.1006 0.8726 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.DD.AADD.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.CC.A9FW.01 3 0.0000 0.8648 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACS.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A9FV.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 7 0.2722 0.6886 0.00 0.04 0.00 0.12 0.00 0.00 0.84
#> TCGA.DD.A4NK.01 6 0.4654 0.6594 0.04 0.00 0.00 0.16 0.06 0.72 0.02
#> TCGA.ED.A97K.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.T1.A6J8.01 3 0.2081 0.7838 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.DD.AACV.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A4NF.01 6 0.1363 0.7205 0.00 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.DD.A3A8.01 6 0.3413 0.3359 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.WX.AA46.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 1 0.3388 0.6693 0.76 0.00 0.00 0.20 0.00 0.00 0.04
#> TCGA.DD.AACH.01 3 0.0000 0.8648 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NO.01 5 0.1006 0.8812 0.00 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.G3.A7M9.01 7 0.2376 0.6158 0.00 0.00 0.12 0.02 0.00 0.00 0.86
#> TCGA.CC.5261.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CG.01 6 0.2376 0.6898 0.00 0.00 0.00 0.02 0.00 0.86 0.12
#> TCGA.CC.A123.01 7 0.3994 -0.0133 0.00 0.00 0.00 0.02 0.48 0.00 0.50
#> TCGA.5R.AA1D.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 3 0.3294 0.5142 0.00 0.00 0.66 0.00 0.00 0.00 0.34
#> TCGA.DD.AAVZ.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD0.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.EP.A2KA.01 7 0.3525 0.2626 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.2Y.A9HA.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.AACD.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE7.01 4 0.0504 0.8742 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BC.A8YO.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.AAE2.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.AAEG.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.CC.A5UC.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KR.A7K0.01 4 0.0504 0.8742 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.K7.A5RG.01 2 0.1433 0.8916 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.G3.AAV4.01 6 0.0863 0.7175 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.ED.A627.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0504 0.9348 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AACX.01 6 0.0863 0.7175 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.DD.AAVR.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H3.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A8JO.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 6 0.2259 0.6497 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.DD.AACL.01 4 0.3459 0.2600 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.KR.A7K8.01 4 0.2572 0.5722 0.00 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.DD.A115.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11B.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 4 0.2081 0.7743 0.00 0.00 0.00 0.86 0.14 0.00 0.00
#> TCGA.G3.A3CH.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAUZ.01 4 0.4175 0.3800 0.38 0.00 0.00 0.58 0.00 0.00 0.04
#> TCGA.DD.AAVV.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NP.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 1 0.2569 0.8176 0.84 0.00 0.14 0.00 0.00 0.00 0.02
#> TCGA.DD.AAE4.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HP.A5MZ.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SI.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV1.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EF.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CC.A9FS.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A5W4.01 3 0.0000 0.8648 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H5.01 2 0.0863 0.9437 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.BW.A5NO.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CC.A7IE.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 3 0.0504 0.8595 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.AADM.01 3 0.4707 0.5133 0.00 0.00 0.66 0.22 0.00 0.02 0.10
#> TCGA.CC.5258.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BW.A5NQ.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9GX.01 2 0.1433 0.8916 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.LG.A9QC.01 2 0.1671 0.8750 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.DD.A11C.01 1 0.0504 0.9348 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BC.A10Q.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4R.AA8I.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FV.A4ZQ.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.4073.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADQ.01 3 0.4998 0.4296 0.00 0.00 0.54 0.00 0.00 0.14 0.32
#> TCGA.DD.AAD2.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.1363 0.8596 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.RC.A7SH.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10T.01 4 0.1718 0.8515 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.DD.A11A.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A6M5.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MD.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WX.AA44.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5264.01 1 0.0504 0.9348 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AADE.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QA.A7B7.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAEB.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A6.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5263.01 4 0.2512 0.8024 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.DD.AACW.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M6.01 4 0.2278 0.8192 0.08 0.00 0.00 0.88 0.00 0.00 0.04
#> TCGA.GJ.A6C0.01 4 0.1718 0.8515 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.BC.4072.01 7 0.3413 0.4209 0.00 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.DD.A116.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A520.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A12J.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADK.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 1 0.1363 0.9232 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.ES.A2HS.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HS.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.CC.A7IH.01 1 0.3815 0.4669 0.62 0.00 0.00 0.00 0.00 0.36 0.02
#> TCGA.BC.A69I.01 6 0.3413 0.4150 0.00 0.00 0.00 0.00 0.38 0.62 0.00
#> TCGA.K7.A6G5.01 4 0.0504 0.8742 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BC.A10U.01 1 0.1363 0.9142 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.DD.A4NG.01 4 0.1363 0.8666 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.BD.A2L6.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MC.01 5 0.3526 0.6579 0.00 0.00 0.00 0.00 0.76 0.18 0.06
#> TCGA.UB.AA0U.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NB.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A8O6.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACQ.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.AAV6.01 3 0.0504 0.8609 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A4.01 2 0.1671 0.8746 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.UB.A7MF.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EK.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.A114.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.WJ.A86L.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.MI.A75C.01 7 0.4505 -0.0918 0.00 0.00 0.44 0.00 0.00 0.06 0.50
#> TCGA.DD.A4NJ.01 4 0.0504 0.8756 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.G3.A25V.01 2 0.2259 0.7761 0.00 0.84 0.00 0.16 0.00 0.00 0.00
#> TCGA.BC.A10X.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A496.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A4ND.01 4 0.2259 0.6513 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.DD.A11D.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD5.01 7 0.2945 0.4573 0.00 0.00 0.26 0.00 0.00 0.00 0.74
#> TCGA.DD.AAE8.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A118.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEH.01 6 0.4681 0.5168 0.00 0.00 0.00 0.32 0.10 0.58 0.00
#> TCGA.G3.A25U.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.2Y.A9GW.01 4 0.1166 0.8497 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.ZS.A9CE.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.NI.A4U2.01 4 0.0504 0.8742 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.5C.AAPD.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVW.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KC.01 1 0.1363 0.9142 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.MI.A75E.01 2 0.2081 0.8065 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.DD.A116.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GJ.A9DB.01 4 0.2912 0.7597 0.14 0.00 0.00 0.82 0.00 0.00 0.04
#> TCGA.CC.A7IL.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.AACC.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5N0.01 5 0.3517 0.5282 0.00 0.00 0.00 0.28 0.70 0.02 0.00
#> TCGA.K7.A5RF.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.YA.A8S7.01 4 0.1433 0.8349 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.DD.A39X.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACF.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EC.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 6 0.3139 0.5067 0.30 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.XR.A8TD.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UE.01 3 0.1166 0.8425 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.DD.AACJ.01 1 0.2163 0.8813 0.88 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.G3.AAV5.01 6 0.3358 0.4515 0.00 0.00 0.00 0.00 0.36 0.64 0.00
#> TCGA.DD.A1EB.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11B.01 3 0.2376 0.7980 0.00 0.00 0.86 0.00 0.00 0.12 0.02
#> TCGA.DD.A4NS.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW3.01 1 0.2945 0.6808 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.G3.A5SK.01 4 0.0504 0.8742 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BC.A110.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A7.01 7 0.2512 0.6566 0.00 0.00 0.00 0.10 0.00 0.04 0.86
#> TCGA.BC.A10R.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25S.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A73A.01 4 0.1363 0.8614 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.DD.AADI.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IG.01 7 0.2422 0.5729 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.G3.AAV3.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1ED.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75H.01 4 0.2769 0.8132 0.02 0.00 0.00 0.86 0.00 0.08 0.04
#> TCGA.DD.A73E.01 1 0.1664 0.9117 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.2Y.A9H7.01 3 0.0000 0.8648 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HV.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 4 0.1433 0.8349 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.DD.AAD6.01 1 0.2569 0.8345 0.84 0.00 0.00 0.00 0.00 0.14 0.02
#> TCGA.BC.A10S.01 5 0.1886 0.8104 0.00 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.DD.A11C.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A9QD.01 7 0.4547 0.3900 0.00 0.34 0.00 0.08 0.00 0.00 0.58
#> TCGA.DD.A3A1.01 4 0.3745 0.5885 0.26 0.00 0.00 0.70 0.00 0.00 0.04
#> TCGA.DD.A73F.01 4 0.1363 0.8614 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.CC.A7IK.01 1 0.0504 0.9348 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AADO.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7II.01 3 0.4070 0.5627 0.00 0.00 0.66 0.02 0.02 0.00 0.30
#> TCGA.RC.A6M3.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.1886 0.8016 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.NI.A8LF.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.01 3 0.0000 0.8648 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADC.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A3CJ.01 6 0.3449 0.6591 0.14 0.00 0.00 0.00 0.08 0.78 0.00
#> TCGA.ZP.A9D1.01 4 0.1928 0.8324 0.00 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.DD.A73C.01 5 0.2945 0.4356 0.00 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.DD.AADU.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A25X.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACP.01 1 0.1671 0.8942 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.UB.A7MB.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADG.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.RC.A6M6.01 7 0.2081 0.5940 0.00 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.DD.A4NH.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A12J.01 6 0.1886 0.6852 0.00 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.CC.5262.01 4 0.1166 0.8219 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.DD.AADJ.01 3 0.0000 0.8648 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 5 0.3052 0.6692 0.00 0.00 0.00 0.20 0.78 0.02 0.00
#> TCGA.DD.AAE9.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BD.A2L6.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.AAEI.01 4 0.2213 0.8436 0.04 0.00 0.00 0.90 0.00 0.02 0.04
#> TCGA.G3.A25T.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GV.01 5 0.3052 0.6690 0.00 0.00 0.00 0.20 0.78 0.02 0.00
#> TCGA.DD.AADS.01 6 0.3867 0.4051 0.00 0.00 0.00 0.38 0.00 0.60 0.02
#> TCGA.DD.A114.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.01 6 0.1363 0.7091 0.00 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.UB.A7MA.01 7 0.3047 0.4615 0.00 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.EP.A2KB.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEA.01 4 0.1006 0.8693 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.UB.AA0V.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A3EP.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3R2.01 4 0.3052 0.7016 0.00 0.00 0.00 0.78 0.00 0.20 0.02
#> TCGA.2Y.A9GY.01 4 0.0863 0.8698 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.XR.A8TE.01 2 0.2081 0.8223 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.DD.AACZ.01 4 0.0504 0.8707 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ED.A4XI.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACG.01 3 0.0504 0.8609 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BW.A5NP.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC9.01 2 0.3558 0.0723 0.00 0.52 0.00 0.00 0.48 0.00 0.00
#> TCGA.DD.AAE1.01 3 0.0000 0.8648 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11D.01 1 0.2912 0.7666 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.DD.AADY.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9D4.01 6 0.2376 0.6745 0.12 0.00 0.00 0.00 0.00 0.86 0.02
#> TCGA.DD.AAED.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACK.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.AAVQ.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A118.01 7 0.3294 0.3912 0.00 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.DD.AACO.01 2 0.1671 0.8748 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.DD.A4NL.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A3JL.01 4 0.1166 0.8497 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.DD.AAD8.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.5R.AA1C.01 6 0.1433 0.7197 0.00 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.G3.A3CI.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 6 0.3927 0.5504 0.00 0.00 0.00 0.30 0.04 0.66 0.00
#> TCGA.2Y.A9H0.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.MI.A75G.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.G3.A5SJ.01 4 0.0504 0.8756 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BC.A216.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 4 0.1363 0.8596 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.BC.A3KG.01 3 0.0504 0.8609 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A1EH.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GS.01 4 0.1363 0.8614 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.BD.A3ER.01 5 0.2163 0.8028 0.00 0.00 0.00 0.10 0.88 0.02 0.00
#> TCGA.BC.A10X.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A2QR.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.A1EC.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IF.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACE.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAVY.01 5 0.2708 0.6648 0.00 0.00 0.00 0.00 0.78 0.22 0.00
#> TCGA.EP.A26S.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.01 4 0.0504 0.8756 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ED.A7PX.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADN.01 4 0.0504 0.8729 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.DD.A3A3.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Z.01 4 0.2722 0.7831 0.12 0.00 0.00 0.84 0.00 0.00 0.04
#> TCGA.BC.A10U.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A5.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BC.A110.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10R.01 7 0.2376 0.5985 0.00 0.00 0.12 0.00 0.00 0.02 0.86
#> TCGA.ED.A7XO.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV7.01 7 0.2722 0.6886 0.00 0.04 0.00 0.12 0.00 0.00 0.84
#> TCGA.GJ.A3OU.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADB.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A7SK.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.A4NE.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39V.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACT.01 7 0.3263 0.6402 0.00 0.12 0.00 0.08 0.00 0.00 0.80
#> TCGA.ZP.A9D0.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADF.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A1EJ.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.AAVU.01 6 0.3617 0.5726 0.00 0.00 0.16 0.00 0.00 0.76 0.08
#> TCGA.G3.A3CG.01 4 0.3667 0.6608 0.00 0.00 0.00 0.74 0.00 0.06 0.20
#> TCGA.DD.AAW1.01 6 0.0863 0.7175 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.O8.A75V.01 7 0.2259 0.6530 0.00 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.DD.A3A9.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0863 0.9285 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.A4NI.01 5 0.2163 0.7997 0.00 0.00 0.00 0.10 0.88 0.02 0.00
#> TCGA.2Y.A9H8.01 7 0.2804 0.6732 0.00 0.06 0.00 0.06 0.00 0.02 0.86
#> TCGA.DD.A1E9.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GT.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10S.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75I.01 4 0.1718 0.8515 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.2Y.A9H1.01 4 0.0504 0.8756 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CC.A8HT.01 4 0.0000 0.8765 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADL.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.XR.A8TC.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7XP.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADR.01 4 0.1006 0.8693 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.2Y.A9HB.01 4 0.1664 0.8480 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.DD.AAE3.01 1 0.1006 0.9348 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.G3.A25X.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NA.01 7 0.2722 0.6886 0.00 0.04 0.00 0.12 0.00 0.00 0.84
#> TCGA.DD.AACI.01 4 0.5875 0.0193 0.00 0.00 0.00 0.44 0.30 0.02 0.24
#> TCGA.CC.A9FU.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.EP.A3RK.01 2 0.3358 0.3840 0.00 0.64 0.00 0.36 0.00 0.00 0.00
#> TCGA.CC.A5UD.01 5 0.0000 0.9086 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0504 0.9336 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAEE.01 3 0.4278 0.2615 0.00 0.00 0.50 0.00 0.00 0.46 0.04
#> TCGA.ZS.A9CF.02 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.ZS.A9CF.01 1 0.0863 0.9332 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.RC.A6M4.01 6 0.0863 0.7175 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.G3.A7M8.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 7 0.2722 0.6886 0.00 0.04 0.00 0.12 0.00 0.00 0.84
#> TCGA.DD.A4NR.01 7 0.2722 0.6886 0.00 0.04 0.00 0.12 0.00 0.00 0.84
#> TCGA.2Y.A9H2.01 7 0.2572 0.5506 0.00 0.20 0.00 0.00 0.00 0.00 0.80
#> TCGA.DD.AAE6.01 3 0.0504 0.8605 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.G3.AAV2.01 6 0.3459 0.3468 0.00 0.00 0.00 0.00 0.40 0.60 0.00
#> TCGA.BC.A10Z.11 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 4 0.1363 0.8614 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.DD.A115.01 1 0.2278 0.8501 0.88 0.00 0.00 0.08 0.00 0.00 0.04
#> TCGA.DD.A39Y.01 4 0.1860 0.8550 0.02 0.00 0.00 0.92 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.FV.A495.01 4 0.0471 0.7777 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.KR.A7K7.01 7 0.1557 0.6215 0.00 0.02 0.06 0.00 0.00 0.00 0.92 0.00
#> TCGA.BC.A3KF.01 6 0.3314 0.6765 0.08 0.10 0.00 0.02 0.00 0.80 0.00 0.00
#> TCGA.DD.A4NV.01 4 0.0808 0.7676 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.DD.A4NQ.01 4 0.1607 0.7504 0.00 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.CC.A1HT.01 4 0.3404 0.4126 0.00 0.00 0.00 0.72 0.00 0.00 0.04 0.24
#> TCGA.BD.A3EP.01 4 0.1275 0.7575 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.ES.A2HT.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A3MA.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZP.A9CV.01 4 0.2862 0.7106 0.00 0.00 0.00 0.82 0.00 0.10 0.08 0.00
#> TCGA.DD.AACY.01 6 0.3589 0.5912 0.00 0.10 0.00 0.00 0.00 0.74 0.16 0.00
#> TCGA.XR.A8TG.01 1 0.1091 0.8045 0.94 0.06 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Y.01 1 0.0471 0.8067 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MB.01 5 0.0471 0.8272 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.ED.A459.01 5 0.0941 0.8120 0.00 0.00 0.00 0.02 0.96 0.02 0.00 0.00
#> TCGA.PD.A5DF.01 4 0.2534 0.7006 0.00 0.22 0.00 0.78 0.00 0.00 0.00 0.00
#> TCGA.ED.A5KG.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAVX.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A0.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SF.01 4 0.4799 0.4227 0.16 0.32 0.00 0.52 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW0.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ED.A66X.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAC8.01 7 0.5788 0.0479 0.00 0.20 0.22 0.00 0.00 0.08 0.50 0.00
#> TCGA.DD.AACM.01 4 0.0808 0.7730 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.FV.A3I1.01 4 0.1091 0.7715 0.00 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.RC.A7S9.01 8 0.3142 0.4365 0.00 0.00 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.ZP.A9D2.01 7 0.1341 0.6281 0.00 0.00 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.G3.A5SL.01 6 0.3270 0.6423 0.02 0.12 0.00 0.06 0.00 0.80 0.00 0.00
#> TCGA.DD.A3A2.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A3M9.01 7 0.5063 0.3519 0.00 0.00 0.00 0.26 0.00 0.00 0.48 0.26
#> TCGA.BC.A216.01 4 0.5308 0.4295 0.02 0.32 0.00 0.48 0.00 0.00 0.18 0.00
#> TCGA.ED.A82E.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10T.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A11A.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A73B.01 7 0.3601 0.4910 0.00 0.06 0.02 0.00 0.00 0.16 0.76 0.00
#> TCGA.DD.AACA.02 6 0.6665 0.2374 0.28 0.10 0.00 0.00 0.28 0.32 0.02 0.00
#> TCGA.DD.AACA.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AA3A.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.RG.A7D4.01 7 0.2114 0.6384 0.00 0.00 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.FV.A2QR.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A25W.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9H4.01 4 0.4847 0.5360 0.08 0.30 0.00 0.58 0.00 0.04 0.00 0.00
#> TCGA.K7.AAU7.01 7 0.1563 0.6759 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.DD.A3A2.01 6 0.4394 0.6135 0.00 0.06 0.00 0.16 0.08 0.70 0.00 0.00
#> TCGA.EP.A26S.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A2QQ.01 4 0.0471 0.7777 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.3K.AAZ8.01 3 0.4764 0.6332 0.00 0.12 0.66 0.00 0.00 0.16 0.06 0.00
#> TCGA.BC.A217.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADP.01 6 0.3630 0.6556 0.00 0.04 0.00 0.10 0.08 0.78 0.00 0.00
#> TCGA.CC.5259.01 5 0.2348 0.7638 0.00 0.04 0.00 0.00 0.88 0.02 0.06 0.00
#> TCGA.DD.A1EA.01 1 0.6166 0.3393 0.38 0.34 0.00 0.16 0.00 0.12 0.00 0.00
#> TCGA.CC.A8HU.01 1 0.3913 0.5604 0.74 0.16 0.04 0.00 0.00 0.06 0.00 0.00
#> TCGA.ES.A2HS.01 5 0.3570 0.3834 0.00 0.00 0.00 0.02 0.62 0.36 0.00 0.00
#> TCGA.G3.A25W.01 4 0.1275 0.7652 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.2V.A95S.01 4 0.2852 0.5251 0.00 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.2Y.A9GU.01 8 0.0471 0.9599 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.RC.A7SB.01 4 0.4677 0.4503 0.14 0.32 0.00 0.54 0.00 0.00 0.00 0.00
#> TCGA.FV.A4ZP.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAD3.01 4 0.0471 0.7784 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H9.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW2.01 6 0.2994 0.6564 0.06 0.14 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.DD.A39V.01 4 0.2719 0.7219 0.00 0.18 0.00 0.80 0.00 0.02 0.00 0.00
#> TCGA.DD.AADD.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FW.01 3 0.0471 0.8352 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AACS.01 5 0.0471 0.8272 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.CC.A9FV.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A7M7.01 7 0.2025 0.6764 0.00 0.00 0.00 0.10 0.00 0.00 0.88 0.02
#> TCGA.DD.A4NK.01 6 0.3675 0.6276 0.02 0.08 0.00 0.14 0.00 0.76 0.00 0.00
#> TCGA.ED.A97K.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.T1.A6J8.01 3 0.2994 0.7756 0.00 0.06 0.80 0.00 0.00 0.00 0.14 0.00
#> TCGA.DD.AACV.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NF.01 6 0.2807 0.6635 0.00 0.10 0.00 0.02 0.00 0.84 0.04 0.00
#> TCGA.DD.A3A8.01 6 0.4100 0.3447 0.00 0.06 0.00 0.00 0.00 0.58 0.36 0.00
#> TCGA.WX.AA46.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EL.01 1 0.4904 0.5239 0.50 0.32 0.00 0.18 0.00 0.00 0.00 0.00
#> TCGA.DD.AACH.01 3 0.0000 0.8366 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.WQ.A9G7.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A4NO.01 5 0.3385 0.6364 0.00 0.00 0.00 0.16 0.76 0.08 0.00 0.00
#> TCGA.G3.A7M9.01 7 0.1557 0.6215 0.00 0.02 0.06 0.00 0.00 0.00 0.92 0.00
#> TCGA.CC.5261.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZS.A9CG.01 6 0.3073 0.6317 0.00 0.10 0.00 0.00 0.00 0.80 0.10 0.00
#> TCGA.CC.A123.01 7 0.5646 0.1394 0.00 0.06 0.00 0.08 0.38 0.02 0.46 0.00
#> TCGA.5R.AA1D.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A69H.01 3 0.3514 0.5391 0.00 0.02 0.64 0.00 0.00 0.00 0.34 0.00
#> TCGA.DD.AAVZ.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAD0.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KA.01 7 0.3808 0.4125 0.00 0.00 0.00 0.34 0.00 0.04 0.62 0.00
#> TCGA.2Y.A9HA.01 1 0.3449 0.7236 0.66 0.32 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.AACD.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAE7.01 4 0.1765 0.7278 0.00 0.00 0.00 0.88 0.00 0.12 0.00 0.00
#> TCGA.BC.A8YO.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE2.01 1 0.3015 0.7361 0.68 0.32 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEG.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.XR.A8TF.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.KR.A7K0.01 4 0.0808 0.7676 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.K7.A5RG.01 8 0.2981 0.6463 0.00 0.00 0.00 0.22 0.00 0.00 0.02 0.76
#> TCGA.G3.AAV4.01 6 0.3504 0.6023 0.00 0.26 0.00 0.00 0.00 0.70 0.04 0.00
#> TCGA.ED.A627.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACX.01 6 0.3293 0.6182 0.00 0.22 0.00 0.00 0.00 0.74 0.04 0.00
#> TCGA.DD.AAVR.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9H3.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MR.A8JO.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAEK.01 4 0.0471 0.7728 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DD.A1EE.01 6 0.3675 0.6518 0.14 0.08 0.00 0.02 0.00 0.76 0.00 0.00
#> TCGA.DD.AACL.01 4 0.3514 0.3708 0.00 0.02 0.00 0.64 0.00 0.00 0.34 0.00
#> TCGA.KR.A7K8.01 4 0.2025 0.6842 0.00 0.00 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.DD.A115.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A3I0.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A11B.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADA.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A5SM.01 4 0.1947 0.7009 0.00 0.00 0.00 0.86 0.14 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.AAUZ.01 1 0.5276 0.1917 0.36 0.32 0.00 0.32 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVV.01 8 0.0471 0.9607 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DD.A4NP.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ED.A66Y.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.LG.A6GG.01 1 0.3054 0.7625 0.80 0.12 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE4.01 1 0.3015 0.7361 0.68 0.32 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A5SI.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A112.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.AAV1.01 5 0.0471 0.8272 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DD.A1EF.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A113.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Y.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACB.01 1 0.3015 0.7361 0.68 0.32 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FS.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A5W4.01 3 0.0471 0.8332 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.2Y.A9H5.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BW.A5NO.01 1 0.3015 0.7361 0.68 0.32 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.KR.A7K2.01 3 0.1804 0.8201 0.00 0.00 0.90 0.00 0.00 0.02 0.08 0.00
#> TCGA.DD.AADM.01 3 0.5831 0.3702 0.00 0.02 0.50 0.26 0.00 0.04 0.18 0.00
#> TCGA.CC.5258.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BW.A5NQ.01 4 0.0471 0.7777 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.2Y.A9GX.01 8 0.3374 0.4902 0.00 0.00 0.00 0.30 0.00 0.00 0.02 0.68
#> TCGA.LG.A9QC.01 8 0.2406 0.7348 0.00 0.00 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.DD.A11C.01 1 0.0471 0.8067 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.4R.AA8I.01 1 0.3746 0.7064 0.64 0.32 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.FV.A4ZQ.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.4073.01 4 0.0808 0.7730 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DD.AADQ.01 7 0.5836 -0.2639 0.00 0.04 0.34 0.00 0.00 0.26 0.36 0.00
#> TCGA.DD.AAD2.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.WQ.AB4B.01 4 0.2025 0.7324 0.00 0.00 0.00 0.88 0.00 0.10 0.02 0.00
#> TCGA.RC.A7SH.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10T.01 4 0.3015 0.6261 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A39W.01 5 0.0471 0.8272 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.RC.A6M5.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.UB.A7MD.01 4 0.0471 0.7784 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.WX.AA44.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.5C.A9VG.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.5264.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADE.01 5 0.0471 0.8231 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DD.AAD1.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.QA.A7B7.01 1 0.2114 0.7889 0.84 0.16 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.1091 0.8045 0.94 0.06 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A6.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.5263.01 4 0.3015 0.6261 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.DD.AACW.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A7M6.01 4 0.3015 0.6261 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.GJ.A6C0.01 4 0.3015 0.6261 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.BC.4072.01 7 0.3714 0.1953 0.00 0.00 0.00 0.44 0.00 0.00 0.54 0.02
#> TCGA.DD.A116.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9H6.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MR.A520.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EP.A12J.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADK.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A73D.01 1 0.0471 0.7944 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HS.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A4NN.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZP.A9CZ.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A8HS.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A6UC.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IH.01 1 0.3808 0.3771 0.62 0.04 0.00 0.00 0.00 0.34 0.00 0.00
#> TCGA.BC.A69I.01 6 0.3374 0.4454 0.00 0.00 0.00 0.02 0.30 0.68 0.00 0.00
#> TCGA.K7.A6G5.01 4 0.0471 0.7728 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.BC.A10U.01 1 0.3746 0.7064 0.64 0.32 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.3660 0.6582 0.00 0.24 0.00 0.70 0.00 0.06 0.00 0.00
#> TCGA.BD.A2L6.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.UB.A7MC.01 5 0.4779 0.5193 0.02 0.18 0.00 0.00 0.66 0.12 0.02 0.00
#> TCGA.UB.AA0U.01 4 0.0471 0.7777 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DD.A4NB.01 8 0.0471 0.9596 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.ED.A8O6.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACQ.01 5 0.2224 0.7538 0.00 0.12 0.00 0.00 0.86 0.00 0.02 0.00
#> TCGA.G3.AAV6.01 3 0.0471 0.8338 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A4.01 8 0.1765 0.8467 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.UB.A7MF.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EK.01 1 0.3449 0.7236 0.66 0.32 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ES.A2HT.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A39Z.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Z.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Y.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EI.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACU.01 1 0.3746 0.7064 0.64 0.32 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.MI.A75C.01 7 0.4764 0.3066 0.00 0.04 0.20 0.00 0.00 0.12 0.64 0.00
#> TCGA.DD.A4NJ.01 4 0.1341 0.7652 0.00 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.G3.A25V.01 8 0.3714 0.1511 0.00 0.00 0.00 0.44 0.00 0.00 0.02 0.54
#> TCGA.BC.A10X.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A496.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4ND.01 4 0.1887 0.7293 0.00 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.DD.A11D.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAD5.01 7 0.2406 0.5065 0.00 0.00 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.DD.AAE8.01 4 0.0471 0.7777 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DD.A118.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAEH.01 6 0.3735 0.5923 0.00 0.02 0.00 0.22 0.04 0.72 0.00 0.00
#> TCGA.G3.A25U.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GW.01 4 0.1557 0.7594 0.00 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.ZS.A9CE.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NI.A4U2.01 4 0.1341 0.7512 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.5C.AAPD.01 4 0.0808 0.7730 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DD.AAVW.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EP.A2KC.01 1 0.3746 0.7064 0.64 0.32 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.MI.A75E.01 8 0.3570 0.3535 0.00 0.00 0.00 0.36 0.00 0.00 0.02 0.62
#> TCGA.DD.A116.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.GJ.A9DB.01 4 0.4380 0.5047 0.10 0.32 0.00 0.58 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACC.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A3R3.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HP.A5N0.01 5 0.4100 0.3817 0.00 0.00 0.00 0.36 0.58 0.06 0.00 0.00
#> TCGA.K7.A5RF.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YA.A8S7.01 4 0.0808 0.7730 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DD.A39X.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACF.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAE0.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.AAV0.01 6 0.4050 0.4454 0.34 0.06 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.XR.A8TD.01 4 0.0808 0.7730 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DD.A1EE.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A5UE.01 3 0.2807 0.8070 0.00 0.04 0.84 0.00 0.00 0.02 0.10 0.00
#> TCGA.DD.AACJ.01 1 0.1341 0.7526 0.92 0.08 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV5.01 6 0.3991 0.5607 0.00 0.06 0.00 0.02 0.22 0.70 0.00 0.00
#> TCGA.DD.A1EB.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A7IJ.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAVS.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A11B.01 3 0.4590 0.6523 0.00 0.10 0.68 0.00 0.00 0.16 0.06 0.00
#> TCGA.DD.A4NS.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ED.A8O5.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A3.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAW3.01 1 0.3299 0.5951 0.76 0.06 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.G3.A5SK.01 4 0.1341 0.7512 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.BC.A110.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A7.01 7 0.1091 0.6683 0.00 0.00 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.BC.A10R.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A112.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACN.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EF.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A3MC.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A113.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EJ.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A25S.01 1 0.2938 0.7454 0.70 0.30 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 4 0.2938 0.6417 0.00 0.30 0.00 0.70 0.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A7IG.01 7 0.3928 0.5276 0.00 0.02 0.00 0.04 0.02 0.00 0.74 0.18
#> TCGA.G3.AAV3.01 5 0.0471 0.8131 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.A1ED.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MI.A75H.01 4 0.4557 0.5346 0.00 0.28 0.00 0.58 0.00 0.14 0.00 0.00
#> TCGA.DD.A73E.01 1 0.0471 0.7944 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 3 0.0000 0.8366 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HV.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1E9.01 4 0.1557 0.7594 0.00 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.DD.AAD6.01 1 0.2407 0.7085 0.86 0.06 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.BC.A10S.01 5 0.3594 0.5232 0.00 0.00 0.00 0.04 0.68 0.28 0.00 0.00
#> TCGA.DD.A11C.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Q.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.LG.A9QD.01 7 0.5037 0.3646 0.00 0.00 0.00 0.14 0.00 0.02 0.54 0.30
#> TCGA.DD.A3A1.01 4 0.4904 0.3710 0.18 0.32 0.00 0.50 0.00 0.00 0.00 0.00
#> TCGA.DD.A73F.01 4 0.2534 0.7006 0.00 0.22 0.00 0.78 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IK.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADO.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A7II.01 3 0.4433 0.4214 0.00 0.10 0.56 0.00 0.00 0.00 0.34 0.00
#> TCGA.RC.A6M3.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A39W.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10W.01 3 0.1947 0.7913 0.00 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.NI.A8LF.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A23B.01 3 0.0000 0.8366 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADC.01 5 0.0941 0.8079 0.00 0.02 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.G3.A3CJ.01 6 0.3970 0.6202 0.18 0.08 0.00 0.02 0.00 0.72 0.00 0.00
#> TCGA.ZP.A9D1.01 4 0.2862 0.7175 0.00 0.00 0.00 0.82 0.00 0.10 0.08 0.00
#> TCGA.DD.A73C.01 5 0.4040 0.2195 0.00 0.00 0.00 0.02 0.58 0.02 0.00 0.38
#> TCGA.DD.AADU.01 5 0.0471 0.8272 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.G3.A25X.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACP.01 1 0.3021 0.7070 0.80 0.16 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.UB.A7MB.01 5 0.0471 0.8272 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DD.AADG.01 1 0.1947 0.7940 0.86 0.14 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 7 0.1804 0.6006 0.00 0.02 0.08 0.00 0.00 0.00 0.90 0.00
#> TCGA.DD.A4NH.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EP.A12J.01 6 0.4033 0.5468 0.00 0.12 0.00 0.00 0.00 0.68 0.20 0.00
#> TCGA.CC.5262.01 4 0.1607 0.7504 0.00 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.DD.AADJ.01 3 0.0000 0.8366 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 4 0.4803 -0.1284 0.00 0.02 0.00 0.46 0.44 0.08 0.00 0.00
#> TCGA.DD.AAE9.01 1 0.2938 0.7454 0.70 0.30 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A2L6.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEI.01 4 0.3845 0.6237 0.00 0.28 0.00 0.66 0.00 0.06 0.00 0.00
#> TCGA.G3.A25T.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9GV.01 5 0.4100 0.3821 0.00 0.00 0.00 0.36 0.58 0.06 0.00 0.00
#> TCGA.DD.AADS.01 6 0.3193 0.3688 0.00 0.00 0.00 0.38 0.00 0.62 0.00 0.00
#> TCGA.DD.A114.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A39Z.01 6 0.3078 0.6538 0.00 0.10 0.00 0.02 0.00 0.82 0.06 0.00
#> TCGA.UB.A7MA.01 7 0.3449 0.3657 0.00 0.02 0.00 0.00 0.00 0.00 0.66 0.32
#> TCGA.EP.A2KB.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEA.01 4 0.2807 0.7042 0.00 0.02 0.00 0.84 0.04 0.10 0.00 0.00
#> TCGA.UB.AA0V.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BD.A3EP.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A3R2.01 4 0.4910 0.1446 0.00 0.16 0.00 0.44 0.00 0.40 0.00 0.00
#> TCGA.2Y.A9GY.01 4 0.2406 0.7122 0.00 0.20 0.00 0.80 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TE.01 8 0.2650 0.6727 0.00 0.00 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.DD.AACZ.01 4 0.1607 0.7661 0.00 0.04 0.00 0.92 0.00 0.00 0.04 0.00
#> TCGA.ED.A4XI.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACG.01 3 0.1275 0.8306 0.00 0.02 0.94 0.00 0.00 0.00 0.04 0.00
#> TCGA.BW.A5NP.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAC9.01 8 0.3193 0.3828 0.00 0.00 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.DD.AAE1.01 3 0.0000 0.8366 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11D.01 1 0.4199 0.6614 0.60 0.32 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.DD.AADY.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZP.A9D4.01 6 0.3909 0.6025 0.18 0.12 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.DD.AAED.01 5 0.0000 0.8302 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACK.01 1 0.3449 0.7236 0.66 0.32 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EI.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A118.01 7 0.3142 0.3263 0.00 0.00 0.00 0.00 0.00 0.00 0.64 0.36
#> TCGA.DD.AACO.01 8 0.1563 0.8724 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.DD.A4NL.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EP.A3JL.01 4 0.1091 0.7675 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.DD.AAD8.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1C.01 6 0.2674 0.6773 0.00 0.06 0.00 0.04 0.04 0.86 0.00 0.00
#> TCGA.G3.A3CI.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A3CK.01 6 0.3198 0.5642 0.00 0.00 0.00 0.26 0.02 0.72 0.00 0.00
#> TCGA.2Y.A9H0.01 1 0.2852 0.7535 0.72 0.28 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75G.01 1 0.3015 0.7361 0.68 0.32 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SJ.01 4 0.0471 0.7784 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.BC.A216.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.5R.AAAM.01 4 0.2807 0.7164 0.00 0.02 0.00 0.84 0.00 0.10 0.04 0.00
#> TCGA.BC.A3KG.01 3 0.1557 0.8269 0.00 0.02 0.92 0.00 0.00 0.00 0.06 0.00
#> TCGA.DD.A1EH.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9GS.01 4 0.2534 0.7006 0.00 0.22 0.00 0.78 0.00 0.00 0.00 0.00
#> TCGA.BD.A3ER.01 5 0.4314 0.5236 0.00 0.02 0.00 0.24 0.66 0.08 0.00 0.00
#> TCGA.BC.A10X.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A2QR.01 1 0.3746 0.7064 0.64 0.32 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A7IF.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACE.01 1 0.2267 0.7849 0.82 0.18 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVY.01 5 0.3570 0.3736 0.00 0.02 0.00 0.00 0.62 0.36 0.00 0.00
#> TCGA.EP.A26S.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EG.01 4 0.1091 0.7715 0.00 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PX.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EB.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADN.01 4 0.0941 0.7732 0.00 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.DD.A3A3.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A39X.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A25Z.01 4 0.3449 0.6070 0.02 0.32 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.BC.A10U.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A5.01 1 0.2938 0.7454 0.70 0.30 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10R.01 7 0.0808 0.6327 0.00 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.ED.A7XO.01 4 0.1275 0.7652 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.G3.AAV7.01 7 0.2025 0.6718 0.00 0.02 0.00 0.10 0.00 0.00 0.88 0.00
#> TCGA.GJ.A3OU.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADB.01 5 0.0808 0.8181 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.RC.A7SK.01 1 0.3449 0.7236 0.66 0.32 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NE.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A39V.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACT.01 7 0.2623 0.6559 0.00 0.00 0.00 0.10 0.00 0.00 0.84 0.06
#> TCGA.ZP.A9D0.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADF.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.01 1 0.3015 0.7361 0.68 0.32 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVU.01 6 0.5448 0.4574 0.02 0.40 0.04 0.00 0.02 0.48 0.04 0.00
#> TCGA.G3.A3CG.01 4 0.5433 0.1648 0.00 0.02 0.00 0.46 0.00 0.22 0.30 0.00
#> TCGA.DD.AAW1.01 6 0.3170 0.6245 0.00 0.20 0.00 0.00 0.00 0.76 0.04 0.00
#> TCGA.O8.A75V.01 7 0.1563 0.6759 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.DD.A3A9.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A73G.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1ED.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.WX.AA47.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A7M5.01 1 0.3449 0.7236 0.66 0.32 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 5 0.3880 0.5357 0.00 0.00 0.00 0.24 0.68 0.08 0.00 0.00
#> TCGA.2Y.A9H8.01 7 0.1557 0.6756 0.00 0.00 0.00 0.06 0.00 0.00 0.92 0.02
#> TCGA.DD.A1E9.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9GT.01 4 0.0471 0.7777 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BC.A10S.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.UB.A7ME.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EL.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A1.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A119.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MI.A75I.01 4 0.3015 0.6261 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H1.01 4 0.1947 0.7427 0.00 0.14 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HT.01 4 0.0808 0.7730 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DD.AADL.01 1 0.2756 0.7605 0.74 0.26 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TC.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ED.A7XP.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10W.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FV.A23B.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.5C.A9VH.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADR.01 4 0.2862 0.7131 0.00 0.00 0.00 0.82 0.00 0.10 0.08 0.00
#> TCGA.2Y.A9HB.01 4 0.2680 0.7050 0.00 0.02 0.00 0.84 0.00 0.12 0.02 0.00
#> TCGA.DD.AAE3.01 1 0.0808 0.8061 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25X.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A4NA.01 7 0.1563 0.6759 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.DD.AACI.01 4 0.5591 0.4093 0.00 0.02 0.00 0.60 0.16 0.12 0.10 0.00
#> TCGA.CC.A9FU.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A3RK.01 4 0.3514 0.2378 0.00 0.00 0.00 0.64 0.00 0.00 0.02 0.34
#> TCGA.CC.A5UD.01 5 0.0808 0.8218 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.1091 0.8045 0.94 0.06 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 3 0.5898 0.2447 0.00 0.16 0.42 0.00 0.00 0.34 0.08 0.00
#> TCGA.ZS.A9CF.02 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 1 0.0000 0.8063 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M4.01 6 0.3594 0.5978 0.00 0.28 0.00 0.00 0.00 0.68 0.04 0.00
#> TCGA.G3.A7M8.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAVP.01 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.5260.01 7 0.1563 0.6759 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.DD.A4NR.01 7 0.1563 0.6759 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.2Y.A9H2.01 7 0.2888 0.5586 0.00 0.00 0.00 0.04 0.00 0.00 0.80 0.16
#> TCGA.DD.AAE6.01 3 0.3128 0.7938 0.00 0.10 0.82 0.00 0.00 0.04 0.04 0.00
#> TCGA.G3.AAV2.01 6 0.3570 0.3339 0.00 0.00 0.00 0.02 0.36 0.62 0.00 0.00
#> TCGA.BC.A10Z.11 8 0.0000 0.9809 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZP.A9CY.01 4 0.2852 0.6581 0.00 0.28 0.00 0.72 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.3991 0.6863 0.62 0.32 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Y.01 4 0.4059 0.6181 0.00 0.28 0.00 0.64 0.08 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node025 , Node031-leaf , Node032 , Node041 , Node042 .
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 87 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.966 0.987 0.4771 0.530 0.530
#> 3 3 1.000 0.991 0.996 0.3951 0.735 0.531
#> 4 4 0.756 0.730 0.811 0.0844 0.928 0.793
#> 5 5 0.776 0.652 0.815 0.0667 0.870 0.608
#> 6 6 0.796 0.690 0.789 0.0367 0.917 0.683
#> 7 7 0.846 0.738 0.831 0.0257 0.948 0.753
#> 8 8 0.824 0.648 0.748 0.0240 0.941 0.727
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.BC.A3KF.01 2 0.000 1.000 0.00 1.00
#> TCGA.XR.A8TG.01 1 0.000 0.979 1.00 0.00
#> TCGA.BC.A10Y.01 1 0.000 0.979 1.00 0.00
#> TCGA.RC.A7SF.01 2 0.000 1.000 0.00 1.00
#> TCGA.BC.A216.01 1 0.995 0.177 0.54 0.46
#> TCGA.DD.AACA.02 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AACA.01 2 0.000 1.000 0.00 1.00
#> TCGA.2Y.A9H4.01 2 0.000 1.000 0.00 1.00
#> TCGA.EP.A26S.01 2 0.000 1.000 0.00 1.00
#> TCGA.BC.A217.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A1EA.01 2 0.000 1.000 0.00 1.00
#> TCGA.CC.A8HU.01 1 0.000 0.979 1.00 0.00
#> TCGA.RC.A7SB.01 1 0.000 0.979 1.00 0.00
#> TCGA.2Y.A9H9.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAW2.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AADD.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AACV.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A1EL.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AAD0.01 2 0.000 1.000 0.00 1.00
#> TCGA.2Y.A9HA.01 1 0.000 0.979 1.00 0.00
#> TCGA.BC.A8YO.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AAE2.01 1 0.000 0.979 1.00 0.00
#> TCGA.XR.A8TF.01 1 0.000 0.979 1.00 0.00
#> TCGA.G3.AAV4.01 2 0.000 1.000 0.00 1.00
#> TCGA.2Y.A9GZ.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A1EE.01 2 0.000 1.000 0.00 1.00
#> TCGA.G3.AAUZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.LG.A6GG.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AAE4.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AACB.01 1 0.000 0.979 1.00 0.00
#> TCGA.BW.A5NO.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A11C.01 1 0.000 0.979 1.00 0.00
#> TCGA.4R.AA8I.01 2 0.000 1.000 0.00 1.00
#> TCGA.CC.5264.01 1 0.000 0.979 1.00 0.00
#> TCGA.QA.A7B7.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAEB.01 1 0.000 0.979 1.00 0.00
#> TCGA.CC.5263.01 1 0.000 0.979 1.00 0.00
#> TCGA.G3.A7M6.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A73D.01 2 0.000 1.000 0.00 1.00
#> TCGA.G3.A6UC.01 1 0.000 0.979 1.00 0.00
#> TCGA.CC.A7IH.01 2 0.000 1.000 0.00 1.00
#> TCGA.BC.A10U.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A1EK.01 1 0.000 0.979 1.00 0.00
#> TCGA.BC.A10Z.01 1 0.000 0.979 1.00 0.00
#> TCGA.WJ.A86L.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AACU.01 1 0.981 0.299 0.58 0.42
#> TCGA.G3.A25U.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZS.A9CE.01 2 0.000 1.000 0.00 1.00
#> TCGA.EP.A2KC.01 2 0.000 1.000 0.00 1.00
#> TCGA.GJ.A9DB.01 1 0.000 0.979 1.00 0.00
#> TCGA.CC.A7IL.01 1 0.000 0.979 1.00 0.00
#> TCGA.ED.A7PZ.01 1 0.000 0.979 1.00 0.00
#> TCGA.G3.AAV0.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AACJ.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAW3.01 2 0.000 1.000 0.00 1.00
#> TCGA.G3.A25S.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A73E.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAD6.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.A3A1.01 1 0.000 0.979 1.00 0.00
#> TCGA.CC.A7IK.01 1 0.000 0.979 1.00 0.00
#> TCGA.G3.A3CJ.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AACP.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AADG.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AAE9.01 1 0.000 0.979 1.00 0.00
#> TCGA.BD.A2L6.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A11D.01 1 0.000 0.979 1.00 0.00
#> TCGA.ZP.A9D4.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AACK.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAD8.01 1 0.000 0.979 1.00 0.00
#> TCGA.2Y.A9H0.01 1 0.000 0.979 1.00 0.00
#> TCGA.MI.A75G.01 2 0.000 1.000 0.00 1.00
#> TCGA.FV.A2QR.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AACE.01 1 0.000 0.979 1.00 0.00
#> TCGA.G3.A25Z.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.A3A5.01 1 0.000 0.979 1.00 0.00
#> TCGA.RC.A7SK.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AADF.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.A1EJ.01 1 0.000 0.979 1.00 0.00
#> TCGA.G3.A7M5.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AADL.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AAE3.01 1 0.795 0.683 0.76 0.24
#> TCGA.CC.A9FU.01 1 0.000 0.979 1.00 0.00
#> TCGA.DD.AADV.01 1 0.000 0.979 1.00 0.00
#> TCGA.ZS.A9CF.02 1 0.000 0.979 1.00 0.00
#> TCGA.ZS.A9CF.01 2 0.000 1.000 0.00 1.00
#> TCGA.RC.A6M4.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.A115.01 1 0.000 0.979 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BC.A3KF.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.XR.A8TG.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BC.A10Y.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.RC.A7SF.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.BC.A216.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.AACA.02 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.AACA.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.2Y.A9H4.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.EP.A26S.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.BC.A217.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.A1EA.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.CC.A8HU.01 1 0.4796 0.725 0.78 0.00 0.22
#> TCGA.RC.A7SB.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.2Y.A9H9.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.AAW2.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.AADD.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AACV.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.A1EL.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AAD0.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.2Y.A9HA.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BC.A8YO.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.AAE2.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.XR.A8TF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.G3.AAV4.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.G3.AAUZ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.LG.A6GG.01 1 0.3340 0.864 0.88 0.00 0.12
#> TCGA.DD.AAE4.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AACB.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BW.A5NO.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.A11C.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.4R.AA8I.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CC.5264.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.QA.A7B7.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.AAEB.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CC.5263.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.G3.A7M6.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.A73D.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.G3.A6UC.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CC.A7IH.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.BC.A10U.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.A1EK.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AACU.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.G3.A25U.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.ZS.A9CE.01 2 0.0892 0.980 0.00 0.98 0.02
#> TCGA.EP.A2KC.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.GJ.A9DB.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.G3.AAV0.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.AACJ.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.AAW3.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.G3.A25S.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.A73E.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.AAD6.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.A3A1.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CC.A7IK.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.G3.A3CJ.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.AACP.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.AADG.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AAE9.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BD.A2L6.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.A11D.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZP.A9D4.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.AACK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.AAD8.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.2Y.A9H0.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.MI.A75G.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.FV.A2QR.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.AACE.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.G3.A25Z.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.A3A5.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.RC.A7SK.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AADF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DD.A1EJ.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AADL.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AAE3.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CC.A9FU.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.ZS.A9CF.02 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZS.A9CF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.RC.A6M4.01 2 0.0000 0.999 0.00 1.00 0.00
#> TCGA.DD.A115.01 1 0.0000 0.990 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.BC.A3KF.01 4 0.5271 -0.00053 0.00 0.34 0.02 0.64
#> TCGA.XR.A8TG.01 3 0.2011 0.64477 0.00 0.00 0.92 0.08
#> TCGA.BC.A10Y.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SF.01 2 0.4790 0.55977 0.00 0.62 0.00 0.38
#> TCGA.BC.A216.01 3 0.3975 0.48461 0.00 0.00 0.76 0.24
#> TCGA.DD.AACA.02 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.DD.AACA.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.2Y.A9H4.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.EP.A26S.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.BC.A217.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EA.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.CC.A8HU.01 3 0.6449 0.37247 0.22 0.00 0.64 0.14
#> TCGA.RC.A7SB.01 1 0.3935 0.83394 0.84 0.00 0.10 0.06
#> TCGA.2Y.A9H9.01 4 0.4277 0.51045 0.00 0.00 0.28 0.72
#> TCGA.DD.AAW2.01 2 0.4713 0.66994 0.00 0.64 0.00 0.36
#> TCGA.DD.AADD.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.AACV.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 1 0.5986 0.49584 0.62 0.00 0.32 0.06
#> TCGA.DD.AAD0.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9HA.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.BC.A8YO.01 3 0.0707 0.66360 0.00 0.00 0.98 0.02
#> TCGA.DD.AAE2.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 3 0.4406 0.40460 0.00 0.00 0.70 0.30
#> TCGA.G3.AAV4.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.G3.AAUZ.01 4 0.4277 0.51045 0.00 0.00 0.28 0.72
#> TCGA.LG.A6GG.01 3 0.5489 0.38384 0.24 0.00 0.70 0.06
#> TCGA.DD.AAE4.01 1 0.4491 0.79272 0.80 0.00 0.14 0.06
#> TCGA.DD.AACB.01 1 0.1637 0.91276 0.94 0.00 0.00 0.06
#> TCGA.BW.A5NO.01 1 0.5767 0.57756 0.66 0.00 0.28 0.06
#> TCGA.DD.A11C.01 3 0.4406 0.40460 0.00 0.00 0.70 0.30
#> TCGA.4R.AA8I.01 3 0.4134 0.45910 0.00 0.00 0.74 0.26
#> TCGA.CC.5264.01 1 0.4949 0.74445 0.76 0.00 0.18 0.06
#> TCGA.QA.A7B7.01 4 0.4994 -0.10206 0.00 0.00 0.48 0.52
#> TCGA.DD.AAEB.01 3 0.2011 0.65191 0.00 0.00 0.92 0.08
#> TCGA.CC.5263.01 1 0.3935 0.83394 0.84 0.00 0.10 0.06
#> TCGA.G3.A7M6.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.G3.A6UC.01 3 0.4790 0.36272 0.00 0.00 0.62 0.38
#> TCGA.CC.A7IH.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.BC.A10U.01 3 0.2647 0.63975 0.00 0.00 0.88 0.12
#> TCGA.DD.A1EK.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 3 0.4277 0.47701 0.00 0.00 0.72 0.28
#> TCGA.G3.A25U.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.ZS.A9CE.01 4 0.5392 0.34495 0.00 0.28 0.04 0.68
#> TCGA.EP.A2KC.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.GJ.A9DB.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.DD.AACJ.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.DD.AAW3.01 4 0.4713 0.14754 0.00 0.00 0.36 0.64
#> TCGA.G3.A25S.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.A73E.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD6.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.DD.A3A1.01 3 0.0707 0.66435 0.00 0.00 0.98 0.02
#> TCGA.CC.A7IK.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.G3.A3CJ.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.DD.AACP.01 3 0.4624 0.34727 0.00 0.00 0.66 0.34
#> TCGA.DD.AADG.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.AAE9.01 3 0.2011 0.65191 0.00 0.00 0.92 0.08
#> TCGA.BD.A2L6.01 3 0.0707 0.66435 0.00 0.00 0.98 0.02
#> TCGA.DD.A11D.01 3 0.0707 0.66435 0.00 0.00 0.98 0.02
#> TCGA.ZP.A9D4.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.DD.AACK.01 3 0.4994 -0.00342 0.00 0.00 0.52 0.48
#> TCGA.DD.AAD8.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.MI.A75G.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.FV.A2QR.01 3 0.0707 0.66435 0.00 0.00 0.98 0.02
#> TCGA.DD.AACE.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.G3.A25Z.01 2 0.3400 0.86079 0.00 0.82 0.00 0.18
#> TCGA.DD.A3A5.01 3 0.2921 0.62791 0.00 0.00 0.86 0.14
#> TCGA.RC.A7SK.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.AADF.01 3 0.4406 0.40460 0.00 0.00 0.70 0.30
#> TCGA.DD.A1EJ.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.AADL.01 1 0.3247 0.86946 0.88 0.00 0.06 0.06
#> TCGA.DD.AAE3.01 3 0.4277 0.47701 0.00 0.00 0.72 0.28
#> TCGA.CC.A9FU.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.94953 1.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.02 3 0.4624 0.34727 0.00 0.00 0.66 0.34
#> TCGA.ZS.A9CF.01 4 0.4277 0.51045 0.00 0.00 0.28 0.72
#> TCGA.RC.A6M4.01 2 0.0000 0.86706 0.00 1.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.0000 0.94953 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.BC.A3KF.01 5 0.5607 0.525 0.00 0.38 0.00 0.08 0.54
#> TCGA.XR.A8TG.01 3 0.2020 0.583 0.00 0.00 0.90 0.10 0.00
#> TCGA.BC.A10Y.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SF.01 2 0.2331 0.511 0.00 0.90 0.00 0.02 0.08
#> TCGA.BC.A216.01 3 0.6824 -0.234 0.00 0.00 0.34 0.34 0.32
#> TCGA.DD.AACA.02 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.DD.AACA.01 2 0.0000 0.628 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H4.01 2 0.0609 0.633 0.00 0.98 0.00 0.00 0.02
#> TCGA.EP.A26S.01 2 0.0609 0.615 0.00 0.98 0.00 0.00 0.02
#> TCGA.BC.A217.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EA.01 2 0.0000 0.628 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A8HU.01 3 0.1410 0.567 0.06 0.00 0.94 0.00 0.00
#> TCGA.RC.A7SB.01 3 0.3796 0.477 0.30 0.00 0.70 0.00 0.00
#> TCGA.2Y.A9H9.01 4 0.5245 0.447 0.00 0.28 0.00 0.64 0.08
#> TCGA.DD.AAW2.01 2 0.4876 0.203 0.00 0.70 0.00 0.08 0.22
#> TCGA.DD.AADD.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACV.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 3 0.2929 0.539 0.18 0.00 0.82 0.00 0.00
#> TCGA.DD.AAD0.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.2Y.A9HA.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A8YO.01 3 0.3641 0.573 0.00 0.00 0.82 0.12 0.06
#> TCGA.DD.AAE2.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 4 0.2732 0.722 0.00 0.00 0.16 0.84 0.00
#> TCGA.G3.AAV4.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.2Y.A9GZ.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.G3.AAUZ.01 4 0.5425 0.382 0.00 0.32 0.00 0.60 0.08
#> TCGA.LG.A6GG.01 3 0.1216 0.582 0.02 0.00 0.96 0.02 0.00
#> TCGA.DD.AAE4.01 3 0.3796 0.477 0.30 0.00 0.70 0.00 0.00
#> TCGA.DD.AACB.01 1 0.4126 0.317 0.62 0.00 0.38 0.00 0.00
#> TCGA.BW.A5NO.01 3 0.4132 0.499 0.26 0.00 0.72 0.02 0.00
#> TCGA.DD.A11C.01 4 0.2732 0.722 0.00 0.00 0.16 0.84 0.00
#> TCGA.4R.AA8I.01 4 0.6816 -0.138 0.00 0.00 0.32 0.36 0.32
#> TCGA.CC.5264.01 3 0.4675 0.388 0.38 0.00 0.60 0.02 0.00
#> TCGA.QA.A7B7.01 4 0.3421 0.677 0.00 0.00 0.08 0.84 0.08
#> TCGA.DD.AAEB.01 3 0.4982 0.411 0.00 0.00 0.70 0.10 0.20
#> TCGA.CC.5263.01 3 0.3561 0.503 0.26 0.00 0.74 0.00 0.00
#> TCGA.G3.A7M6.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.G3.A6UC.01 5 0.6530 0.109 0.00 0.00 0.36 0.20 0.44
#> TCGA.CC.A7IH.01 2 0.0609 0.615 0.00 0.98 0.00 0.00 0.02
#> TCGA.BC.A10U.01 3 0.3521 0.534 0.00 0.00 0.82 0.04 0.14
#> TCGA.DD.A1EK.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 3 0.6254 0.013 0.00 0.00 0.50 0.16 0.34
#> TCGA.G3.A25U.01 2 0.0609 0.615 0.00 0.98 0.00 0.00 0.02
#> TCGA.ZS.A9CE.01 2 0.5457 -0.379 0.00 0.48 0.00 0.46 0.06
#> TCGA.EP.A2KC.01 2 0.0000 0.628 0.00 1.00 0.00 0.00 0.00
#> TCGA.GJ.A9DB.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.DD.AACJ.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.DD.AAW3.01 5 0.7003 0.586 0.00 0.26 0.06 0.14 0.54
#> TCGA.G3.A25S.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73E.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.DD.AAD6.01 2 0.0000 0.628 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.01 3 0.4637 0.537 0.00 0.00 0.74 0.16 0.10
#> TCGA.CC.A7IK.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CJ.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.DD.AACP.01 4 0.2516 0.729 0.00 0.00 0.14 0.86 0.00
#> TCGA.DD.AADG.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE9.01 3 0.4170 0.510 0.00 0.00 0.78 0.08 0.14
#> TCGA.BD.A2L6.01 3 0.4373 0.551 0.00 0.00 0.76 0.16 0.08
#> TCGA.DD.A11D.01 3 0.4373 0.551 0.00 0.00 0.76 0.16 0.08
#> TCGA.ZP.A9D4.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.DD.AACK.01 4 0.2331 0.706 0.00 0.00 0.08 0.90 0.02
#> TCGA.DD.AAD8.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75G.01 2 0.0609 0.633 0.00 0.98 0.00 0.00 0.02
#> TCGA.FV.A2QR.01 3 0.4373 0.551 0.00 0.00 0.76 0.16 0.08
#> TCGA.DD.AACE.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Z.01 2 0.0000 0.628 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A5.01 3 0.0000 0.573 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A7SK.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADF.01 4 0.2732 0.722 0.00 0.00 0.16 0.84 0.00
#> TCGA.DD.A1EJ.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADL.01 3 0.4126 0.401 0.38 0.00 0.62 0.00 0.00
#> TCGA.DD.AAE3.01 3 0.6254 0.013 0.00 0.00 0.50 0.16 0.34
#> TCGA.CC.A9FU.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.02 4 0.2516 0.729 0.00 0.00 0.14 0.86 0.00
#> TCGA.ZS.A9CF.01 4 0.4876 0.517 0.00 0.22 0.00 0.70 0.08
#> TCGA.RC.A6M4.01 2 0.4287 0.657 0.00 0.54 0.00 0.00 0.46
#> TCGA.DD.A115.01 1 0.0000 0.983 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.BC.A3KF.01 5 0.7488 0.1117 0.00 0.04 0.10 0.14 0.46 0.26
#> TCGA.XR.A8TG.01 3 0.4078 0.2515 0.00 0.00 0.64 0.00 0.02 0.34
#> TCGA.BC.A10Y.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SF.01 4 0.4613 -0.0482 0.00 0.26 0.00 0.66 0.08 0.00
#> TCGA.BC.A216.01 6 0.4575 0.3401 0.00 0.00 0.02 0.34 0.02 0.62
#> TCGA.DD.AACA.02 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACA.01 2 0.4758 0.6636 0.00 0.58 0.00 0.36 0.06 0.00
#> TCGA.2Y.A9H4.01 2 0.4482 0.6701 0.00 0.60 0.00 0.36 0.04 0.00
#> TCGA.EP.A26S.01 2 0.5195 0.6369 0.00 0.54 0.00 0.36 0.10 0.00
#> TCGA.BC.A217.01 1 0.0547 0.9752 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DD.A1EA.01 2 0.4993 0.6533 0.00 0.56 0.00 0.36 0.08 0.00
#> TCGA.CC.A8HU.01 3 0.2048 0.6835 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.RC.A7SB.01 3 0.2956 0.7704 0.12 0.00 0.84 0.00 0.00 0.04
#> TCGA.2Y.A9H9.01 4 0.2512 0.6003 0.00 0.00 0.00 0.88 0.06 0.06
#> TCGA.DD.AAW2.01 5 0.8080 0.0189 0.00 0.18 0.10 0.16 0.44 0.12
#> TCGA.DD.AADD.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AACV.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.A1EL.01 3 0.2048 0.6835 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.DD.AAD0.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9HA.01 1 0.0547 0.9752 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BC.A8YO.01 6 0.4348 0.5615 0.00 0.00 0.32 0.00 0.04 0.64
#> TCGA.DD.AAE2.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 5 0.6105 0.3943 0.00 0.00 0.02 0.22 0.52 0.24
#> TCGA.G3.AAV4.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.A1EE.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAUZ.01 4 0.2190 0.5987 0.00 0.00 0.00 0.90 0.04 0.06
#> TCGA.LG.A6GG.01 3 0.2048 0.6811 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.DD.AAE4.01 3 0.2956 0.7704 0.12 0.00 0.84 0.00 0.00 0.04
#> TCGA.DD.AACB.01 3 0.3198 0.6311 0.26 0.00 0.74 0.00 0.00 0.00
#> TCGA.BW.A5NO.01 3 0.3270 0.7609 0.12 0.00 0.82 0.00 0.00 0.06
#> TCGA.DD.A11C.01 5 0.6105 0.3943 0.00 0.00 0.02 0.22 0.52 0.24
#> TCGA.4R.AA8I.01 6 0.4575 0.3401 0.00 0.00 0.02 0.34 0.02 0.62
#> TCGA.CC.5264.01 3 0.2793 0.7042 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.QA.A7B7.01 4 0.5721 0.2781 0.00 0.00 0.00 0.52 0.24 0.24
#> TCGA.DD.AAEB.01 6 0.3647 0.5611 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.CC.5263.01 3 0.2260 0.7626 0.14 0.00 0.86 0.00 0.00 0.00
#> TCGA.G3.A7M6.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 6 0.4536 0.5361 0.00 0.00 0.12 0.00 0.18 0.70
#> TCGA.CC.A7IH.01 2 0.5371 0.6177 0.00 0.52 0.00 0.36 0.12 0.00
#> TCGA.BC.A10U.01 6 0.3706 0.5319 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.DD.A1EK.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BC.A10Z.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.WJ.A86L.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AACU.01 6 0.4887 0.5793 0.00 0.00 0.08 0.22 0.02 0.68
#> TCGA.G3.A25U.01 2 0.5235 0.6154 0.00 0.52 0.00 0.38 0.10 0.00
#> TCGA.ZS.A9CE.01 4 0.0547 0.5368 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.EP.A2KC.01 2 0.4758 0.6636 0.00 0.58 0.00 0.36 0.06 0.00
#> TCGA.GJ.A9DB.01 1 0.0547 0.9752 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.ED.A7PZ.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G3.AAV0.01 2 0.0547 0.7423 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DD.AACJ.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW3.01 5 0.5906 -0.0322 0.00 0.00 0.12 0.02 0.44 0.42
#> TCGA.G3.A25S.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.A73E.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD6.01 2 0.4993 0.6533 0.00 0.56 0.00 0.36 0.08 0.00
#> TCGA.DD.A3A1.01 6 0.4238 0.6457 0.00 0.00 0.16 0.04 0.04 0.76
#> TCGA.CC.A7IK.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G3.A3CJ.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACP.01 5 0.5684 0.3071 0.00 0.00 0.00 0.28 0.52 0.20
#> TCGA.DD.AADG.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AAE9.01 6 0.3647 0.5611 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.BD.A2L6.01 6 0.4552 0.6247 0.00 0.00 0.30 0.00 0.06 0.64
#> TCGA.DD.A11D.01 6 0.4265 0.6326 0.00 0.00 0.30 0.00 0.04 0.66
#> TCGA.ZP.A9D4.01 2 0.0547 0.7424 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DD.AACK.01 4 0.5202 0.2851 0.00 0.00 0.00 0.60 0.26 0.14
#> TCGA.DD.AAD8.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 1 0.0937 0.9572 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.MI.A75G.01 2 0.4482 0.6701 0.00 0.60 0.00 0.36 0.04 0.00
#> TCGA.FV.A2QR.01 6 0.4552 0.6247 0.00 0.00 0.30 0.00 0.06 0.64
#> TCGA.DD.AACE.01 1 0.0547 0.9752 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.G3.A25Z.01 2 0.4806 0.6489 0.00 0.56 0.00 0.38 0.06 0.00
#> TCGA.DD.A3A5.01 3 0.3198 0.5088 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.RC.A7SK.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADF.01 5 0.6105 0.3943 0.00 0.00 0.02 0.22 0.52 0.24
#> TCGA.DD.A1EJ.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0547 0.9752 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DD.AADL.01 3 0.2631 0.7337 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.DD.AAE3.01 6 0.4495 0.5737 0.00 0.00 0.06 0.20 0.02 0.72
#> TCGA.CC.A9FU.01 1 0.0547 0.9851 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.02 5 0.6105 0.3719 0.00 0.00 0.02 0.24 0.52 0.22
#> TCGA.ZS.A9CF.01 4 0.3746 0.5409 0.00 0.00 0.00 0.78 0.14 0.08
#> TCGA.RC.A6M4.01 2 0.0000 0.7430 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.0000 0.9846 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.BC.A3KF.01 7 0.3755 0.6871 0.00 0.00 0.00 0.34 0.00 0.02 0.64
#> TCGA.XR.A8TG.01 3 0.5490 0.2292 0.00 0.00 0.54 0.00 0.06 0.32 0.08
#> TCGA.BC.A10Y.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SF.01 4 0.1166 0.3606 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.BC.A216.01 6 0.5135 0.4372 0.00 0.00 0.02 0.14 0.02 0.66 0.16
#> TCGA.DD.AACA.02 2 0.0504 0.9659 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AACA.01 4 0.4772 0.6279 0.00 0.32 0.00 0.60 0.00 0.04 0.04
#> TCGA.2Y.A9H4.01 4 0.3221 0.6383 0.00 0.32 0.00 0.68 0.00 0.00 0.00
#> TCGA.EP.A26S.01 4 0.4845 0.6269 0.00 0.30 0.02 0.62 0.00 0.04 0.02
#> TCGA.BC.A217.01 1 0.0504 0.9776 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EA.01 4 0.4461 0.6319 0.00 0.32 0.02 0.62 0.00 0.04 0.00
#> TCGA.CC.A8HU.01 3 0.1664 0.7329 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.RC.A7SB.01 3 0.4358 0.7092 0.06 0.00 0.74 0.00 0.00 0.12 0.08
#> TCGA.2Y.A9H9.01 4 0.5605 -0.0039 0.00 0.00 0.00 0.58 0.24 0.10 0.08
#> TCGA.DD.AAW2.01 7 0.5571 0.5110 0.00 0.10 0.02 0.32 0.00 0.02 0.54
#> TCGA.DD.AADD.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACV.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 3 0.2159 0.7434 0.02 0.00 0.90 0.00 0.00 0.06 0.02
#> TCGA.DD.AAD0.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9HA.01 1 0.0863 0.9631 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.BC.A8YO.01 6 0.5430 0.6054 0.00 0.00 0.20 0.02 0.06 0.64 0.08
#> TCGA.DD.AAE2.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 5 0.1363 0.7880 0.00 0.00 0.04 0.00 0.94 0.00 0.02
#> TCGA.G3.AAV4.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAUZ.01 4 0.5605 -0.0039 0.00 0.00 0.00 0.58 0.24 0.10 0.08
#> TCGA.LG.A6GG.01 3 0.0504 0.7378 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DD.AAE4.01 3 0.4536 0.7060 0.06 0.00 0.72 0.00 0.00 0.14 0.08
#> TCGA.DD.AACB.01 3 0.2422 0.6326 0.18 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.BW.A5NO.01 3 0.3744 0.6884 0.02 0.00 0.78 0.00 0.00 0.12 0.08
#> TCGA.DD.A11C.01 5 0.0863 0.7887 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.4R.AA8I.01 6 0.4825 0.4057 0.00 0.00 0.00 0.16 0.02 0.66 0.16
#> TCGA.CC.5264.01 3 0.1886 0.6919 0.12 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.QA.A7B7.01 5 0.6824 0.3413 0.00 0.00 0.00 0.24 0.38 0.24 0.14
#> TCGA.DD.AAEB.01 6 0.3991 0.5987 0.00 0.00 0.22 0.02 0.00 0.72 0.04
#> TCGA.CC.5263.01 3 0.1166 0.7544 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M6.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 6 0.4778 0.4379 0.00 0.00 0.06 0.02 0.00 0.58 0.34
#> TCGA.CC.A7IH.01 4 0.4993 0.5869 0.00 0.26 0.02 0.64 0.00 0.04 0.04
#> TCGA.BC.A10U.01 6 0.4908 0.4847 0.00 0.00 0.26 0.02 0.00 0.62 0.10
#> TCGA.DD.A1EK.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 6 0.4831 0.5534 0.00 0.00 0.06 0.08 0.02 0.72 0.12
#> TCGA.G3.A25U.01 4 0.4845 0.6269 0.00 0.30 0.02 0.62 0.00 0.04 0.02
#> TCGA.ZS.A9CE.01 4 0.3744 0.2105 0.00 0.00 0.00 0.78 0.12 0.02 0.08
#> TCGA.EP.A2KC.01 4 0.4003 0.6384 0.00 0.32 0.00 0.64 0.00 0.04 0.00
#> TCGA.GJ.A9DB.01 1 0.0863 0.9631 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PZ.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 2 0.1433 0.8848 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.DD.AACJ.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW3.01 7 0.4348 0.5125 0.00 0.00 0.00 0.14 0.00 0.18 0.68
#> TCGA.G3.A25S.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73E.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD6.01 4 0.4915 0.6303 0.00 0.32 0.02 0.60 0.00 0.04 0.02
#> TCGA.DD.A3A1.01 6 0.4892 0.6388 0.00 0.00 0.16 0.02 0.08 0.70 0.04
#> TCGA.CC.A7IK.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CJ.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACP.01 5 0.1363 0.7781 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.DD.AADG.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE9.01 6 0.3661 0.5929 0.00 0.00 0.22 0.02 0.00 0.74 0.02
#> TCGA.BD.A2L6.01 6 0.5856 0.5072 0.00 0.00 0.26 0.00 0.12 0.54 0.08
#> TCGA.DD.A11D.01 6 0.5856 0.5072 0.00 0.00 0.26 0.00 0.12 0.54 0.08
#> TCGA.ZP.A9D4.01 2 0.1363 0.9203 0.00 0.94 0.02 0.04 0.00 0.00 0.00
#> TCGA.DD.AACK.01 5 0.5386 0.5317 0.00 0.00 0.00 0.24 0.60 0.06 0.10
#> TCGA.DD.AAD8.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 1 0.0863 0.9625 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.MI.A75G.01 4 0.3221 0.6383 0.00 0.32 0.00 0.68 0.00 0.00 0.00
#> TCGA.FV.A2QR.01 6 0.5856 0.5072 0.00 0.00 0.26 0.00 0.12 0.54 0.08
#> TCGA.DD.AACE.01 1 0.0863 0.9631 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Z.01 4 0.3221 0.6383 0.00 0.32 0.00 0.68 0.00 0.00 0.00
#> TCGA.DD.A3A5.01 3 0.4487 0.4368 0.00 0.00 0.60 0.00 0.00 0.32 0.08
#> TCGA.RC.A7SK.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADF.01 5 0.0863 0.7887 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.DD.A1EJ.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0863 0.9631 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.DD.AADL.01 3 0.1433 0.7446 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE3.01 6 0.4555 0.5398 0.00 0.00 0.04 0.08 0.02 0.74 0.12
#> TCGA.CC.A9FU.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.02 5 0.0000 0.7860 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZS.A9CF.01 4 0.5605 -0.0039 0.00 0.00 0.00 0.58 0.24 0.10 0.08
#> TCGA.RC.A6M4.01 2 0.0000 0.9791 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.0000 0.9905 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.BC.A3KF.01 5 0.6185 0.2013 0.00 0.38 0.00 0.04 0.40 0.12 0.06 0.00
#> TCGA.XR.A8TG.01 6 0.5455 0.5055 0.38 0.00 0.20 0.00 0.02 0.40 0.00 0.00
#> TCGA.BC.A10Y.01 8 0.0941 0.8977 0.02 0.02 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.RC.A7SF.01 4 0.3514 0.4338 0.00 0.00 0.00 0.64 0.02 0.00 0.34 0.00
#> TCGA.BC.A216.01 6 0.3083 0.0801 0.00 0.00 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.DD.AACA.02 7 0.3449 0.6465 0.00 0.32 0.00 0.00 0.02 0.00 0.66 0.00
#> TCGA.DD.AACA.01 7 0.3170 0.5498 0.00 0.00 0.00 0.20 0.04 0.00 0.76 0.00
#> TCGA.2Y.A9H4.01 7 0.2534 0.5439 0.00 0.00 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.EP.A26S.01 7 0.3615 0.5298 0.00 0.02 0.00 0.20 0.04 0.00 0.74 0.00
#> TCGA.BC.A217.01 8 0.3941 0.7274 0.02 0.26 0.04 0.00 0.00 0.00 0.00 0.68
#> TCGA.DD.A1EA.01 7 0.3615 0.5298 0.00 0.02 0.00 0.20 0.04 0.00 0.74 0.00
#> TCGA.CC.A8HU.01 3 0.2224 0.7304 0.12 0.00 0.86 0.00 0.00 0.02 0.00 0.00
#> TCGA.RC.A7SB.01 3 0.4276 0.6870 0.06 0.28 0.64 0.00 0.00 0.00 0.00 0.02
#> TCGA.2Y.A9H9.01 4 0.0471 0.7235 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DD.AAW2.01 5 0.5768 0.1667 0.00 0.38 0.00 0.02 0.40 0.02 0.18 0.00
#> TCGA.DD.AADD.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACV.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EL.01 3 0.2224 0.7304 0.12 0.00 0.86 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAD0.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.2Y.A9HA.01 8 0.3941 0.7274 0.02 0.26 0.04 0.00 0.00 0.00 0.00 0.68
#> TCGA.BC.A8YO.01 6 0.4097 0.4727 0.08 0.00 0.20 0.02 0.00 0.70 0.00 0.00
#> TCGA.DD.AAE2.01 8 0.1341 0.8847 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.92
#> TCGA.XR.A8TF.01 5 0.4174 0.5628 0.40 0.00 0.00 0.06 0.54 0.00 0.00 0.00
#> TCGA.G3.AAV4.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.2Y.A9GZ.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EE.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.G3.AAUZ.01 4 0.0471 0.7235 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.LG.A6GG.01 3 0.0471 0.7578 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAE4.01 3 0.4487 0.6850 0.08 0.28 0.62 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AACB.01 3 0.2165 0.7259 0.06 0.00 0.88 0.00 0.00 0.00 0.00 0.06
#> TCGA.BW.A5NO.01 3 0.4165 0.6737 0.10 0.26 0.64 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11C.01 5 0.4199 0.5652 0.42 0.00 0.00 0.06 0.52 0.00 0.00 0.00
#> TCGA.4R.AA8I.01 6 0.3015 0.1222 0.00 0.00 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.CC.5264.01 3 0.0941 0.7643 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.QA.A7B7.01 4 0.4284 0.3781 0.04 0.00 0.00 0.58 0.02 0.36 0.00 0.00
#> TCGA.DD.AAEB.01 6 0.4370 0.6353 0.40 0.00 0.08 0.00 0.00 0.52 0.00 0.00
#> TCGA.CC.5263.01 3 0.0941 0.7610 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.G3.A7M6.01 8 0.0941 0.8977 0.02 0.02 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.DD.A73D.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.G3.A6UC.01 6 0.4100 0.5969 0.36 0.00 0.00 0.00 0.06 0.58 0.00 0.00
#> TCGA.CC.A7IH.01 7 0.4180 0.4886 0.00 0.06 0.00 0.20 0.04 0.00 0.70 0.00
#> TCGA.BC.A10U.01 6 0.4391 0.6252 0.42 0.00 0.08 0.00 0.00 0.50 0.00 0.00
#> TCGA.DD.A1EK.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Z.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.WJ.A86L.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACU.01 6 0.1804 0.5239 0.02 0.00 0.00 0.08 0.00 0.90 0.00 0.00
#> TCGA.G3.A25U.01 7 0.3843 0.4811 0.00 0.02 0.00 0.24 0.04 0.00 0.70 0.00
#> TCGA.ZS.A9CE.01 4 0.1947 0.6384 0.00 0.00 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.EP.A2KC.01 7 0.3170 0.5409 0.00 0.00 0.00 0.20 0.04 0.00 0.76 0.00
#> TCGA.GJ.A9DB.01 8 0.3594 0.7259 0.00 0.28 0.04 0.00 0.00 0.00 0.00 0.68
#> TCGA.CC.A7IL.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ED.A7PZ.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.AAV0.01 7 0.3198 0.6456 0.00 0.26 0.00 0.02 0.00 0.00 0.72 0.00
#> TCGA.DD.AACJ.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.DD.AAW3.01 5 0.5768 0.2120 0.02 0.38 0.00 0.02 0.40 0.18 0.00 0.00
#> TCGA.G3.A25S.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A73E.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.DD.AAD6.01 7 0.3615 0.5298 0.00 0.02 0.00 0.20 0.04 0.00 0.74 0.00
#> TCGA.DD.A3A1.01 6 0.3262 0.5794 0.10 0.00 0.02 0.04 0.02 0.82 0.00 0.00
#> TCGA.CC.A7IK.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.A3CJ.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.DD.AACP.01 5 0.4586 0.5259 0.40 0.00 0.02 0.06 0.52 0.00 0.00 0.00
#> TCGA.DD.AADG.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAE9.01 6 0.4370 0.6353 0.40 0.00 0.08 0.00 0.00 0.52 0.00 0.00
#> TCGA.BD.A2L6.01 6 0.4803 0.6244 0.44 0.00 0.08 0.00 0.02 0.46 0.00 0.00
#> TCGA.DD.A11D.01 6 0.4794 0.6348 0.42 0.00 0.08 0.00 0.02 0.48 0.00 0.00
#> TCGA.ZP.A9D4.01 7 0.2852 0.6516 0.00 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.DD.AACK.01 4 0.3528 0.4389 0.08 0.00 0.00 0.74 0.18 0.00 0.00 0.00
#> TCGA.DD.AAD8.01 8 0.2267 0.8310 0.00 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.2Y.A9H0.01 8 0.2624 0.8552 0.02 0.06 0.06 0.00 0.00 0.00 0.00 0.86
#> TCGA.MI.A75G.01 7 0.2534 0.5439 0.00 0.00 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.FV.A2QR.01 6 0.4794 0.6348 0.42 0.00 0.08 0.00 0.02 0.48 0.00 0.00
#> TCGA.DD.AACE.01 8 0.3594 0.7259 0.00 0.28 0.04 0.00 0.00 0.00 0.00 0.68
#> TCGA.G3.A25Z.01 7 0.3198 0.4884 0.00 0.00 0.00 0.26 0.02 0.00 0.72 0.00
#> TCGA.DD.A3A5.01 3 0.5203 -0.1356 0.30 0.00 0.42 0.00 0.00 0.28 0.00 0.00
#> TCGA.RC.A7SK.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADF.01 5 0.4199 0.5652 0.42 0.00 0.00 0.06 0.52 0.00 0.00 0.00
#> TCGA.DD.A1EJ.01 8 0.1741 0.8828 0.02 0.02 0.04 0.00 0.00 0.00 0.00 0.92
#> TCGA.G3.A7M5.01 8 0.3594 0.7259 0.00 0.28 0.04 0.00 0.00 0.00 0.00 0.68
#> TCGA.DD.AADL.01 3 0.2856 0.7297 0.00 0.20 0.78 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAE3.01 6 0.1341 0.5097 0.00 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.CC.A9FU.01 8 0.0000 0.9051 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADV.01 8 0.0471 0.9019 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.ZS.A9CF.02 5 0.4216 0.5608 0.44 0.00 0.00 0.06 0.50 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 4 0.1275 0.7110 0.04 0.00 0.00 0.94 0.00 0.02 0.00 0.00
#> TCGA.RC.A6M4.01 7 0.3083 0.6506 0.00 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.DD.A115.01 8 0.2852 0.7556 0.00 0.28 0.00 0.00 0.00 0.00 0.00 0.72
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 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 36 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5084 0.492 0.492
#> 3 3 0.988 0.968 0.979 0.2294 0.865 0.731
#> 4 4 0.863 0.950 0.970 0.0803 0.956 0.882
#> 5 5 0.815 0.828 0.897 0.1306 0.897 0.692
#> 6 6 0.843 0.832 0.893 0.0546 0.941 0.755
#> 7 7 0.781 0.659 0.858 0.0284 0.954 0.775
#> 8 8 0.798 0.682 0.857 0.0148 0.987 0.927
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.BC.A10Y.01 1 0 1 1 0
#> TCGA.BC.A217.01 1 0 1 1 0
#> TCGA.CC.A8HU.01 2 0 1 0 1
#> TCGA.RC.A7SB.01 1 0 1 1 0
#> TCGA.DD.AADD.01 2 0 1 0 1
#> TCGA.DD.AACV.01 1 0 1 1 0
#> TCGA.DD.A1EL.01 2 0 1 0 1
#> TCGA.2Y.A9HA.01 2 0 1 0 1
#> TCGA.DD.AAE2.01 1 0 1 1 0
#> TCGA.2Y.A9GZ.01 1 0 1 1 0
#> TCGA.LG.A6GG.01 2 0 1 0 1
#> TCGA.DD.AAE4.01 1 0 1 1 0
#> TCGA.DD.AACB.01 2 0 1 0 1
#> TCGA.BW.A5NO.01 1 0 1 1 0
#> TCGA.CC.5264.01 2 0 1 0 1
#> TCGA.CC.5263.01 2 0 1 0 1
#> TCGA.G3.A7M6.01 2 0 1 0 1
#> TCGA.DD.A1EK.01 1 0 1 1 0
#> TCGA.BC.A10Z.01 1 0 1 1 0
#> TCGA.WJ.A86L.01 1 0 1 1 0
#> TCGA.GJ.A9DB.01 1 0 1 1 0
#> TCGA.CC.A7IL.01 1 0 1 1 0
#> TCGA.ED.A7PZ.01 2 0 1 0 1
#> TCGA.G3.A25S.01 2 0 1 0 1
#> TCGA.CC.A7IK.01 2 0 1 0 1
#> TCGA.DD.AADG.01 1 0 1 1 0
#> TCGA.DD.AAD8.01 1 0 1 1 0
#> TCGA.2Y.A9H0.01 2 0 1 0 1
#> TCGA.DD.AACE.01 1 0 1 1 0
#> TCGA.RC.A7SK.01 2 0 1 0 1
#> TCGA.DD.A1EJ.01 2 0 1 0 1
#> TCGA.G3.A7M5.01 1 0 1 1 0
#> TCGA.DD.AADL.01 1 0 1 1 0
#> TCGA.CC.A9FU.01 2 0 1 0 1
#> TCGA.DD.AADV.01 1 0 1 1 0
#> TCGA.DD.A115.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BC.A10Y.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.BC.A217.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.CC.A8HU.01 2 0.207 0.964 0.00 0.94 0.06
#> TCGA.RC.A7SB.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DD.AADD.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.DD.AACV.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DD.A1EL.01 2 0.207 0.964 0.00 0.94 0.06
#> TCGA.2Y.A9HA.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.DD.AAE2.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.LG.A6GG.01 3 0.000 0.974 0.00 0.00 1.00
#> TCGA.DD.AAE4.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DD.AACB.01 2 0.207 0.964 0.00 0.94 0.06
#> TCGA.BW.A5NO.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.CC.5264.01 3 0.000 0.974 0.00 0.00 1.00
#> TCGA.CC.5263.01 3 0.207 0.921 0.00 0.06 0.94
#> TCGA.G3.A7M6.01 2 0.207 0.964 0.00 0.94 0.06
#> TCGA.DD.A1EK.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.BC.A10Z.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.WJ.A86L.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.GJ.A9DB.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.ED.A7PZ.01 2 0.000 0.945 0.00 1.00 0.00
#> TCGA.G3.A25S.01 3 0.000 0.974 0.00 0.00 1.00
#> TCGA.CC.A7IK.01 2 0.296 0.869 0.00 0.90 0.10
#> TCGA.DD.AADG.01 1 0.497 0.825 0.84 0.06 0.10
#> TCGA.DD.AAD8.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.2Y.A9H0.01 3 0.000 0.974 0.00 0.00 1.00
#> TCGA.DD.AACE.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.RC.A7SK.01 3 0.000 0.974 0.00 0.00 1.00
#> TCGA.DD.A1EJ.01 2 0.207 0.964 0.00 0.94 0.06
#> TCGA.G3.A7M5.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DD.AADL.01 3 0.207 0.908 0.06 0.00 0.94
#> TCGA.CC.A9FU.01 2 0.207 0.964 0.00 0.94 0.06
#> TCGA.DD.AADV.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DD.A115.01 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.BC.A10Y.01 1 0.2345 0.927 0.90 0.00 0.00 0.10
#> TCGA.BC.A217.01 1 0.2345 0.927 0.90 0.00 0.00 0.10
#> TCGA.CC.A8HU.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.RC.A7SB.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.DD.AADD.01 2 0.0707 0.963 0.00 0.98 0.00 0.02
#> TCGA.DD.AACV.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9HA.01 2 0.3172 0.809 0.00 0.84 0.00 0.16
#> TCGA.DD.AAE2.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 3 0.0000 0.987 0.00 0.00 1.00 0.00
#> TCGA.DD.AAE4.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.BW.A5NO.01 1 0.2345 0.927 0.90 0.00 0.00 0.10
#> TCGA.CC.5264.01 3 0.0000 0.987 0.00 0.00 1.00 0.00
#> TCGA.CC.5263.01 3 0.1637 0.921 0.00 0.06 0.94 0.00
#> TCGA.G3.A7M6.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EK.01 1 0.2345 0.927 0.90 0.00 0.00 0.10
#> TCGA.BC.A10Z.01 1 0.2345 0.927 0.90 0.00 0.00 0.10
#> TCGA.WJ.A86L.01 1 0.2345 0.927 0.90 0.00 0.00 0.10
#> TCGA.GJ.A9DB.01 1 0.0707 0.957 0.98 0.00 0.00 0.02
#> TCGA.CC.A7IL.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.ED.A7PZ.01 2 0.0707 0.963 0.00 0.98 0.00 0.02
#> TCGA.G3.A25S.01 3 0.0000 0.987 0.00 0.00 1.00 0.00
#> TCGA.CC.A7IK.01 4 0.2345 0.832 0.00 0.10 0.00 0.90
#> TCGA.DD.AADG.01 4 0.2345 0.839 0.10 0.00 0.00 0.90
#> TCGA.DD.AAD8.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 3 0.0000 0.987 0.00 0.00 1.00 0.00
#> TCGA.DD.AACE.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SK.01 3 0.0000 0.987 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EJ.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.DD.AADL.01 3 0.0000 0.987 0.00 0.00 1.00 0.00
#> TCGA.CC.A9FU.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 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.BC.A10Y.01 5 0.3684 0.975 0.28 0.00 0.00 0.00 0.72
#> TCGA.BC.A217.01 5 0.3684 0.975 0.28 0.00 0.00 0.00 0.72
#> TCGA.CC.A8HU.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SB.01 1 0.4613 0.374 0.62 0.00 0.00 0.02 0.36
#> TCGA.DD.AADD.01 2 0.3037 0.855 0.00 0.86 0.00 0.04 0.10
#> TCGA.DD.AACV.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9HA.01 2 0.4252 0.628 0.00 0.70 0.00 0.28 0.02
#> TCGA.DD.AAE2.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE4.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.BW.A5NO.01 5 0.3561 0.966 0.26 0.00 0.00 0.00 0.74
#> TCGA.CC.5264.01 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.5263.01 3 0.2929 0.751 0.00 0.18 0.82 0.00 0.00
#> TCGA.G3.A7M6.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EK.01 1 0.4798 -0.167 0.54 0.00 0.00 0.02 0.44
#> TCGA.BC.A10Z.01 5 0.3684 0.975 0.28 0.00 0.00 0.00 0.72
#> TCGA.WJ.A86L.01 5 0.3424 0.944 0.24 0.00 0.00 0.00 0.76
#> TCGA.GJ.A9DB.01 1 0.4767 0.203 0.56 0.00 0.00 0.02 0.42
#> TCGA.CC.A7IL.01 1 0.1648 0.810 0.94 0.00 0.00 0.02 0.04
#> TCGA.ED.A7PZ.01 2 0.3291 0.843 0.00 0.84 0.00 0.04 0.12
#> TCGA.G3.A25S.01 3 0.0609 0.927 0.00 0.00 0.98 0.00 0.02
#> TCGA.CC.A7IK.01 4 0.0609 0.971 0.00 0.02 0.00 0.98 0.00
#> TCGA.DD.AADG.01 4 0.0000 0.971 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD8.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 3 0.0609 0.930 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AACE.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SK.01 3 0.1043 0.925 0.00 0.00 0.96 0.00 0.04
#> TCGA.DD.A1EJ.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADL.01 3 0.2616 0.867 0.00 0.00 0.88 0.02 0.10
#> TCGA.CC.A9FU.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.0609 0.842 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.BC.A10Y.01 5 0.1807 0.885 0.06 0.00 0.00 0.00 0.92 0.02
#> TCGA.BC.A217.01 5 0.1807 0.885 0.06 0.00 0.00 0.00 0.92 0.02
#> TCGA.CC.A8HU.01 2 0.0000 0.905 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SB.01 6 0.5295 0.688 0.44 0.00 0.00 0.00 0.10 0.46
#> TCGA.DD.AADD.01 2 0.2454 0.842 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.DD.AACV.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 2 0.1267 0.889 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.2Y.A9HA.01 2 0.4890 0.661 0.00 0.66 0.00 0.16 0.00 0.18
#> TCGA.DD.AAE2.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 3 0.0000 0.776 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAE4.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 2 0.0000 0.905 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BW.A5NO.01 5 0.0937 0.888 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.CC.5264.01 3 0.0000 0.776 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.5263.01 3 0.3706 0.364 0.00 0.38 0.62 0.00 0.00 0.00
#> TCGA.G3.A7M6.01 2 0.0000 0.905 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EK.01 5 0.3950 0.474 0.24 0.00 0.00 0.00 0.72 0.04
#> TCGA.BC.A10Z.01 5 0.0547 0.877 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.WJ.A86L.01 5 0.1092 0.874 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.GJ.A9DB.01 6 0.5921 0.697 0.30 0.00 0.00 0.00 0.24 0.46
#> TCGA.CC.A7IL.01 1 0.2725 0.792 0.88 0.00 0.00 0.02 0.04 0.06
#> TCGA.ED.A7PZ.01 2 0.3409 0.738 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.G3.A25S.01 3 0.3156 0.714 0.00 0.00 0.80 0.00 0.02 0.18
#> TCGA.CC.A7IK.01 4 0.0547 0.981 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AADG.01 4 0.0000 0.981 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD8.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 3 0.0547 0.772 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.AACE.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SK.01 3 0.2981 0.729 0.00 0.00 0.82 0.00 0.02 0.16
#> TCGA.DD.A1EJ.01 2 0.0000 0.905 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.0547 0.947 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AADL.01 3 0.3797 0.395 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.CC.A9FU.01 2 0.0000 0.905 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.0000 0.976 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.BC.A10Y.01 5 0.1928 0.8163 0.08 0.00 0.00 0.00 0.90 0.02 0.00
#> TCGA.BC.A217.01 5 0.2163 0.8062 0.10 0.00 0.00 0.00 0.88 0.02 0.00
#> TCGA.CC.A8HU.01 2 0.0863 0.6171 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SB.01 6 0.4030 0.6542 0.16 0.00 0.00 0.00 0.12 0.72 0.00
#> TCGA.DD.AADD.01 2 0.4718 -0.3807 0.00 0.60 0.00 0.00 0.02 0.06 0.32
#> TCGA.DD.AACV.01 1 0.0000 0.9398 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 2 0.1664 0.5636 0.00 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.2Y.A9HA.01 2 0.5830 -0.3209 0.00 0.46 0.00 0.28 0.00 0.02 0.24
#> TCGA.DD.AAE2.01 1 0.0000 0.9398 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.9398 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 3 0.1006 0.8461 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.DD.AAE4.01 1 0.0000 0.9398 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 2 0.0504 0.6233 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BW.A5NO.01 5 0.1860 0.8147 0.04 0.00 0.00 0.00 0.92 0.02 0.02
#> TCGA.CC.5264.01 3 0.0504 0.8405 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CC.5263.01 2 0.3546 0.0642 0.00 0.54 0.46 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M6.01 2 0.0504 0.6313 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EK.01 5 0.5915 0.1734 0.22 0.00 0.00 0.00 0.50 0.24 0.04
#> TCGA.BC.A10Z.01 5 0.1363 0.8198 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.WJ.A86L.01 5 0.2159 0.7844 0.02 0.00 0.00 0.00 0.90 0.06 0.02
#> TCGA.GJ.A9DB.01 6 0.3617 0.6578 0.08 0.00 0.00 0.00 0.16 0.76 0.00
#> TCGA.CC.A7IL.01 1 0.3386 0.7703 0.78 0.00 0.00 0.00 0.02 0.18 0.02
#> TCGA.ED.A7PZ.01 7 0.3459 0.0000 0.00 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.G3.A25S.01 3 0.2572 0.8238 0.00 0.00 0.86 0.00 0.00 0.06 0.08
#> TCGA.CC.A7IK.01 4 0.0000 0.9167 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADG.01 4 0.2163 0.9167 0.00 0.00 0.00 0.88 0.02 0.00 0.10
#> TCGA.DD.AAD8.01 1 0.0000 0.9398 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 3 0.2722 0.7548 0.00 0.00 0.84 0.00 0.00 0.12 0.04
#> TCGA.DD.AACE.01 1 0.0000 0.9398 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SK.01 3 0.4177 0.7087 0.00 0.00 0.70 0.00 0.00 0.18 0.12
#> TCGA.DD.A1EJ.01 2 0.0000 0.6347 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.2163 0.8637 0.88 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.DD.AADL.01 6 0.4461 0.3185 0.00 0.00 0.32 0.00 0.04 0.62 0.02
#> TCGA.CC.A9FU.01 2 0.0000 0.6347 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.9398 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.2745 0.8063 0.82 0.00 0.00 0.00 0.02 0.16 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.BC.A10Y.01 5 0.2204 0.8199 0.02 0.00 0.00 0.00 0.90 0.02 0.02 0.04
#> TCGA.BC.A217.01 5 0.1804 0.8115 0.00 0.00 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.CC.A8HU.01 2 0.0941 0.6817 0.00 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.RC.A7SB.01 6 0.3434 0.7502 0.14 0.00 0.00 0.00 0.10 0.76 0.00 0.00
#> TCGA.DD.AADD.01 8 0.4804 0.0000 0.00 0.40 0.00 0.00 0.00 0.00 0.14 0.46
#> TCGA.DD.AACV.01 1 0.0000 0.9449 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.01 2 0.1341 0.6096 0.00 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.2Y.A9HA.01 2 0.5211 -0.3075 0.00 0.40 0.00 0.34 0.00 0.00 0.26 0.00
#> TCGA.DD.AAE2.01 1 0.0000 0.9449 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GZ.01 1 0.0000 0.9449 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A6GG.01 3 0.1557 0.7960 0.00 0.00 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.DD.AAE4.01 1 0.0000 0.9449 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACB.01 2 0.0000 0.6997 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BW.A5NO.01 5 0.0941 0.8316 0.02 0.00 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.CC.5264.01 3 0.0941 0.7881 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.CC.5263.01 2 0.4284 0.0858 0.00 0.58 0.36 0.00 0.00 0.00 0.02 0.04
#> TCGA.G3.A7M6.01 2 0.0471 0.6929 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EK.01 5 0.4482 0.3126 0.26 0.00 0.00 0.00 0.60 0.14 0.00 0.00
#> TCGA.BC.A10Z.01 5 0.0941 0.8343 0.02 0.00 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.WJ.A86L.01 5 0.1741 0.8122 0.00 0.00 0.00 0.00 0.92 0.02 0.02 0.04
#> TCGA.GJ.A9DB.01 6 0.3450 0.7611 0.12 0.00 0.00 0.00 0.12 0.76 0.00 0.00
#> TCGA.CC.A7IL.01 1 0.4096 0.7051 0.74 0.00 0.00 0.04 0.04 0.16 0.02 0.00
#> TCGA.ED.A7PZ.01 7 0.2406 0.0000 0.00 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.G3.A25S.01 3 0.3619 0.6954 0.00 0.00 0.74 0.00 0.00 0.12 0.00 0.14
#> TCGA.CC.A7IK.01 4 0.2623 0.7761 0.00 0.00 0.00 0.84 0.00 0.00 0.10 0.06
#> TCGA.DD.AADG.01 4 0.1557 0.7824 0.00 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.DD.AAD8.01 1 0.0000 0.9449 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H0.01 3 0.3397 0.7396 0.00 0.00 0.80 0.00 0.00 0.10 0.04 0.06
#> TCGA.DD.AACE.01 1 0.0000 0.9449 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SK.01 3 0.5289 0.6590 0.00 0.00 0.58 0.00 0.00 0.16 0.06 0.20
#> TCGA.DD.A1EJ.01 2 0.0000 0.6997 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M5.01 1 0.1804 0.8837 0.90 0.00 0.00 0.00 0.00 0.08 0.02 0.00
#> TCGA.DD.AADL.01 6 0.4478 0.4616 0.00 0.00 0.22 0.00 0.04 0.68 0.04 0.02
#> TCGA.CC.A9FU.01 2 0.0000 0.6997 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADV.01 1 0.0000 0.9449 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.01 1 0.2265 0.8631 0.88 0.00 0.00 0.00 0.02 0.08 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: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 25 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.4539 0.547 0.547
#> 3 3 0.630 0.793 0.712 0.4377 0.780 0.598
#> 4 4 0.810 0.961 0.913 0.1618 0.900 0.694
#> 5 5 0.905 0.924 0.889 0.0689 0.950 0.779
#> 6 6 0.851 0.854 0.849 0.0312 1.000 1.000
#> 7 7 0.810 0.785 0.818 0.0259 0.953 0.736
#> 8 8 0.806 0.676 0.830 0.0221 0.983 0.884
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2
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.BC.A3KF.01 1 0 1 1 0
#> TCGA.RC.A7SF.01 1 0 1 1 0
#> TCGA.DD.AACA.02 2 0 1 0 1
#> TCGA.DD.AACA.01 2 0 1 0 1
#> TCGA.2Y.A9H4.01 1 0 1 1 0
#> TCGA.EP.A26S.01 2 0 1 0 1
#> TCGA.DD.A1EA.01 2 0 1 0 1
#> TCGA.DD.AAW2.01 2 0 1 0 1
#> TCGA.DD.AAD0.01 2 0 1 0 1
#> TCGA.G3.AAV4.01 2 0 1 0 1
#> TCGA.DD.A1EE.01 2 0 1 0 1
#> TCGA.DD.A73D.01 2 0 1 0 1
#> TCGA.CC.A7IH.01 2 0 1 0 1
#> TCGA.G3.A25U.01 1 0 1 1 0
#> TCGA.ZS.A9CE.01 1 0 1 1 0
#> TCGA.EP.A2KC.01 2 0 1 0 1
#> TCGA.G3.AAV0.01 1 0 1 1 0
#> TCGA.DD.AACJ.01 2 0 1 0 1
#> TCGA.DD.A73E.01 2 0 1 0 1
#> TCGA.DD.AAD6.01 2 0 1 0 1
#> TCGA.G3.A3CJ.01 2 0 1 0 1
#> TCGA.ZP.A9D4.01 2 0 1 0 1
#> TCGA.MI.A75G.01 1 0 1 1 0
#> TCGA.G3.A25Z.01 1 0 1 1 0
#> TCGA.RC.A6M4.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BC.A3KF.01 1 0.000 0.969 1.0 0.00 0.00
#> TCGA.RC.A7SF.01 1 0.296 0.947 0.9 0.10 0.00
#> TCGA.DD.AACA.02 2 0.556 0.520 0.0 0.70 0.30
#> TCGA.DD.AACA.01 2 0.604 0.477 0.0 0.62 0.38
#> TCGA.2Y.A9H4.01 1 0.296 0.947 0.9 0.10 0.00
#> TCGA.EP.A26S.01 3 0.000 1.000 0.0 0.00 1.00
#> TCGA.DD.A1EA.01 3 0.000 1.000 0.0 0.00 1.00
#> TCGA.DD.AAW2.01 3 0.000 1.000 0.0 0.00 1.00
#> TCGA.DD.AAD0.01 2 0.595 0.618 0.0 0.64 0.36
#> TCGA.G3.AAV4.01 2 0.595 0.618 0.0 0.64 0.36
#> TCGA.DD.A1EE.01 2 0.595 0.618 0.0 0.64 0.36
#> TCGA.DD.A73D.01 2 0.595 0.618 0.0 0.64 0.36
#> TCGA.CC.A7IH.01 3 0.000 1.000 0.0 0.00 1.00
#> TCGA.G3.A25U.01 1 0.000 0.969 1.0 0.00 0.00
#> TCGA.ZS.A9CE.01 1 0.000 0.969 1.0 0.00 0.00
#> TCGA.EP.A2KC.01 2 0.604 0.477 0.0 0.62 0.38
#> TCGA.G3.AAV0.01 1 0.000 0.969 1.0 0.00 0.00
#> TCGA.DD.AACJ.01 2 0.604 0.477 0.0 0.62 0.38
#> TCGA.DD.A73E.01 2 0.595 0.618 0.0 0.64 0.36
#> TCGA.DD.AAD6.01 2 0.604 0.477 0.0 0.62 0.38
#> TCGA.G3.A3CJ.01 3 0.000 1.000 0.0 0.00 1.00
#> TCGA.ZP.A9D4.01 3 0.000 1.000 0.0 0.00 1.00
#> TCGA.MI.A75G.01 1 0.000 0.969 1.0 0.00 0.00
#> TCGA.G3.A25Z.01 1 0.296 0.947 0.9 0.10 0.00
#> TCGA.RC.A6M4.01 2 0.595 0.618 0.0 0.64 0.36
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BC.A3KF.01 1 0.0707 0.912 0.98 0.00 0.00 0.02
#> TCGA.RC.A7SF.01 1 0.4894 0.868 0.78 0.10 0.00 0.12
#> TCGA.DD.AACA.02 4 0.3606 0.938 0.00 0.14 0.02 0.84
#> TCGA.DD.AACA.01 4 0.3935 0.975 0.00 0.10 0.06 0.84
#> TCGA.2Y.A9H4.01 1 0.4894 0.868 0.78 0.10 0.00 0.12
#> TCGA.EP.A26S.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EA.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DD.AAW2.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD0.01 2 0.2647 1.000 0.00 0.88 0.12 0.00
#> TCGA.G3.AAV4.01 2 0.2647 1.000 0.00 0.88 0.12 0.00
#> TCGA.DD.A1EE.01 2 0.2647 1.000 0.00 0.88 0.12 0.00
#> TCGA.DD.A73D.01 2 0.2647 1.000 0.00 0.88 0.12 0.00
#> TCGA.CC.A7IH.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.G3.A25U.01 1 0.0707 0.912 0.98 0.00 0.00 0.02
#> TCGA.ZS.A9CE.01 1 0.0000 0.916 1.00 0.00 0.00 0.00
#> TCGA.EP.A2KC.01 4 0.3611 0.981 0.00 0.08 0.06 0.86
#> TCGA.G3.AAV0.01 1 0.0000 0.916 1.00 0.00 0.00 0.00
#> TCGA.DD.AACJ.01 4 0.3611 0.981 0.00 0.08 0.06 0.86
#> TCGA.DD.A73E.01 2 0.2647 1.000 0.00 0.88 0.12 0.00
#> TCGA.DD.AAD6.01 4 0.3611 0.981 0.00 0.08 0.06 0.86
#> TCGA.G3.A3CJ.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.ZP.A9D4.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.MI.A75G.01 1 0.0707 0.916 0.98 0.00 0.00 0.02
#> TCGA.G3.A25Z.01 1 0.4894 0.868 0.78 0.10 0.00 0.12
#> TCGA.RC.A6M4.01 2 0.2647 1.000 0.00 0.88 0.12 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BC.A3KF.01 1 0.0609 0.798 0.98 0.00 0.00 0.02 0.00
#> TCGA.RC.A7SF.01 5 0.4227 1.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.DD.AACA.02 4 0.3513 0.895 0.00 0.00 0.02 0.80 0.18
#> TCGA.DD.AACA.01 4 0.3513 0.895 0.00 0.00 0.02 0.80 0.18
#> TCGA.2Y.A9H4.01 5 0.4227 1.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.EP.A26S.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EA.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAW2.01 3 0.2929 0.907 0.00 0.00 0.82 0.00 0.18
#> TCGA.DD.AAD0.01 2 0.1043 0.970 0.00 0.96 0.00 0.00 0.04
#> TCGA.G3.AAV4.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.0609 0.982 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.A73D.01 2 0.0000 0.985 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IH.01 3 0.2929 0.907 0.00 0.00 0.82 0.00 0.18
#> TCGA.G3.A25U.01 1 0.0000 0.812 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CE.01 1 0.2280 0.864 0.88 0.00 0.00 0.00 0.12
#> TCGA.EP.A2KC.01 4 0.0609 0.931 0.00 0.00 0.02 0.98 0.00
#> TCGA.G3.AAV0.01 1 0.2280 0.864 0.88 0.00 0.00 0.00 0.12
#> TCGA.DD.AACJ.01 4 0.0609 0.931 0.00 0.00 0.02 0.98 0.00
#> TCGA.DD.A73E.01 2 0.0609 0.980 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.AAD6.01 4 0.0609 0.931 0.00 0.00 0.02 0.98 0.00
#> TCGA.G3.A3CJ.01 3 0.0609 0.903 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZP.A9D4.01 3 0.3109 0.903 0.00 0.00 0.80 0.00 0.20
#> TCGA.MI.A75G.01 1 0.2280 0.864 0.88 0.00 0.00 0.00 0.12
#> TCGA.G3.A25Z.01 5 0.4227 1.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.RC.A6M4.01 2 0.0609 0.982 0.00 0.98 0.00 0.00 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BC.A3KF.01 1 0.607 0.653 0.40 0.00 0.28 0.00 0.32 0.00
#> TCGA.RC.A7SF.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACA.02 4 0.000 0.742 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACA.01 4 0.000 0.742 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H4.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EP.A26S.01 6 0.000 0.855 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EA.01 6 0.127 0.845 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.DD.AAW2.01 6 0.308 0.851 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.DD.AAD0.01 2 0.369 0.848 0.02 0.80 0.14 0.04 0.00 0.00
#> TCGA.G3.AAV4.01 2 0.000 0.921 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.127 0.911 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.DD.A73D.01 2 0.000 0.921 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IH.01 6 0.279 0.856 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.G3.A25U.01 1 0.508 0.800 0.58 0.00 0.10 0.00 0.32 0.00
#> TCGA.ZS.A9CE.01 1 0.376 0.841 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.EP.A2KC.01 4 0.487 0.836 0.32 0.00 0.08 0.60 0.00 0.00
#> TCGA.G3.AAV0.01 1 0.376 0.841 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.DD.AACJ.01 4 0.487 0.836 0.32 0.00 0.08 0.60 0.00 0.00
#> TCGA.DD.A73E.01 2 0.279 0.871 0.02 0.84 0.14 0.00 0.00 0.00
#> TCGA.DD.AAD6.01 4 0.487 0.836 0.32 0.00 0.08 0.60 0.00 0.00
#> TCGA.G3.A3CJ.01 6 0.335 0.785 0.04 0.00 0.16 0.00 0.00 0.80
#> TCGA.ZP.A9D4.01 6 0.331 0.840 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.MI.A75G.01 1 0.461 0.797 0.54 0.00 0.04 0.00 0.42 0.00
#> TCGA.G3.A25Z.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.RC.A6M4.01 2 0.127 0.911 0.00 0.94 0.06 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.BC.A3KF.01 1 0.467 0.671 0.70 0.0 0.12 0.0 0.04 0.00 0.14
#> TCGA.RC.A7SF.01 5 0.329 1.000 0.34 0.0 0.00 0.0 0.66 0.00 0.00
#> TCGA.DD.AACA.02 3 0.314 1.000 0.00 0.0 0.70 0.3 0.00 0.00 0.00
#> TCGA.DD.AACA.01 3 0.314 1.000 0.00 0.0 0.70 0.3 0.00 0.00 0.00
#> TCGA.2Y.A9H4.01 5 0.329 1.000 0.34 0.0 0.00 0.0 0.66 0.00 0.00
#> TCGA.EP.A26S.01 6 0.346 -0.475 0.00 0.0 0.00 0.0 0.00 0.60 0.40
#> TCGA.DD.A1EA.01 7 0.442 0.617 0.00 0.0 0.02 0.0 0.02 0.46 0.50
#> TCGA.DD.AAW2.01 6 0.136 0.681 0.00 0.0 0.02 0.0 0.04 0.94 0.00
#> TCGA.DD.AAD0.01 2 0.340 0.827 0.00 0.8 0.02 0.0 0.14 0.00 0.04
#> TCGA.G3.AAV4.01 2 0.000 0.890 0.00 1.0 0.00 0.0 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.221 0.869 0.00 0.9 0.02 0.0 0.04 0.00 0.04
#> TCGA.DD.A73D.01 2 0.000 0.890 0.00 1.0 0.00 0.0 0.00 0.00 0.00
#> TCGA.CC.A7IH.01 6 0.000 0.662 0.00 0.0 0.00 0.0 0.00 1.00 0.00
#> TCGA.G3.A25U.01 1 0.286 0.793 0.86 0.0 0.06 0.0 0.04 0.00 0.04
#> TCGA.ZS.A9CE.01 1 0.000 0.830 1.00 0.0 0.00 0.0 0.00 0.00 0.00
#> TCGA.EP.A2KC.01 4 0.000 0.943 0.00 0.0 0.00 1.0 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 1 0.000 0.830 1.00 0.0 0.00 0.0 0.00 0.00 0.00
#> TCGA.DD.AACJ.01 4 0.000 0.943 0.00 0.0 0.00 1.0 0.00 0.00 0.00
#> TCGA.DD.A73E.01 2 0.340 0.827 0.00 0.8 0.02 0.0 0.14 0.00 0.04
#> TCGA.DD.AAD6.01 4 0.202 0.883 0.00 0.0 0.00 0.9 0.06 0.00 0.04
#> TCGA.G3.A3CJ.01 7 0.305 0.668 0.00 0.0 0.00 0.0 0.00 0.28 0.72
#> TCGA.ZP.A9D4.01 6 0.251 0.652 0.00 0.0 0.02 0.0 0.04 0.88 0.06
#> TCGA.MI.A75G.01 1 0.242 0.754 0.88 0.0 0.08 0.0 0.02 0.00 0.02
#> TCGA.G3.A25Z.01 5 0.329 1.000 0.34 0.0 0.00 0.0 0.66 0.00 0.00
#> TCGA.RC.A6M4.01 2 0.221 0.869 0.00 0.9 0.02 0.0 0.04 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.BC.A3KF.01 1 0.6163 0.606 0.48 0.00 0.28 0.00 0.14 0.00 0.04 0.06
#> TCGA.RC.A7SF.01 5 0.0941 0.965 0.00 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.DD.AACA.02 8 0.2267 1.000 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.DD.AACA.01 8 0.2267 1.000 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.2Y.A9H4.01 5 0.0000 0.983 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A26S.01 6 0.3618 -0.296 0.00 0.00 0.00 0.00 0.00 0.60 0.38 0.02
#> TCGA.DD.A1EA.01 6 0.5496 -0.395 0.02 0.00 0.14 0.00 0.00 0.50 0.32 0.02
#> TCGA.DD.AAW2.01 6 0.2624 0.487 0.06 0.00 0.06 0.00 0.00 0.86 0.00 0.02
#> TCGA.DD.AAD0.01 2 0.3374 0.734 0.00 0.68 0.30 0.00 0.00 0.00 0.00 0.02
#> TCGA.G3.AAV4.01 2 0.0000 0.834 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EE.01 2 0.2888 0.802 0.04 0.80 0.16 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73D.01 2 0.0000 0.834 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IH.01 6 0.0471 0.461 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.G3.A25U.01 1 0.3986 0.769 0.74 0.00 0.04 0.00 0.14 0.00 0.08 0.00
#> TCGA.ZS.A9CE.01 1 0.2267 0.803 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.EP.A2KC.01 4 0.0000 0.952 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV0.01 1 0.2267 0.803 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DD.AACJ.01 4 0.0000 0.952 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73E.01 2 0.2852 0.754 0.00 0.72 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD6.01 4 0.2071 0.901 0.02 0.00 0.04 0.90 0.00 0.00 0.04 0.00
#> TCGA.G3.A3CJ.01 7 0.2938 0.000 0.00 0.00 0.00 0.00 0.00 0.30 0.70 0.00
#> TCGA.ZP.A9D4.01 6 0.3080 0.475 0.06 0.00 0.06 0.00 0.00 0.84 0.02 0.02
#> TCGA.MI.A75G.01 1 0.5758 0.687 0.58 0.00 0.06 0.00 0.18 0.00 0.14 0.04
#> TCGA.G3.A25Z.01 5 0.0000 0.983 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RC.A6M4.01 2 0.2547 0.798 0.04 0.84 0.12 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 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 26 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.837 0.877 0.946 0.4680 0.557 0.557
#> 3 3 0.953 0.946 0.977 0.4481 0.763 0.575
#> 4 4 0.837 0.744 0.904 0.1342 0.852 0.575
#> 5 5 0.746 0.571 0.821 0.0621 0.849 0.449
#> 6 6 0.804 0.626 0.822 0.0361 0.914 0.562
#> 7 7 0.812 0.540 0.758 0.0249 0.951 0.692
#> 8 8 0.833 0.515 0.733 0.0178 0.972 0.800
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.XR.A8TG.01 2 0.000 0.918 0.00 1.00
#> TCGA.BC.A216.01 2 0.000 0.918 0.00 1.00
#> TCGA.2Y.A9H9.01 2 0.000 0.918 0.00 1.00
#> TCGA.BC.A8YO.01 2 0.000 0.918 0.00 1.00
#> TCGA.XR.A8TF.01 1 0.402 0.899 0.92 0.08
#> TCGA.G3.AAUZ.01 2 0.000 0.918 0.00 1.00
#> TCGA.DD.A11C.01 2 0.000 0.918 0.00 1.00
#> TCGA.4R.AA8I.01 2 0.827 0.672 0.26 0.74
#> TCGA.QA.A7B7.01 2 0.000 0.918 0.00 1.00
#> TCGA.DD.AAEB.01 1 0.000 0.987 1.00 0.00
#> TCGA.G3.A6UC.01 1 0.000 0.987 1.00 0.00
#> TCGA.BC.A10U.01 1 0.000 0.987 1.00 0.00
#> TCGA.DD.AACU.01 2 0.995 0.260 0.46 0.54
#> TCGA.DD.AAW3.01 1 0.000 0.987 1.00 0.00
#> TCGA.DD.A3A1.01 2 0.000 0.918 0.00 1.00
#> TCGA.DD.AACP.01 2 0.000 0.918 0.00 1.00
#> TCGA.DD.AAE9.01 1 0.000 0.987 1.00 0.00
#> TCGA.BD.A2L6.01 2 0.000 0.918 0.00 1.00
#> TCGA.DD.A11D.01 2 0.943 0.507 0.36 0.64
#> TCGA.DD.AACK.01 2 0.000 0.918 0.00 1.00
#> TCGA.FV.A2QR.01 1 0.000 0.987 1.00 0.00
#> TCGA.DD.A3A5.01 2 0.795 0.699 0.24 0.76
#> TCGA.DD.AADF.01 2 0.000 0.918 0.00 1.00
#> TCGA.DD.AAE3.01 1 0.000 0.987 1.00 0.00
#> TCGA.ZS.A9CF.02 2 0.000 0.918 0.00 1.00
#> TCGA.ZS.A9CF.01 2 0.000 0.918 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.XR.A8TG.01 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.BC.A216.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.2Y.A9H9.01 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.BC.A8YO.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.XR.A8TF.01 1 0.540 0.600 0.72 0.28 0.0
#> TCGA.G3.AAUZ.01 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.DD.A11C.01 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.4R.AA8I.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.QA.A7B7.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.DD.AAEB.01 1 0.000 0.940 1.00 0.00 0.0
#> TCGA.G3.A6UC.01 1 0.000 0.940 1.00 0.00 0.0
#> TCGA.BC.A10U.01 1 0.000 0.940 1.00 0.00 0.0
#> TCGA.DD.AACU.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.DD.AAW3.01 1 0.000 0.940 1.00 0.00 0.0
#> TCGA.DD.A3A1.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.DD.AACP.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.DD.AAE9.01 1 0.000 0.940 1.00 0.00 0.0
#> TCGA.BD.A2L6.01 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.DD.A11D.01 2 0.429 0.772 0.18 0.82 0.0
#> TCGA.DD.AACK.01 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.FV.A2QR.01 1 0.000 0.940 1.00 0.00 0.0
#> TCGA.DD.A3A5.01 2 0.153 0.944 0.04 0.96 0.0
#> TCGA.DD.AADF.01 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.DD.AAE3.01 1 0.296 0.860 0.90 0.00 0.1
#> TCGA.ZS.A9CF.02 2 0.000 0.976 0.00 1.00 0.0
#> TCGA.ZS.A9CF.01 2 0.000 0.976 0.00 1.00 0.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.XR.A8TG.01 4 0.4855 -0.0609 0.00 0.40 0.00 0.60
#> TCGA.BC.A216.01 3 0.0000 0.9517 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9H9.01 2 0.4790 0.4520 0.00 0.62 0.00 0.38
#> TCGA.BC.A8YO.01 3 0.0000 0.9517 0.00 0.00 1.00 0.00
#> TCGA.XR.A8TF.01 4 0.0707 0.7625 0.02 0.00 0.00 0.98
#> TCGA.G3.AAUZ.01 2 0.0000 0.7755 0.00 1.00 0.00 0.00
#> TCGA.DD.A11C.01 2 0.0000 0.7755 0.00 1.00 0.00 0.00
#> TCGA.4R.AA8I.01 3 0.0000 0.9517 0.00 0.00 1.00 0.00
#> TCGA.QA.A7B7.01 3 0.0000 0.9517 0.00 0.00 1.00 0.00
#> TCGA.DD.AAEB.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00
#> TCGA.BC.A10U.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 3 0.3975 0.6663 0.00 0.00 0.76 0.24
#> TCGA.DD.AAW3.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.01 3 0.0707 0.9386 0.00 0.00 0.98 0.02
#> TCGA.DD.AACP.01 3 0.0000 0.9517 0.00 0.00 1.00 0.00
#> TCGA.DD.AAE9.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00
#> TCGA.BD.A2L6.01 2 0.6005 0.1881 0.00 0.50 0.04 0.46
#> TCGA.DD.A11D.01 4 0.0000 0.7655 0.00 0.00 0.00 1.00
#> TCGA.DD.AACK.01 2 0.4994 0.2714 0.00 0.52 0.00 0.48
#> TCGA.FV.A2QR.01 4 0.0707 0.7623 0.02 0.00 0.00 0.98
#> TCGA.DD.A3A5.01 4 0.0000 0.7655 0.00 0.00 0.00 1.00
#> TCGA.DD.AADF.01 2 0.0000 0.7755 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE3.01 4 0.6649 0.1962 0.10 0.00 0.34 0.56
#> TCGA.ZS.A9CF.02 2 0.0000 0.7755 0.00 1.00 0.00 0.00
#> TCGA.ZS.A9CF.01 2 0.0000 0.7755 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.XR.A8TG.01 4 0.397 0.5662 0.00 0.10 0.00 0.80 0.10
#> TCGA.BC.A216.01 3 0.000 0.8068 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H9.01 4 0.425 0.4408 0.00 0.28 0.00 0.70 0.02
#> TCGA.BC.A8YO.01 3 0.000 0.8068 0.00 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TF.01 5 0.430 -0.2834 0.00 0.00 0.00 0.48 0.52
#> TCGA.G3.AAUZ.01 2 0.380 0.5596 0.00 0.70 0.00 0.30 0.00
#> TCGA.DD.A11C.01 2 0.141 0.8785 0.00 0.94 0.00 0.06 0.00
#> TCGA.4R.AA8I.01 3 0.429 0.1034 0.00 0.00 0.54 0.00 0.46
#> TCGA.QA.A7B7.01 3 0.000 0.8068 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10U.01 1 0.000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 5 0.413 0.0086 0.00 0.00 0.38 0.00 0.62
#> TCGA.DD.AAW3.01 1 0.000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.01 5 0.429 -0.2179 0.00 0.00 0.46 0.00 0.54
#> TCGA.DD.AACP.01 3 0.252 0.7274 0.00 0.00 0.86 0.00 0.14
#> TCGA.DD.AAE9.01 1 0.000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A2L6.01 4 0.560 0.4786 0.00 0.16 0.04 0.70 0.10
#> TCGA.DD.A11D.01 4 0.426 0.2652 0.00 0.00 0.00 0.56 0.44
#> TCGA.DD.AACK.01 4 0.489 0.5392 0.00 0.14 0.00 0.72 0.14
#> TCGA.FV.A2QR.01 5 0.425 0.0173 0.02 0.00 0.00 0.28 0.70
#> TCGA.DD.A3A5.01 4 0.423 0.3022 0.00 0.00 0.00 0.58 0.42
#> TCGA.DD.AADF.01 2 0.104 0.8858 0.00 0.96 0.00 0.04 0.00
#> TCGA.DD.AAE3.01 5 0.335 0.3851 0.08 0.00 0.04 0.02 0.86
#> TCGA.ZS.A9CF.02 2 0.000 0.8825 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 2 0.000 0.8825 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.XR.A8TG.01 6 0.4962 0.3448 0.00 0.08 0.00 0.18 0.04 0.70
#> TCGA.BC.A216.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H9.01 4 0.6200 0.0385 0.00 0.18 0.00 0.46 0.02 0.34
#> TCGA.BC.A8YO.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 4 0.2981 0.3667 0.00 0.00 0.00 0.82 0.16 0.02
#> TCGA.G3.AAUZ.01 2 0.4503 0.6019 0.00 0.68 0.00 0.08 0.00 0.24
#> TCGA.DD.A11C.01 2 0.2048 0.8404 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.4R.AA8I.01 5 0.3076 0.8147 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.QA.A7B7.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.0000 0.9948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.0000 0.9948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10U.01 1 0.0000 0.9948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACU.01 5 0.3156 0.8268 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.DD.AAW3.01 1 0.0000 0.9948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.01 5 0.3916 0.7427 0.00 0.00 0.30 0.00 0.68 0.02
#> TCGA.DD.AACP.01 3 0.3706 0.0397 0.00 0.00 0.62 0.00 0.38 0.00
#> TCGA.DD.AAE9.01 1 0.0547 0.9789 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BD.A2L6.01 6 0.3851 0.3848 0.00 0.08 0.02 0.06 0.02 0.82
#> TCGA.DD.A11D.01 4 0.4503 0.2892 0.00 0.00 0.00 0.68 0.08 0.24
#> TCGA.DD.AACK.01 4 0.3600 0.3944 0.00 0.08 0.00 0.82 0.02 0.08
#> TCGA.FV.A2QR.01 6 0.6526 -0.1945 0.02 0.00 0.00 0.34 0.28 0.36
#> TCGA.DD.A3A5.01 4 0.5037 0.1347 0.00 0.00 0.00 0.54 0.08 0.38
#> TCGA.DD.AADF.01 2 0.1814 0.8474 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.DD.AAE3.01 5 0.2020 0.7129 0.02 0.00 0.04 0.02 0.92 0.00
#> TCGA.ZS.A9CF.02 2 0.0547 0.8393 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.ZS.A9CF.01 2 0.0547 0.8393 0.00 0.98 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.XR.A8TG.01 4 0.3985 -0.3808 0.00 0.00 0.00 0.52 0.02 0.46 0.00
#> TCGA.BC.A216.01 3 0.0000 0.7957 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H9.01 4 0.4499 0.1044 0.00 0.12 0.00 0.70 0.00 0.02 0.16
#> TCGA.BC.A8YO.01 3 0.0000 0.7957 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 7 0.3911 0.5025 0.00 0.00 0.00 0.24 0.06 0.00 0.70
#> TCGA.G3.AAUZ.01 2 0.5776 0.2548 0.00 0.46 0.00 0.38 0.00 0.10 0.06
#> TCGA.DD.A11C.01 2 0.4145 0.7247 0.00 0.74 0.00 0.14 0.00 0.02 0.10
#> TCGA.4R.AA8I.01 5 0.3052 0.5847 0.00 0.00 0.20 0.00 0.78 0.02 0.00
#> TCGA.QA.A7B7.01 3 0.0000 0.7957 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A6UC.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10U.01 1 0.0504 0.9857 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AACU.01 5 0.1433 0.6659 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.DD.AAW3.01 1 0.0000 0.9905 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.01 5 0.3991 0.5482 0.00 0.00 0.22 0.00 0.72 0.02 0.04
#> TCGA.DD.AACP.01 3 0.3985 -0.0798 0.00 0.00 0.52 0.00 0.46 0.00 0.02
#> TCGA.DD.AAE9.01 1 0.0504 0.9857 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BD.A2L6.01 6 0.2832 0.0000 0.00 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.DD.A11D.01 4 0.4092 0.1186 0.00 0.00 0.00 0.74 0.08 0.02 0.16
#> TCGA.DD.AACK.01 7 0.3943 0.4186 0.00 0.00 0.00 0.42 0.00 0.02 0.56
#> TCGA.FV.A2QR.01 5 0.6745 0.0252 0.00 0.00 0.00 0.22 0.42 0.16 0.20
#> TCGA.DD.A3A5.01 4 0.4905 0.2712 0.00 0.00 0.00 0.68 0.06 0.16 0.10
#> TCGA.DD.AADF.01 2 0.3000 0.7690 0.00 0.84 0.00 0.10 0.00 0.02 0.04
#> TCGA.DD.AAE3.01 5 0.0504 0.6532 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZS.A9CF.02 2 0.0000 0.7673 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 2 0.0000 0.7673 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.XR.A8TG.01 4 0.6086 -0.3036 0.00 0.00 0.00 0.48 0.04 0.30 0.12 0.06
#> TCGA.BC.A216.01 3 0.0000 0.8225 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H9.01 7 0.4722 0.0692 0.00 0.10 0.00 0.18 0.00 0.06 0.66 0.00
#> TCGA.BC.A8YO.01 3 0.0000 0.8225 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TF.01 7 0.6455 0.0709 0.00 0.00 0.00 0.30 0.02 0.22 0.38 0.08
#> TCGA.G3.AAUZ.01 2 0.6505 -0.1332 0.00 0.34 0.00 0.16 0.00 0.24 0.26 0.00
#> TCGA.DD.A11C.01 2 0.5640 0.6046 0.00 0.62 0.00 0.08 0.00 0.06 0.14 0.10
#> TCGA.4R.AA8I.01 5 0.2224 0.8062 0.00 0.00 0.12 0.00 0.86 0.02 0.00 0.00
#> TCGA.QA.A7B7.01 3 0.0000 0.8225 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEB.01 1 0.0471 0.9726 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G3.A6UC.01 1 0.0941 0.9694 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.BC.A10U.01 1 0.0471 0.9726 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AACU.01 5 0.1887 0.8057 0.00 0.00 0.06 0.04 0.90 0.00 0.00 0.00
#> TCGA.DD.AAW3.01 1 0.0000 0.9730 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.01 5 0.4492 0.7086 0.00 0.00 0.18 0.02 0.70 0.06 0.00 0.04
#> TCGA.DD.AACP.01 3 0.3272 0.1052 0.00 0.00 0.58 0.00 0.42 0.00 0.00 0.00
#> TCGA.DD.AAE9.01 1 0.0941 0.9493 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.BD.A2L6.01 6 0.4404 0.0000 0.00 0.00 0.00 0.22 0.00 0.66 0.10 0.02
#> TCGA.DD.A11D.01 4 0.6024 0.1177 0.00 0.00 0.00 0.34 0.00 0.06 0.34 0.26
#> TCGA.DD.AACK.01 7 0.0941 0.3096 0.00 0.00 0.00 0.02 0.00 0.00 0.96 0.02
#> TCGA.FV.A2QR.01 8 0.3337 0.0000 0.00 0.00 0.00 0.04 0.16 0.00 0.02 0.78
#> TCGA.DD.A3A5.01 4 0.3128 0.2673 0.00 0.00 0.00 0.82 0.04 0.00 0.10 0.04
#> TCGA.DD.AADF.01 2 0.4846 0.6433 0.00 0.70 0.00 0.06 0.00 0.04 0.10 0.10
#> TCGA.DD.AAE3.01 5 0.2071 0.7108 0.00 0.00 0.00 0.04 0.90 0.02 0.00 0.04
#> TCGA.ZS.A9CF.02 2 0.0000 0.6559 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CF.01 2 0.0000 0.6559 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 , Node021 , Node022 , Node023 , Node024 , Node025 , Node031-leaf , Node032 , Node041 , Node042 .
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 200 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 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.989 0.996 0.4803 0.520 0.520
#> 3 3 0.747 0.917 0.930 0.1995 0.910 0.829
#> 4 4 1.000 0.973 0.986 0.2397 0.804 0.575
#> 5 5 0.979 0.954 0.974 0.0998 0.911 0.697
#> 6 6 0.909 0.815 0.916 0.0314 0.963 0.829
#> 7 7 0.874 0.818 0.894 0.0205 0.972 0.857
#> 8 8 0.839 0.700 0.834 0.0169 0.982 0.897
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 4 5
There is also optional best \(k\) = 2 4 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.DD.A4NQ.01 1 0.000 0.993 1.00 0.00
#> TCGA.CC.A1HT.01 1 0.000 0.993 1.00 0.00
#> TCGA.BD.A3EP.01 2 0.000 0.997 0.00 1.00
#> TCGA.ES.A2HT.01 1 0.000 0.993 1.00 0.00
#> TCGA.CC.A3MA.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AADW.01 2 0.000 0.997 0.00 1.00
#> TCGA.ED.A5KG.01 2 0.000 0.997 0.00 1.00
#> TCGA.ED.A7PY.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAW0.01 2 0.000 0.997 0.00 1.00
#> TCGA.ED.A66X.01 2 0.000 0.997 0.00 1.00
#> TCGA.RC.A7S9.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A3A2.11 1 0.000 0.993 1.00 0.00
#> TCGA.CC.A3M9.01 2 0.000 0.997 0.00 1.00
#> TCGA.ED.A82E.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.A10T.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A1EH.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AA3A.01 2 0.000 0.997 0.00 1.00
#> TCGA.RG.A7D4.01 2 0.000 0.997 0.00 1.00
#> TCGA.FV.A2QR.11 1 0.000 0.993 1.00 0.00
#> TCGA.G3.A25W.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A1EG.11 1 0.000 0.993 1.00 0.00
#> TCGA.G3.A25W.01 2 0.000 0.997 0.00 1.00
#> TCGA.2Y.A9GU.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.A9FV.01 1 0.000 0.993 1.00 0.00
#> TCGA.G3.A7M7.01 2 0.000 0.997 0.00 1.00
#> TCGA.ED.A97K.01 2 0.000 0.997 0.00 1.00
#> TCGA.WX.AA46.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A119.11 1 0.000 0.993 1.00 0.00
#> TCGA.WQ.A9G7.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.5261.01 2 0.000 0.997 0.00 1.00
#> TCGA.5R.AA1D.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AAVZ.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AACD.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAEG.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.A5UC.01 2 0.000 0.997 0.00 1.00
#> TCGA.K7.A5RG.01 2 0.000 0.997 0.00 1.00
#> TCGA.ED.A627.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AAVR.01 2 0.000 0.997 0.00 1.00
#> TCGA.2Y.A9H3.01 2 0.000 0.997 0.00 1.00
#> TCGA.MR.A8JO.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AACL.01 2 0.000 0.997 0.00 1.00
#> TCGA.KR.A7K8.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A115.11 1 0.000 0.993 1.00 0.00
#> TCGA.FV.A3I0.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A11B.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AADA.01 2 0.000 0.997 0.00 1.00
#> TCGA.G3.A3CH.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAVV.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A4NP.01 1 0.000 0.993 1.00 0.00
#> TCGA.ED.A66Y.01 2 0.000 0.997 0.00 1.00
#> TCGA.HP.A5MZ.01 2 0.000 0.997 0.00 1.00
#> TCGA.G3.A5SI.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.A112.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1EF.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A113.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.A10Y.11 1 0.000 0.993 1.00 0.00
#> TCGA.CC.A9FS.01 2 0.000 0.997 0.00 1.00
#> TCGA.2Y.A9H5.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.A7IE.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.5258.01 2 0.000 0.997 0.00 1.00
#> TCGA.BW.A5NQ.01 2 0.000 0.997 0.00 1.00
#> TCGA.2Y.A9GX.01 1 0.000 0.993 1.00 0.00
#> TCGA.LG.A9QC.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.A10Q.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.4073.01 1 0.925 0.486 0.66 0.34
#> TCGA.DD.AAD2.01 2 0.000 0.997 0.00 1.00
#> TCGA.RC.A7SH.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A11A.11 1 0.000 0.993 1.00 0.00
#> TCGA.RC.A6M5.01 1 0.000 0.993 1.00 0.00
#> TCGA.WX.AA44.01 2 0.000 0.997 0.00 1.00
#> TCGA.5C.A9VG.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAD1.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A3A6.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AACW.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.4072.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A116.11 1 0.000 0.993 1.00 0.00
#> TCGA.2Y.A9H6.01 2 0.000 0.997 0.00 1.00
#> TCGA.MR.A520.01 1 0.000 0.993 1.00 0.00
#> TCGA.EP.A12J.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AADK.01 2 0.000 0.997 0.00 1.00
#> TCGA.ES.A2HS.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A4NN.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZP.A9CZ.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.A8HS.01 2 0.000 0.997 0.00 1.00
#> TCGA.BD.A2L6.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A4NB.01 1 0.000 0.993 1.00 0.00
#> TCGA.ED.A8O6.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A3A4.01 2 0.000 0.997 0.00 1.00
#> TCGA.UB.A7MF.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A114.11 1 0.000 0.993 1.00 0.00
#> TCGA.ES.A2HT.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A39Z.11 1 0.000 0.993 1.00 0.00
#> TCGA.G3.A25Y.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1EI.11 1 0.000 0.993 1.00 0.00
#> TCGA.G3.A25V.01 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A10X.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A4ND.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A11D.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A118.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AAVW.01 2 0.000 0.997 0.00 1.00
#> TCGA.MI.A75E.01 2 0.904 0.523 0.32 0.68
#> TCGA.DD.A116.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AACC.01 2 0.000 0.997 0.00 1.00
#> TCGA.FV.A3R3.01 2 0.000 0.997 0.00 1.00
#> TCGA.K7.A5RF.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A39X.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1EC.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAE0.01 2 0.000 0.997 0.00 1.00
#> TCGA.XR.A8TD.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A1EE.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A1EB.11 1 0.000 0.993 1.00 0.00
#> TCGA.CC.A7IJ.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAVS.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A4NS.01 1 0.000 0.993 1.00 0.00
#> TCGA.ED.A8O5.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A3A3.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.A110.01 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A10R.11 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A112.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AACN.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1EF.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.A3MC.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A113.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A1EJ.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AADI.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.A7IG.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1ED.11 1 0.000 0.993 1.00 0.00
#> TCGA.CC.A8HV.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1E9.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A11C.11 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A10Q.11 1 0.000 0.993 1.00 0.00
#> TCGA.LG.A9QD.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AADO.01 2 0.000 0.997 0.00 1.00
#> TCGA.RC.A6M3.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A39W.11 1 0.000 0.993 1.00 0.00
#> TCGA.NI.A8LF.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AADC.01 2 0.000 0.997 0.00 1.00
#> TCGA.G3.A25X.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A4NH.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.5262.01 2 0.000 0.997 0.00 1.00
#> TCGA.G3.A25T.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A114.01 2 0.000 0.997 0.00 1.00
#> TCGA.UB.A7MA.01 2 0.000 0.997 0.00 1.00
#> TCGA.UB.AA0V.01 1 0.000 0.993 1.00 0.00
#> TCGA.BD.A3EP.11 1 0.000 0.993 1.00 0.00
#> TCGA.XR.A8TE.01 1 0.760 0.718 0.78 0.22
#> TCGA.ED.A4XI.01 2 0.000 0.997 0.00 1.00
#> TCGA.BW.A5NP.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAC9.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AADY.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AAVQ.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1EI.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A118.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.AACO.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A4NL.01 1 0.000 0.993 1.00 0.00
#> TCGA.G3.A3CI.01 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A216.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A1EH.11 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A10X.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A1EC.11 1 0.000 0.993 1.00 0.00
#> TCGA.CC.A7IF.01 2 0.000 0.997 0.00 1.00
#> TCGA.EP.A26S.11 1 0.000 0.993 1.00 0.00
#> TCGA.ED.A7PX.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1EB.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A3A3.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A39X.11 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A10U.11 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A110.11 1 0.000 0.993 1.00 0.00
#> TCGA.ED.A7XO.01 1 0.000 0.993 1.00 0.00
#> TCGA.G3.AAV7.01 2 0.000 0.997 0.00 1.00
#> TCGA.GJ.A3OU.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A4NE.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A39V.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AACT.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZP.A9D0.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A3A9.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A73G.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1ED.01 1 0.000 0.993 1.00 0.00
#> TCGA.WX.AA47.01 2 0.000 0.997 0.00 1.00
#> TCGA.2Y.A9H8.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1E9.11 1 0.000 0.993 1.00 0.00
#> TCGA.BC.A10S.11 1 0.000 0.993 1.00 0.00
#> TCGA.UB.A7ME.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A1EL.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A3A1.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A119.01 2 0.000 0.997 0.00 1.00
#> TCGA.XR.A8TC.01 2 0.000 0.997 0.00 1.00
#> TCGA.ED.A7XP.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.A10W.11 1 0.000 0.993 1.00 0.00
#> TCGA.FV.A23B.11 1 0.000 0.993 1.00 0.00
#> TCGA.5C.A9VH.01 2 0.000 0.997 0.00 1.00
#> TCGA.G3.A25X.11 1 0.000 0.993 1.00 0.00
#> TCGA.DD.A4NA.01 2 0.000 0.997 0.00 1.00
#> TCGA.EP.A3RK.01 2 0.000 0.997 0.00 1.00
#> TCGA.G3.A7M8.01 1 0.000 0.993 1.00 0.00
#> TCGA.DD.AAVP.01 2 0.000 0.997 0.00 1.00
#> TCGA.CC.5260.01 2 0.000 0.997 0.00 1.00
#> TCGA.DD.A4NR.01 2 0.000 0.997 0.00 1.00
#> TCGA.2Y.A9H2.01 2 0.000 0.997 0.00 1.00
#> TCGA.BC.A10Z.11 1 0.000 0.993 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DD.A4NQ.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.CC.A1HT.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.BD.A3EP.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.ES.A2HT.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.CC.A3MA.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AADW.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.ED.A5KG.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.ED.A7PY.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AAW0.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.ED.A66X.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.RC.A7S9.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A3A2.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.CC.A3M9.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.ED.A82E.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.A10T.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AA3A.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.RG.A7D4.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.FV.A2QR.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.G3.A25W.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.A1EG.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.G3.A25W.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.2Y.A9GU.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.A9FV.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.G3.A7M7.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.ED.A97K.01 2 0.254 0.914 0.00 0.92 0.08
#> TCGA.WX.AA46.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A119.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.5261.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.5R.AA1D.01 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.AAVZ.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AACD.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AAEG.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.A5UC.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.K7.A5RG.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.ED.A627.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.AAVR.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.2Y.A9H3.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.MR.A8JO.01 1 0.941 0.164 0.46 0.36 0.18
#> TCGA.DD.AACL.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.KR.A7K8.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.DD.A115.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.FV.A3I0.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A11B.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.G3.A3CH.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AAVV.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.A4NP.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.HP.A5MZ.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.G3.A5SI.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.A112.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1EF.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.A113.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.A10Y.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.CC.A9FS.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.2Y.A9H5.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.A7IE.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.5258.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BW.A5NQ.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.2Y.A9GX.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.LG.A9QC.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.BC.A10Q.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.4073.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.DD.AAD2.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.RC.A7SH.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A11A.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.RC.A6M5.01 3 0.000 0.755 0.00 0.00 1.00
#> TCGA.WX.AA44.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.5C.A9VG.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AAD1.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A3A6.01 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.AACW.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.4072.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.A116.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.MR.A520.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.EP.A12J.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.AADK.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.ES.A2HS.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.A8HS.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BD.A2L6.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A4NB.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.ED.A8O6.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A3A4.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.UB.A7MF.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A114.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.ES.A2HT.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A39Z.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.G3.A25Y.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1EI.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.G3.A25V.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.BC.A10X.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.A4ND.01 3 0.000 0.755 0.00 0.00 1.00
#> TCGA.DD.A11D.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.A118.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.AAVW.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.MI.A75E.01 1 0.770 0.580 0.68 0.14 0.18
#> TCGA.DD.A116.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AACC.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.FV.A3R3.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.K7.A5RF.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.DD.A39X.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1EC.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.AAE0.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.XR.A8TD.01 3 0.400 0.956 0.16 0.00 0.84
#> TCGA.DD.A1EE.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A1EB.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.CC.A7IJ.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AAVS.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A4NS.01 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.ED.A8O5.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A3A3.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.A110.01 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.BC.A10R.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.BC.A112.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1EF.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.A3MC.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A113.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.A1EJ.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.AADI.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.A7IG.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1ED.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.CC.A8HV.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1E9.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.A11C.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.BC.A10Q.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.LG.A9QD.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.AADO.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.RC.A6M3.01 2 0.296 0.906 0.00 0.90 0.10
#> TCGA.DD.A39W.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.NI.A8LF.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.AADC.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.G3.A25X.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A4NH.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.CC.5262.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.G3.A25T.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A114.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.UB.A7MA.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.UB.AA0V.01 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.BD.A3EP.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.XR.A8TE.01 1 0.429 0.774 0.82 0.00 0.18
#> TCGA.ED.A4XI.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.BW.A5NP.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AAC9.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.AADY.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AAVQ.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1EI.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.A118.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.AACO.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A4NL.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.G3.A3CI.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.BC.A216.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.A1EH.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.BC.A10X.01 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.DD.A1EC.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.CC.A7IF.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.EP.A26S.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.ED.A7PX.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1EB.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.A3A3.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A39X.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.BC.A10U.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.BC.A110.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.ED.A7XO.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.G3.AAV7.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.GJ.A3OU.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.DD.A4NE.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A39V.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.AACT.01 2 0.296 0.906 0.00 0.90 0.10
#> TCGA.ZP.A9D0.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A3A9.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A73G.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1ED.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.WX.AA47.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.2Y.A9H8.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1E9.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.BC.A10S.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A1EL.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A3A1.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A119.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.XR.A8TC.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.ED.A7XP.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.A10W.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.FV.A23B.11 3 0.429 0.980 0.18 0.00 0.82
#> TCGA.5C.A9VH.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.G3.A25X.11 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.A4NA.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.EP.A3RK.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.G3.A7M8.01 1 0.000 0.929 1.00 0.00 0.00
#> TCGA.DD.AAVP.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.CC.5260.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.DD.A4NR.01 2 0.429 0.870 0.00 0.82 0.18
#> TCGA.2Y.A9H2.01 2 0.000 0.946 0.00 1.00 0.00
#> TCGA.BC.A10Z.11 3 0.429 0.980 0.18 0.00 0.82
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DD.A4NQ.01 4 0.0707 0.951 0.02 0.00 0.00 0.98
#> TCGA.CC.A1HT.01 4 0.0707 0.951 0.02 0.00 0.00 0.98
#> TCGA.BD.A3EP.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.ES.A2HT.01 4 0.0707 0.951 0.02 0.00 0.00 0.98
#> TCGA.CC.A3MA.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.ED.A5KG.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.ED.A7PY.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AAW0.01 2 0.1211 0.967 0.00 0.96 0.00 0.04
#> TCGA.ED.A66X.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.RC.A7S9.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A2.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.CC.A3M9.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.ED.A82E.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.BC.A10T.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.RG.A7D4.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.FV.A2QR.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EG.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G3.A25W.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.2Y.A9GU.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.A9FV.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.ED.A97K.01 4 0.4855 0.324 0.00 0.40 0.00 0.60
#> TCGA.WX.AA46.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.AAVZ.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.AACD.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.AAEG.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.A5UC.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.K7.A5RG.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.ED.A627.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVR.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.2Y.A9H3.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.MR.A8JO.01 4 0.0707 0.951 0.02 0.00 0.00 0.98
#> TCGA.DD.AACL.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.KR.A7K8.01 4 0.3610 0.748 0.20 0.00 0.00 0.80
#> TCGA.DD.A115.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A11B.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.G3.A3CH.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.AAVV.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.DD.A4NP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.HP.A5MZ.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.G3.A5SI.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EF.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.BC.A10Y.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CC.A9FS.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.2Y.A9H5.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.CC.5258.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.BW.A5NQ.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.2Y.A9GX.01 4 0.0707 0.951 0.02 0.00 0.00 0.98
#> TCGA.LG.A9QC.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.BC.A10Q.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.BC.4073.01 4 0.0707 0.951 0.02 0.00 0.00 0.98
#> TCGA.DD.AAD2.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.RC.A7SH.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.A11A.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.RC.A6M5.01 3 0.1211 0.959 0.00 0.00 0.96 0.04
#> TCGA.WX.AA44.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A6.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.AACW.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.BC.4072.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.A116.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.MR.A520.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EP.A12J.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AADK.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.ES.A2HS.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.A8HS.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.BD.A2L6.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NB.01 4 0.2011 0.898 0.08 0.00 0.00 0.92
#> TCGA.ED.A8O6.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.A3A4.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.UB.A7MF.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A114.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EI.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G3.A25V.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BC.A10X.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A4ND.01 3 0.0707 0.979 0.00 0.00 0.98 0.02
#> TCGA.DD.A11D.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A118.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.AAVW.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.MI.A75E.01 4 0.0707 0.951 0.02 0.00 0.00 0.98
#> TCGA.DD.A116.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.AACC.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.FV.A3R3.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.K7.A5RF.01 4 0.1211 0.936 0.04 0.00 0.00 0.96
#> TCGA.DD.A39X.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EC.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.AAE0.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TD.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EE.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.CC.A7IJ.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVS.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.A4NS.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A3.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.BC.A110.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BC.A10R.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BC.A112.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.A1EF.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.A3MC.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.A113.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EJ.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IG.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CC.A8HV.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1E9.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.A11C.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.LG.A9QD.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.AADO.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.RC.A6M3.01 4 0.4948 0.253 0.00 0.44 0.00 0.56
#> TCGA.DD.A39W.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.NI.A8LF.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.AADC.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.G3.A25X.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.CC.5262.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.G3.A25T.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A114.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.UB.A7MA.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.UB.AA0V.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BD.A3EP.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.XR.A8TE.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.ED.A4XI.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.BW.A5NP.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AAC9.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.AADY.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVQ.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.A1EI.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.DD.A118.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G3.A3CI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BC.A216.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EH.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BC.A10X.01 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EC.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.CC.A7IF.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.EP.A26S.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.ED.A7PX.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EB.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.A3A3.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BC.A10U.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.ED.A7XO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV7.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.GJ.A3OU.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.DD.A4NE.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A39V.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AACT.01 2 0.4522 0.506 0.00 0.68 0.00 0.32
#> TCGA.ZP.A9D0.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.2Y.A9H8.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A1E9.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BC.A10S.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.DD.A1EL.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A119.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.XR.A8TC.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.ED.A7XP.01 2 0.1211 0.952 0.00 0.96 0.00 0.04
#> TCGA.BC.A10W.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.G3.A25X.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NA.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.EP.A3RK.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.G3.A7M8.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 4 0.0000 0.953 0.00 0.00 0.00 1.00
#> TCGA.CC.5260.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NR.01 4 0.0707 0.960 0.00 0.02 0.00 0.98
#> TCGA.2Y.A9H2.01 2 0.0000 0.989 0.00 1.00 0.00 0.00
#> TCGA.BC.A10Z.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DD.A4NQ.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.CC.A1HT.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.BD.A3EP.01 4 0.1043 0.945 0.00 0.00 0.00 0.96 0.04
#> TCGA.ES.A2HT.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.CC.A3MA.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A5KG.01 4 0.3731 0.755 0.00 0.16 0.00 0.80 0.04
#> TCGA.ED.A7PY.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAW0.01 5 0.1216 0.935 0.00 0.02 0.00 0.02 0.96
#> TCGA.ED.A66X.01 5 0.1410 0.933 0.00 0.06 0.00 0.00 0.94
#> TCGA.RC.A7S9.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A2.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A3M9.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A82E.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10T.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.RG.A7D4.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.FV.A2QR.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EG.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.01 4 0.1043 0.945 0.00 0.00 0.00 0.96 0.04
#> TCGA.2Y.A9GU.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A9FV.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.ED.A97K.01 5 0.1043 0.921 0.00 0.00 0.00 0.04 0.96
#> TCGA.WX.AA46.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVZ.01 5 0.3274 0.765 0.00 0.22 0.00 0.00 0.78
#> TCGA.DD.AACD.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.DD.AAEG.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 5 0.1043 0.921 0.00 0.00 0.00 0.04 0.96
#> TCGA.K7.A5RG.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A627.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVR.01 5 0.1732 0.919 0.00 0.08 0.00 0.00 0.92
#> TCGA.2Y.A9H3.01 5 0.1732 0.919 0.00 0.08 0.00 0.00 0.92
#> TCGA.MR.A8JO.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACL.01 4 0.1043 0.945 0.00 0.00 0.00 0.96 0.04
#> TCGA.KR.A7K8.01 4 0.2020 0.874 0.10 0.00 0.00 0.90 0.00
#> TCGA.DD.A115.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11B.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.DD.AAVV.01 5 0.3561 0.670 0.00 0.00 0.00 0.26 0.74
#> TCGA.DD.A4NP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.G3.A5SI.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FS.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.2Y.A9H5.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.CC.5258.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.BW.A5NQ.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9GX.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.LG.A9QC.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.BC.A10Q.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.4073.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAD2.01 5 0.1043 0.921 0.00 0.00 0.00 0.04 0.96
#> TCGA.RC.A7SH.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11A.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M5.01 3 0.3037 0.852 0.00 0.00 0.86 0.10 0.04
#> TCGA.WX.AA44.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A6.01 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACW.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.BC.4072.01 4 0.1043 0.945 0.00 0.00 0.00 0.96 0.04
#> TCGA.DD.A116.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.MR.A520.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A12J.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADK.01 5 0.0609 0.920 0.00 0.02 0.00 0.00 0.98
#> TCGA.ES.A2HS.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A8HS.01 5 0.1410 0.930 0.00 0.06 0.00 0.00 0.94
#> TCGA.BD.A2L6.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NB.01 4 0.2516 0.825 0.14 0.00 0.00 0.86 0.00
#> TCGA.ED.A8O6.01 5 0.3274 0.761 0.00 0.22 0.00 0.00 0.78
#> TCGA.DD.A3A4.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.UB.A7MF.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A114.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25V.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10X.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A4ND.01 3 0.4096 0.720 0.00 0.00 0.76 0.20 0.04
#> TCGA.DD.A11D.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A118.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVW.01 5 0.1043 0.921 0.00 0.00 0.00 0.04 0.96
#> TCGA.MI.A75E.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A116.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.DD.AACC.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.FV.A3R3.01 2 0.1043 0.943 0.00 0.96 0.00 0.00 0.04
#> TCGA.K7.A5RF.01 4 0.1410 0.919 0.06 0.00 0.00 0.94 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.01 4 0.1410 0.944 0.00 0.00 0.00 0.94 0.06
#> TCGA.DD.AAE0.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TD.01 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EE.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 2 0.4262 0.144 0.00 0.56 0.00 0.00 0.44
#> TCGA.DD.A4NS.01 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.BC.A110.01 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A10R.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A112.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.3561 0.621 0.00 0.74 0.00 0.00 0.26
#> TCGA.DD.A1EF.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.DD.A113.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EJ.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IG.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HV.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A11C.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.LG.A9QD.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.AADO.01 2 0.0609 0.962 0.00 0.98 0.00 0.00 0.02
#> TCGA.RC.A6M3.01 5 0.3037 0.879 0.00 0.04 0.00 0.10 0.86
#> TCGA.DD.A39W.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.NI.A8LF.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.AADC.01 4 0.1043 0.943 0.00 0.00 0.00 0.96 0.04
#> TCGA.G3.A25X.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.5262.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.G3.A25T.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A114.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.UB.A7MA.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.UB.AA0V.01 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.BD.A3EP.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TE.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.ED.A4XI.01 5 0.2516 0.843 0.00 0.00 0.00 0.14 0.86
#> TCGA.BW.A5NP.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAC9.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.AADY.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.DD.A1EI.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.A118.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A216.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EH.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10X.01 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EC.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IF.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.EP.A26S.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PX.01 2 0.1043 0.943 0.00 0.96 0.00 0.00 0.04
#> TCGA.DD.A1EB.01 4 0.1410 0.944 0.00 0.00 0.00 0.94 0.06
#> TCGA.DD.A3A3.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A7XO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV7.01 4 0.4126 0.362 0.00 0.00 0.00 0.62 0.38
#> TCGA.GJ.A3OU.01 4 0.0609 0.957 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.A4NE.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39V.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACT.01 2 0.3390 0.814 0.00 0.84 0.00 0.10 0.06
#> TCGA.ZP.A9D0.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 4 0.2012 0.931 0.00 0.02 0.00 0.92 0.06
#> TCGA.2Y.A9H8.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.DD.A1EL.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.01 5 0.1043 0.944 0.00 0.04 0.00 0.00 0.96
#> TCGA.XR.A8TC.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A7XP.01 2 0.3037 0.848 0.00 0.86 0.00 0.04 0.10
#> TCGA.BC.A10W.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A25X.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NA.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A3RK.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00
#> TCGA.G3.A7M8.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 5 0.2020 0.881 0.00 0.00 0.00 0.10 0.90
#> TCGA.CC.5260.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NR.01 4 0.1043 0.945 0.00 0.00 0.00 0.96 0.04
#> TCGA.2Y.A9H2.01 2 0.0000 0.981 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Z.11 3 0.0000 0.986 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DD.A4NQ.01 4 0.0000 0.6752 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A1HT.01 4 0.0000 0.6752 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BD.A3EP.01 4 0.3828 0.2665 0.00 0.00 0.00 0.56 0.00 0.44
#> TCGA.ES.A2HT.01 4 0.1556 0.6369 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.CC.A3MA.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A5KG.01 6 0.1092 0.4817 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.ED.A7PY.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAW0.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A66X.01 5 0.0937 0.8732 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.RC.A7S9.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A2.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 4 0.1267 0.6484 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.ED.A82E.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10T.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A1EH.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RG.A7D4.01 4 0.3409 0.2679 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.FV.A2QR.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.01 6 0.3499 0.1622 0.00 0.00 0.00 0.32 0.00 0.68
#> TCGA.2Y.A9GU.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FV.01 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.ED.A97K.01 5 0.2048 0.8033 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.WX.AA46.01 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A119.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.WQ.A9G7.01 2 0.0547 0.9598 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CC.5261.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVZ.01 5 0.3409 0.5665 0.00 0.30 0.00 0.00 0.70 0.00
#> TCGA.DD.AACD.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAEG.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.K7.A5RG.01 4 0.3409 0.2679 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.ED.A627.01 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVR.01 5 0.3156 0.7155 0.00 0.18 0.00 0.00 0.80 0.02
#> TCGA.2Y.A9H3.01 5 0.2941 0.6774 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.MR.A8JO.01 4 0.3499 0.2515 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.DD.AACL.01 6 0.3864 -0.2376 0.00 0.00 0.00 0.48 0.00 0.52
#> TCGA.KR.A7K8.01 4 0.1092 0.6545 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.DD.A115.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FV.A3I0.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11B.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAVV.01 6 0.5304 0.4786 0.00 0.00 0.00 0.20 0.20 0.60
#> TCGA.DD.A4NP.01 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ED.A66Y.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.G3.A5SI.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CC.A9FS.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9H5.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CC.5258.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BW.A5NQ.01 4 0.1267 0.6484 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.2Y.A9GX.01 4 0.0000 0.6752 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.LG.A9QC.01 6 0.3756 0.4841 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.BC.A10Q.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.4073.01 4 0.0000 0.6752 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD2.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.RC.A7SH.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M5.01 3 0.4310 0.4229 0.00 0.00 0.54 0.02 0.00 0.44
#> TCGA.WX.AA44.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A6.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACW.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.4072.01 4 0.3851 0.2554 0.00 0.00 0.00 0.54 0.00 0.46
#> TCGA.DD.A116.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A520.01 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A12J.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADK.01 5 0.2793 0.7321 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.ES.A2HS.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.0547 0.9580 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CC.A8HS.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BD.A2L6.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NB.01 4 0.3270 0.5508 0.12 0.00 0.00 0.82 0.00 0.06
#> TCGA.ED.A8O6.01 5 0.3076 0.6495 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.DD.A3A4.01 6 0.3647 0.5326 0.00 0.00 0.00 0.36 0.00 0.64
#> TCGA.UB.A7MF.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.G3.A25V.01 1 0.4282 0.3148 0.56 0.00 0.00 0.42 0.00 0.02
#> TCGA.BC.A10X.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4ND.01 4 0.5963 0.1930 0.00 0.00 0.24 0.44 0.00 0.32
#> TCGA.DD.A11D.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A118.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVW.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MI.A75E.01 4 0.0000 0.6752 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A116.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACC.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.FV.A3R3.01 2 0.3578 0.5607 0.00 0.66 0.00 0.00 0.00 0.34
#> TCGA.K7.A5RF.01 4 0.1814 0.5973 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.01 6 0.0547 0.4829 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.DD.AAE0.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TD.01 3 0.3351 0.7883 0.00 0.00 0.80 0.04 0.00 0.16
#> TCGA.DD.A1EE.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.2631 0.7659 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.DD.AAVS.01 2 0.3309 0.5960 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.DD.A4NS.01 3 0.2454 0.8274 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.ED.A8O5.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.A110.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10R.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A112.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.3076 0.6685 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.DD.A1EF.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A113.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IG.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CC.A8HV.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 4 0.3706 0.0192 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.DD.A11C.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BC.A10Q.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LG.A9QD.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.DD.AADO.01 2 0.0937 0.9387 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.RC.A6M3.01 6 0.4844 0.3884 0.00 0.02 0.00 0.04 0.32 0.62
#> TCGA.DD.A39W.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NI.A8LF.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.DD.AADC.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.G3.A25X.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5262.01 4 0.0000 0.6752 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A25T.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.01 4 0.3864 -0.3145 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.UB.A7MA.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.AA0V.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BD.A3EP.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TE.01 4 0.2048 0.6157 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.ED.A4XI.01 6 0.5798 0.3514 0.00 0.00 0.00 0.20 0.32 0.48
#> TCGA.BW.A5NP.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC9.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.DD.AADY.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EI.01 6 0.4199 0.5347 0.00 0.00 0.00 0.38 0.02 0.60
#> TCGA.DD.A118.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.0547 0.9580 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A4NL.01 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.G3.A3CI.01 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A216.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10X.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IF.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EP.A26S.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PX.01 2 0.3076 0.7162 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.DD.A1EB.01 6 0.1556 0.4897 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.DD.A3A3.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BC.A110.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A7XO.01 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.G3.AAV7.01 6 0.5267 0.4900 0.00 0.00 0.00 0.32 0.12 0.56
#> TCGA.GJ.A3OU.01 6 0.3756 0.5349 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.DD.A4NE.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39V.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACT.01 6 0.3309 0.3219 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.ZP.A9D0.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.WX.AA47.01 6 0.0547 0.4829 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.2Y.A9H8.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BC.A10S.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.UB.A7ME.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EL.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A1.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.01 5 0.0000 0.9060 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XR.A8TC.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7XP.01 6 0.0937 0.4704 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.BC.A10W.11 1 0.0547 0.9791 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FV.A23B.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25X.11 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NA.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A3RK.01 4 0.3756 -0.0573 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.G3.A7M8.01 1 0.0000 0.9817 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 5 0.5285 -0.1016 0.00 0.00 0.00 0.10 0.48 0.42
#> TCGA.CC.5260.01 2 0.0000 0.9751 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NR.01 6 0.3409 0.2029 0.00 0.00 0.00 0.30 0.00 0.70
#> TCGA.2Y.A9H2.01 2 0.0547 0.9598 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BC.A10Z.11 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DD.A4NQ.01 4 0.1886 0.7646 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.CC.A1HT.01 4 0.1886 0.7646 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.BD.A3EP.01 7 0.4681 0.4754 0.00 0.00 0.00 0.32 0.00 0.10 0.58
#> TCGA.ES.A2HT.01 4 0.3526 0.7124 0.00 0.00 0.00 0.76 0.00 0.18 0.06
#> TCGA.CC.A3MA.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A5KG.01 7 0.3517 0.5568 0.00 0.02 0.00 0.00 0.00 0.28 0.70
#> TCGA.ED.A7PY.01 2 0.0504 0.9456 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAW0.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A66X.01 5 0.2509 0.8471 0.00 0.02 0.00 0.00 0.88 0.04 0.06
#> TCGA.RC.A7S9.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A2.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 4 0.3867 0.5028 0.00 0.00 0.00 0.60 0.00 0.38 0.02
#> TCGA.ED.A82E.01 2 0.0863 0.9370 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.BC.A10T.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.DD.A1EH.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.1363 0.9246 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.RG.A7D4.01 6 0.4127 0.2575 0.00 0.00 0.00 0.36 0.00 0.60 0.04
#> TCGA.FV.A2QR.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.01 7 0.4990 0.5781 0.00 0.00 0.00 0.20 0.00 0.22 0.58
#> TCGA.2Y.A9GU.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FV.01 1 0.1671 0.8640 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.G3.A7M7.01 6 0.1006 0.7797 0.00 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.ED.A97K.01 5 0.4696 0.6622 0.00 0.00 0.00 0.06 0.70 0.16 0.08
#> TCGA.WX.AA46.01 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.DD.A119.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.WQ.A9G7.01 2 0.2163 0.8706 0.00 0.88 0.00 0.02 0.00 0.00 0.10
#> TCGA.CC.5261.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.1166 0.9088 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.DD.AAVZ.01 5 0.4828 0.3806 0.00 0.36 0.00 0.00 0.56 0.02 0.06
#> TCGA.DD.AACD.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 5 0.3114 0.8166 0.00 0.00 0.00 0.04 0.84 0.04 0.08
#> TCGA.K7.A5RG.01 6 0.4127 0.2575 0.00 0.00 0.00 0.36 0.00 0.60 0.04
#> TCGA.ED.A627.01 1 0.1671 0.8640 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.AAVR.01 5 0.4181 0.6946 0.00 0.16 0.00 0.00 0.74 0.04 0.06
#> TCGA.2Y.A9H3.01 5 0.4377 0.5868 0.00 0.24 0.00 0.00 0.68 0.02 0.06
#> TCGA.MR.A8JO.01 4 0.4820 0.3578 0.00 0.00 0.00 0.52 0.00 0.38 0.10
#> TCGA.DD.AACL.01 7 0.4338 0.5570 0.00 0.00 0.00 0.28 0.00 0.08 0.64
#> TCGA.KR.A7K8.01 4 0.1433 0.7402 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.DD.A115.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.FV.A3I0.01 2 0.1363 0.9246 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.DD.A11B.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVV.01 6 0.1928 0.7222 0.00 0.00 0.00 0.02 0.08 0.90 0.00
#> TCGA.DD.A4NP.01 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.ED.A66Y.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 6 0.1006 0.7797 0.00 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.G3.A5SI.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.CC.A9FS.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H5.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.5258.01 5 0.0504 0.8861 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BW.A5NQ.01 4 0.4127 0.4758 0.00 0.00 0.00 0.60 0.00 0.36 0.04
#> TCGA.2Y.A9GX.01 4 0.2376 0.7653 0.00 0.00 0.00 0.86 0.00 0.12 0.02
#> TCGA.LG.A9QC.01 6 0.2278 0.7426 0.00 0.00 0.00 0.08 0.00 0.88 0.04
#> TCGA.BC.A10Q.01 2 0.0863 0.9370 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.BC.4073.01 4 0.1886 0.7646 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.DD.AAD2.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A7SH.01 2 0.1006 0.9333 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.DD.A11A.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M5.01 7 0.4649 0.4262 0.00 0.00 0.30 0.06 0.00 0.02 0.62
#> TCGA.WX.AA44.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0504 0.9456 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAD1.01 2 0.0504 0.9468 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A6.01 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACW.01 5 0.1664 0.8660 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.BC.4072.01 7 0.4070 0.5001 0.00 0.00 0.00 0.34 0.00 0.04 0.62
#> TCGA.DD.A116.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A520.01 1 0.1433 0.8755 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.EP.A12J.11 1 0.1671 0.8640 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.AADK.01 5 0.3927 0.5008 0.00 0.00 0.00 0.00 0.66 0.04 0.30
#> TCGA.ES.A2HS.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.1433 0.8964 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.CC.A8HS.01 5 0.1363 0.8726 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.BD.A2L6.11 1 0.0504 0.9109 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DD.A4NB.01 4 0.4937 0.6039 0.12 0.00 0.00 0.68 0.00 0.06 0.14
#> TCGA.ED.A8O6.01 5 0.2745 0.7231 0.00 0.16 0.00 0.00 0.82 0.00 0.02
#> TCGA.DD.A3A4.01 6 0.1363 0.7782 0.00 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.UB.A7MF.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.11 1 0.1671 0.8640 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.ES.A2HT.11 1 0.1671 0.8640 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.A39Z.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.G3.A25V.01 4 0.3770 0.4895 0.18 0.00 0.00 0.74 0.00 0.00 0.08
#> TCGA.BC.A10X.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4ND.01 7 0.4873 0.4969 0.00 0.00 0.18 0.22 0.00 0.00 0.60
#> TCGA.DD.A11D.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A118.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVW.01 5 0.0504 0.8861 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.MI.A75E.01 4 0.2572 0.7513 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.DD.A116.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACC.01 6 0.0000 0.7789 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FV.A3R3.01 7 0.3994 0.0151 0.00 0.48 0.00 0.00 0.00 0.02 0.50
#> TCGA.K7.A5RF.01 4 0.4405 0.7074 0.08 0.00 0.00 0.74 0.00 0.10 0.08
#> TCGA.DD.A39X.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.01 7 0.3606 0.5347 0.00 0.00 0.00 0.02 0.00 0.30 0.68
#> TCGA.DD.AAE0.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TD.01 3 0.4328 0.3565 0.00 0.00 0.60 0.06 0.00 0.00 0.34
#> TCGA.DD.A1EE.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.3221 0.5341 0.00 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.DD.AAVS.01 2 0.3984 0.5408 0.00 0.68 0.00 0.00 0.28 0.02 0.02
#> TCGA.DD.A4NS.01 3 0.3413 0.3861 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.ED.A8O5.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A110.01 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10R.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.3661 0.6542 0.00 0.74 0.00 0.00 0.22 0.02 0.02
#> TCGA.DD.A1EF.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A113.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IG.01 2 0.0504 0.9446 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.A1ED.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.CC.A8HV.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 6 0.3745 0.4890 0.00 0.00 0.00 0.26 0.00 0.70 0.04
#> TCGA.DD.A11C.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.BC.A10Q.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A9QD.01 6 0.1006 0.7797 0.00 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.DD.AADO.01 2 0.1860 0.8992 0.00 0.92 0.00 0.00 0.04 0.02 0.02
#> TCGA.RC.A6M3.01 6 0.3494 0.6396 0.00 0.00 0.00 0.06 0.12 0.80 0.02
#> TCGA.DD.A39W.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NI.A8LF.01 6 0.0504 0.7813 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.AADC.01 6 0.1166 0.7668 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.G3.A25X.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0504 0.9468 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CC.5262.01 4 0.2572 0.7410 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.G3.A25T.01 2 0.0863 0.9370 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.A114.01 6 0.2906 0.6197 0.00 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.UB.A7MA.01 2 0.1363 0.9246 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.UB.AA0V.01 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A3EP.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TE.01 4 0.4108 0.6096 0.00 0.00 0.00 0.66 0.00 0.28 0.06
#> TCGA.ED.A4XI.01 6 0.4422 0.5773 0.00 0.00 0.00 0.04 0.16 0.72 0.08
#> TCGA.BW.A5NP.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC9.01 6 0.0504 0.7813 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.AADY.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 5 0.1006 0.8795 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.DD.A1EI.01 6 0.1006 0.7756 0.00 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.DD.A118.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.1671 0.8767 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.DD.A4NL.01 1 0.2313 0.9017 0.88 0.00 0.00 0.06 0.00 0.00 0.06
#> TCGA.G3.A3CI.01 1 0.1671 0.8640 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.BC.A216.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.11 1 0.1166 0.9090 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.BC.A10X.01 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IF.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EP.A26S.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PX.01 2 0.3887 0.5964 0.00 0.70 0.00 0.02 0.00 0.02 0.26
#> TCGA.DD.A1EB.01 6 0.3985 -0.1906 0.00 0.00 0.00 0.02 0.00 0.52 0.46
#> TCGA.DD.A3A3.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.BC.A110.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7XO.01 1 0.3835 0.8079 0.74 0.00 0.00 0.16 0.00 0.00 0.10
#> TCGA.G3.AAV7.01 6 0.1363 0.7571 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.GJ.A3OU.01 6 0.1006 0.7797 0.00 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.DD.A4NE.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39V.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACT.01 6 0.2912 0.6297 0.00 0.04 0.00 0.00 0.00 0.82 0.14
#> TCGA.ZP.A9D0.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.WX.AA47.01 7 0.4070 0.4763 0.00 0.00 0.00 0.04 0.00 0.34 0.62
#> TCGA.2Y.A9H8.01 2 0.0000 0.9555 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.BC.A10S.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.UB.A7ME.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EL.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.DD.A3A1.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.01 5 0.0000 0.8910 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TC.01 2 0.0504 0.9456 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ED.A7XP.01 7 0.5383 0.4299 0.00 0.14 0.00 0.00 0.02 0.30 0.54
#> TCGA.BC.A10W.11 1 0.2803 0.8952 0.84 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.FV.A23B.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.1886 0.8550 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.G3.A25X.11 1 0.0000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NA.01 2 0.0863 0.9370 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EP.A3RK.01 6 0.3519 0.5603 0.00 0.00 0.00 0.22 0.00 0.74 0.04
#> TCGA.G3.A7M8.01 1 0.1671 0.8640 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.AAVP.01 6 0.4461 0.3934 0.00 0.00 0.00 0.04 0.32 0.62 0.02
#> TCGA.CC.5260.01 2 0.0863 0.9370 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.A4NR.01 7 0.4970 0.5672 0.00 0.00 0.00 0.18 0.00 0.24 0.58
#> TCGA.2Y.A9H2.01 2 0.2163 0.8706 0.00 0.88 0.00 0.02 0.00 0.00 0.10
#> TCGA.BC.A10Z.11 3 0.0000 0.9654 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DD.A4NQ.01 4 0.1947 0.7888 0.00 0.00 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.CC.A1HT.01 4 0.2404 0.7890 0.00 0.00 0.00 0.84 0.00 0.14 0.02 0.00
#> TCGA.BD.A3EP.01 7 0.3523 0.6815 0.00 0.00 0.00 0.10 0.00 0.10 0.78 0.02
#> TCGA.ES.A2HT.01 4 0.3178 0.7686 0.00 0.00 0.00 0.80 0.00 0.14 0.02 0.04
#> TCGA.CC.A3MA.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A5KG.01 7 0.2224 0.7260 0.00 0.00 0.00 0.00 0.00 0.12 0.86 0.02
#> TCGA.ED.A7PY.01 2 0.0471 0.9109 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AAW0.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A66X.01 5 0.4720 0.6941 0.00 0.10 0.00 0.00 0.70 0.06 0.02 0.12
#> TCGA.RC.A7S9.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A2.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 4 0.4004 0.3044 0.00 0.00 0.00 0.50 0.00 0.46 0.04 0.00
#> TCGA.ED.A82E.01 2 0.1557 0.8830 0.00 0.92 0.00 0.02 0.00 0.00 0.00 0.06
#> TCGA.BC.A10T.11 1 0.0471 0.5803 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A1EH.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 2 0.2623 0.8277 0.00 0.84 0.00 0.06 0.00 0.00 0.00 0.10
#> TCGA.RG.A7D4.01 6 0.3991 0.2209 0.00 0.00 0.00 0.32 0.00 0.62 0.06 0.00
#> TCGA.FV.A2QR.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.G3.A25W.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.G3.A25W.01 7 0.3170 0.6699 0.00 0.00 0.00 0.04 0.00 0.20 0.76 0.00
#> TCGA.2Y.A9GU.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FV.01 8 0.3318 0.9815 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.G3.A7M7.01 6 0.0471 0.7641 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.ED.A97K.01 5 0.5818 0.4412 0.00 0.00 0.00 0.04 0.56 0.22 0.06 0.12
#> TCGA.WX.AA46.01 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.4098 0.7212 0.00 0.74 0.00 0.06 0.00 0.00 0.10 0.10
#> TCGA.CC.5261.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.0808 0.9596 0.00 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.AAVZ.01 5 0.5462 0.3292 0.00 0.38 0.00 0.00 0.46 0.02 0.02 0.12
#> TCGA.DD.AACD.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.0471 0.9123 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CC.A5UC.01 5 0.3337 0.7567 0.00 0.00 0.00 0.04 0.78 0.02 0.00 0.16
#> TCGA.K7.A5RG.01 6 0.4100 0.0799 0.00 0.00 0.00 0.36 0.00 0.58 0.06 0.00
#> TCGA.ED.A627.01 8 0.3318 0.9815 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.DD.AAVR.01 5 0.5321 0.6065 0.00 0.18 0.00 0.00 0.62 0.06 0.02 0.12
#> TCGA.2Y.A9H3.01 5 0.5385 0.5444 0.00 0.24 0.00 0.00 0.58 0.04 0.02 0.12
#> TCGA.MR.A8JO.01 4 0.5971 0.3814 0.00 0.00 0.00 0.44 0.00 0.28 0.08 0.20
#> TCGA.DD.AACL.01 7 0.2864 0.7089 0.00 0.00 0.00 0.08 0.00 0.06 0.84 0.02
#> TCGA.KR.A7K8.01 4 0.3131 0.7646 0.04 0.00 0.00 0.84 0.00 0.06 0.02 0.04
#> TCGA.DD.A115.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 2 0.2623 0.8277 0.00 0.84 0.00 0.06 0.00 0.00 0.00 0.10
#> TCGA.DD.A11B.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.AADA.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVV.01 6 0.1557 0.7353 0.00 0.00 0.00 0.00 0.06 0.92 0.00 0.02
#> TCGA.DD.A4NP.01 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 6 0.0000 0.7695 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A5SI.01 2 0.0471 0.9105 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BC.A112.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Y.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FS.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H5.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 5 0.1275 0.8275 0.00 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.CC.5258.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BW.A5NQ.01 4 0.4174 0.4358 0.00 0.00 0.00 0.54 0.00 0.40 0.06 0.00
#> TCGA.2Y.A9GX.01 4 0.2404 0.7890 0.00 0.00 0.00 0.84 0.00 0.14 0.02 0.00
#> TCGA.LG.A9QC.01 6 0.4764 0.5235 0.00 0.00 0.00 0.12 0.00 0.66 0.06 0.16
#> TCGA.BC.A10Q.01 2 0.1804 0.8702 0.00 0.90 0.00 0.02 0.00 0.00 0.00 0.08
#> TCGA.BC.4073.01 4 0.2725 0.7847 0.00 0.00 0.00 0.82 0.00 0.14 0.04 0.00
#> TCGA.DD.AAD2.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SH.01 2 0.2025 0.8452 0.00 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.DD.A11A.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.RC.A6M5.01 7 0.2858 0.7090 0.00 0.00 0.04 0.04 0.00 0.02 0.86 0.04
#> TCGA.WX.AA44.01 2 0.0471 0.9123 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.5C.A9VG.01 2 0.0471 0.9105 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAD1.01 2 0.0471 0.9123 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A6.01 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACW.01 5 0.3311 0.7740 0.00 0.02 0.00 0.00 0.80 0.02 0.02 0.14
#> TCGA.BC.4072.01 7 0.2407 0.7141 0.00 0.00 0.00 0.08 0.00 0.06 0.86 0.00
#> TCGA.DD.A116.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.2Y.A9H6.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A520.01 8 0.3329 0.9421 0.48 0.00 0.00 0.00 0.00 0.00 0.00 0.52
#> TCGA.EP.A12J.11 8 0.3318 0.9815 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.DD.AADK.01 5 0.3843 0.5440 0.00 0.00 0.00 0.00 0.70 0.02 0.24 0.04
#> TCGA.ES.A2HS.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.A4NN.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CZ.01 2 0.3551 0.6660 0.00 0.72 0.00 0.00 0.00 0.22 0.00 0.06
#> TCGA.CC.A8HS.01 5 0.2224 0.7997 0.00 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.BD.A2L6.11 1 0.3083 -0.1533 0.66 0.00 0.00 0.00 0.00 0.00 0.00 0.34
#> TCGA.DD.A4NB.01 4 0.4233 0.5609 0.00 0.00 0.00 0.60 0.00 0.04 0.02 0.34
#> TCGA.ED.A8O6.01 5 0.4487 0.5260 0.00 0.28 0.00 0.00 0.62 0.00 0.02 0.08
#> TCGA.DD.A3A4.01 6 0.0000 0.7695 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.UB.A7MF.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.11 8 0.3318 0.9815 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.ES.A2HT.11 8 0.3318 0.9815 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.DD.A39Z.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25V.01 4 0.3314 0.6921 0.10 0.00 0.00 0.80 0.00 0.02 0.00 0.08
#> TCGA.BC.A10X.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4ND.01 7 0.3675 0.6667 0.00 0.00 0.14 0.08 0.00 0.00 0.76 0.02
#> TCGA.DD.A11D.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A118.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVW.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MI.A75E.01 4 0.3291 0.6836 0.00 0.00 0.00 0.70 0.00 0.28 0.02 0.00
#> TCGA.DD.A116.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACC.01 6 0.0000 0.7695 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FV.A3R3.01 7 0.4534 0.4013 0.00 0.30 0.00 0.02 0.00 0.02 0.62 0.04
#> TCGA.K7.A5RF.01 4 0.2623 0.7780 0.00 0.00 0.00 0.84 0.00 0.10 0.00 0.06
#> TCGA.DD.A39X.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.01 7 0.2025 0.7253 0.00 0.00 0.00 0.00 0.00 0.10 0.88 0.02
#> TCGA.DD.AAE0.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TD.01 7 0.4040 0.4159 0.00 0.00 0.38 0.02 0.00 0.00 0.58 0.02
#> TCGA.DD.A1EE.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.A1EB.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.4216 0.1553 0.00 0.50 0.00 0.00 0.00 0.44 0.00 0.06
#> TCGA.DD.AAVS.01 2 0.4948 0.5483 0.00 0.66 0.00 0.00 0.16 0.04 0.02 0.12
#> TCGA.DD.A4NS.01 7 0.3618 0.4222 0.00 0.00 0.38 0.00 0.00 0.00 0.60 0.02
#> TCGA.ED.A8O5.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A110.01 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10R.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A112.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.AACN.01 2 0.4467 0.5247 0.00 0.66 0.00 0.00 0.20 0.00 0.02 0.12
#> TCGA.DD.A1EF.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A113.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IG.01 2 0.1091 0.8865 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.DD.A1ED.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HV.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 6 0.3170 0.5302 0.00 0.00 0.00 0.20 0.00 0.76 0.04 0.00
#> TCGA.DD.A11C.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LG.A9QD.01 6 0.0471 0.7584 0.00 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DD.AADO.01 2 0.2484 0.8277 0.00 0.86 0.00 0.00 0.02 0.00 0.02 0.10
#> TCGA.RC.A6M3.01 6 0.4253 0.6056 0.00 0.00 0.00 0.04 0.14 0.74 0.04 0.04
#> TCGA.DD.A39W.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NI.A8LF.01 6 0.0000 0.7695 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADC.01 6 0.1741 0.7501 0.00 0.00 0.00 0.00 0.04 0.92 0.02 0.02
#> TCGA.G3.A25X.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0808 0.9058 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CC.5262.01 4 0.2569 0.7830 0.00 0.00 0.00 0.82 0.00 0.16 0.02 0.00
#> TCGA.G3.A25T.01 2 0.1804 0.8702 0.00 0.90 0.00 0.02 0.00 0.00 0.00 0.08
#> TCGA.DD.A114.01 6 0.2756 0.4551 0.00 0.00 0.00 0.26 0.00 0.74 0.00 0.00
#> TCGA.UB.A7MA.01 2 0.2623 0.8277 0.00 0.84 0.00 0.06 0.00 0.00 0.00 0.10
#> TCGA.UB.AA0V.01 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A3EP.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TE.01 4 0.5062 0.5896 0.00 0.00 0.00 0.60 0.00 0.18 0.04 0.18
#> TCGA.ED.A4XI.01 6 0.4415 0.3858 0.00 0.00 0.00 0.02 0.32 0.60 0.00 0.06
#> TCGA.BW.A5NP.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC9.01 6 0.0000 0.7695 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADY.01 2 0.0471 0.9123 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAVQ.01 5 0.2025 0.8077 0.00 0.00 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.DD.A1EI.01 6 0.0471 0.7641 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.DD.A118.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACO.01 2 0.3299 0.7195 0.00 0.76 0.00 0.00 0.00 0.18 0.00 0.06
#> TCGA.DD.A4NL.01 1 0.1341 0.5221 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.G3.A3CI.01 8 0.3318 0.9815 0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.BC.A216.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.11 1 0.2114 0.4038 0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.BC.A10X.01 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IF.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A26S.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.ED.A7PX.01 2 0.5317 0.4562 0.00 0.58 0.00 0.08 0.00 0.00 0.22 0.12
#> TCGA.DD.A1EB.01 7 0.3658 0.4032 0.00 0.00 0.00 0.02 0.00 0.40 0.58 0.00
#> TCGA.DD.A3A3.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.A39X.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7XO.01 1 0.1563 0.4486 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV7.01 6 0.1804 0.7347 0.00 0.00 0.00 0.00 0.08 0.90 0.02 0.00
#> TCGA.GJ.A3OU.01 6 0.0000 0.7695 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NE.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39V.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.AACT.01 6 0.2404 0.6103 0.00 0.14 0.00 0.00 0.00 0.84 0.02 0.00
#> TCGA.ZP.A9D0.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 7 0.4138 0.6521 0.00 0.00 0.00 0.04 0.00 0.16 0.72 0.08
#> TCGA.2Y.A9H8.01 2 0.0000 0.9190 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A1.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.A119.01 5 0.0000 0.8439 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TC.01 2 0.1804 0.8603 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.ED.A7XP.01 7 0.3924 0.6603 0.00 0.04 0.00 0.00 0.00 0.20 0.72 0.04
#> TCGA.BC.A10W.11 1 0.0000 0.5954 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 2 0.3660 0.6365 0.00 0.70 0.00 0.00 0.00 0.24 0.00 0.06
#> TCGA.G3.A25X.11 1 0.3193 -0.2503 0.62 0.00 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DD.A4NA.01 2 0.2623 0.8277 0.00 0.84 0.00 0.06 0.00 0.00 0.00 0.10
#> TCGA.EP.A3RK.01 6 0.2888 0.5944 0.00 0.00 0.00 0.16 0.00 0.80 0.04 0.00
#> TCGA.G3.A7M8.01 8 0.3329 0.9421 0.48 0.00 0.00 0.00 0.00 0.00 0.00 0.52
#> TCGA.DD.AAVP.01 6 0.6114 0.1542 0.00 0.00 0.00 0.06 0.34 0.42 0.02 0.16
#> TCGA.CC.5260.01 2 0.1804 0.8702 0.00 0.90 0.00 0.02 0.00 0.00 0.00 0.08
#> TCGA.DD.A4NR.01 7 0.3170 0.6699 0.00 0.00 0.00 0.04 0.00 0.20 0.76 0.00
#> TCGA.2Y.A9H2.01 2 0.4098 0.7212 0.00 0.74 0.00 0.06 0.00 0.00 0.10 0.10
#> TCGA.BC.A10Z.11 3 0.0000 0.9984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 41 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 0.5127 0.488 0.488
#> 3 3 1.000 0.990 0.996 0.2718 0.702 0.475
#> 4 4 0.834 0.856 0.920 0.1167 0.873 0.658
#> 5 5 0.767 0.747 0.855 0.0362 0.968 0.886
#> 6 6 0.653 0.576 0.786 0.0449 0.959 0.841
#> 7 7 0.599 0.537 0.735 0.0230 0.960 0.826
#> 8 8 0.638 0.424 0.714 0.0304 0.952 0.786
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.BC.A10T.11 2 0 1 0 1
#> TCGA.FV.A2QR.11 1 0 1 1 0
#> TCGA.DD.A1EG.11 1 0 1 1 0
#> TCGA.CC.A9FV.01 1 0 1 1 0
#> TCGA.WX.AA46.01 2 0 1 0 1
#> TCGA.DD.A119.11 2 0 1 0 1
#> TCGA.ED.A627.01 1 0 1 1 0
#> TCGA.DD.A115.11 2 0 1 0 1
#> TCGA.DD.A11B.11 1 0 1 1 0
#> TCGA.DD.A4NP.01 2 0 1 0 1
#> TCGA.BC.A10Y.11 2 0 1 0 1
#> TCGA.DD.A11A.11 1 0 1 1 0
#> TCGA.DD.A116.11 1 0 1 1 0
#> TCGA.MR.A520.01 1 0 1 1 0
#> TCGA.EP.A12J.11 1 0 1 1 0
#> TCGA.ES.A2HS.11 1 0 1 1 0
#> TCGA.BD.A2L6.11 2 0 1 0 1
#> TCGA.DD.A114.11 1 0 1 1 0
#> TCGA.ES.A2HT.11 1 0 1 1 0
#> TCGA.DD.A1EI.11 2 0 1 0 1
#> TCGA.G3.A25V.01 2 0 1 0 1
#> TCGA.DD.A1EE.11 1 0 1 1 0
#> TCGA.BC.A112.11 1 0 1 1 0
#> TCGA.DD.A1ED.11 2 0 1 0 1
#> TCGA.DD.A11C.11 2 0 1 0 1
#> TCGA.DD.A4NL.01 2 0 1 0 1
#> TCGA.G3.A3CI.01 1 0 1 1 0
#> TCGA.DD.A1EH.11 2 0 1 0 1
#> TCGA.EP.A26S.11 1 0 1 1 0
#> TCGA.DD.A3A3.11 1 0 1 1 0
#> TCGA.BC.A10U.11 2 0 1 0 1
#> TCGA.ED.A7XO.01 2 0 1 0 1
#> TCGA.DD.A39V.11 1 0 1 1 0
#> TCGA.DD.A1ED.01 2 0 1 0 1
#> TCGA.DD.A1E9.11 2 0 1 0 1
#> TCGA.BC.A10S.11 2 0 1 0 1
#> TCGA.DD.A1EL.11 2 0 1 0 1
#> TCGA.DD.A3A1.11 1 0 1 1 0
#> TCGA.BC.A10W.11 2 0 1 0 1
#> TCGA.G3.A25X.11 1 0 1 1 0
#> TCGA.G3.A7M8.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BC.A10T.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.FV.A2QR.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.DD.A1EG.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.CC.A9FV.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.WX.AA46.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A119.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.ED.A627.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.DD.A115.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A11B.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.DD.A4NP.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.BC.A10Y.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.DD.A11A.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.DD.A116.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.MR.A520.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.EP.A12J.11 3 0.000 1.000 0.00 0.00 1
#> TCGA.ES.A2HS.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.BD.A2L6.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A114.11 3 0.000 1.000 0.00 0.00 1
#> TCGA.ES.A2HT.11 3 0.000 1.000 0.00 0.00 1
#> TCGA.DD.A1EI.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.G3.A25V.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A1EE.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.BC.A112.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.DD.A1ED.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A11C.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A4NL.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.G3.A3CI.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.DD.A1EH.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.EP.A26S.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.DD.A3A3.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.BC.A10U.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.ED.A7XO.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A39V.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.DD.A1ED.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A1E9.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.BC.A10S.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A1EL.11 2 0.000 1.000 0.00 1.00 0
#> TCGA.DD.A3A1.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.BC.A10W.11 1 0.429 0.774 0.82 0.18 0
#> TCGA.G3.A25X.11 1 0.000 0.988 1.00 0.00 0
#> TCGA.G3.A7M8.01 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.BC.A10T.11 1 0.2345 0.8781 0.90 0.10 0.00 0.00
#> TCGA.FV.A2QR.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.CC.A9FV.01 3 0.0000 0.9851 0.00 0.00 1.00 0.00
#> TCGA.WX.AA46.01 2 0.3172 0.7864 0.00 0.84 0.00 0.16
#> TCGA.DD.A119.11 2 0.1637 0.8158 0.00 0.94 0.00 0.06
#> TCGA.ED.A627.01 3 0.0000 0.9851 0.00 0.00 1.00 0.00
#> TCGA.DD.A115.11 2 0.2921 0.8038 0.00 0.86 0.00 0.14
#> TCGA.DD.A11B.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NP.01 4 0.2011 0.8941 0.00 0.08 0.00 0.92
#> TCGA.BC.A10Y.11 2 0.4713 0.3619 0.36 0.64 0.00 0.00
#> TCGA.DD.A11A.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.DD.A116.11 1 0.0707 0.9401 0.98 0.00 0.00 0.02
#> TCGA.MR.A520.01 3 0.1637 0.9633 0.00 0.00 0.94 0.06
#> TCGA.EP.A12J.11 3 0.0000 0.9851 0.00 0.00 1.00 0.00
#> TCGA.ES.A2HS.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.BD.A2L6.11 4 0.5062 0.7228 0.02 0.30 0.00 0.68
#> TCGA.DD.A114.11 3 0.0000 0.9851 0.00 0.00 1.00 0.00
#> TCGA.ES.A2HT.11 3 0.0000 0.9851 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EI.11 2 0.0707 0.8085 0.00 0.98 0.00 0.02
#> TCGA.G3.A25V.01 4 0.2647 0.8848 0.00 0.12 0.00 0.88
#> TCGA.DD.A1EE.11 1 0.0707 0.9354 0.98 0.00 0.02 0.00
#> TCGA.BC.A112.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.11 2 0.2921 0.8038 0.00 0.86 0.00 0.14
#> TCGA.DD.A11C.11 2 0.2647 0.8122 0.00 0.88 0.00 0.12
#> TCGA.DD.A4NL.01 4 0.2011 0.8941 0.00 0.08 0.00 0.92
#> TCGA.G3.A3CI.01 3 0.0707 0.9798 0.00 0.00 0.98 0.02
#> TCGA.DD.A1EH.11 1 0.2011 0.8954 0.92 0.08 0.00 0.00
#> TCGA.EP.A26S.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.11 1 0.0707 0.9401 0.98 0.00 0.00 0.02
#> TCGA.BC.A10U.11 2 0.0707 0.8045 0.00 0.98 0.00 0.02
#> TCGA.ED.A7XO.01 2 0.2921 0.7901 0.00 0.86 0.00 0.14
#> TCGA.DD.A39V.11 1 0.0000 0.9467 1.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 4 0.2011 0.8941 0.00 0.08 0.00 0.92
#> TCGA.DD.A1E9.11 1 0.4994 0.0744 0.52 0.48 0.00 0.00
#> TCGA.BC.A10S.11 2 0.0707 0.8045 0.00 0.98 0.00 0.02
#> TCGA.DD.A1EL.11 4 0.4277 0.7058 0.00 0.28 0.00 0.72
#> TCGA.DD.A3A1.11 1 0.0707 0.9379 0.98 0.02 0.00 0.00
#> TCGA.BC.A10W.11 2 0.4284 0.5777 0.20 0.78 0.00 0.02
#> TCGA.G3.A25X.11 1 0.0707 0.9401 0.98 0.00 0.00 0.02
#> TCGA.G3.A7M8.01 3 0.1637 0.9633 0.00 0.00 0.94 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BC.A10T.11 1 0.4872 0.675873 0.72 0.16 0.00 0.00 0.12
#> TCGA.FV.A2QR.11 1 0.0000 0.939008 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EG.11 1 0.0000 0.939008 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FV.01 3 0.2020 0.847034 0.00 0.00 0.90 0.00 0.10
#> TCGA.WX.AA46.01 2 0.2754 0.705948 0.00 0.88 0.00 0.04 0.08
#> TCGA.DD.A119.11 2 0.1648 0.727189 0.00 0.94 0.00 0.02 0.04
#> TCGA.ED.A627.01 3 0.1410 0.815733 0.06 0.00 0.94 0.00 0.00
#> TCGA.DD.A115.11 2 0.2331 0.719914 0.00 0.90 0.00 0.02 0.08
#> TCGA.DD.A11B.11 1 0.0000 0.939008 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NP.01 4 0.1043 0.742906 0.00 0.04 0.00 0.96 0.00
#> TCGA.BC.A10Y.11 2 0.5210 0.511533 0.20 0.68 0.00 0.00 0.12
#> TCGA.DD.A11A.11 1 0.1043 0.934082 0.96 0.00 0.00 0.00 0.04
#> TCGA.DD.A116.11 1 0.1043 0.932530 0.96 0.00 0.00 0.00 0.04
#> TCGA.MR.A520.01 3 0.4126 0.735660 0.00 0.00 0.62 0.00 0.38
#> TCGA.EP.A12J.11 3 0.0000 0.854303 0.00 0.00 1.00 0.00 0.00
#> TCGA.ES.A2HS.11 1 0.0609 0.935644 0.98 0.00 0.00 0.00 0.02
#> TCGA.BD.A2L6.11 4 0.7570 0.401363 0.08 0.30 0.02 0.50 0.10
#> TCGA.DD.A114.11 3 0.0000 0.854303 0.00 0.00 1.00 0.00 0.00
#> TCGA.ES.A2HT.11 3 0.0000 0.854303 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EI.11 2 0.1216 0.729704 0.00 0.96 0.00 0.02 0.02
#> TCGA.G3.A25V.01 4 0.4902 0.686532 0.00 0.04 0.04 0.74 0.18
#> TCGA.DD.A1EE.11 1 0.0609 0.932389 0.98 0.00 0.02 0.00 0.00
#> TCGA.BC.A112.11 1 0.0609 0.935644 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A1ED.11 2 0.2331 0.719914 0.00 0.90 0.00 0.02 0.08
#> TCGA.DD.A11C.11 2 0.2331 0.719914 0.00 0.90 0.00 0.02 0.08
#> TCGA.DD.A4NL.01 4 0.1410 0.746303 0.00 0.06 0.00 0.94 0.00
#> TCGA.G3.A3CI.01 3 0.3274 0.813037 0.00 0.00 0.78 0.00 0.22
#> TCGA.DD.A1EH.11 1 0.4725 0.670290 0.72 0.20 0.00 0.00 0.08
#> TCGA.EP.A26S.11 1 0.0609 0.936301 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A3.11 1 0.1043 0.932530 0.96 0.00 0.00 0.00 0.04
#> TCGA.BC.A10U.11 2 0.2020 0.695366 0.00 0.90 0.00 0.00 0.10
#> TCGA.ED.A7XO.01 2 0.6671 0.000736 0.00 0.42 0.00 0.24 0.34
#> TCGA.DD.A39V.11 1 0.1043 0.929170 0.96 0.00 0.00 0.00 0.04
#> TCGA.DD.A1ED.01 4 0.3291 0.736852 0.00 0.12 0.00 0.84 0.04
#> TCGA.DD.A1E9.11 2 0.6019 0.242601 0.38 0.50 0.00 0.00 0.12
#> TCGA.BC.A10S.11 2 0.1410 0.726110 0.00 0.94 0.00 0.00 0.06
#> TCGA.DD.A1EL.11 4 0.5895 0.266315 0.00 0.44 0.00 0.46 0.10
#> TCGA.DD.A3A1.11 1 0.0609 0.935598 0.98 0.00 0.00 0.00 0.02
#> TCGA.BC.A10W.11 2 0.4458 0.611577 0.12 0.76 0.00 0.00 0.12
#> TCGA.G3.A25X.11 1 0.1043 0.932530 0.96 0.00 0.00 0.00 0.04
#> TCGA.G3.A7M8.01 3 0.4287 0.680064 0.00 0.00 0.54 0.00 0.46
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BC.A10T.11 1 0.5324 -0.2063 0.54 0.12 0.00 0.00 0.00 0.34
#> TCGA.FV.A2QR.11 1 0.0937 0.8161 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A1EG.11 1 0.1807 0.8159 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.CC.A9FV.01 3 0.4042 0.4838 0.00 0.00 0.76 0.02 0.18 0.04
#> TCGA.WX.AA46.01 2 0.3073 0.6814 0.00 0.84 0.00 0.08 0.00 0.08
#> TCGA.DD.A119.11 2 0.2260 0.6946 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.ED.A627.01 3 0.4361 0.3603 0.14 0.00 0.76 0.00 0.06 0.04
#> TCGA.DD.A115.11 2 0.1480 0.7320 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.DD.A11B.11 1 0.1267 0.8122 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DD.A4NP.01 4 0.1807 0.6219 0.00 0.02 0.00 0.92 0.00 0.06
#> TCGA.BC.A10Y.11 6 0.5921 0.7274 0.30 0.24 0.00 0.00 0.00 0.46
#> TCGA.DD.A11A.11 1 0.2048 0.7927 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.DD.A116.11 1 0.3321 0.7759 0.82 0.00 0.00 0.00 0.08 0.10
#> TCGA.MR.A520.01 3 0.3409 -0.0568 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.EP.A12J.11 3 0.0547 0.7066 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.ES.A2HS.11 1 0.0937 0.8059 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.BD.A2L6.11 4 0.8301 0.0817 0.04 0.22 0.06 0.34 0.04 0.30
#> TCGA.DD.A114.11 3 0.0000 0.7104 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 3 0.0000 0.7104 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 2 0.2631 0.6667 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.G3.A25V.01 4 0.6480 0.5376 0.00 0.04 0.04 0.58 0.12 0.22
#> TCGA.DD.A1EE.11 1 0.2784 0.7961 0.88 0.00 0.04 0.00 0.04 0.04
#> TCGA.BC.A112.11 1 0.0937 0.8072 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.A1ED.11 2 0.2629 0.7076 0.00 0.88 0.00 0.08 0.02 0.02
#> TCGA.DD.A11C.11 2 0.0547 0.7343 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DD.A4NL.01 4 0.2020 0.6409 0.00 0.04 0.00 0.92 0.02 0.02
#> TCGA.G3.A3CI.01 3 0.1556 0.6615 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.DD.A1EH.11 1 0.6073 0.4004 0.58 0.06 0.00 0.02 0.06 0.28
#> TCGA.EP.A26S.11 1 0.2190 0.8054 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.DD.A3A3.11 1 0.3321 0.7759 0.82 0.00 0.00 0.00 0.08 0.10
#> TCGA.BC.A10U.11 2 0.4246 0.0531 0.02 0.58 0.00 0.00 0.00 0.40
#> TCGA.ED.A7XO.01 2 0.5663 0.4095 0.00 0.58 0.00 0.06 0.06 0.30
#> TCGA.DD.A39V.11 1 0.1814 0.7759 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.A1ED.01 4 0.2784 0.6396 0.00 0.04 0.00 0.88 0.04 0.04
#> TCGA.DD.A1E9.11 6 0.5963 0.7253 0.32 0.24 0.00 0.00 0.00 0.44
#> TCGA.BC.A10S.11 2 0.2793 0.6424 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.DD.A1EL.11 4 0.4902 0.0868 0.00 0.46 0.00 0.48 0.00 0.06
#> TCGA.DD.A3A1.11 1 0.2260 0.7252 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.BC.A10W.11 6 0.5295 0.1808 0.10 0.44 0.00 0.00 0.00 0.46
#> TCGA.G3.A25X.11 1 0.3321 0.7759 0.82 0.00 0.00 0.00 0.08 0.10
#> TCGA.G3.A7M8.01 5 0.3797 0.0000 0.00 0.00 0.42 0.00 0.58 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BC.A10T.11 1 0.4974 0.0625 0.58 0.04 0.00 0.00 0.02 0.34 0.02
#> TCGA.FV.A2QR.11 1 0.2706 0.7683 0.88 0.00 0.04 0.00 0.04 0.02 0.02
#> TCGA.DD.A1EG.11 1 0.2769 0.7620 0.86 0.00 0.04 0.00 0.02 0.08 0.00
#> TCGA.CC.A9FV.01 3 0.5625 0.1592 0.00 0.00 0.48 0.02 0.04 0.06 0.40
#> TCGA.WX.AA46.01 2 0.1664 0.7028 0.00 0.92 0.00 0.06 0.00 0.02 0.00
#> TCGA.DD.A119.11 2 0.4643 0.6547 0.00 0.74 0.00 0.04 0.04 0.12 0.06
#> TCGA.ED.A627.01 3 0.3000 0.5424 0.06 0.00 0.86 0.00 0.04 0.02 0.02
#> TCGA.DD.A115.11 2 0.2509 0.7247 0.00 0.88 0.00 0.04 0.02 0.06 0.00
#> TCGA.DD.A11B.11 1 0.0863 0.7573 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A4NP.01 4 0.2163 0.5138 0.00 0.10 0.00 0.88 0.00 0.02 0.00
#> TCGA.BC.A10Y.11 6 0.5930 0.5869 0.26 0.30 0.00 0.00 0.02 0.42 0.00
#> TCGA.DD.A11A.11 1 0.3396 0.7442 0.80 0.00 0.00 0.00 0.02 0.14 0.04
#> TCGA.DD.A116.11 1 0.4663 0.6491 0.70 0.00 0.04 0.02 0.04 0.20 0.00
#> TCGA.MR.A520.01 5 0.3943 0.6875 0.00 0.00 0.42 0.00 0.56 0.00 0.02
#> TCGA.EP.A12J.11 3 0.0000 0.6470 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HS.11 1 0.0000 0.7654 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A2L6.11 4 0.7898 -0.0116 0.02 0.12 0.02 0.32 0.02 0.30 0.20
#> TCGA.DD.A114.11 3 0.0000 0.6470 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.11 3 0.0504 0.6302 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DD.A1EI.11 2 0.4643 0.6397 0.00 0.74 0.00 0.04 0.04 0.12 0.06
#> TCGA.G3.A25V.01 7 0.4569 -0.0605 0.00 0.06 0.00 0.28 0.00 0.02 0.64
#> TCGA.DD.A1EE.11 1 0.4212 0.6766 0.76 0.00 0.14 0.00 0.04 0.04 0.02
#> TCGA.BC.A112.11 1 0.1664 0.7464 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.DD.A1ED.11 2 0.1363 0.7186 0.00 0.94 0.00 0.04 0.00 0.02 0.00
#> TCGA.DD.A11C.11 2 0.1363 0.7283 0.00 0.94 0.00 0.02 0.00 0.04 0.00
#> TCGA.DD.A4NL.01 4 0.3879 0.5251 0.00 0.10 0.00 0.78 0.04 0.00 0.08
#> TCGA.G3.A3CI.01 3 0.3755 -0.2428 0.00 0.00 0.64 0.00 0.34 0.00 0.02
#> TCGA.DD.A1EH.11 1 0.5626 0.4293 0.64 0.08 0.00 0.04 0.02 0.20 0.02
#> TCGA.EP.A26S.11 1 0.2355 0.7668 0.90 0.00 0.02 0.02 0.02 0.04 0.00
#> TCGA.DD.A3A3.11 1 0.5447 0.6459 0.68 0.00 0.04 0.02 0.06 0.16 0.04
#> TCGA.BC.A10U.11 2 0.3815 0.2869 0.02 0.62 0.00 0.00 0.00 0.36 0.00
#> TCGA.ED.A7XO.01 7 0.7243 0.2389 0.00 0.26 0.00 0.08 0.06 0.20 0.40
#> TCGA.DD.A39V.11 1 0.2421 0.7244 0.88 0.00 0.00 0.00 0.02 0.08 0.02
#> TCGA.DD.A1ED.01 4 0.4033 0.4984 0.00 0.22 0.00 0.70 0.00 0.00 0.08
#> TCGA.DD.A1E9.11 6 0.5342 0.5533 0.40 0.18 0.00 0.00 0.00 0.42 0.00
#> TCGA.BC.A10S.11 2 0.2572 0.6203 0.00 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.DD.A1EL.11 2 0.5371 0.1053 0.00 0.50 0.00 0.38 0.00 0.08 0.04
#> TCGA.DD.A3A1.11 1 0.2864 0.6958 0.84 0.00 0.00 0.00 0.02 0.12 0.02
#> TCGA.BC.A10W.11 6 0.7347 0.3357 0.16 0.32 0.00 0.00 0.08 0.36 0.08
#> TCGA.G3.A25X.11 1 0.4654 0.6742 0.72 0.00 0.04 0.02 0.06 0.16 0.00
#> TCGA.G3.A7M8.01 5 0.3221 0.7263 0.00 0.00 0.32 0.00 0.68 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BC.A10T.11 6 0.4403 0.25707 0.44 0.08 0.00 0.00 0.00 0.48 0.00 0.00
#> TCGA.FV.A2QR.11 1 0.1804 0.72898 0.90 0.00 0.00 0.00 0.02 0.08 0.00 0.00
#> TCGA.DD.A1EG.11 1 0.1607 0.73727 0.92 0.00 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.CC.A9FV.01 8 0.3193 0.00000 0.00 0.00 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.WX.AA46.01 2 0.4057 0.31420 0.00 0.72 0.00 0.04 0.02 0.00 0.20 0.02
#> TCGA.DD.A119.11 2 0.5243 0.36868 0.00 0.58 0.02 0.00 0.00 0.14 0.24 0.02
#> TCGA.ED.A627.01 3 0.4188 0.34134 0.14 0.00 0.72 0.00 0.00 0.04 0.00 0.10
#> TCGA.DD.A115.11 2 0.1408 0.58610 0.00 0.94 0.00 0.02 0.00 0.02 0.00 0.02
#> TCGA.DD.A11B.11 1 0.0808 0.73641 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DD.A4NP.01 4 0.4781 0.47043 0.00 0.06 0.00 0.72 0.02 0.08 0.10 0.02
#> TCGA.BC.A10Y.11 6 0.4723 0.26946 0.14 0.34 0.00 0.00 0.00 0.52 0.00 0.00
#> TCGA.DD.A11A.11 1 0.2265 0.70325 0.88 0.02 0.00 0.00 0.02 0.08 0.00 0.00
#> TCGA.DD.A116.11 1 0.5114 0.60535 0.58 0.00 0.00 0.00 0.04 0.30 0.04 0.04
#> TCGA.MR.A520.01 3 0.3729 -0.04019 0.00 0.00 0.52 0.00 0.46 0.00 0.02 0.00
#> TCGA.EP.A12J.11 3 0.0808 0.60157 0.04 0.00 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HS.11 1 0.1091 0.71926 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.BD.A2L6.11 6 0.8230 -0.00535 0.06 0.08 0.00 0.22 0.02 0.28 0.10 0.24
#> TCGA.DD.A114.11 3 0.1275 0.58685 0.04 0.00 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.ES.A2HT.11 3 0.0808 0.60157 0.04 0.00 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 2 0.5267 0.37633 0.00 0.56 0.00 0.00 0.00 0.18 0.22 0.04
#> TCGA.G3.A25V.01 4 0.6648 0.04961 0.00 0.00 0.00 0.40 0.06 0.06 0.20 0.28
#> TCGA.DD.A1EE.11 1 0.4808 0.58743 0.66 0.00 0.16 0.00 0.00 0.08 0.00 0.10
#> TCGA.BC.A112.11 1 0.1275 0.71902 0.94 0.00 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.DD.A1ED.11 2 0.1765 0.54626 0.00 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.DD.A11C.11 2 0.1275 0.56908 0.00 0.94 0.00 0.02 0.00 0.00 0.04 0.00
#> TCGA.DD.A4NL.01 4 0.2807 0.55654 0.00 0.06 0.00 0.86 0.02 0.00 0.02 0.04
#> TCGA.G3.A3CI.01 3 0.4028 0.35644 0.00 0.00 0.66 0.00 0.28 0.00 0.02 0.04
#> TCGA.DD.A1EH.11 1 0.6877 0.18368 0.40 0.04 0.00 0.10 0.00 0.34 0.06 0.06
#> TCGA.EP.A26S.11 1 0.4046 0.70152 0.74 0.00 0.00 0.00 0.02 0.16 0.02 0.06
#> TCGA.DD.A3A3.11 1 0.4375 0.65707 0.66 0.00 0.00 0.00 0.04 0.26 0.02 0.02
#> TCGA.BC.A10U.11 2 0.3995 0.23416 0.00 0.60 0.00 0.02 0.00 0.36 0.02 0.00
#> TCGA.ED.A7XO.01 7 0.1563 0.00000 0.00 0.10 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.DD.A39V.11 1 0.2224 0.67093 0.86 0.00 0.00 0.00 0.02 0.12 0.00 0.00
#> TCGA.DD.A1ED.01 4 0.2981 0.50679 0.00 0.22 0.00 0.76 0.00 0.00 0.00 0.02
#> TCGA.DD.A1E9.11 6 0.4747 0.47447 0.30 0.16 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.BC.A10S.11 2 0.2938 0.40148 0.00 0.70 0.00 0.00 0.00 0.30 0.00 0.00
#> TCGA.DD.A1EL.11 2 0.5264 -0.05298 0.00 0.48 0.02 0.40 0.00 0.00 0.04 0.06
#> TCGA.DD.A3A1.11 1 0.4174 0.60447 0.70 0.00 0.00 0.02 0.02 0.22 0.00 0.04
#> TCGA.BC.A10W.11 6 0.5903 0.02826 0.00 0.28 0.00 0.02 0.00 0.42 0.26 0.02
#> TCGA.G3.A25X.11 1 0.4028 0.64996 0.66 0.00 0.00 0.00 0.04 0.28 0.02 0.00
#> TCGA.G3.A7M8.01 5 0.2569 0.00000 0.00 0.00 0.16 0.00 0.82 0.02 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node02121 , Node02122-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221 , Node02222-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02411-leaf , Node02412-leaf , Node02421-leaf , Node02422-leaf , Node02431-leaf , Node02432-leaf , Node02433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0212"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 15 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 7.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.2484 0.752 0.752
#> 3 3 0.790 0.864 0.965 0.5944 0.886 0.848
#> 4 4 1.000 0.933 1.000 0.6843 0.695 0.522
#> 5 5 0.790 0.662 0.880 0.0964 0.971 0.914
#> 6 6 0.781 0.766 0.908 0.0985 0.810 0.429
#> 7 7 0.990 0.769 0.963 0.0611 0.971 0.833
#> 8 8 0.905 0.622 0.892 0.0425 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] 7
#> 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.WX.AA46.01 1 0 1 1 0
#> TCGA.DD.A119.11 1 0 1 1 0
#> TCGA.DD.A115.11 1 0 1 1 0
#> TCGA.DD.A4NP.01 1 0 1 1 0
#> TCGA.BD.A2L6.11 1 0 1 1 0
#> TCGA.DD.A1EI.11 1 0 1 1 0
#> TCGA.G3.A25V.01 2 0 1 0 1
#> TCGA.DD.A1ED.11 1 0 1 1 0
#> TCGA.DD.A11C.11 1 0 1 1 0
#> TCGA.DD.A4NL.01 1 0 1 1 0
#> TCGA.BC.A10U.11 1 0 1 1 0
#> TCGA.ED.A7XO.01 2 0 1 0 1
#> TCGA.DD.A1ED.01 1 0 1 1 0
#> TCGA.BC.A10S.11 1 0 1 1 0
#> TCGA.DD.A1EL.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.WX.AA46.01 3 0.153 0.000 0.04 0.00 0.96
#> TCGA.DD.A119.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.DD.A115.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.DD.A4NP.01 1 0.480 0.730 0.78 0.00 0.22
#> TCGA.BD.A2L6.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.DD.A1EI.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.G3.A25V.01 2 0.153 0.968 0.00 0.96 0.04
#> TCGA.DD.A1ED.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.DD.A11C.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.DD.A4NL.01 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.ED.A7XO.01 2 0.000 0.968 0.00 1.00 0.00
#> TCGA.DD.A1ED.01 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.BC.A10S.11 1 0.000 0.956 1.00 0.00 0.00
#> TCGA.DD.A1EL.11 1 0.480 0.730 0.78 0.00 0.22
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.WX.AA46.01 3 0 0 0 0 1 0
#> TCGA.DD.A119.11 4 0 1 0 0 0 1
#> TCGA.DD.A115.11 1 0 1 1 0 0 0
#> TCGA.DD.A4NP.01 4 0 1 0 0 0 1
#> TCGA.BD.A2L6.11 1 0 1 1 0 0 0
#> TCGA.DD.A1EI.11 1 0 1 1 0 0 0
#> TCGA.G3.A25V.01 2 0 1 0 1 0 0
#> TCGA.DD.A1ED.11 1 0 1 1 0 0 0
#> TCGA.DD.A11C.11 1 0 1 1 0 0 0
#> TCGA.DD.A4NL.01 1 0 1 1 0 0 0
#> TCGA.BC.A10U.11 1 0 1 1 0 0 0
#> TCGA.ED.A7XO.01 2 0 1 0 1 0 0
#> TCGA.DD.A1ED.01 1 0 1 1 0 0 0
#> TCGA.BC.A10S.11 4 0 1 0 0 0 1
#> TCGA.DD.A1EL.11 4 0 1 0 0 0 1
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.WX.AA46.01 3 0.406 0.000 0.00 0.00 0.64 0.00 0.36
#> TCGA.DD.A119.11 4 0.000 0.595 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A115.11 1 0.389 0.849 0.68 0.32 0.00 0.00 0.00
#> TCGA.DD.A4NP.01 5 0.423 0.000 0.00 0.00 0.00 0.42 0.58
#> TCGA.BD.A2L6.11 1 0.000 0.729 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.11 1 0.000 0.729 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25V.01 2 0.389 0.967 0.00 0.68 0.32 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.389 0.849 0.68 0.32 0.00 0.00 0.00
#> TCGA.DD.A11C.11 1 0.389 0.849 0.68 0.32 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 1 0.000 0.729 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.389 0.849 0.68 0.32 0.00 0.00 0.00
#> TCGA.ED.A7XO.01 2 0.406 0.967 0.00 0.64 0.36 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.389 0.849 0.68 0.32 0.00 0.00 0.00
#> TCGA.BC.A10S.11 4 0.516 0.370 0.32 0.00 0.00 0.62 0.06
#> TCGA.DD.A1EL.11 4 0.000 0.595 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.WX.AA46.01 3 0.000 0.000 0.00 0.0 1 0.00 0.00 0.00
#> TCGA.DD.A119.11 4 0.000 1.000 0.00 0.0 0 1.00 0.00 0.00
#> TCGA.DD.A115.11 1 0.308 1.000 0.76 0.0 0 0.00 0.00 0.24
#> TCGA.DD.A4NP.01 5 0.294 0.000 0.00 0.0 0 0.22 0.78 0.00
#> TCGA.BD.A2L6.11 6 0.000 0.806 0.00 0.0 0 0.00 0.00 1.00
#> TCGA.DD.A1EI.11 6 0.000 0.806 0.00 0.0 0 0.00 0.00 1.00
#> TCGA.G3.A25V.01 2 0.219 0.916 0.04 0.9 0 0.00 0.06 0.00
#> TCGA.DD.A1ED.11 1 0.308 1.000 0.76 0.0 0 0.00 0.00 0.24
#> TCGA.DD.A11C.11 1 0.308 1.000 0.76 0.0 0 0.00 0.00 0.24
#> TCGA.DD.A4NL.01 6 0.000 0.806 0.00 0.0 0 0.00 0.00 1.00
#> TCGA.BC.A10U.11 1 0.308 1.000 0.76 0.0 0 0.00 0.00 0.24
#> TCGA.ED.A7XO.01 2 0.000 0.916 0.00 1.0 0 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.308 1.000 0.76 0.0 0 0.00 0.00 0.24
#> TCGA.BC.A10S.11 6 0.715 0.241 0.20 0.0 0 0.18 0.16 0.46
#> TCGA.DD.A1EL.11 4 0.000 1.000 0.00 0.0 0 1.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.WX.AA46.01 3 0.0000 0.000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 4 0.0000 1.000 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.DD.A115.11 1 0.1363 0.957 0.94 0.00 0 0.00 0.02 0.00 0.04
#> TCGA.DD.A4NP.01 5 0.0504 0.000 0.00 0.00 0 0.02 0.98 0.00 0.00
#> TCGA.BD.A2L6.11 6 0.0863 0.987 0.04 0.00 0 0.00 0.00 0.96 0.00
#> TCGA.DD.A1EI.11 6 0.1166 0.973 0.06 0.00 0 0.00 0.00 0.94 0.00
#> TCGA.G3.A25V.01 2 0.0000 0.880 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.0000 0.972 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DD.A11C.11 1 0.0000 0.972 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 6 0.0863 0.987 0.04 0.00 0 0.00 0.00 0.96 0.00
#> TCGA.BC.A10U.11 1 0.1363 0.957 0.94 0.00 0 0.00 0.02 0.00 0.04
#> TCGA.ED.A7XO.01 2 0.2512 0.880 0.00 0.86 0 0.00 0.00 0.04 0.10
#> TCGA.DD.A1ED.01 1 0.0000 0.972 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.11 7 0.2572 0.000 0.00 0.00 0 0.06 0.00 0.08 0.86
#> TCGA.DD.A1EL.11 4 0.0000 1.000 0.00 0.00 0 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.WX.AA46.01 3 0.0000 0.000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 4 0.2114 0.856 0.00 0.00 0 0.84 0.00 0.00 0.00 0.16
#> TCGA.DD.A115.11 1 0.3299 0.628 0.56 0.00 0 0.00 0.00 0.00 0.00 0.44
#> TCGA.DD.A4NP.01 5 0.0808 0.000 0.00 0.00 0 0.04 0.96 0.00 0.00 0.00
#> TCGA.BD.A2L6.11 6 0.0000 0.859 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EI.11 6 0.1091 0.841 0.06 0.00 0 0.00 0.00 0.94 0.00 0.00
#> TCGA.G3.A25V.01 2 0.0000 0.789 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.0000 0.771 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11C.11 1 0.0000 0.771 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 6 0.2534 0.768 0.00 0.00 0 0.00 0.00 0.78 0.00 0.22
#> TCGA.BC.A10U.11 1 0.3299 0.628 0.56 0.00 0 0.00 0.00 0.00 0.00 0.44
#> TCGA.ED.A7XO.01 2 0.3483 0.789 0.00 0.76 0 0.00 0.04 0.00 0.02 0.18
#> TCGA.DD.A1ED.01 1 0.0000 0.771 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.11 7 0.0471 0.000 0.00 0.00 0 0.02 0.00 0.00 0.98 0.00
#> TCGA.DD.A1EL.11 4 0.0000 0.856 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0212. Child nodes: Node021211-leaf , Node021212-leaf , Node022211-leaf , Node022212-leaf , Node022213-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02121"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 13 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.2828 0.718 0.718
#> 3 3 0.615 0.680 0.738 0.8280 1.000 1.000
#> 4 4 0.949 0.898 0.974 0.2928 0.603 0.446
#> 5 5 0.808 0.629 0.895 0.0884 0.987 0.960
#> 6 6 0.782 0.476 0.611 0.0698 0.821 0.462
#> 7 7 0.756 0.376 0.863 0.0695 0.821 0.364
#> 8 8 0.795 0.490 0.877 0.0527 0.897 0.500
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.WX.AA46.01 2 0 1 0 1
#> TCGA.DD.A119.11 1 0 1 1 0
#> TCGA.DD.A115.11 1 0 1 1 0
#> TCGA.DD.A4NP.01 2 0 1 0 1
#> TCGA.BD.A2L6.11 1 0 1 1 0
#> TCGA.DD.A1EI.11 1 0 1 1 0
#> TCGA.DD.A1ED.11 1 0 1 1 0
#> TCGA.DD.A11C.11 1 0 1 1 0
#> TCGA.DD.A4NL.01 1 0 1 1 0
#> TCGA.BC.A10U.11 1 0 1 1 0
#> TCGA.DD.A1ED.01 1 0 1 1 0
#> TCGA.BC.A10S.11 1 0 1 1 0
#> TCGA.DD.A1EL.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.WX.AA46.01 2 0.000 0.980 0.00 1.00 0.00
#> TCGA.DD.A119.11 1 0.000 0.739 1.00 0.00 0.00
#> TCGA.DD.A115.11 1 0.000 0.739 1.00 0.00 0.00
#> TCGA.DD.A4NP.01 2 0.153 0.980 0.00 0.96 0.04
#> TCGA.BD.A2L6.11 1 0.630 0.574 0.52 0.00 0.48
#> TCGA.DD.A1EI.11 1 0.000 0.739 1.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.000 0.739 1.00 0.00 0.00
#> TCGA.DD.A11C.11 1 0.000 0.739 1.00 0.00 0.00
#> TCGA.DD.A4NL.01 1 0.630 0.574 0.52 0.00 0.48
#> TCGA.BC.A10U.11 1 0.000 0.739 1.00 0.00 0.00
#> TCGA.DD.A1ED.01 1 0.630 0.574 0.52 0.00 0.48
#> TCGA.BC.A10S.11 1 0.630 0.150 0.52 0.00 0.48
#> TCGA.DD.A1EL.11 1 0.630 0.574 0.52 0.00 0.48
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.WX.AA46.01 2 0.000 0.916 0.00 1.0 0.00 0.00
#> TCGA.DD.A119.11 1 0.000 0.988 1.00 0.0 0.00 0.00
#> TCGA.DD.A115.11 1 0.000 0.988 1.00 0.0 0.00 0.00
#> TCGA.DD.A4NP.01 2 0.283 0.916 0.00 0.9 0.06 0.04
#> TCGA.BD.A2L6.11 1 0.164 0.923 0.94 0.0 0.00 0.06
#> TCGA.DD.A1EI.11 1 0.000 0.988 1.00 0.0 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.000 0.988 1.00 0.0 0.00 0.00
#> TCGA.DD.A11C.11 1 0.000 0.988 1.00 0.0 0.00 0.00
#> TCGA.DD.A4NL.01 4 0.121 1.000 0.04 0.0 0.00 0.96
#> TCGA.BC.A10U.11 1 0.000 0.988 1.00 0.0 0.00 0.00
#> TCGA.DD.A1ED.01 4 0.121 1.000 0.04 0.0 0.00 0.96
#> TCGA.BC.A10S.11 3 0.164 0.000 0.06 0.0 0.94 0.00
#> TCGA.DD.A1EL.11 4 0.121 1.000 0.04 0.0 0.00 0.96
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.WX.AA46.01 2 0.418 0.000 0.00 0.60 0 0.00 0.4
#> TCGA.DD.A119.11 1 0.368 0.754 0.72 0.28 0 0.00 0.0
#> TCGA.DD.A115.11 1 0.000 0.894 1.00 0.00 0 0.00 0.0
#> TCGA.DD.A4NP.01 5 0.000 0.000 0.00 0.00 0 0.00 1.0
#> TCGA.BD.A2L6.11 1 0.000 0.894 1.00 0.00 0 0.00 0.0
#> TCGA.DD.A1EI.11 1 0.368 0.754 0.72 0.28 0 0.00 0.0
#> TCGA.DD.A1ED.11 1 0.104 0.894 0.96 0.04 0 0.00 0.0
#> TCGA.DD.A11C.11 1 0.104 0.894 0.96 0.04 0 0.00 0.0
#> TCGA.DD.A4NL.01 4 0.000 0.808 0.00 0.00 0 1.00 0.0
#> TCGA.BC.A10U.11 1 0.000 0.894 1.00 0.00 0 0.00 0.0
#> TCGA.DD.A1ED.01 4 0.000 0.808 0.00 0.00 0 1.00 0.0
#> TCGA.BC.A10S.11 3 0.000 0.000 0.00 0.00 1 0.00 0.0
#> TCGA.DD.A1EL.11 4 0.406 0.586 0.00 0.36 0 0.64 0.0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.WX.AA46.01 2 0.0000 0.000 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 3 0.3869 0.138 0.50 0.0 0.50 0.00 0.00 0.00
#> TCGA.DD.A115.11 1 0.0000 0.899 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NP.01 5 0.2793 0.000 0.00 0.2 0.00 0.00 0.80 0.00
#> TCGA.BD.A2L6.11 1 0.1814 0.802 0.90 0.0 0.00 0.00 0.10 0.00
#> TCGA.DD.A1EI.11 3 0.3869 0.138 0.50 0.0 0.50 0.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.1556 0.874 0.92 0.0 0.08 0.00 0.00 0.00
#> TCGA.DD.A11C.11 1 0.1556 0.874 0.92 0.0 0.08 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 4 0.0937 0.949 0.00 0.0 0.00 0.96 0.04 0.00
#> TCGA.BC.A10U.11 1 0.0000 0.899 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.01 4 0.0547 0.949 0.00 0.0 0.00 0.98 0.02 0.00
#> TCGA.BC.A10S.11 3 0.4892 -0.327 0.00 0.0 0.50 0.00 0.06 0.44
#> TCGA.DD.A1EL.11 6 0.4576 0.000 0.00 0.0 0.40 0.04 0.00 0.56
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.WX.AA46.01 2 0.2259 0.000 0.00 0.84 0 0.00 0.16 0.00 0.00
#> TCGA.DD.A119.11 1 0.1886 0.495 0.88 0.12 0 0.00 0.00 0.00 0.00
#> TCGA.DD.A115.11 1 0.3525 0.524 0.56 0.00 0 0.00 0.00 0.00 0.44
#> TCGA.DD.A4NP.01 5 0.0000 0.000 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BD.A2L6.11 7 0.0000 0.000 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EI.11 1 0.1886 0.495 0.88 0.12 0 0.00 0.00 0.00 0.00
#> TCGA.DD.A1ED.11 1 0.3047 0.644 0.72 0.00 0 0.00 0.00 0.00 0.28
#> TCGA.DD.A11C.11 1 0.3047 0.644 0.72 0.00 0 0.00 0.00 0.00 0.28
#> TCGA.DD.A4NL.01 4 0.0000 0.783 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.3525 0.524 0.56 0.00 0 0.00 0.00 0.00 0.44
#> TCGA.DD.A1ED.01 4 0.3566 0.781 0.00 0.04 0 0.78 0.00 0.02 0.16
#> TCGA.BC.A10S.11 3 0.0000 0.000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.11 6 0.0504 0.000 0.02 0.00 0 0.00 0.00 0.98 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.WX.AA46.01 2 0.000 0.000 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A119.11 8 0.435 0.950 0.30 0.00 0 0.00 0.06 0.02 0.00 0.62
#> TCGA.DD.A115.11 1 0.222 0.875 0.86 0.00 0 0.00 0.02 0.00 0.12 0.00
#> TCGA.DD.A4NP.01 5 0.558 0.000 0.00 0.14 0 0.00 0.48 0.00 0.06 0.32
#> TCGA.BD.A2L6.11 7 0.109 0.000 0.06 0.00 0 0.00 0.00 0.00 0.94 0.00
#> TCGA.DD.A1EI.11 8 0.337 0.950 0.30 0.00 0 0.00 0.00 0.02 0.00 0.68
#> TCGA.DD.A1ED.11 1 0.000 0.868 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11C.11 1 0.000 0.868 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NL.01 4 0.330 0.505 0.00 0.00 0 0.56 0.44 0.00 0.00 0.00
#> TCGA.BC.A10U.11 1 0.222 0.875 0.86 0.00 0 0.00 0.02 0.00 0.12 0.00
#> TCGA.DD.A1ED.01 4 0.134 0.476 0.00 0.00 0 0.92 0.00 0.00 0.08 0.00
#> TCGA.BC.A10S.11 3 0.000 0.000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EL.11 6 0.000 0.000 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 61 columns.
#> Top rows (1000) are extracted by '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 0.933 0.934 0.971 0.5035 0.498 0.498
#> 3 3 1.000 0.974 0.990 0.3003 0.763 0.562
#> 4 4 0.983 0.937 0.965 0.1393 0.822 0.542
#> 5 5 0.776 0.788 0.892 0.0256 0.975 0.902
#> 6 6 0.744 0.681 0.873 0.0130 0.993 0.972
#> 7 7 0.701 0.657 0.838 0.0156 0.984 0.932
#> 8 8 0.711 0.537 0.796 0.0233 0.962 0.850
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.CC.A3MA.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.AADW.01 2 0.000 0.960 0.00 1.00
#> TCGA.ED.A7PY.01 2 0.000 0.960 0.00 1.00
#> TCGA.RC.A7S9.01 2 0.242 0.940 0.04 0.96
#> TCGA.ED.A82E.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.A1EH.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.AA3A.01 1 0.000 0.980 1.00 0.00
#> TCGA.2Y.A9GU.01 2 0.000 0.960 0.00 1.00
#> TCGA.WQ.A9G7.01 1 0.000 0.980 1.00 0.00
#> TCGA.CC.5261.01 2 0.242 0.940 0.04 0.96
#> TCGA.DD.AAEG.01 2 0.141 0.950 0.02 0.98
#> TCGA.FV.A3I0.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.AADA.01 2 0.000 0.960 0.00 1.00
#> TCGA.ED.A66Y.01 2 0.000 0.960 0.00 1.00
#> TCGA.G3.A5SI.01 2 0.000 0.960 0.00 1.00
#> TCGA.BC.A112.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.A113.01 2 0.242 0.940 0.04 0.96
#> TCGA.2Y.A9H5.01 2 0.327 0.926 0.06 0.94
#> TCGA.BC.A10Q.01 1 0.000 0.980 1.00 0.00
#> TCGA.RC.A7SH.01 2 0.000 0.960 0.00 1.00
#> TCGA.WX.AA44.01 1 0.000 0.980 1.00 0.00
#> TCGA.5C.A9VG.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.AAD1.01 1 0.000 0.980 1.00 0.00
#> TCGA.2Y.A9H6.01 1 0.327 0.922 0.94 0.06
#> TCGA.DD.A4NN.01 2 0.000 0.960 0.00 1.00
#> TCGA.ZP.A9CZ.01 1 0.971 0.288 0.60 0.40
#> TCGA.UB.A7MF.01 2 0.327 0.926 0.06 0.94
#> TCGA.G3.A25Y.01 2 0.760 0.722 0.22 0.78
#> TCGA.FV.A3R3.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.A39X.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.AAE0.01 2 0.760 0.722 0.22 0.78
#> TCGA.CC.A7IJ.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.AAVS.01 2 0.000 0.960 0.00 1.00
#> TCGA.ED.A8O5.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.AACN.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.A1EF.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.AADI.01 2 0.000 0.960 0.00 1.00
#> TCGA.CC.A7IG.01 1 0.000 0.980 1.00 0.00
#> TCGA.CC.A8HV.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.AADO.01 2 0.000 0.960 0.00 1.00
#> TCGA.G3.A25X.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.A4NH.01 1 0.000 0.980 1.00 0.00
#> TCGA.G3.A25T.01 1 0.000 0.980 1.00 0.00
#> TCGA.UB.A7MA.01 1 0.000 0.980 1.00 0.00
#> TCGA.BW.A5NP.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.AADY.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.A118.01 2 0.990 0.241 0.44 0.56
#> TCGA.DD.AACO.01 2 0.327 0.926 0.06 0.94
#> TCGA.ED.A7PX.01 1 0.000 0.980 1.00 0.00
#> TCGA.DD.A4NE.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.AACT.01 1 0.000 0.980 1.00 0.00
#> TCGA.ZP.A9D0.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.A3A9.01 1 0.141 0.962 0.98 0.02
#> TCGA.DD.A73G.01 2 0.000 0.960 0.00 1.00
#> TCGA.2Y.A9H8.01 2 0.327 0.926 0.06 0.94
#> TCGA.XR.A8TC.01 2 0.000 0.960 0.00 1.00
#> TCGA.ED.A7XP.01 1 0.000 0.980 1.00 0.00
#> TCGA.5C.A9VH.01 2 0.000 0.960 0.00 1.00
#> TCGA.DD.A4NA.01 1 0.000 0.980 1.00 0.00
#> TCGA.CC.5260.01 1 0.000 0.980 1.00 0.00
#> TCGA.2Y.A9H2.01 1 0.000 0.980 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CC.A3MA.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.AADW.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.ED.A7PY.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.RC.A7S9.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.ED.A82E.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.A1EH.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.AA3A.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.2Y.A9GU.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.WQ.A9G7.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.CC.5261.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.AAEG.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.FV.A3I0.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.AADA.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.ED.A66Y.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.G3.A5SI.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.BC.A112.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.A113.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.2Y.A9H5.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.BC.A10Q.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.RC.A7SH.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.WX.AA44.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.5C.A9VG.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.AAD1.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.2Y.A9H6.01 2 0.400 0.798 0.16 0.84 0
#> TCGA.DD.A4NN.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.ZP.A9CZ.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.UB.A7MF.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.G3.A25Y.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.FV.A3R3.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.A39X.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.AAE0.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.CC.A7IJ.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.AAVS.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.ED.A8O5.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.AACN.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.A1EF.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.AADI.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.CC.A7IG.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.CC.A8HV.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.AADO.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.G3.A25X.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.A4NH.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.G3.A25T.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.UB.A7MA.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.BW.A5NP.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.AADY.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.A118.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.DD.AACO.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.ED.A7PX.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.DD.A4NE.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.DD.AACT.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.ZP.A9D0.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.DD.A3A9.01 2 0.624 0.233 0.44 0.56 0
#> TCGA.DD.A73G.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.2Y.A9H8.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.XR.A8TC.01 2 0.000 0.973 0.00 1.00 0
#> TCGA.ED.A7XP.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.5C.A9VH.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.DD.A4NA.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.CC.5260.01 1 0.000 1.000 1.00 0.00 0
#> TCGA.2Y.A9H2.01 1 0.000 1.000 1.00 0.00 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CC.A3MA.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.4624 0.444 0.00 0.66 0.00 0.34
#> TCGA.ED.A7PY.01 4 0.1637 0.983 0.00 0.06 0.00 0.94
#> TCGA.RC.A7S9.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.ED.A82E.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.DD.AA3A.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9GU.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.WQ.A9G7.01 2 0.3801 0.740 0.22 0.78 0.00 0.00
#> TCGA.CC.5261.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.0707 0.934 0.02 0.98 0.00 0.00
#> TCGA.FV.A3I0.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.3172 0.778 0.00 0.84 0.00 0.16
#> TCGA.ED.A66Y.01 4 0.1637 0.983 0.00 0.06 0.00 0.94
#> TCGA.G3.A5SI.01 3 0.0707 0.945 0.00 0.00 0.98 0.02
#> TCGA.BC.A112.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9H5.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.BC.A10Q.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SH.01 4 0.1211 0.985 0.00 0.04 0.00 0.96
#> TCGA.WX.AA44.01 1 0.0707 0.977 0.98 0.02 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.1637 0.914 0.06 0.94 0.00 0.00
#> TCGA.DD.AAD1.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.1211 0.927 0.04 0.96 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.1211 0.985 0.00 0.04 0.00 0.96
#> TCGA.ZP.A9CZ.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.UB.A7MF.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.1637 0.914 0.06 0.94 0.00 0.00
#> TCGA.DD.A39X.01 2 0.1211 0.927 0.04 0.96 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IJ.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.1211 0.985 0.00 0.04 0.00 0.96
#> TCGA.ED.A8O5.01 4 0.1637 0.983 0.00 0.06 0.00 0.94
#> TCGA.DD.AACN.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EF.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.DD.AADI.01 4 0.1637 0.977 0.00 0.06 0.00 0.94
#> TCGA.CC.A7IG.01 3 0.0707 0.937 0.02 0.00 0.98 0.00
#> TCGA.CC.A8HV.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.DD.AADO.01 4 0.1637 0.983 0.00 0.06 0.00 0.94
#> TCGA.G3.A25X.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 1 0.0707 0.980 0.98 0.00 0.00 0.02
#> TCGA.BW.A5NP.01 4 0.1211 0.985 0.00 0.04 0.00 0.96
#> TCGA.DD.AADY.01 4 0.2335 0.965 0.00 0.06 0.02 0.92
#> TCGA.DD.A118.01 3 0.5535 0.219 0.02 0.42 0.56 0.00
#> TCGA.DD.AACO.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.ED.A7PX.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NE.01 3 0.0707 0.945 0.00 0.00 0.98 0.02
#> TCGA.DD.AACT.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.ZP.A9D0.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.1211 0.927 0.04 0.96 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.938 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H8.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.XR.A8TC.01 4 0.1211 0.985 0.00 0.04 0.00 0.96
#> TCGA.ED.A7XP.01 2 0.1211 0.927 0.04 0.96 0.00 0.00
#> TCGA.5C.A9VH.01 3 0.0000 0.953 0.00 0.00 1.00 0.00
#> TCGA.DD.A4NA.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CC.A3MA.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 4 0.5689 0.171 0.00 0.44 0.00 0.48 0.08
#> TCGA.ED.A7PY.01 4 0.1648 0.874 0.00 0.04 0.00 0.94 0.02
#> TCGA.RC.A7S9.01 3 0.1410 0.855 0.00 0.00 0.94 0.00 0.06
#> TCGA.ED.A82E.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.1216 0.886 0.00 0.96 0.00 0.02 0.02
#> TCGA.DD.AA3A.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GU.01 2 0.3731 0.793 0.00 0.80 0.00 0.04 0.16
#> TCGA.WQ.A9G7.01 2 0.4060 0.274 0.36 0.64 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.1732 0.853 0.00 0.92 0.00 0.00 0.08
#> TCGA.DD.AAEG.01 2 0.0609 0.885 0.00 0.98 0.00 0.00 0.02
#> TCGA.FV.A3I0.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.5297 0.268 0.00 0.58 0.00 0.36 0.06
#> TCGA.ED.A66Y.01 4 0.2438 0.860 0.00 0.04 0.00 0.90 0.06
#> TCGA.G3.A5SI.01 3 0.2516 0.819 0.00 0.00 0.86 0.00 0.14
#> TCGA.BC.A112.01 1 0.1732 0.780 0.92 0.08 0.00 0.00 0.00
#> TCGA.DD.A113.01 3 0.0000 0.867 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H5.01 3 0.0000 0.867 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A10Q.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SH.01 4 0.1648 0.865 0.00 0.04 0.00 0.94 0.02
#> TCGA.WX.AA44.01 1 0.4588 0.352 0.72 0.22 0.00 0.00 0.06
#> TCGA.5C.A9VG.01 2 0.0609 0.883 0.02 0.98 0.00 0.00 0.00
#> TCGA.DD.AAD1.01 1 0.2929 0.582 0.82 0.18 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0609 0.883 0.02 0.98 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.1648 0.865 0.00 0.04 0.00 0.94 0.02
#> TCGA.ZP.A9CZ.01 3 0.1410 0.856 0.00 0.00 0.94 0.00 0.06
#> TCGA.UB.A7MF.01 3 0.0000 0.867 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0609 0.887 0.00 0.98 0.00 0.02 0.00
#> TCGA.FV.A3R3.01 2 0.1043 0.867 0.04 0.96 0.00 0.00 0.00
#> TCGA.DD.A39X.01 2 0.0609 0.883 0.02 0.98 0.00 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.0609 0.887 0.00 0.98 0.00 0.02 0.00
#> TCGA.CC.A7IJ.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.2438 0.867 0.00 0.06 0.00 0.90 0.04
#> TCGA.ED.A8O5.01 4 0.2012 0.874 0.00 0.06 0.00 0.92 0.02
#> TCGA.DD.AACN.01 2 0.3110 0.828 0.00 0.86 0.00 0.08 0.06
#> TCGA.DD.A1EF.01 2 0.1216 0.886 0.00 0.96 0.00 0.02 0.02
#> TCGA.DD.AADI.01 4 0.3868 0.809 0.00 0.14 0.00 0.80 0.06
#> TCGA.CC.A7IG.01 3 0.4967 0.660 0.06 0.00 0.66 0.00 0.28
#> TCGA.CC.A8HV.01 2 0.2438 0.856 0.00 0.90 0.00 0.06 0.04
#> TCGA.DD.AADO.01 4 0.2754 0.860 0.00 0.08 0.00 0.88 0.04
#> TCGA.G3.A25X.01 1 0.0609 0.870 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A4NH.01 1 0.2516 0.670 0.86 0.14 0.00 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 5 0.5330 0.000 0.44 0.02 0.02 0.00 0.52
#> TCGA.BW.A5NP.01 4 0.1648 0.874 0.00 0.04 0.00 0.94 0.02
#> TCGA.DD.AADY.01 4 0.6867 0.622 0.00 0.14 0.10 0.60 0.16
#> TCGA.DD.A118.01 3 0.6458 0.400 0.00 0.24 0.50 0.00 0.26
#> TCGA.DD.AACO.01 3 0.0609 0.864 0.00 0.00 0.98 0.00 0.02
#> TCGA.ED.A7PX.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NE.01 3 0.4398 0.732 0.00 0.00 0.72 0.04 0.24
#> TCGA.DD.AACT.01 3 0.2873 0.823 0.02 0.00 0.86 0.00 0.12
#> TCGA.ZP.A9D0.01 2 0.2754 0.849 0.00 0.88 0.00 0.04 0.08
#> TCGA.DD.A3A9.01 2 0.0609 0.883 0.02 0.98 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.2438 0.863 0.00 0.90 0.00 0.04 0.06
#> TCGA.2Y.A9H8.01 3 0.2929 0.806 0.00 0.00 0.82 0.00 0.18
#> TCGA.XR.A8TC.01 4 0.1043 0.872 0.00 0.04 0.00 0.96 0.00
#> TCGA.ED.A7XP.01 2 0.1043 0.867 0.04 0.96 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 3 0.1043 0.866 0.00 0.00 0.96 0.00 0.04
#> TCGA.DD.A4NA.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 1 0.0000 0.895 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.CC.A3MA.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 4 0.5087 0.2800 0.00 0.42 0.00 0.52 0.02 0.04
#> TCGA.ED.A7PY.01 4 0.2403 0.7840 0.00 0.04 0.00 0.90 0.02 0.04
#> TCGA.RC.A7S9.01 3 0.2048 0.5266 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.ED.A82E.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.0000 0.8697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GU.01 2 0.4703 0.7044 0.00 0.72 0.00 0.04 0.06 0.18
#> TCGA.WQ.A9G7.01 2 0.3647 0.3170 0.36 0.64 0.00 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.0937 0.8573 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.0937 0.8640 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.FV.A3I0.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.4892 -0.0714 0.00 0.50 0.00 0.44 0.00 0.06
#> TCGA.ED.A66Y.01 4 0.3007 0.7761 0.00 0.04 0.00 0.86 0.02 0.08
#> TCGA.G3.A5SI.01 3 0.3309 0.1575 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.BC.A112.01 1 0.2048 0.7953 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.01 3 0.2474 0.5923 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.2Y.A9H5.01 3 0.0000 0.6330 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SH.01 4 0.2350 0.7251 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.WX.AA44.01 1 0.5175 0.4358 0.64 0.28 0.04 0.00 0.02 0.02
#> TCGA.5C.A9VG.01 2 0.1865 0.8324 0.04 0.92 0.00 0.00 0.00 0.04
#> TCGA.DD.AAD1.01 1 0.2793 0.6931 0.80 0.20 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.8697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.1480 0.7553 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.ZP.A9CZ.01 3 0.1807 0.6178 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.UB.A7MF.01 3 0.0000 0.6330 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.0000 0.8697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.0937 0.8455 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.8697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.1092 0.8635 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.CC.A7IJ.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.1865 0.7804 0.00 0.04 0.00 0.92 0.00 0.04
#> TCGA.ED.A8O5.01 4 0.1480 0.7806 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.DD.AACN.01 2 0.3258 0.7794 0.00 0.84 0.00 0.10 0.02 0.04
#> TCGA.DD.A1EF.01 2 0.0000 0.8697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 4 0.3821 0.6709 0.00 0.22 0.00 0.74 0.00 0.04
#> TCGA.CC.A7IG.01 3 0.4887 0.2325 0.08 0.00 0.68 0.00 0.22 0.02
#> TCGA.CC.A8HV.01 2 0.2403 0.8324 0.00 0.90 0.00 0.04 0.02 0.04
#> TCGA.DD.AADO.01 4 0.3156 0.7205 0.00 0.18 0.00 0.80 0.00 0.02
#> TCGA.G3.A25X.01 1 0.0937 0.8710 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A4NH.01 1 0.2631 0.7230 0.82 0.18 0.00 0.00 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 5 0.2454 0.0000 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.BW.A5NP.01 4 0.1807 0.7770 0.00 0.02 0.00 0.92 0.00 0.06
#> TCGA.DD.AADY.01 4 0.7628 0.3640 0.00 0.22 0.16 0.46 0.04 0.12
#> TCGA.DD.A118.01 3 0.6549 -0.0990 0.00 0.32 0.48 0.00 0.12 0.08
#> TCGA.DD.AACO.01 3 0.0937 0.6206 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.ED.A7PX.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NE.01 6 0.3864 0.0000 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.DD.AACT.01 3 0.2882 0.5743 0.02 0.00 0.86 0.00 0.10 0.02
#> TCGA.ZP.A9D0.01 2 0.4361 0.7394 0.00 0.76 0.00 0.04 0.06 0.14
#> TCGA.DD.A3A9.01 2 0.0000 0.8697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.2784 0.8236 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.2Y.A9H8.01 3 0.4377 0.2902 0.00 0.00 0.72 0.00 0.16 0.12
#> TCGA.XR.A8TC.01 4 0.1480 0.7731 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.ED.A7XP.01 2 0.0937 0.8455 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 3 0.1480 0.6112 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.DD.A4NA.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 1 0.0000 0.9097 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 1 0.0000 0.9097 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.CC.A3MA.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 2 0.5408 -0.0830 0.00 0.46 0.08 0.42 0.00 0.04 0.00
#> TCGA.ED.A7PY.01 4 0.1928 0.7357 0.00 0.02 0.08 0.90 0.00 0.00 0.00
#> TCGA.RC.A7S9.01 7 0.2278 0.6556 0.00 0.00 0.04 0.00 0.00 0.08 0.88
#> TCGA.ED.A82E.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.1363 0.8062 0.00 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.DD.AA3A.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GU.01 2 0.4457 0.6904 0.00 0.72 0.16 0.06 0.00 0.06 0.00
#> TCGA.WQ.A9G7.01 2 0.3994 -0.1335 0.48 0.50 0.00 0.00 0.00 0.02 0.00
#> TCGA.CC.5261.01 2 0.2421 0.7650 0.00 0.88 0.08 0.02 0.00 0.02 0.00
#> TCGA.DD.AAEG.01 2 0.0863 0.8065 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.4175 0.2682 0.00 0.58 0.04 0.38 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 4 0.5102 0.6578 0.00 0.10 0.16 0.68 0.04 0.02 0.00
#> TCGA.G3.A5SI.01 7 0.4535 0.3254 0.00 0.00 0.12 0.00 0.00 0.24 0.64
#> TCGA.BC.A112.01 1 0.3417 0.6430 0.72 0.26 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.A113.01 7 0.1433 0.6927 0.00 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.2Y.A9H5.01 7 0.0504 0.6962 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.BC.A10Q.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SH.01 4 0.3284 0.6943 0.00 0.00 0.10 0.80 0.00 0.10 0.00
#> TCGA.WX.AA44.01 1 0.5813 0.4557 0.58 0.26 0.10 0.00 0.02 0.02 0.02
#> TCGA.5C.A9VG.01 2 0.1664 0.7746 0.06 0.92 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD1.01 1 0.3186 0.6956 0.76 0.22 0.00 0.00 0.00 0.02 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.8075 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.2016 0.7096 0.00 0.00 0.04 0.90 0.00 0.06 0.00
#> TCGA.ZP.A9CZ.01 7 0.1664 0.6885 0.00 0.00 0.06 0.00 0.02 0.00 0.92
#> TCGA.UB.A7MF.01 7 0.1006 0.6956 0.00 0.00 0.02 0.00 0.00 0.02 0.96
#> TCGA.G3.A25Y.01 2 0.0000 0.8075 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.2569 0.6886 0.14 0.84 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.A39X.01 2 0.1006 0.7972 0.02 0.96 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.AAE0.01 2 0.1363 0.8057 0.00 0.94 0.00 0.04 0.00 0.02 0.00
#> TCGA.CC.A7IJ.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.3879 0.7191 0.00 0.10 0.04 0.78 0.00 0.08 0.00
#> TCGA.ED.A8O5.01 4 0.2829 0.7400 0.00 0.08 0.08 0.84 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.3965 0.6956 0.00 0.76 0.10 0.12 0.00 0.02 0.00
#> TCGA.DD.A1EF.01 2 0.1363 0.8033 0.00 0.94 0.04 0.02 0.00 0.00 0.00
#> TCGA.DD.AADI.01 4 0.4813 0.6124 0.00 0.24 0.10 0.64 0.00 0.02 0.00
#> TCGA.CC.A7IG.01 7 0.5659 0.3141 0.02 0.02 0.36 0.00 0.10 0.00 0.50
#> TCGA.CC.A8HV.01 2 0.2769 0.7737 0.00 0.86 0.08 0.04 0.00 0.02 0.00
#> TCGA.DD.AADO.01 4 0.4809 0.6989 0.00 0.12 0.14 0.70 0.02 0.02 0.00
#> TCGA.G3.A25X.01 1 0.0504 0.8871 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 1 0.3052 0.7180 0.78 0.20 0.00 0.00 0.00 0.02 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 5 0.0504 0.0000 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.BW.A5NP.01 4 0.1363 0.7420 0.00 0.02 0.04 0.94 0.00 0.00 0.00
#> TCGA.DD.AADY.01 4 0.8156 0.1801 0.00 0.16 0.28 0.32 0.04 0.06 0.14
#> TCGA.DD.A118.01 7 0.6923 0.0367 0.00 0.30 0.20 0.00 0.06 0.04 0.40
#> TCGA.DD.AACO.01 7 0.1928 0.6661 0.00 0.00 0.02 0.00 0.00 0.08 0.90
#> TCGA.ED.A7PX.01 1 0.0504 0.8894 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DD.A4NE.01 6 0.3086 0.0000 0.00 0.00 0.04 0.00 0.00 0.80 0.16
#> TCGA.DD.AACT.01 7 0.3566 0.6126 0.02 0.00 0.16 0.00 0.04 0.00 0.78
#> TCGA.ZP.A9D0.01 2 0.3680 0.7269 0.00 0.78 0.14 0.06 0.00 0.02 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.8075 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.2512 0.7721 0.00 0.86 0.10 0.04 0.00 0.00 0.00
#> TCGA.2Y.A9H8.01 7 0.4266 0.3303 0.00 0.00 0.44 0.00 0.04 0.00 0.52
#> TCGA.XR.A8TC.01 4 0.3149 0.7367 0.00 0.06 0.06 0.84 0.00 0.04 0.00
#> TCGA.ED.A7XP.01 2 0.1433 0.7660 0.08 0.92 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 7 0.2509 0.6776 0.00 0.00 0.06 0.02 0.00 0.04 0.88
#> TCGA.DD.A4NA.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 1 0.0000 0.9003 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 1 0.0000 0.9003 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.CC.A3MA.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADW.01 4 0.5270 -0.14324 0.00 0.34 0.30 0.36 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.2265 0.41556 0.00 0.00 0.08 0.88 0.00 0.02 0.00 0.02
#> TCGA.RC.A7S9.01 7 0.2569 0.69587 0.00 0.00 0.00 0.00 0.00 0.02 0.82 0.16
#> TCGA.ED.A82E.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.1563 0.70588 0.00 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GU.01 2 0.4459 0.54480 0.00 0.64 0.28 0.04 0.00 0.02 0.00 0.02
#> TCGA.WQ.A9G7.01 2 0.3570 0.24719 0.36 0.62 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.3774 0.52000 0.00 0.70 0.22 0.08 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEG.01 2 0.2856 0.62500 0.00 0.78 0.20 0.02 0.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.5635 -0.23063 0.00 0.36 0.32 0.30 0.00 0.00 0.00 0.02
#> TCGA.ED.A66Y.01 4 0.4750 0.30950 0.00 0.02 0.20 0.68 0.02 0.02 0.00 0.06
#> TCGA.G3.A5SI.01 7 0.4848 0.31955 0.00 0.00 0.10 0.00 0.00 0.02 0.54 0.34
#> TCGA.BC.A112.01 1 0.3794 0.69072 0.74 0.18 0.04 0.00 0.04 0.00 0.00 0.00
#> TCGA.DD.A113.01 7 0.1275 0.75350 0.00 0.00 0.04 0.00 0.00 0.00 0.94 0.02
#> TCGA.2Y.A9H5.01 7 0.0000 0.75597 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.A10Q.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A7SH.01 4 0.5209 0.27023 0.00 0.00 0.14 0.64 0.02 0.06 0.00 0.14
#> TCGA.WX.AA44.01 1 0.5740 0.37749 0.54 0.26 0.08 0.00 0.00 0.00 0.02 0.10
#> TCGA.5C.A9VG.01 2 0.2020 0.69569 0.02 0.90 0.06 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAD1.01 1 0.2981 0.69573 0.76 0.22 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.71059 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.3169 0.32034 0.00 0.00 0.00 0.78 0.02 0.02 0.00 0.18
#> TCGA.ZP.A9CZ.01 7 0.2020 0.74478 0.00 0.00 0.02 0.00 0.02 0.00 0.90 0.06
#> TCGA.UB.A7MF.01 7 0.0471 0.75557 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.G3.A25Y.01 2 0.1563 0.70530 0.00 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.1275 0.69543 0.02 0.94 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.01 2 0.0471 0.70607 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.4169 0.59221 0.00 0.70 0.18 0.10 0.00 0.02 0.00 0.00
#> TCGA.CC.A7IJ.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.6528 0.00594 0.00 0.10 0.24 0.48 0.00 0.08 0.00 0.10
#> TCGA.ED.A8O5.01 4 0.3036 0.34490 0.00 0.04 0.18 0.78 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.5097 0.42953 0.00 0.60 0.12 0.24 0.00 0.02 0.00 0.02
#> TCGA.DD.A1EF.01 2 0.2404 0.69584 0.00 0.84 0.14 0.02 0.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 4 0.4918 -0.21496 0.00 0.10 0.38 0.50 0.00 0.02 0.00 0.00
#> TCGA.CC.A7IG.01 7 0.6889 0.27797 0.08 0.02 0.06 0.00 0.04 0.04 0.44 0.32
#> TCGA.CC.A8HV.01 2 0.3589 0.63236 0.00 0.74 0.16 0.10 0.00 0.00 0.00 0.00
#> TCGA.DD.AADO.01 4 0.5390 -0.12711 0.00 0.14 0.28 0.54 0.02 0.00 0.00 0.02
#> TCGA.G3.A25X.01 1 0.0808 0.87031 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 1 0.2981 0.69573 0.76 0.22 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 5 0.0808 0.00000 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.BW.A5NP.01 4 0.1557 0.41684 0.00 0.00 0.06 0.92 0.00 0.00 0.00 0.02
#> TCGA.DD.AADY.01 3 0.6483 0.00000 0.00 0.10 0.48 0.28 0.04 0.02 0.08 0.00
#> TCGA.DD.A118.01 2 0.7077 -0.12702 0.00 0.36 0.14 0.00 0.02 0.02 0.26 0.20
#> TCGA.DD.AACO.01 7 0.0808 0.75159 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.ED.A7PX.01 1 0.0471 0.88785 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NE.01 6 0.1804 0.00000 0.00 0.00 0.02 0.00 0.00 0.90 0.08 0.00
#> TCGA.DD.AACT.01 7 0.3758 0.66337 0.04 0.00 0.06 0.00 0.00 0.00 0.76 0.14
#> TCGA.ZP.A9D0.01 2 0.4028 0.57465 0.00 0.66 0.28 0.04 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A9.01 2 0.0000 0.71059 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.3227 0.65439 0.00 0.78 0.14 0.08 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H8.01 7 0.4518 0.43978 0.00 0.00 0.00 0.00 0.02 0.06 0.56 0.36
#> TCGA.XR.A8TC.01 4 0.5775 0.31842 0.00 0.06 0.16 0.60 0.00 0.08 0.00 0.10
#> TCGA.ED.A7XP.01 2 0.0471 0.70607 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VH.01 7 0.3503 0.68692 0.00 0.00 0.12 0.00 0.00 0.02 0.78 0.08
#> TCGA.DD.A4NA.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5260.01 1 0.0000 0.89950 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 1 0.0000 0.89950 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: Node022. Child nodes: Node02121 , Node02122-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221 , Node02222-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02411-leaf , Node02412-leaf , Node02421-leaf , Node02422-leaf , Node02431-leaf , Node02432-leaf , Node02433-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 22 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.442 0.796 0.841 0.4027 0.632 0.632
#> 3 3 1.000 0.995 0.993 0.6607 0.697 0.521
#> 4 4 0.848 0.867 0.902 0.0881 1.000 1.000
#> 5 5 0.805 0.847 0.897 0.0691 0.883 0.645
#> 6 6 0.721 0.736 0.848 0.0535 1.000 1.000
#> 7 7 0.819 0.616 0.819 0.0247 0.978 0.898
#> 8 8 0.816 0.621 0.759 0.0284 0.926 0.622
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.CC.A3MA.01 2 0.000 0.720 0.00 1.00
#> TCGA.ED.A82E.01 1 0.000 1.000 1.00 0.00
#> TCGA.DD.AA3A.01 2 0.000 0.720 0.00 1.00
#> TCGA.WQ.A9G7.01 2 0.000 0.720 0.00 1.00
#> TCGA.FV.A3I0.01 2 0.000 0.720 0.00 1.00
#> TCGA.BC.A112.01 2 0.943 0.749 0.36 0.64
#> TCGA.BC.A10Q.01 1 0.000 1.000 1.00 0.00
#> TCGA.WX.AA44.01 2 0.943 0.749 0.36 0.64
#> TCGA.5C.A9VG.01 2 0.943 0.749 0.36 0.64
#> TCGA.DD.AAD1.01 2 0.943 0.749 0.36 0.64
#> TCGA.FV.A3R3.01 2 0.827 0.745 0.26 0.74
#> TCGA.DD.A39X.01 2 0.943 0.749 0.36 0.64
#> TCGA.CC.A7IJ.01 2 0.943 0.749 0.36 0.64
#> TCGA.G3.A25X.01 2 0.943 0.749 0.36 0.64
#> TCGA.DD.A4NH.01 2 0.943 0.749 0.36 0.64
#> TCGA.G3.A25T.01 1 0.000 1.000 1.00 0.00
#> TCGA.UB.A7MA.01 2 0.000 0.720 0.00 1.00
#> TCGA.ED.A7PX.01 2 0.000 0.720 0.00 1.00
#> TCGA.ED.A7XP.01 2 0.943 0.749 0.36 0.64
#> TCGA.DD.A4NA.01 1 0.000 1.000 1.00 0.00
#> TCGA.CC.5260.01 1 0.000 1.000 1.00 0.00
#> TCGA.2Y.A9H2.01 2 0.000 0.720 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CC.A3MA.01 3 0.0892 0.986 0.02 0.00 0.98
#> TCGA.ED.A82E.01 1 0.0892 1.000 0.98 0.02 0.00
#> TCGA.DD.AA3A.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.WQ.A9G7.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.FV.A3I0.01 3 0.0892 0.986 0.02 0.00 0.98
#> TCGA.BC.A112.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BC.A10Q.01 1 0.0892 1.000 0.98 0.02 0.00
#> TCGA.WX.AA44.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.FV.A3R3.01 2 0.0892 0.976 0.00 0.98 0.02
#> TCGA.DD.A39X.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CC.A7IJ.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.G3.A25X.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.G3.A25T.01 1 0.0892 1.000 0.98 0.02 0.00
#> TCGA.UB.A7MA.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.ED.A7PX.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.ED.A7XP.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.DD.A4NA.01 1 0.0892 1.000 0.98 0.02 0.00
#> TCGA.CC.5260.01 1 0.0892 1.000 0.98 0.02 0.00
#> TCGA.2Y.A9H2.01 3 0.0000 0.995 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.CC.A3MA.01 4 0.4790 0.617 0.00 0.00 0.38 0.62
#> TCGA.ED.A82E.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.DD.AA3A.01 4 0.0000 0.877 0.00 0.00 0.00 1.00
#> TCGA.WQ.A9G7.01 4 0.2921 0.870 0.00 0.00 0.14 0.86
#> TCGA.FV.A3I0.01 4 0.1211 0.874 0.00 0.00 0.04 0.96
#> TCGA.BC.A112.01 2 0.4855 0.697 0.00 0.60 0.40 0.00
#> TCGA.BC.A10Q.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.WX.AA44.01 2 0.0707 0.878 0.00 0.98 0.02 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.884 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD1.01 2 0.0000 0.884 0.00 1.00 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.0000 0.884 0.00 1.00 0.00 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.884 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IJ.01 2 0.4790 0.710 0.00 0.62 0.38 0.00
#> TCGA.G3.A25X.01 2 0.4855 0.697 0.00 0.60 0.40 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.884 0.00 1.00 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 4 0.3975 0.834 0.00 0.00 0.24 0.76
#> TCGA.ED.A7PX.01 4 0.2921 0.870 0.00 0.00 0.14 0.86
#> TCGA.ED.A7XP.01 2 0.0000 0.884 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NA.01 1 0.0707 0.986 0.98 0.00 0.02 0.00
#> TCGA.CC.5260.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 4 0.0000 0.877 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CC.A3MA.01 5 0.4182 0.000 0.00 0.00 0.00 0.40 0.60
#> TCGA.ED.A82E.01 1 0.1216 0.920 0.96 0.00 0.02 0.00 0.02
#> TCGA.DD.AA3A.01 4 0.1410 0.807 0.00 0.00 0.00 0.94 0.06
#> TCGA.WQ.A9G7.01 4 0.0609 0.818 0.00 0.00 0.02 0.98 0.00
#> TCGA.FV.A3I0.01 4 0.3513 0.734 0.00 0.00 0.02 0.80 0.18
#> TCGA.BC.A112.01 3 0.3852 0.985 0.00 0.22 0.76 0.00 0.02
#> TCGA.BC.A10Q.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA44.01 2 0.2754 0.896 0.00 0.88 0.04 0.00 0.08
#> TCGA.5C.A9VG.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAD1.01 2 0.0609 0.939 0.00 0.98 0.00 0.00 0.02
#> TCGA.FV.A3R3.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39X.01 2 0.1732 0.926 0.00 0.92 0.00 0.00 0.08
#> TCGA.CC.A7IJ.01 3 0.3274 0.992 0.00 0.22 0.78 0.00 0.00
#> TCGA.G3.A25X.01 3 0.3274 0.992 0.00 0.22 0.78 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.945 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 4 0.3922 0.653 0.00 0.00 0.04 0.78 0.18
#> TCGA.ED.A7PX.01 4 0.0609 0.818 0.00 0.00 0.02 0.98 0.00
#> TCGA.ED.A7XP.01 2 0.2020 0.922 0.00 0.90 0.00 0.00 0.10
#> TCGA.DD.A4NA.01 1 0.4373 0.765 0.76 0.00 0.16 0.00 0.08
#> TCGA.CC.5260.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 4 0.1410 0.807 0.00 0.00 0.00 0.94 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CC.A3MA.01 5 0.5083 0.000 0.00 0.00 0.00 0.10 0.58 0.32
#> TCGA.ED.A82E.01 1 0.2794 0.832 0.86 0.00 0.06 0.00 0.00 0.08
#> TCGA.DD.AA3A.01 4 0.3985 0.688 0.00 0.00 0.00 0.76 0.14 0.10
#> TCGA.WQ.A9G7.01 4 0.0000 0.717 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FV.A3I0.01 4 0.6022 0.581 0.00 0.00 0.04 0.56 0.14 0.26
#> TCGA.BC.A112.01 3 0.2728 0.903 0.00 0.10 0.86 0.00 0.00 0.04
#> TCGA.BC.A10Q.01 1 0.0000 0.904 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA44.01 2 0.4420 0.757 0.00 0.62 0.04 0.00 0.34 0.00
#> TCGA.5C.A9VG.01 2 0.0547 0.742 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.AAD1.01 2 0.3309 0.785 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.FV.A3R3.01 2 0.0547 0.742 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A39X.01 2 0.3578 0.780 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.CC.A7IJ.01 3 0.2941 0.846 0.00 0.22 0.78 0.00 0.00 0.00
#> TCGA.G3.A25X.01 3 0.1814 0.910 0.00 0.10 0.90 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0000 0.750 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.904 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 4 0.3198 0.561 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.ED.A7PX.01 4 0.0000 0.717 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A7XP.01 2 0.3706 0.767 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.DD.A4NA.01 1 0.3950 0.705 0.72 0.00 0.00 0.00 0.04 0.24
#> TCGA.CC.5260.01 1 0.0000 0.904 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 4 0.3985 0.688 0.00 0.00 0.00 0.76 0.14 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CC.A3MA.01 5 0.2259 0.000 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.ED.A82E.01 1 0.3600 0.791 0.82 0.00 0.02 0.00 0.04 0.04 0.08
#> TCGA.DD.AA3A.01 4 0.0000 0.709 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WQ.A9G7.01 4 0.1433 0.695 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.FV.A3I0.01 4 0.5128 -0.562 0.00 0.00 0.02 0.56 0.00 0.10 0.32
#> TCGA.BC.A112.01 3 0.5423 0.659 0.00 0.04 0.66 0.00 0.04 0.10 0.16
#> TCGA.BC.A10Q.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA44.01 2 0.0504 0.732 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.3413 0.736 0.00 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.DD.AAD1.01 2 0.4429 0.711 0.00 0.66 0.00 0.00 0.00 0.22 0.12
#> TCGA.FV.A3R3.01 2 0.3413 0.736 0.00 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.DD.A39X.01 2 0.0000 0.740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IJ.01 3 0.3548 0.731 0.00 0.04 0.80 0.00 0.00 0.12 0.04
#> TCGA.G3.A25X.01 3 0.0863 0.777 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.3221 0.749 0.00 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 7 0.3459 0.000 0.00 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.ED.A7PX.01 4 0.1433 0.695 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.ED.A7XP.01 2 0.3263 0.674 0.00 0.80 0.00 0.00 0.00 0.08 0.12
#> TCGA.DD.A4NA.01 1 0.4248 0.636 0.66 0.00 0.00 0.00 0.08 0.26 0.00
#> TCGA.CC.5260.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 4 0.0000 0.709 0.00 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CC.A3MA.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A82E.01 1 0.3272 0.499 0.58 0.00 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.DD.AA3A.01 4 0.3128 0.784 0.00 0.00 0.00 0.82 0.04 0.04 0.10 0.00
#> TCGA.WQ.A9G7.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A3I0.01 7 0.3514 0.409 0.00 0.00 0.00 0.34 0.02 0.00 0.64 0.00
#> TCGA.BC.A112.01 3 0.4704 0.534 0.00 0.02 0.62 0.00 0.00 0.06 0.02 0.28
#> TCGA.BC.A10Q.01 1 0.0000 0.770 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA44.01 6 0.3299 0.909 0.00 0.44 0.00 0.00 0.00 0.56 0.00 0.00
#> TCGA.5C.A9VG.01 2 0.0000 0.747 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD1.01 2 0.3272 -0.403 0.00 0.58 0.00 0.00 0.00 0.42 0.00 0.00
#> TCGA.FV.A3R3.01 2 0.0000 0.747 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.01 6 0.3299 0.909 0.00 0.44 0.00 0.00 0.00 0.56 0.00 0.00
#> TCGA.CC.A7IJ.01 3 0.3770 0.651 0.00 0.12 0.78 0.00 0.00 0.02 0.04 0.04
#> TCGA.G3.A25X.01 3 0.0941 0.710 0.00 0.02 0.96 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A4NH.01 2 0.0471 0.735 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.G3.A25T.01 1 0.0000 0.770 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MA.01 7 0.5724 0.489 0.00 0.00 0.02 0.38 0.00 0.04 0.44 0.12
#> TCGA.ED.A7PX.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7XP.01 6 0.3142 0.827 0.00 0.36 0.00 0.00 0.00 0.64 0.00 0.00
#> TCGA.DD.A4NA.01 1 0.6128 0.348 0.46 0.00 0.00 0.00 0.00 0.22 0.18 0.14
#> TCGA.CC.5260.01 1 0.0000 0.770 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H2.01 4 0.2350 0.812 0.00 0.00 0.00 0.86 0.04 0.00 0.10 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node02121 , Node02122-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221 , Node02222-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02411-leaf , Node02412-leaf , Node02421-leaf , Node02422-leaf , Node02431-leaf , Node02432-leaf , Node02433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0222"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 26 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4436 0.557 0.557
#> 3 3 0.717 0.816 0.858 0.3344 0.825 0.702
#> 4 4 0.949 0.923 0.959 0.2294 0.760 0.490
#> 5 5 0.851 0.925 0.959 0.0510 0.954 0.824
#> 6 6 0.837 0.839 0.951 0.0323 0.997 0.986
#> 7 7 0.833 0.609 0.849 0.0420 0.982 0.914
#> 8 8 0.819 0.577 0.848 0.0339 0.898 0.542
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.DD.AADW.01 1 0 1 1 0
#> TCGA.ED.A7PY.01 1 0 1 1 0
#> TCGA.DD.A1EH.01 1 0 1 1 0
#> TCGA.2Y.A9GU.01 2 0 1 0 1
#> TCGA.CC.5261.01 1 0 1 1 0
#> TCGA.DD.AAEG.01 2 0 1 0 1
#> TCGA.DD.AADA.01 2 0 1 0 1
#> TCGA.ED.A66Y.01 1 0 1 1 0
#> TCGA.RC.A7SH.01 1 0 1 1 0
#> TCGA.2Y.A9H6.01 2 0 1 0 1
#> TCGA.DD.A4NN.01 1 0 1 1 0
#> TCGA.G3.A25Y.01 1 0 1 1 0
#> TCGA.DD.AAE0.01 1 0 1 1 0
#> TCGA.DD.AAVS.01 1 0 1 1 0
#> TCGA.ED.A8O5.01 1 0 1 1 0
#> TCGA.DD.AACN.01 1 0 1 1 0
#> TCGA.DD.A1EF.01 2 0 1 0 1
#> TCGA.DD.AADI.01 1 0 1 1 0
#> TCGA.CC.A8HV.01 1 0 1 1 0
#> TCGA.DD.AADO.01 1 0 1 1 0
#> TCGA.BW.A5NP.01 1 0 1 1 0
#> TCGA.DD.AADY.01 1 0 1 1 0
#> TCGA.ZP.A9D0.01 2 0 1 0 1
#> TCGA.DD.A3A9.01 2 0 1 0 1
#> TCGA.DD.A73G.01 2 0 1 0 1
#> TCGA.XR.A8TC.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DD.AADW.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.ED.A7PY.01 1 0.0000 0.803 1.00 0.00 0.00
#> TCGA.DD.A1EH.01 2 0.6387 0.537 0.02 0.68 0.30
#> TCGA.2Y.A9GU.01 3 0.5560 1.000 0.00 0.30 0.70
#> TCGA.CC.5261.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.DD.AAEG.01 3 0.5560 1.000 0.00 0.30 0.70
#> TCGA.DD.AADA.01 2 0.0000 0.782 0.00 1.00 0.00
#> TCGA.ED.A66Y.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.RC.A7SH.01 1 0.0000 0.803 1.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 0.782 0.00 1.00 0.00
#> TCGA.DD.A4NN.01 1 0.0000 0.803 1.00 0.00 0.00
#> TCGA.G3.A25Y.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.DD.AAE0.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.DD.AAVS.01 1 0.0000 0.803 1.00 0.00 0.00
#> TCGA.ED.A8O5.01 1 0.6387 0.834 0.68 0.02 0.30
#> TCGA.DD.AACN.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.DD.A1EF.01 2 0.0000 0.782 0.00 1.00 0.00
#> TCGA.DD.AADI.01 1 0.0892 0.807 0.98 0.00 0.02
#> TCGA.CC.A8HV.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.DD.AADO.01 1 0.0000 0.803 1.00 0.00 0.00
#> TCGA.BW.A5NP.01 1 0.5560 0.850 0.70 0.00 0.30
#> TCGA.DD.AADY.01 2 0.7683 0.503 0.08 0.64 0.28
#> TCGA.ZP.A9D0.01 3 0.5560 1.000 0.00 0.30 0.70
#> TCGA.DD.A3A9.01 2 0.0000 0.782 0.00 1.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.782 0.00 1.00 0.00
#> TCGA.XR.A8TC.01 1 0.0000 0.803 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.DD.AADW.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.1637 0.917 0.06 0.00 0.00 0.94
#> TCGA.DD.A1EH.01 1 0.0707 0.974 0.98 0.02 0.00 0.00
#> TCGA.2Y.A9GU.01 3 0.0707 1.000 0.00 0.02 0.98 0.00
#> TCGA.CC.5261.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEG.01 3 0.0707 1.000 0.00 0.02 0.98 0.00
#> TCGA.DD.AADA.01 2 0.0000 0.893 0.00 1.00 0.00 0.00
#> TCGA.ED.A66Y.01 1 0.1411 0.962 0.96 0.00 0.02 0.02
#> TCGA.RC.A7SH.01 4 0.0707 0.922 0.02 0.00 0.00 0.98
#> TCGA.2Y.A9H6.01 2 0.0000 0.893 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.1211 0.923 0.04 0.00 0.00 0.96
#> TCGA.G3.A25Y.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DD.AAE0.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.0707 0.922 0.02 0.00 0.00 0.98
#> TCGA.ED.A8O5.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.01 2 0.0000 0.893 0.00 1.00 0.00 0.00
#> TCGA.DD.AADI.01 4 0.3801 0.766 0.22 0.00 0.00 0.78
#> TCGA.CC.A8HV.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DD.AADO.01 4 0.2647 0.878 0.12 0.00 0.00 0.88
#> TCGA.BW.A5NP.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DD.AADY.01 2 0.7198 0.405 0.32 0.56 0.02 0.10
#> TCGA.ZP.A9D0.01 3 0.0707 1.000 0.00 0.02 0.98 0.00
#> TCGA.DD.A3A9.01 2 0.0000 0.893 0.00 1.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 0.893 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TC.01 4 0.0707 0.922 0.02 0.00 0.00 0.98
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DD.AADW.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.202 0.864 0.10 0.00 0 0.90 0.00
#> TCGA.DD.A1EH.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.2Y.A9GU.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.CC.5261.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.DD.AAEG.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DD.AADA.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.ED.A66Y.01 5 0.273 0.561 0.16 0.00 0 0.00 0.84
#> TCGA.RC.A7SH.01 4 0.000 0.884 0.00 0.00 0 1.00 0.00
#> TCGA.2Y.A9H6.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.104 0.887 0.04 0.00 0 0.96 0.00
#> TCGA.G3.A25Y.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.DD.AAE0.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.000 0.884 0.00 0.00 0 1.00 0.00
#> TCGA.ED.A8O5.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.DD.AACN.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.DD.A1EF.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.DD.AADI.01 4 0.385 0.698 0.22 0.00 0 0.76 0.02
#> TCGA.CC.A8HV.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.DD.AADO.01 4 0.287 0.841 0.12 0.00 0 0.86 0.02
#> TCGA.BW.A5NP.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.DD.AADY.01 5 0.629 0.538 0.12 0.22 0 0.04 0.62
#> TCGA.ZP.A9D0.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.DD.A73G.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.XR.A8TC.01 4 0.000 0.884 0.00 0.00 0 1.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DD.AADW.01 1 0.0000 0.957 1.00 0 0 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.3045 0.799 0.06 0 0 0.84 0.10 0.00
#> TCGA.DD.A1EH.01 1 0.0000 0.957 1.00 0 0 0.00 0.00 0.00
#> TCGA.2Y.A9GU.01 3 0.0000 1.000 0.00 0 1 0.00 0.00 0.00
#> TCGA.CC.5261.01 1 0.0000 0.957 1.00 0 0 0.00 0.00 0.00
#> TCGA.DD.AAEG.01 3 0.0000 1.000 0.00 0 1 0.00 0.00 0.00
#> TCGA.DD.AADA.01 2 0.0000 1.000 0.00 1 0 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 5 0.0937 0.000 0.00 0 0 0.00 0.96 0.04
#> TCGA.RC.A7SH.01 4 0.0000 0.831 0.00 0 0 1.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 1.000 0.00 1 0 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.2094 0.824 0.02 0 0 0.90 0.08 0.00
#> TCGA.G3.A25Y.01 1 0.1556 0.919 0.92 0 0 0.00 0.08 0.00
#> TCGA.DD.AAE0.01 1 0.0000 0.957 1.00 0 0 0.00 0.00 0.00
#> TCGA.DD.AAVS.01 4 0.0000 0.831 0.00 0 0 1.00 0.00 0.00
#> TCGA.ED.A8O5.01 1 0.0000 0.957 1.00 0 0 0.00 0.00 0.00
#> TCGA.DD.AACN.01 1 0.1814 0.905 0.90 0 0 0.00 0.10 0.00
#> TCGA.DD.A1EF.01 2 0.0000 1.000 0.00 1 0 0.00 0.00 0.00
#> TCGA.DD.AADI.01 4 0.5862 0.543 0.20 0 0 0.60 0.16 0.04
#> TCGA.CC.A8HV.01 1 0.2260 0.871 0.86 0 0 0.00 0.14 0.00
#> TCGA.DD.AADO.01 4 0.4444 0.714 0.08 0 0 0.74 0.16 0.02
#> TCGA.BW.A5NP.01 1 0.0000 0.957 1.00 0 0 0.00 0.00 0.00
#> TCGA.DD.AADY.01 6 0.0000 0.000 0.00 0 0 0.00 0.00 1.00
#> TCGA.ZP.A9D0.01 3 0.0000 1.000 0.00 0 1 0.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 1.000 0.00 1 0 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 1.000 0.00 1 0 0.00 0.00 0.00
#> TCGA.XR.A8TC.01 4 0.0000 0.831 0.00 0 0 1.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DD.AADW.01 1 0.0000 0.8305 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.4003 -0.0889 0.04 0 0.00 0.64 0.00 0.00 0.32
#> TCGA.DD.A1EH.01 1 0.0000 0.8305 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GU.01 3 0.0000 0.9913 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5261.01 1 0.1671 0.8316 0.90 0 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.AAEG.01 3 0.0504 0.9825 0.00 0 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.AADA.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 5 0.0000 0.0000 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A7SH.01 4 0.0000 0.5104 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H6.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.3994 0.1311 0.02 0 0.00 0.50 0.00 0.00 0.48
#> TCGA.G3.A25Y.01 1 0.2832 0.7670 0.76 0 0.00 0.00 0.00 0.00 0.24
#> TCGA.DD.AAE0.01 1 0.1886 0.8311 0.88 0 0.00 0.00 0.00 0.00 0.12
#> TCGA.DD.AAVS.01 4 0.0504 0.4966 0.00 0 0.00 0.98 0.00 0.00 0.02
#> TCGA.ED.A8O5.01 1 0.0000 0.8305 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 1 0.3459 0.6234 0.60 0 0.00 0.00 0.00 0.00 0.40
#> TCGA.DD.A1EF.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 4 0.5716 -0.6253 0.10 0 0.00 0.44 0.02 0.02 0.42
#> TCGA.CC.A8HV.01 1 0.3525 0.5680 0.56 0 0.00 0.00 0.00 0.00 0.44
#> TCGA.DD.AADO.01 7 0.3943 0.0000 0.02 0 0.00 0.42 0.00 0.00 0.56
#> TCGA.BW.A5NP.01 1 0.1671 0.8093 0.90 0 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.AADY.01 6 0.0000 0.0000 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZP.A9D0.01 3 0.0000 0.9913 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 1.0000 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TC.01 4 0.0000 0.5104 0.00 0 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DD.AADW.01 1 0.0000 0.731 1.00 0 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 7 0.5035 0.062 0.02 0 0.0 0.36 0.00 0.00 0.50 0.12
#> TCGA.DD.A1EH.01 1 0.0808 0.721 0.96 0 0.0 0.00 0.00 0.00 0.00 0.04
#> TCGA.2Y.A9GU.01 3 0.0000 0.956 0.00 0 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5261.01 1 0.3293 0.637 0.74 0 0.0 0.00 0.00 0.00 0.22 0.04
#> TCGA.DD.AAEG.01 3 0.1887 0.909 0.00 0 0.9 0.00 0.00 0.00 0.04 0.06
#> TCGA.DD.AADA.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A66Y.01 5 0.0000 0.000 0.00 0 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.RC.A7SH.01 4 0.0941 0.921 0.00 0 0.0 0.96 0.00 0.00 0.02 0.02
#> TCGA.2Y.A9H6.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 8 0.3154 0.000 0.00 0 0.0 0.16 0.00 0.00 0.06 0.78
#> TCGA.G3.A25Y.01 1 0.3690 0.272 0.56 0 0.0 0.00 0.00 0.00 0.42 0.02
#> TCGA.DD.AAE0.01 1 0.2888 0.690 0.80 0 0.0 0.00 0.00 0.00 0.16 0.04
#> TCGA.DD.AAVS.01 4 0.0808 0.919 0.00 0 0.0 0.96 0.00 0.00 0.04 0.00
#> TCGA.ED.A8O5.01 1 0.0808 0.721 0.96 0 0.0 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.AACN.01 7 0.4008 -0.229 0.48 0 0.0 0.00 0.00 0.00 0.48 0.04
#> TCGA.DD.A1EF.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADI.01 7 0.6319 0.188 0.10 0 0.0 0.22 0.00 0.04 0.50 0.14
#> TCGA.CC.A8HV.01 7 0.4358 -0.120 0.40 0 0.0 0.00 0.02 0.00 0.54 0.04
#> TCGA.DD.AADO.01 7 0.3991 0.136 0.00 0 0.0 0.32 0.00 0.00 0.62 0.06
#> TCGA.BW.A5NP.01 1 0.3619 0.597 0.74 0 0.0 0.00 0.00 0.00 0.12 0.14
#> TCGA.DD.AADY.01 6 0.0000 0.000 0.00 0 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9D0.01 3 0.0000 0.956 0.00 0 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A9.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73G.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TC.01 4 0.0000 0.942 0.00 0 0.0 1.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0222. Child nodes: Node021211-leaf , Node021212-leaf , Node022211-leaf , Node022212-leaf , Node022213-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02221"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 18 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.634 0.926 0.959 0.3337 0.706 0.706
#> 3 3 0.993 0.986 0.993 0.5961 0.765 0.667
#> 4 4 0.699 0.736 0.886 0.1715 0.908 0.808
#> 5 5 0.627 0.716 0.866 0.1887 0.817 0.533
#> 6 6 0.654 0.675 0.834 0.0485 1.000 1.000
#> 7 7 0.706 0.533 0.823 0.0184 0.980 0.906
#> 8 8 0.686 0.408 0.789 0.0472 0.967 0.833
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.DD.AADW.01 2 0.000 0.944 0.00 1.00
#> TCGA.ED.A7PY.01 2 0.722 0.804 0.20 0.80
#> TCGA.DD.A1EH.01 2 0.000 0.944 0.00 1.00
#> TCGA.CC.5261.01 2 0.000 0.944 0.00 1.00
#> TCGA.ED.A66Y.01 2 0.000 0.944 0.00 1.00
#> TCGA.RC.A7SH.01 1 0.000 1.000 1.00 0.00
#> TCGA.DD.A4NN.01 2 0.680 0.825 0.18 0.82
#> TCGA.G3.A25Y.01 2 0.000 0.944 0.00 1.00
#> TCGA.DD.AAE0.01 2 0.000 0.944 0.00 1.00
#> TCGA.DD.AAVS.01 1 0.000 1.000 1.00 0.00
#> TCGA.ED.A8O5.01 2 0.000 0.944 0.00 1.00
#> TCGA.DD.AACN.01 2 0.000 0.944 0.00 1.00
#> TCGA.DD.AADI.01 2 0.680 0.825 0.18 0.82
#> TCGA.CC.A8HV.01 2 0.000 0.944 0.00 1.00
#> TCGA.DD.AADO.01 2 0.000 0.944 0.00 1.00
#> TCGA.BW.A5NP.01 2 0.000 0.944 0.00 1.00
#> TCGA.DD.AADY.01 2 0.680 0.825 0.18 0.82
#> TCGA.XR.A8TC.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.DD.AADW.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.ED.A7PY.01 2 0.254 0.912 0.00 0.92 0.08
#> TCGA.DD.A1EH.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.CC.5261.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.ED.A66Y.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.RC.A7SH.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DD.A4NN.01 3 0.178 0.956 0.02 0.02 0.96
#> TCGA.G3.A25Y.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.DD.AAE0.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.DD.AAVS.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.DD.AACN.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.DD.AADI.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.CC.A8HV.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.DD.AADO.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BW.A5NP.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.DD.AADY.01 3 0.000 0.979 0.00 0.00 1.00
#> TCGA.XR.A8TC.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.DD.AADW.01 2 0.0000 0.8675 0.00 1.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.6005 0.0624 0.04 0.46 0.00 0.50
#> TCGA.DD.A1EH.01 2 0.0000 0.8675 0.00 1.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.0000 0.8675 0.00 1.00 0.00 0.00
#> TCGA.ED.A66Y.01 2 0.4522 0.6618 0.00 0.68 0.00 0.32
#> TCGA.RC.A7SH.01 1 0.1211 0.9654 0.96 0.00 0.00 0.04
#> TCGA.DD.A4NN.01 4 0.5062 -0.3459 0.00 0.02 0.30 0.68
#> TCGA.G3.A25Y.01 2 0.0000 0.8675 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE0.01 2 0.3801 0.7678 0.00 0.78 0.00 0.22
#> TCGA.DD.AAVS.01 1 0.0000 0.9829 1.00 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.8675 0.00 1.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.0707 0.8601 0.00 0.98 0.00 0.02
#> TCGA.DD.AADI.01 3 0.3606 0.7899 0.00 0.02 0.84 0.14
#> TCGA.CC.A8HV.01 2 0.3801 0.7678 0.00 0.78 0.00 0.22
#> TCGA.DD.AADO.01 2 0.4134 0.7331 0.00 0.74 0.00 0.26
#> TCGA.BW.A5NP.01 2 0.0000 0.8675 0.00 1.00 0.00 0.00
#> TCGA.DD.AADY.01 3 0.0000 0.8074 0.00 0.00 1.00 0.00
#> TCGA.XR.A8TC.01 1 0.0000 0.9829 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.DD.AADW.01 2 0.000 0.847 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.717 0.035 0.04 0.38 0.00 0.42 0.16
#> TCGA.DD.A1EH.01 2 0.000 0.847 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.311 0.835 0.00 0.84 0.00 0.02 0.14
#> TCGA.ED.A66Y.01 5 0.201 0.696 0.00 0.06 0.00 0.02 0.92
#> TCGA.RC.A7SH.01 1 0.122 0.965 0.96 0.00 0.00 0.02 0.02
#> TCGA.DD.A4NN.01 4 0.141 -0.127 0.00 0.00 0.06 0.94 0.00
#> TCGA.G3.A25Y.01 2 0.332 0.821 0.00 0.82 0.00 0.02 0.16
#> TCGA.DD.AAE0.01 5 0.380 0.732 0.00 0.30 0.00 0.00 0.70
#> TCGA.DD.AAVS.01 1 0.000 0.983 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.000 0.847 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.173 0.859 0.00 0.92 0.00 0.00 0.08
#> TCGA.DD.AADI.01 3 0.520 0.581 0.00 0.04 0.66 0.28 0.02
#> TCGA.CC.A8HV.01 5 0.342 0.796 0.00 0.24 0.00 0.00 0.76
#> TCGA.DD.AADO.01 5 0.287 0.775 0.00 0.12 0.00 0.02 0.86
#> TCGA.BW.A5NP.01 2 0.369 0.770 0.00 0.78 0.00 0.02 0.20
#> TCGA.DD.AADY.01 3 0.000 0.644 0.00 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TC.01 1 0.000 0.983 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.DD.AADW.01 2 0.0937 0.849 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.6990 0.321 0.00 0.16 0.32 0.42 0.10 0.00
#> TCGA.DD.A1EH.01 2 0.0937 0.849 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.2260 0.849 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.ED.A66Y.01 5 0.3711 0.440 0.00 0.02 0.26 0.00 0.72 0.00
#> TCGA.RC.A7SH.01 1 0.0000 0.690 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 4 0.0000 0.282 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A25Y.01 2 0.2048 0.860 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.DD.AAE0.01 5 0.3499 0.558 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.DD.AAVS.01 1 0.3578 0.843 0.66 0.00 0.34 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.0937 0.849 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.1814 0.866 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.DD.AADI.01 6 0.6011 0.429 0.00 0.02 0.12 0.26 0.02 0.58
#> TCGA.CC.A8HV.01 5 0.2941 0.673 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.DD.AADO.01 5 0.2794 0.614 0.00 0.06 0.08 0.00 0.86 0.00
#> TCGA.BW.A5NP.01 2 0.2793 0.781 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.DD.AADY.01 6 0.0000 0.544 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.XR.A8TC.01 1 0.3499 0.847 0.68 0.00 0.32 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.DD.AADW.01 2 0.1363 0.9000 0.00 0.94 0.02 0.04 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.3879 0.0000 0.00 0.08 0.00 0.78 0.04 0.00 0.10
#> TCGA.DD.A1EH.01 2 0.1363 0.9000 0.00 0.94 0.02 0.04 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.0504 0.9051 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.ED.A66Y.01 5 0.3055 0.1287 0.00 0.00 0.14 0.02 0.82 0.00 0.02
#> TCGA.RC.A7SH.01 3 0.3413 0.0000 0.38 0.00 0.62 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 7 0.0504 0.0000 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.G3.A25Y.01 2 0.1166 0.8951 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DD.AAE0.01 5 0.3525 0.2606 0.00 0.44 0.00 0.00 0.56 0.00 0.00
#> TCGA.DD.AAVS.01 1 0.1363 0.8521 0.94 0.00 0.04 0.02 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.1363 0.9000 0.00 0.94 0.02 0.04 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.1166 0.8951 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DD.AADI.01 6 0.5989 0.4201 0.00 0.00 0.08 0.18 0.00 0.54 0.20
#> TCGA.CC.A8HV.01 5 0.4127 0.4169 0.00 0.36 0.00 0.04 0.60 0.00 0.00
#> TCGA.DD.AADO.01 5 0.5542 -0.0537 0.00 0.02 0.14 0.38 0.46 0.00 0.00
#> TCGA.BW.A5NP.01 2 0.1886 0.8196 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.DD.AADY.01 6 0.0000 0.5023 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XR.A8TC.01 1 0.0863 0.8499 0.96 0.00 0.04 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.DD.AADW.01 2 0.0000 0.6442 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A7PY.01 4 0.6603 0.2086 0.00 0.02 0.08 0.54 0.14 0.00 0.12 0.10
#> TCGA.DD.A1EH.01 2 0.0000 0.6442 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5261.01 2 0.4308 0.6358 0.00 0.62 0.02 0.02 0.32 0.00 0.00 0.02
#> TCGA.ED.A66Y.01 8 0.2938 0.0000 0.00 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.RC.A7SH.01 3 0.1765 0.0000 0.12 0.00 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NN.01 7 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G3.A25Y.01 2 0.4367 0.6208 0.00 0.60 0.02 0.02 0.34 0.00 0.00 0.02
#> TCGA.DD.AAE0.01 5 0.2725 0.5035 0.00 0.14 0.00 0.00 0.82 0.00 0.00 0.04
#> TCGA.DD.AAVS.01 1 0.0471 0.9594 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A8O5.01 2 0.0000 0.6442 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACN.01 2 0.4162 0.6510 0.00 0.66 0.02 0.02 0.28 0.00 0.00 0.02
#> TCGA.DD.AADI.01 4 0.3970 0.0981 0.00 0.00 0.00 0.68 0.00 0.22 0.10 0.00
#> TCGA.CC.A8HV.01 5 0.1765 0.5230 0.00 0.12 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.DD.AADO.01 5 0.5539 -0.1609 0.00 0.00 0.06 0.14 0.50 0.00 0.00 0.30
#> TCGA.BW.A5NP.01 2 0.4541 0.4203 0.00 0.48 0.02 0.02 0.46 0.00 0.00 0.02
#> TCGA.DD.AADY.01 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TC.01 1 0.0471 0.9597 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 29 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.2963 0.704 0.704
#> 3 3 0.889 0.959 0.979 0.1356 0.985 0.979
#> 4 4 0.735 0.935 0.903 0.3744 0.766 0.661
#> 5 5 0.920 0.904 0.962 0.1799 0.995 0.989
#> 6 6 0.933 0.871 0.985 0.0248 0.998 0.995
#> 7 7 0.835 0.775 0.941 0.0747 0.990 0.978
#> 8 8 0.714 0.679 0.908 0.0372 0.998 0.994
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.DD.A3A2.11 1 0 1 1 0
#> TCGA.G3.A25W.11 1 0 1 1 0
#> TCGA.5R.AA1D.01 2 0 1 0 1
#> TCGA.DD.A1EF.11 1 0 1 1 0
#> TCGA.RC.A6M5.01 2 0 1 0 1
#> TCGA.DD.A3A6.01 2 0 1 0 1
#> TCGA.DD.A39Z.11 1 0 1 1 0
#> TCGA.BC.A10X.11 1 0 1 1 0
#> TCGA.DD.A4ND.01 2 0 1 0 1
#> TCGA.DD.A11D.11 1 0 1 1 0
#> TCGA.DD.A118.11 1 0 1 1 0
#> TCGA.XR.A8TD.01 2 0 1 0 1
#> TCGA.DD.A1EB.11 1 0 1 1 0
#> TCGA.DD.A4NS.01 1 0 1 1 0
#> TCGA.BC.A110.01 1 0 1 1 0
#> TCGA.BC.A10R.11 1 0 1 1 0
#> TCGA.DD.A113.11 1 0 1 1 0
#> TCGA.DD.A1EJ.11 1 0 1 1 0
#> TCGA.BC.A10Q.11 1 0 1 1 0
#> TCGA.DD.A39W.11 1 0 1 1 0
#> TCGA.UB.AA0V.01 1 0 1 1 0
#> TCGA.BD.A3EP.11 1 0 1 1 0
#> TCGA.BC.A216.11 1 0 1 1 0
#> TCGA.BC.A10X.01 1 0 1 1 0
#> TCGA.DD.A1EC.11 1 0 1 1 0
#> TCGA.DD.A39X.11 1 0 1 1 0
#> TCGA.BC.A110.11 1 0 1 1 0
#> TCGA.FV.A23B.11 1 0 1 1 0
#> TCGA.BC.A10Z.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DD.A3A2.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.G3.A25W.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.0000 0.971 0.00 0.00 1.00
#> TCGA.DD.A1EF.11 1 0.1529 0.949 0.96 0.00 0.04
#> TCGA.RC.A6M5.01 3 0.0892 0.971 0.00 0.02 0.98
#> TCGA.DD.A3A6.01 2 0.0892 0.975 0.00 0.98 0.02
#> TCGA.DD.A39Z.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.BC.A10X.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DD.A4ND.01 2 0.0892 0.976 0.00 0.98 0.02
#> TCGA.DD.A11D.11 1 0.2066 0.934 0.94 0.00 0.06
#> TCGA.DD.A118.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.XR.A8TD.01 2 0.0000 0.979 0.00 1.00 0.00
#> TCGA.DD.A1EB.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DD.A4NS.01 1 0.3340 0.880 0.88 0.00 0.12
#> TCGA.BC.A110.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.BC.A10R.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DD.A113.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DD.A1EJ.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.BC.A10Q.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DD.A39W.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.UB.AA0V.01 1 0.3340 0.880 0.88 0.00 0.12
#> TCGA.BD.A3EP.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.BC.A216.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.BC.A10X.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DD.A1EC.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DD.A39X.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.BC.A110.11 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FV.A23B.11 1 0.4796 0.755 0.78 0.00 0.22
#> TCGA.BC.A10Z.11 1 0.0000 0.976 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.DD.A3A2.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.0707 1.000 0.00 0.00 0.98 0.02
#> TCGA.DD.A1EF.11 4 0.4907 0.918 0.42 0.00 0.00 0.58
#> TCGA.RC.A6M5.01 3 0.0707 1.000 0.00 0.00 0.98 0.02
#> TCGA.DD.A3A6.01 2 0.4088 0.781 0.00 0.82 0.04 0.14
#> TCGA.DD.A39Z.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.BC.A10X.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DD.A4ND.01 2 0.5860 0.677 0.00 0.58 0.04 0.38
#> TCGA.DD.A11D.11 4 0.4907 0.918 0.42 0.00 0.00 0.58
#> TCGA.DD.A118.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TD.01 2 0.0000 0.775 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EB.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NS.01 4 0.5860 0.939 0.38 0.00 0.04 0.58
#> TCGA.BC.A110.01 1 0.3400 0.581 0.82 0.00 0.00 0.18
#> TCGA.BC.A10R.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DD.A113.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DD.A39W.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.UB.AA0V.01 4 0.6150 0.931 0.36 0.00 0.06 0.58
#> TCGA.BD.A3EP.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.BC.A216.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.BC.A10X.01 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EC.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 1 0.0000 0.983 1.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 4 0.6382 0.904 0.34 0.00 0.08 0.58
#> TCGA.BC.A10Z.11 1 0.0000 0.983 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.DD.A3A2.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EF.11 4 0.141 0.986 0.06 0.00 0.00 0.94 0.00
#> TCGA.RC.A6M5.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A6.01 2 0.459 0.573 0.00 0.72 0.00 0.06 0.22
#> TCGA.DD.A39Z.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10X.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4ND.01 5 0.104 0.000 0.00 0.00 0.00 0.04 0.96
#> TCGA.DD.A11D.11 4 0.141 0.986 0.06 0.00 0.00 0.94 0.00
#> TCGA.DD.A118.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TD.01 2 0.202 0.597 0.00 0.90 0.00 0.00 0.10
#> TCGA.DD.A1EB.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NS.01 4 0.141 0.986 0.06 0.00 0.00 0.94 0.00
#> TCGA.BC.A110.01 1 0.368 0.582 0.72 0.00 0.00 0.28 0.00
#> TCGA.BC.A10R.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.AA0V.01 4 0.233 0.945 0.08 0.00 0.02 0.90 0.00
#> TCGA.BD.A3EP.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A216.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10X.01 1 0.141 0.920 0.94 0.00 0.00 0.06 0.00
#> TCGA.DD.A1EC.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 1 0.000 0.979 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 4 0.141 0.986 0.06 0.00 0.00 0.94 0.00
#> TCGA.BC.A10Z.11 1 0.000 0.979 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.DD.A3A2.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A25W.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EF.11 4 0.0000 0.967 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A6M5.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A6.01 2 0.0000 0.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Z.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10X.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4ND.01 5 0.0547 0.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.DD.A11D.11 4 0.0000 0.967 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A118.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TD.01 6 0.1267 0.000 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.DD.A1EB.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NS.01 4 0.0547 0.961 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BC.A110.01 1 0.2454 0.808 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.BC.A10R.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A113.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A1EJ.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10Q.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.AA0V.01 4 0.2880 0.885 0.02 0.00 0.02 0.88 0.02 0.06
#> TCGA.BD.A3EP.11 1 0.0547 0.970 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BC.A216.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10X.01 1 0.0937 0.951 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DD.A1EC.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39X.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A110.11 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.11 4 0.0000 0.967 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A10Z.11 1 0.0000 0.987 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.DD.A3A2.11 1 0.0863 0.924 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.G3.A25W.11 1 0.0504 0.924 0.98 0 0.00 0.00 0 0 0.02
#> TCGA.5R.AA1D.01 3 0.1433 0.933 0.00 0 0.92 0.00 0 0 0.08
#> TCGA.DD.A1EF.11 4 0.0000 0.992 0.00 0 0.00 1.00 0 0 0.00
#> TCGA.RC.A6M5.01 3 0.0000 0.933 0.00 0 1.00 0.00 0 0 0.00
#> TCGA.DD.A3A6.01 2 0.0000 0.000 0.00 1 0.00 0.00 0 0 0.00
#> TCGA.DD.A39Z.11 1 0.0863 0.924 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.BC.A10X.11 1 0.0504 0.926 0.98 0 0.00 0.00 0 0 0.02
#> TCGA.DD.A4ND.01 5 0.0000 0.000 0.00 0 0.00 0.00 1 0 0.00
#> TCGA.DD.A11D.11 4 0.0000 0.992 0.00 0 0.00 1.00 0 0 0.00
#> TCGA.DD.A118.11 1 0.0863 0.920 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.XR.A8TD.01 6 0.0000 0.000 0.00 0 0.00 0.00 0 1 0.00
#> TCGA.DD.A1EB.11 1 0.0504 0.926 0.98 0 0.00 0.00 0 0 0.02
#> TCGA.DD.A4NS.01 4 0.0504 0.976 0.00 0 0.00 0.98 0 0 0.02
#> TCGA.BC.A110.01 1 0.4487 0.204 0.52 0 0.00 0.42 0 0 0.06
#> TCGA.BC.A10R.11 1 0.0863 0.920 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.DD.A113.11 1 0.0863 0.924 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.DD.A1EJ.11 1 0.1166 0.923 0.94 0 0.00 0.00 0 0 0.06
#> TCGA.BC.A10Q.11 1 0.0863 0.924 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.DD.A39W.11 1 0.0863 0.924 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.UB.AA0V.01 7 0.2259 0.000 0.00 0 0.00 0.16 0 0 0.84
#> TCGA.BD.A3EP.11 1 0.1928 0.890 0.90 0 0.00 0.02 0 0 0.08
#> TCGA.BC.A216.11 1 0.0863 0.920 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.BC.A10X.01 1 0.2829 0.831 0.84 0 0.00 0.08 0 0 0.08
#> TCGA.DD.A1EC.11 1 0.0863 0.924 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.DD.A39X.11 1 0.0863 0.924 0.96 0 0.00 0.00 0 0 0.04
#> TCGA.BC.A110.11 1 0.1166 0.912 0.94 0 0.00 0.00 0 0 0.06
#> TCGA.FV.A23B.11 4 0.0000 0.992 0.00 0 0.00 1.00 0 0 0.00
#> TCGA.BC.A10Z.11 1 0.1433 0.901 0.92 0 0.00 0.00 0 0 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DD.A3A2.11 1 0.1341 0.890 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.G3.A25W.11 1 0.0471 0.899 0.98 0 0.02 0.00 0 0 0.00 0.00
#> TCGA.5R.AA1D.01 3 0.3142 0.000 0.00 0 0.64 0.00 0 0 0.00 0.36
#> TCGA.DD.A1EF.11 4 0.0000 0.893 0.00 0 0.00 1.00 0 0 0.00 0.00
#> TCGA.RC.A6M5.01 8 0.0000 0.000 0.00 0 0.00 0.00 0 0 0.00 1.00
#> TCGA.DD.A3A6.01 2 0.0000 0.000 0.00 1 0.00 0.00 0 0 0.00 0.00
#> TCGA.DD.A39Z.11 1 0.1341 0.890 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.BC.A10X.11 1 0.0808 0.900 0.96 0 0.04 0.00 0 0 0.00 0.00
#> TCGA.DD.A4ND.01 5 0.0000 0.000 0.00 0 0.00 0.00 1 0 0.00 0.00
#> TCGA.DD.A11D.11 4 0.0808 0.888 0.00 0 0.00 0.96 0 0 0.04 0.00
#> TCGA.DD.A118.11 1 0.0471 0.899 0.98 0 0.02 0.00 0 0 0.00 0.00
#> TCGA.XR.A8TD.01 6 0.0000 0.000 0.00 0 0.00 0.00 0 1 0.00 0.00
#> TCGA.DD.A1EB.11 1 0.0471 0.900 0.98 0 0.02 0.00 0 0 0.00 0.00
#> TCGA.DD.A4NS.01 4 0.3434 0.754 0.00 0 0.14 0.76 0 0 0.10 0.00
#> TCGA.BC.A110.01 1 0.5480 0.386 0.54 0 0.12 0.26 0 0 0.08 0.00
#> TCGA.BC.A10R.11 1 0.1563 0.882 0.90 0 0.10 0.00 0 0 0.00 0.00
#> TCGA.DD.A113.11 1 0.1341 0.890 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.DD.A1EJ.11 1 0.1091 0.892 0.94 0 0.06 0.00 0 0 0.00 0.00
#> TCGA.BC.A10Q.11 1 0.1341 0.890 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.DD.A39W.11 1 0.1341 0.890 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.UB.AA0V.01 7 0.0808 0.000 0.00 0 0.00 0.04 0 0 0.96 0.00
#> TCGA.BD.A3EP.11 1 0.2547 0.844 0.84 0 0.12 0.04 0 0 0.00 0.00
#> TCGA.BC.A216.11 1 0.1563 0.882 0.90 0 0.10 0.00 0 0 0.00 0.00
#> TCGA.BC.A10X.01 1 0.3227 0.791 0.78 0 0.14 0.08 0 0 0.00 0.00
#> TCGA.DD.A1EC.11 1 0.1341 0.896 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.DD.A39X.11 1 0.1341 0.890 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.BC.A110.11 1 0.1341 0.887 0.92 0 0.08 0.00 0 0 0.00 0.00
#> TCGA.FV.A23B.11 4 0.0941 0.878 0.00 0 0.02 0.96 0 0 0.02 0.00
#> TCGA.BC.A10Z.11 1 0.1563 0.880 0.90 0 0.10 0.00 0 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node023. Child nodes: Node02121 , Node02122-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221 , Node02222-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02411-leaf , Node02412-leaf , Node02421-leaf , Node02422-leaf , Node02431-leaf , Node02432-leaf , Node02433-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 24 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3449 0.656 0.656
#> 3 3 0.768 0.892 0.947 0.7103 0.754 0.632
#> 4 4 1.000 1.000 1.000 0.2720 0.754 0.473
#> 5 5 1.000 0.927 0.988 0.0118 0.989 0.957
#> 6 6 0.775 0.813 0.932 0.0243 0.993 0.970
#> 7 7 0.791 0.622 0.786 0.0324 0.989 0.953
#> 8 8 0.823 0.482 0.792 0.0222 0.924 0.682
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.DD.A3A2.11 1 0 1 1 0
#> TCGA.G3.A25W.11 1 0 1 1 0
#> TCGA.DD.A1EF.11 2 0 1 0 1
#> TCGA.DD.A39Z.11 1 0 1 1 0
#> TCGA.BC.A10X.11 1 0 1 1 0
#> TCGA.DD.A11D.11 2 0 1 0 1
#> TCGA.DD.A118.11 1 0 1 1 0
#> TCGA.DD.A1EB.11 1 0 1 1 0
#> TCGA.DD.A4NS.01 2 0 1 0 1
#> TCGA.BC.A110.01 1 0 1 1 0
#> TCGA.BC.A10R.11 1 0 1 1 0
#> TCGA.DD.A113.11 1 0 1 1 0
#> TCGA.DD.A1EJ.11 1 0 1 1 0
#> TCGA.BC.A10Q.11 1 0 1 1 0
#> TCGA.DD.A39W.11 1 0 1 1 0
#> TCGA.UB.AA0V.01 2 0 1 0 1
#> TCGA.BD.A3EP.11 1 0 1 1 0
#> TCGA.BC.A216.11 1 0 1 1 0
#> TCGA.BC.A10X.01 1 0 1 1 0
#> TCGA.DD.A1EC.11 1 0 1 1 0
#> TCGA.DD.A39X.11 1 0 1 1 0
#> TCGA.BC.A110.11 1 0 1 1 0
#> TCGA.FV.A23B.11 2 0 1 0 1
#> TCGA.BC.A10Z.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DD.A3A2.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.G3.A25W.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.DD.A1EF.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.DD.A39Z.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.BC.A10X.11 1 0.571 0.630 0.68 0 0.32
#> TCGA.DD.A11D.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.DD.A118.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.DD.A1EB.11 1 0.571 0.630 0.68 0 0.32
#> TCGA.DD.A4NS.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BC.A110.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BC.A10R.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.DD.A113.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.DD.A1EJ.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.BC.A10Q.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.DD.A39W.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.UB.AA0V.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BD.A3EP.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.BC.A216.11 1 0.571 0.630 0.68 0 0.32
#> TCGA.BC.A10X.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DD.A1EC.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.DD.A39X.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.BC.A110.11 1 0.000 0.899 1.00 0 0.00
#> TCGA.FV.A23B.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.BC.A10Z.11 1 0.571 0.630 0.68 0 0.32
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DD.A3A2.11 4 0 1 0 0 0 1
#> TCGA.G3.A25W.11 1 0 1 1 0 0 0
#> TCGA.DD.A1EF.11 3 0 1 0 0 1 0
#> TCGA.DD.A39Z.11 1 0 1 1 0 0 0
#> TCGA.BC.A10X.11 1 0 1 1 0 0 0
#> TCGA.DD.A11D.11 2 0 1 0 1 0 0
#> TCGA.DD.A118.11 4 0 1 0 0 0 1
#> TCGA.DD.A1EB.11 1 0 1 1 0 0 0
#> TCGA.DD.A4NS.01 2 0 1 0 1 0 0
#> TCGA.BC.A110.01 3 0 1 0 0 1 0
#> TCGA.BC.A10R.11 1 0 1 1 0 0 0
#> TCGA.DD.A113.11 4 0 1 0 0 0 1
#> TCGA.DD.A1EJ.11 1 0 1 1 0 0 0
#> TCGA.BC.A10Q.11 4 0 1 0 0 0 1
#> TCGA.DD.A39W.11 4 0 1 0 0 0 1
#> TCGA.UB.AA0V.01 2 0 1 0 1 0 0
#> TCGA.BD.A3EP.11 3 0 1 0 0 1 0
#> TCGA.BC.A216.11 1 0 1 1 0 0 0
#> TCGA.BC.A10X.01 3 0 1 0 0 1 0
#> TCGA.DD.A1EC.11 1 0 1 1 0 0 0
#> TCGA.DD.A39X.11 4 0 1 0 0 0 1
#> TCGA.BC.A110.11 4 0 1 0 0 0 1
#> TCGA.FV.A23B.11 2 0 1 0 1 0 0
#> TCGA.BC.A10Z.11 1 0 1 1 0 0 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DD.A3A2.11 4 0.000 1.000 0.00 0 0.00 1.00 0
#> TCGA.G3.A25W.11 1 0.173 0.904 0.92 0 0.00 0.08 0
#> TCGA.DD.A1EF.11 3 0.000 0.939 0.00 0 1.00 0.00 0
#> TCGA.DD.A39Z.11 1 0.000 0.974 1.00 0 0.00 0.00 0
#> TCGA.BC.A10X.11 1 0.000 0.974 1.00 0 0.00 0.00 0
#> TCGA.DD.A11D.11 2 0.000 1.000 0.00 1 0.00 0.00 0
#> TCGA.DD.A118.11 4 0.000 1.000 0.00 0 0.00 1.00 0
#> TCGA.DD.A1EB.11 1 0.000 0.974 1.00 0 0.00 0.00 0
#> TCGA.DD.A4NS.01 2 0.000 1.000 0.00 1 0.00 0.00 0
#> TCGA.BC.A110.01 3 0.000 0.939 0.00 0 1.00 0.00 0
#> TCGA.BC.A10R.11 1 0.000 0.974 1.00 0 0.00 0.00 0
#> TCGA.DD.A113.11 4 0.000 1.000 0.00 0 0.00 1.00 0
#> TCGA.DD.A1EJ.11 1 0.173 0.904 0.92 0 0.00 0.08 0
#> TCGA.BC.A10Q.11 4 0.000 1.000 0.00 0 0.00 1.00 0
#> TCGA.DD.A39W.11 4 0.000 1.000 0.00 0 0.00 1.00 0
#> TCGA.UB.AA0V.01 5 0.000 0.000 0.00 0 0.00 0.00 1
#> TCGA.BD.A3EP.11 3 0.000 0.939 0.00 0 1.00 0.00 0
#> TCGA.BC.A216.11 1 0.000 0.974 1.00 0 0.00 0.00 0
#> TCGA.BC.A10X.01 3 0.228 0.809 0.12 0 0.88 0.00 0
#> TCGA.DD.A1EC.11 1 0.000 0.974 1.00 0 0.00 0.00 0
#> TCGA.DD.A39X.11 4 0.000 1.000 0.00 0 0.00 1.00 0
#> TCGA.BC.A110.11 4 0.000 1.000 0.00 0 0.00 1.00 0
#> TCGA.FV.A23B.11 2 0.000 1.000 0.00 1 0.00 0.00 0
#> TCGA.BC.A10Z.11 1 0.000 0.974 1.00 0 0.00 0.00 0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DD.A3A2.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.G3.A25W.11 1 0.4200 0.759 0.74 0.00 0.00 0.14 0 0.12
#> TCGA.DD.A1EF.11 3 0.0000 0.825 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.DD.A39Z.11 1 0.2581 0.851 0.86 0.00 0.00 0.02 0 0.12
#> TCGA.BC.A10X.11 1 0.0000 0.878 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.DD.A11D.11 6 0.3198 0.000 0.00 0.26 0.00 0.00 0 0.74
#> TCGA.DD.A118.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.DD.A1EB.11 1 0.0547 0.879 0.98 0.00 0.00 0.00 0 0.02
#> TCGA.DD.A4NS.01 2 0.0547 0.972 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.BC.A110.01 3 0.0000 0.825 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.BC.A10R.11 1 0.2048 0.792 0.88 0.00 0.00 0.00 0 0.12
#> TCGA.DD.A113.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.DD.A1EJ.11 1 0.4200 0.759 0.74 0.00 0.00 0.14 0 0.12
#> TCGA.BC.A10Q.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.DD.A39W.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.UB.AA0V.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.BD.A3EP.11 3 0.1814 0.808 0.00 0.00 0.90 0.00 0 0.10
#> TCGA.BC.A216.11 1 0.0000 0.878 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.BC.A10X.01 3 0.4989 0.572 0.22 0.00 0.64 0.00 0 0.14
#> TCGA.DD.A1EC.11 1 0.1814 0.865 0.90 0.00 0.00 0.00 0 0.10
#> TCGA.DD.A39X.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.BC.A110.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.FV.A23B.11 2 0.0000 0.972 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.BC.A10Z.11 1 0.0547 0.870 0.98 0.00 0.00 0.00 0 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DD.A3A2.11 4 0.0000 0.996 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.G3.A25W.11 1 0.4644 0.631 0.68 0.00 0.00 0.12 0 0.02 0.18
#> TCGA.DD.A1EF.11 7 0.3755 0.000 0.00 0.00 0.34 0.00 0 0.02 0.64
#> TCGA.DD.A39Z.11 1 0.2906 0.710 0.80 0.00 0.00 0.00 0 0.02 0.18
#> TCGA.BC.A10X.11 1 0.1886 0.718 0.88 0.00 0.00 0.00 0 0.00 0.12
#> TCGA.DD.A11D.11 6 0.0863 0.000 0.00 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.DD.A118.11 4 0.0504 0.977 0.00 0.00 0.00 0.98 0 0.00 0.02
#> TCGA.DD.A1EB.11 1 0.0000 0.739 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DD.A4NS.01 2 0.0863 0.926 0.00 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.BC.A110.01 3 0.3139 -0.301 0.00 0.00 0.70 0.00 0 0.00 0.30
#> TCGA.BC.A10R.11 1 0.4698 0.359 0.62 0.00 0.24 0.00 0 0.00 0.14
#> TCGA.DD.A113.11 4 0.0000 0.996 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DD.A1EJ.11 1 0.4644 0.631 0.68 0.00 0.00 0.12 0 0.02 0.18
#> TCGA.BC.A10Q.11 4 0.0000 0.996 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DD.A39W.11 4 0.0000 0.996 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.UB.AA0V.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.BD.A3EP.11 3 0.0000 0.228 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.BC.A216.11 1 0.1886 0.718 0.88 0.00 0.00 0.00 0 0.00 0.12
#> TCGA.BC.A10X.01 3 0.4930 0.254 0.26 0.00 0.58 0.00 0 0.00 0.16
#> TCGA.DD.A1EC.11 1 0.2745 0.718 0.82 0.00 0.00 0.00 0 0.02 0.16
#> TCGA.DD.A39X.11 4 0.0000 0.996 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.BC.A110.11 4 0.0000 0.996 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.FV.A23B.11 2 0.1006 0.927 0.00 0.96 0.00 0.00 0 0.02 0.02
#> TCGA.BC.A10Z.11 1 0.2081 0.706 0.86 0.00 0.00 0.00 0 0.00 0.14
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DD.A3A2.11 4 0.1091 0.93970 0.06 0.00 0.00 0.94 0.00 0 0.00 0
#> TCGA.G3.A25W.11 1 0.0808 0.60090 0.96 0.00 0.00 0.04 0.00 0 0.00 0
#> TCGA.DD.A1EF.11 7 0.2406 0.46366 0.00 0.00 0.00 0.00 0.20 0 0.80 0
#> TCGA.DD.A39Z.11 1 0.0808 0.58576 0.96 0.00 0.00 0.00 0.04 0 0.00 0
#> TCGA.BC.A10X.11 1 0.3318 0.26954 0.54 0.00 0.46 0.00 0.00 0 0.00 0
#> TCGA.DD.A11D.11 6 0.0000 0.00000 0.00 0.00 0.00 0.00 0.00 1 0.00 0
#> TCGA.DD.A118.11 4 0.1563 0.90338 0.10 0.00 0.00 0.90 0.00 0 0.00 0
#> TCGA.DD.A1EB.11 1 0.3237 0.36097 0.60 0.00 0.40 0.00 0.00 0 0.00 0
#> TCGA.DD.A4NS.01 2 0.0000 0.69190 0.00 1.00 0.00 0.00 0.00 0 0.00 0
#> TCGA.BC.A110.01 7 0.2650 0.49655 0.00 0.00 0.24 0.00 0.00 0 0.76 0
#> TCGA.BC.A10R.11 3 0.2938 -0.00773 0.30 0.00 0.70 0.00 0.00 0 0.00 0
#> TCGA.DD.A113.11 4 0.0000 0.96760 0.00 0.00 0.00 1.00 0.00 0 0.00 0
#> TCGA.DD.A1EJ.11 1 0.1341 0.57681 0.92 0.00 0.00 0.08 0.00 0 0.00 0
#> TCGA.BC.A10Q.11 4 0.0471 0.96231 0.02 0.00 0.00 0.98 0.00 0 0.00 0
#> TCGA.DD.A39W.11 4 0.0000 0.96760 0.00 0.00 0.00 1.00 0.00 0 0.00 0
#> TCGA.UB.AA0V.01 8 0.0000 0.00000 0.00 0.00 0.00 0.00 0.00 0 0.00 1
#> TCGA.BD.A3EP.11 3 0.5163 -0.36627 0.00 0.00 0.42 0.00 0.34 0 0.24 0
#> TCGA.BC.A216.11 1 0.3333 0.15642 0.50 0.00 0.50 0.00 0.00 0 0.00 0
#> TCGA.BC.A10X.01 3 0.1341 0.19595 0.00 0.00 0.92 0.00 0.00 0 0.08 0
#> TCGA.DD.A1EC.11 1 0.2407 0.57929 0.86 0.00 0.06 0.00 0.08 0 0.00 0
#> TCGA.DD.A39X.11 4 0.0000 0.96760 0.00 0.00 0.00 1.00 0.00 0 0.00 0
#> TCGA.BC.A110.11 4 0.0000 0.96760 0.00 0.00 0.00 1.00 0.00 0 0.00 0
#> TCGA.FV.A23B.11 2 0.3083 0.69190 0.00 0.66 0.00 0.00 0.34 0 0.00 0
#> TCGA.BC.A10Z.11 3 0.3329 -0.40901 0.48 0.00 0.52 0.00 0.00 0 0.00 0
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 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 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 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 0.5018 0.499 0.499
#> 3 3 1.000 1.000 1.000 0.3497 0.796 0.603
#> 4 4 0.777 0.808 0.685 0.0942 1.000 1.000
#> 5 5 0.792 0.771 0.842 0.0596 0.862 0.581
#> 6 6 0.802 0.788 0.827 0.0378 0.897 0.556
#> 7 7 0.846 0.777 0.841 0.0316 0.958 0.768
#> 8 8 0.824 0.680 0.744 0.0210 0.929 0.638
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.DD.A4NQ.01 1 0 1 1 0
#> TCGA.CC.A1HT.01 1 0 1 1 0
#> TCGA.BD.A3EP.01 1 0 1 1 0
#> TCGA.ES.A2HT.01 2 0 1 0 1
#> TCGA.ED.A5KG.01 2 0 1 0 1
#> TCGA.CC.A3M9.01 1 0 1 1 0
#> TCGA.RG.A7D4.01 1 0 1 1 0
#> TCGA.G3.A25W.01 1 0 1 1 0
#> TCGA.G3.A7M7.01 2 0 1 0 1
#> TCGA.K7.A5RG.01 1 0 1 1 0
#> TCGA.MR.A8JO.01 2 0 1 0 1
#> TCGA.DD.AACL.01 1 0 1 1 0
#> TCGA.KR.A7K8.01 1 0 1 1 0
#> TCGA.HP.A5MZ.01 2 0 1 0 1
#> TCGA.BW.A5NQ.01 1 0 1 1 0
#> TCGA.2Y.A9GX.01 1 0 1 1 0
#> TCGA.LG.A9QC.01 2 0 1 0 1
#> TCGA.BC.4073.01 1 0 1 1 0
#> TCGA.BC.4072.01 1 0 1 1 0
#> TCGA.DD.A4NB.01 2 0 1 0 1
#> TCGA.DD.A3A4.01 2 0 1 0 1
#> TCGA.MI.A75E.01 2 0 1 0 1
#> TCGA.DD.AACC.01 2 0 1 0 1
#> TCGA.K7.A5RF.01 2 0 1 0 1
#> TCGA.DD.A1EC.01 2 0 1 0 1
#> TCGA.DD.A1E9.01 1 0 1 1 0
#> TCGA.LG.A9QD.01 2 0 1 0 1
#> TCGA.NI.A8LF.01 2 0 1 0 1
#> TCGA.DD.AADC.01 2 0 1 0 1
#> TCGA.CC.5262.01 1 0 1 1 0
#> TCGA.DD.A114.01 2 0 1 0 1
#> TCGA.XR.A8TE.01 2 0 1 0 1
#> TCGA.DD.AAC9.01 2 0 1 0 1
#> TCGA.DD.A1EI.01 2 0 1 0 1
#> TCGA.DD.A1EB.01 2 0 1 0 1
#> TCGA.G3.AAV7.01 2 0 1 0 1
#> TCGA.GJ.A3OU.01 2 0 1 0 1
#> TCGA.WX.AA47.01 2 0 1 0 1
#> TCGA.EP.A3RK.01 1 0 1 1 0
#> TCGA.DD.A4NR.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DD.A4NQ.01 1 0 1 1 0 0
#> TCGA.CC.A1HT.01 1 0 1 1 0 0
#> TCGA.BD.A3EP.01 1 0 1 1 0 0
#> TCGA.ES.A2HT.01 2 0 1 0 1 0
#> TCGA.ED.A5KG.01 3 0 1 0 0 1
#> TCGA.CC.A3M9.01 1 0 1 1 0 0
#> TCGA.RG.A7D4.01 1 0 1 1 0 0
#> TCGA.G3.A25W.01 1 0 1 1 0 0
#> TCGA.G3.A7M7.01 2 0 1 0 1 0
#> TCGA.K7.A5RG.01 1 0 1 1 0 0
#> TCGA.MR.A8JO.01 2 0 1 0 1 0
#> TCGA.DD.AACL.01 1 0 1 1 0 0
#> TCGA.KR.A7K8.01 1 0 1 1 0 0
#> TCGA.HP.A5MZ.01 3 0 1 0 0 1
#> TCGA.BW.A5NQ.01 1 0 1 1 0 0
#> TCGA.2Y.A9GX.01 3 0 1 0 0 1
#> TCGA.LG.A9QC.01 2 0 1 0 1 0
#> TCGA.BC.4073.01 1 0 1 1 0 0
#> TCGA.BC.4072.01 1 0 1 1 0 0
#> TCGA.DD.A4NB.01 3 0 1 0 0 1
#> TCGA.DD.A3A4.01 2 0 1 0 1 0
#> TCGA.MI.A75E.01 3 0 1 0 0 1
#> TCGA.DD.AACC.01 3 0 1 0 0 1
#> TCGA.K7.A5RF.01 3 0 1 0 0 1
#> TCGA.DD.A1EC.01 3 0 1 0 0 1
#> TCGA.DD.A1E9.01 1 0 1 1 0 0
#> TCGA.LG.A9QD.01 2 0 1 0 1 0
#> TCGA.NI.A8LF.01 2 0 1 0 1 0
#> TCGA.DD.AADC.01 3 0 1 0 0 1
#> TCGA.CC.5262.01 1 0 1 1 0 0
#> TCGA.DD.A114.01 3 0 1 0 0 1
#> TCGA.XR.A8TE.01 2 0 1 0 1 0
#> TCGA.DD.AAC9.01 2 0 1 0 1 0
#> TCGA.DD.A1EI.01 2 0 1 0 1 0
#> TCGA.DD.A1EB.01 2 0 1 0 1 0
#> TCGA.G3.AAV7.01 3 0 1 0 0 1
#> TCGA.GJ.A3OU.01 3 0 1 0 0 1
#> TCGA.WX.AA47.01 2 0 1 0 1 0
#> TCGA.EP.A3RK.01 1 0 1 1 0 0
#> TCGA.DD.A4NR.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.DD.A4NQ.01 1 0.4522 0.787 0.68 0.32 0.00 0.00
#> TCGA.CC.A1HT.01 1 0.0000 0.815 1.00 0.00 0.00 0.00
#> TCGA.BD.A3EP.01 1 0.4994 0.736 0.52 0.48 0.00 0.00
#> TCGA.ES.A2HT.01 4 0.0000 0.912 0.00 0.00 0.00 1.00
#> TCGA.ED.A5KG.01 3 0.4790 0.797 0.00 0.38 0.62 0.00
#> TCGA.CC.A3M9.01 1 0.0000 0.815 1.00 0.00 0.00 0.00
#> TCGA.RG.A7D4.01 1 0.4994 0.736 0.52 0.48 0.00 0.00
#> TCGA.G3.A25W.01 1 0.0000 0.815 1.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 4 0.0000 0.912 0.00 0.00 0.00 1.00
#> TCGA.K7.A5RG.01 1 0.0000 0.815 1.00 0.00 0.00 0.00
#> TCGA.MR.A8JO.01 4 0.5428 0.433 0.00 0.38 0.02 0.60
#> TCGA.DD.AACL.01 1 0.2345 0.817 0.90 0.10 0.00 0.00
#> TCGA.KR.A7K8.01 1 0.4522 0.787 0.68 0.32 0.00 0.00
#> TCGA.HP.A5MZ.01 3 0.7179 0.670 0.00 0.38 0.48 0.14
#> TCGA.BW.A5NQ.01 1 0.4994 0.736 0.52 0.48 0.00 0.00
#> TCGA.2Y.A9GX.01 3 0.2345 0.740 0.10 0.00 0.90 0.00
#> TCGA.LG.A9QC.01 4 0.2921 0.879 0.00 0.14 0.00 0.86
#> TCGA.BC.4073.01 1 0.4994 0.736 0.52 0.48 0.00 0.00
#> TCGA.BC.4072.01 1 0.4994 0.736 0.52 0.48 0.00 0.00
#> TCGA.DD.A4NB.01 3 0.0000 0.803 0.00 0.00 1.00 0.00
#> TCGA.DD.A3A4.01 4 0.2921 0.879 0.00 0.14 0.00 0.86
#> TCGA.MI.A75E.01 3 0.0000 0.803 0.00 0.00 1.00 0.00
#> TCGA.DD.AACC.01 3 0.4790 0.797 0.00 0.38 0.62 0.00
#> TCGA.K7.A5RF.01 3 0.0000 0.803 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EC.01 3 0.4790 0.797 0.00 0.38 0.62 0.00
#> TCGA.DD.A1E9.01 1 0.0000 0.815 1.00 0.00 0.00 0.00
#> TCGA.LG.A9QD.01 4 0.0707 0.910 0.00 0.02 0.00 0.98
#> TCGA.NI.A8LF.01 4 0.0000 0.912 0.00 0.00 0.00 1.00
#> TCGA.DD.AADC.01 3 0.0000 0.803 0.00 0.00 1.00 0.00
#> TCGA.CC.5262.01 1 0.2345 0.817 0.90 0.10 0.00 0.00
#> TCGA.DD.A114.01 3 0.4790 0.797 0.00 0.38 0.62 0.00
#> TCGA.XR.A8TE.01 4 0.0707 0.910 0.00 0.02 0.00 0.98
#> TCGA.DD.AAC9.01 4 0.0707 0.910 0.00 0.02 0.00 0.98
#> TCGA.DD.A1EI.01 4 0.0707 0.910 0.00 0.02 0.00 0.98
#> TCGA.DD.A1EB.01 4 0.2921 0.879 0.00 0.14 0.00 0.86
#> TCGA.G3.AAV7.01 3 0.0000 0.803 0.00 0.00 1.00 0.00
#> TCGA.GJ.A3OU.01 3 0.4790 0.797 0.00 0.38 0.62 0.00
#> TCGA.WX.AA47.01 4 0.2921 0.879 0.00 0.14 0.00 0.86
#> TCGA.EP.A3RK.01 1 0.0000 0.815 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NR.01 1 0.0000 0.815 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.DD.A4NQ.01 1 0.5558 -0.378 0.56 0.36 0.08 0.00 0.00
#> TCGA.CC.A1HT.01 1 0.1732 0.774 0.92 0.00 0.08 0.00 0.00
#> TCGA.BD.A3EP.01 2 0.5607 0.860 0.38 0.54 0.08 0.00 0.00
#> TCGA.ES.A2HT.01 4 0.0000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.ED.A5KG.01 3 0.2732 0.831 0.00 0.00 0.84 0.00 0.16
#> TCGA.CC.A3M9.01 1 0.1043 0.772 0.96 0.04 0.00 0.00 0.00
#> TCGA.RG.A7D4.01 2 0.4126 0.960 0.38 0.62 0.00 0.00 0.00
#> TCGA.G3.A25W.01 1 0.0609 0.796 0.98 0.00 0.02 0.00 0.00
#> TCGA.G3.A7M7.01 4 0.0000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.K7.A5RG.01 1 0.0000 0.800 1.00 0.00 0.00 0.00 0.00
#> TCGA.MR.A8JO.01 3 0.4798 0.408 0.00 0.00 0.54 0.44 0.02
#> TCGA.DD.AACL.01 1 0.1732 0.774 0.92 0.00 0.08 0.00 0.00
#> TCGA.KR.A7K8.01 1 0.5558 -0.378 0.56 0.36 0.08 0.00 0.00
#> TCGA.HP.A5MZ.01 3 0.5927 0.596 0.00 0.00 0.54 0.34 0.12
#> TCGA.BW.A5NQ.01 2 0.4126 0.960 0.38 0.62 0.00 0.00 0.00
#> TCGA.2Y.A9GX.01 5 0.1732 0.885 0.08 0.00 0.00 0.00 0.92
#> TCGA.LG.A9QC.01 4 0.4748 0.744 0.00 0.30 0.04 0.66 0.00
#> TCGA.BC.4073.01 2 0.4126 0.960 0.38 0.62 0.00 0.00 0.00
#> TCGA.BC.4072.01 2 0.4675 0.944 0.38 0.60 0.02 0.00 0.00
#> TCGA.DD.A4NB.01 5 0.0000 0.970 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A3A4.01 4 0.4748 0.744 0.00 0.30 0.04 0.66 0.00
#> TCGA.MI.A75E.01 5 0.0000 0.970 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AACC.01 3 0.2732 0.831 0.00 0.00 0.84 0.00 0.16
#> TCGA.K7.A5RF.01 5 0.0000 0.970 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EC.01 3 0.2732 0.831 0.00 0.00 0.84 0.00 0.16
#> TCGA.DD.A1E9.01 1 0.1043 0.787 0.96 0.00 0.04 0.00 0.00
#> TCGA.LG.A9QD.01 4 0.0000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.NI.A8LF.01 4 0.0000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADC.01 5 0.1043 0.949 0.00 0.04 0.00 0.00 0.96
#> TCGA.CC.5262.01 1 0.1732 0.774 0.92 0.00 0.08 0.00 0.00
#> TCGA.DD.A114.01 3 0.2732 0.831 0.00 0.00 0.84 0.00 0.16
#> TCGA.XR.A8TE.01 4 0.0000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAC9.01 4 0.0000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EI.01 4 0.0000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EB.01 4 0.4748 0.744 0.00 0.30 0.04 0.66 0.00
#> TCGA.G3.AAV7.01 5 0.0000 0.970 0.00 0.00 0.00 0.00 1.00
#> TCGA.GJ.A3OU.01 3 0.2732 0.831 0.00 0.00 0.84 0.00 0.16
#> TCGA.WX.AA47.01 4 0.4748 0.744 0.00 0.30 0.04 0.66 0.00
#> TCGA.EP.A3RK.01 1 0.0000 0.800 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NR.01 1 0.0609 0.796 0.98 0.00 0.02 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.DD.A4NQ.01 2 0.5199 0.166 0.30 0.58 0.00 0.00 0.00 0.12
#> TCGA.CC.A1HT.01 1 0.5029 0.816 0.62 0.26 0.00 0.00 0.00 0.12
#> TCGA.BD.A3EP.01 2 0.2260 0.712 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.ES.A2HT.01 4 0.0000 0.700 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ED.A5KG.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 1 0.3660 0.710 0.78 0.16 0.00 0.00 0.00 0.06
#> TCGA.RG.A7D4.01 2 0.0547 0.759 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.G3.A25W.01 1 0.3711 0.869 0.72 0.26 0.00 0.00 0.00 0.02
#> TCGA.G3.A7M7.01 4 0.1480 0.662 0.04 0.00 0.00 0.94 0.02 0.00
#> TCGA.K7.A5RG.01 1 0.3198 0.872 0.74 0.26 0.00 0.00 0.00 0.00
#> TCGA.MR.A8JO.01 4 0.4310 0.246 0.02 0.00 0.44 0.54 0.00 0.00
#> TCGA.DD.AACL.01 1 0.5029 0.816 0.62 0.26 0.00 0.00 0.00 0.12
#> TCGA.KR.A7K8.01 2 0.5289 0.205 0.28 0.58 0.00 0.00 0.00 0.14
#> TCGA.HP.A5MZ.01 4 0.4787 0.234 0.02 0.00 0.44 0.52 0.02 0.00
#> TCGA.BW.A5NQ.01 2 0.0000 0.763 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GX.01 5 0.0547 0.956 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.LG.A9QC.01 6 0.3828 1.000 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.BC.4073.01 2 0.0000 0.763 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.4072.01 2 0.1814 0.728 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.DD.A4NB.01 5 0.0547 0.956 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.DD.A3A4.01 6 0.3828 1.000 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.MI.A75E.01 5 0.0547 0.956 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.DD.AACC.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K7.A5RF.01 5 0.0937 0.923 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.DD.A1EC.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 1 0.4834 0.814 0.64 0.26 0.00 0.00 0.00 0.10
#> TCGA.LG.A9QD.01 4 0.2403 0.702 0.04 0.00 0.04 0.90 0.02 0.00
#> TCGA.NI.A8LF.01 4 0.0000 0.700 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADC.01 5 0.4265 0.822 0.08 0.00 0.02 0.00 0.76 0.14
#> TCGA.CC.5262.01 1 0.5202 0.802 0.60 0.26 0.00 0.00 0.00 0.14
#> TCGA.DD.A114.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XR.A8TE.01 4 0.1865 0.722 0.04 0.00 0.04 0.92 0.00 0.00
#> TCGA.DD.AAC9.01 4 0.1480 0.729 0.02 0.00 0.04 0.94 0.00 0.00
#> TCGA.DD.A1EI.01 4 0.1480 0.729 0.02 0.00 0.04 0.94 0.00 0.00
#> TCGA.DD.A1EB.01 6 0.3828 1.000 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.G3.AAV7.01 5 0.0547 0.956 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.GJ.A3OU.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 6 0.3828 1.000 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.EP.A3RK.01 1 0.3198 0.872 0.74 0.26 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NR.01 1 0.3711 0.869 0.72 0.26 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DD.A4NQ.01 1 0.3637 0.483 0.72 0.24 0.00 0.00 0.00 0.00 0.04
#> TCGA.CC.A1HT.01 1 0.0504 0.729 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BD.A3EP.01 2 0.2832 0.734 0.24 0.76 0.00 0.00 0.00 0.00 0.00
#> TCGA.ES.A2HT.01 4 0.0504 0.749 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ED.A5KG.01 3 0.0504 0.990 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CC.A3M9.01 1 0.4873 0.635 0.60 0.00 0.00 0.00 0.00 0.18 0.22
#> TCGA.RG.A7D4.01 2 0.1718 0.906 0.04 0.92 0.00 0.00 0.00 0.00 0.04
#> TCGA.G3.A25W.01 1 0.4789 0.678 0.60 0.00 0.00 0.00 0.00 0.26 0.14
#> TCGA.G3.A7M7.01 4 0.0863 0.744 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.K7.A5RG.01 1 0.3199 0.740 0.80 0.00 0.00 0.00 0.00 0.14 0.06
#> TCGA.MR.A8JO.01 4 0.3496 0.267 0.00 0.00 0.42 0.58 0.00 0.00 0.00
#> TCGA.DD.AACL.01 1 0.1363 0.719 0.94 0.02 0.00 0.00 0.00 0.00 0.04
#> TCGA.KR.A7K8.01 1 0.2945 0.472 0.74 0.26 0.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 4 0.3943 0.256 0.00 0.00 0.42 0.56 0.00 0.00 0.02
#> TCGA.BW.A5NQ.01 2 0.0863 0.915 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9GX.01 5 0.0000 0.981 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.LG.A9QC.01 6 0.3496 1.000 0.00 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.BC.4073.01 2 0.0863 0.915 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.4072.01 2 0.2213 0.902 0.04 0.90 0.02 0.00 0.00 0.00 0.04
#> TCGA.DD.A4NB.01 5 0.0000 0.981 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A4.01 6 0.3496 1.000 0.00 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.MI.A75E.01 5 0.0000 0.981 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACC.01 3 0.0504 0.990 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.K7.A5RF.01 5 0.0504 0.954 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.A1EC.01 3 0.1363 0.959 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.DD.A1E9.01 1 0.4870 0.665 0.58 0.00 0.00 0.00 0.00 0.28 0.14
#> TCGA.LG.A9QD.01 4 0.0863 0.744 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.NI.A8LF.01 4 0.0504 0.749 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.AADC.01 7 0.3525 0.000 0.00 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.CC.5262.01 1 0.0863 0.721 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.01 3 0.0504 0.990 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.XR.A8TE.01 4 0.1860 0.683 0.00 0.02 0.00 0.92 0.00 0.02 0.04
#> TCGA.DD.AAC9.01 4 0.0000 0.748 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EI.01 4 0.0000 0.748 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1EB.01 6 0.3496 1.000 0.00 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.G3.AAV7.01 5 0.0504 0.962 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.GJ.A3OU.01 3 0.0504 0.990 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.WX.AA47.01 6 0.3496 1.000 0.00 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.EP.A3RK.01 1 0.3199 0.740 0.80 0.00 0.00 0.00 0.00 0.14 0.06
#> TCGA.DD.A4NR.01 1 0.4789 0.678 0.60 0.00 0.00 0.00 0.00 0.26 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.DD.A4NQ.01 2 0.1947 0.3856 0.14 0.86 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A1HT.01 2 0.3714 -0.1749 0.44 0.54 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BD.A3EP.01 2 0.1341 0.4600 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.ES.A2HT.01 4 0.0000 0.8325 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A5KG.01 3 0.0471 0.9830 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3M9.01 1 0.6239 0.4375 0.46 0.10 0.00 0.00 0.00 0.14 0.28 0.02
#> TCGA.RG.A7D4.01 2 0.3329 0.4127 0.00 0.52 0.00 0.00 0.00 0.48 0.00 0.00
#> TCGA.G3.A25W.01 1 0.1091 0.8055 0.94 0.06 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A7M7.01 4 0.1275 0.8203 0.00 0.00 0.00 0.94 0.00 0.04 0.02 0.00
#> TCGA.K7.A5RG.01 1 0.3154 0.7708 0.78 0.16 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.MR.A8JO.01 4 0.4041 0.6820 0.00 0.00 0.22 0.70 0.00 0.04 0.04 0.00
#> TCGA.DD.AACL.01 2 0.4358 -0.0976 0.40 0.54 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.KR.A7K8.01 2 0.1947 0.3856 0.14 0.86 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 4 0.4759 0.6633 0.00 0.00 0.22 0.64 0.00 0.08 0.06 0.00
#> TCGA.BW.A5NQ.01 2 0.3329 0.4127 0.00 0.52 0.00 0.00 0.00 0.48 0.00 0.00
#> TCGA.2Y.A9GX.01 5 0.0000 0.9319 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LG.A9QC.01 8 0.2406 1.0000 0.00 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.BC.4073.01 2 0.3329 0.4127 0.00 0.52 0.00 0.00 0.00 0.48 0.00 0.00
#> TCGA.BC.4072.01 2 0.4860 0.3809 0.00 0.50 0.00 0.00 0.00 0.40 0.04 0.06
#> TCGA.DD.A4NB.01 5 0.0000 0.9319 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A4.01 8 0.2406 1.0000 0.00 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.MI.A75E.01 5 0.0000 0.9319 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACC.01 3 0.0471 0.9830 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.K7.A5RF.01 5 0.1275 0.8607 0.00 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.DD.A1EC.01 3 0.0471 0.9761 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A1E9.01 1 0.1887 0.7822 0.90 0.06 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.LG.A9QD.01 4 0.1275 0.8203 0.00 0.00 0.00 0.94 0.00 0.04 0.02 0.00
#> TCGA.NI.A8LF.01 4 0.0000 0.8325 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADC.01 7 0.3193 0.0000 0.00 0.00 0.00 0.00 0.38 0.00 0.62 0.00
#> TCGA.CC.5262.01 2 0.3299 -0.1275 0.44 0.56 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.01 3 0.0000 0.9846 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XR.A8TE.01 4 0.3843 0.6798 0.00 0.00 0.00 0.70 0.00 0.24 0.04 0.02
#> TCGA.DD.AAC9.01 4 0.1607 0.8299 0.00 0.00 0.00 0.92 0.00 0.04 0.04 0.00
#> TCGA.DD.A1EI.01 4 0.1607 0.8299 0.00 0.00 0.00 0.92 0.00 0.04 0.04 0.00
#> TCGA.DD.A1EB.01 8 0.2406 1.0000 0.00 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.G3.AAV7.01 5 0.1887 0.8280 0.00 0.00 0.00 0.00 0.90 0.06 0.00 0.04
#> TCGA.GJ.A3OU.01 3 0.0000 0.9846 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WX.AA47.01 8 0.2406 1.0000 0.00 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.EP.A3RK.01 1 0.3154 0.7708 0.78 0.16 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.DD.A4NR.01 1 0.1091 0.8055 0.94 0.06 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node024. Child nodes: Node02121 , Node02122-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221 , Node02222-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02411-leaf , Node02412-leaf , Node02421-leaf , Node02422-leaf , Node02431-leaf , Node02432-leaf , Node02433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0241"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'SD' 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 0.976 0.981 0.4613 0.542 0.542
#> 3 3 0.633 0.793 0.819 0.4868 0.750 0.538
#> 4 4 0.500 0.621 0.823 0.0767 0.883 0.650
#> 5 5 0.525 0.551 0.766 0.0691 1.000 1.000
#> 6 6 0.617 0.441 0.772 0.0595 0.842 0.457
#> 7 7 0.758 0.486 0.814 0.0396 0.967 0.800
#> 8 8 0.767 0.516 0.830 0.0345 0.950 0.647
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.DD.A4NQ.01 1 0.242 0.970 0.96 0.04
#> TCGA.CC.A1HT.01 1 0.242 0.970 0.96 0.04
#> TCGA.BD.A3EP.01 2 0.242 0.979 0.04 0.96
#> TCGA.CC.A3M9.01 1 0.242 0.970 0.96 0.04
#> TCGA.RG.A7D4.01 1 0.000 0.981 1.00 0.00
#> TCGA.G3.A25W.01 2 0.242 0.979 0.04 0.96
#> TCGA.K7.A5RG.01 1 0.000 0.981 1.00 0.00
#> TCGA.DD.AACL.01 2 0.000 0.969 0.00 1.00
#> TCGA.KR.A7K8.01 1 0.000 0.981 1.00 0.00
#> TCGA.BW.A5NQ.01 1 0.141 0.968 0.98 0.02
#> TCGA.BC.4073.01 1 0.242 0.970 0.96 0.04
#> TCGA.BC.4072.01 2 0.000 0.969 0.00 1.00
#> TCGA.DD.A1E9.01 1 0.000 0.981 1.00 0.00
#> TCGA.CC.5262.01 1 0.000 0.981 1.00 0.00
#> TCGA.EP.A3RK.01 1 0.000 0.981 1.00 0.00
#> TCGA.DD.A4NR.01 2 0.242 0.979 0.04 0.96
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DD.A4NQ.01 1 0.241 0.755 0.94 0.02 0.04
#> TCGA.CC.A1HT.01 1 0.241 0.758 0.94 0.02 0.04
#> TCGA.BD.A3EP.01 2 0.369 0.893 0.00 0.86 0.14
#> TCGA.CC.A3M9.01 1 0.207 0.763 0.94 0.00 0.06
#> TCGA.RG.A7D4.01 3 0.000 0.910 0.00 0.00 1.00
#> TCGA.G3.A25W.01 2 0.254 0.938 0.00 0.92 0.08
#> TCGA.K7.A5RG.01 3 0.254 0.890 0.08 0.00 0.92
#> TCGA.DD.AACL.01 2 0.000 0.921 0.00 1.00 0.00
#> TCGA.KR.A7K8.01 1 0.502 0.661 0.76 0.00 0.24
#> TCGA.BW.A5NQ.01 3 0.000 0.910 0.00 0.00 1.00
#> TCGA.BC.4073.01 1 0.522 0.595 0.74 0.00 0.26
#> TCGA.BC.4072.01 2 0.000 0.921 0.00 1.00 0.00
#> TCGA.DD.A1E9.01 3 0.400 0.787 0.16 0.00 0.84
#> TCGA.CC.5262.01 1 0.630 0.143 0.52 0.00 0.48
#> TCGA.EP.A3RK.01 3 0.153 0.906 0.04 0.00 0.96
#> TCGA.DD.A4NR.01 2 0.254 0.938 0.00 0.92 0.08
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DD.A4NQ.01 1 0.261 0.566 0.92 0.02 0.02 0.04
#> TCGA.CC.A1HT.01 1 0.304 0.584 0.88 0.00 0.02 0.10
#> TCGA.BD.A3EP.01 2 0.361 0.865 0.00 0.86 0.08 0.06
#> TCGA.CC.A3M9.01 1 0.515 0.608 0.74 0.00 0.20 0.06
#> TCGA.RG.A7D4.01 3 0.476 0.567 0.04 0.00 0.76 0.20
#> TCGA.G3.A25W.01 2 0.121 0.897 0.00 0.96 0.04 0.00
#> TCGA.K7.A5RG.01 3 0.340 0.646 0.18 0.00 0.82 0.00
#> TCGA.DD.AACL.01 2 0.164 0.880 0.00 0.94 0.00 0.06
#> TCGA.KR.A7K8.01 1 0.671 0.325 0.54 0.00 0.36 0.10
#> TCGA.BW.A5NQ.01 3 0.380 0.565 0.00 0.00 0.78 0.22
#> TCGA.BC.4073.01 4 0.515 0.000 0.14 0.00 0.10 0.76
#> TCGA.BC.4072.01 2 0.164 0.880 0.00 0.94 0.00 0.06
#> TCGA.DD.A1E9.01 3 0.385 0.665 0.16 0.00 0.82 0.02
#> TCGA.CC.5262.01 3 0.527 0.322 0.34 0.00 0.64 0.02
#> TCGA.EP.A3RK.01 3 0.201 0.692 0.08 0.00 0.92 0.00
#> TCGA.DD.A4NR.01 2 0.325 0.880 0.00 0.88 0.06 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DD.A4NQ.01 1 0.401 0.605 0.82 0.00 0.08 0.02 0.08
#> TCGA.CC.A1HT.01 1 0.165 0.625 0.94 0.00 0.04 0.02 0.00
#> TCGA.BD.A3EP.01 2 0.262 0.724 0.00 0.88 0.10 0.00 0.02
#> TCGA.CC.A3M9.01 1 0.398 0.624 0.82 0.00 0.10 0.02 0.06
#> TCGA.RG.A7D4.01 3 0.651 0.530 0.00 0.06 0.60 0.10 0.24
#> TCGA.G3.A25W.01 2 0.233 0.750 0.00 0.90 0.08 0.00 0.02
#> TCGA.K7.A5RG.01 3 0.335 0.619 0.08 0.00 0.86 0.02 0.04
#> TCGA.DD.AACL.01 2 0.398 0.623 0.00 0.66 0.00 0.00 0.34
#> TCGA.KR.A7K8.01 1 0.803 0.206 0.38 0.00 0.30 0.10 0.22
#> TCGA.BW.A5NQ.01 3 0.754 0.408 0.02 0.04 0.48 0.16 0.30
#> TCGA.BC.4073.01 4 0.202 0.000 0.10 0.00 0.00 0.90 0.00
#> TCGA.BC.4072.01 2 0.418 0.583 0.00 0.60 0.00 0.00 0.40
#> TCGA.DD.A1E9.01 3 0.394 0.642 0.02 0.08 0.84 0.02 0.04
#> TCGA.CC.5262.01 3 0.581 0.456 0.14 0.02 0.70 0.02 0.12
#> TCGA.EP.A3RK.01 3 0.225 0.668 0.00 0.04 0.92 0.02 0.02
#> TCGA.DD.A4NR.01 2 0.202 0.745 0.00 0.90 0.10 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.DD.A4NQ.01 1 0.410 0.7310 0.80 0.00 0.06 0.02 0.10 0.02
#> TCGA.CC.A1HT.01 1 0.226 0.7332 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.BD.A3EP.01 2 0.109 0.6890 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.CC.A3M9.01 1 0.251 0.7280 0.88 0.00 0.06 0.00 0.00 0.06
#> TCGA.RG.A7D4.01 6 0.288 0.8382 0.02 0.10 0.02 0.00 0.00 0.86
#> TCGA.G3.A25W.01 2 0.301 0.6146 0.00 0.86 0.08 0.00 0.04 0.02
#> TCGA.K7.A5RG.01 3 0.649 0.2470 0.14 0.02 0.42 0.00 0.02 0.40
#> TCGA.DD.AACL.01 2 0.420 -0.0397 0.00 0.60 0.02 0.00 0.38 0.00
#> TCGA.KR.A7K8.01 3 0.550 -0.0972 0.30 0.00 0.58 0.02 0.10 0.00
#> TCGA.BW.A5NQ.01 6 0.219 0.8410 0.00 0.06 0.04 0.00 0.00 0.90
#> TCGA.BC.4073.01 4 0.000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.4072.01 5 0.350 0.0000 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.DD.A1E9.01 3 0.665 0.3355 0.06 0.04 0.46 0.00 0.06 0.38
#> TCGA.CC.5262.01 3 0.327 0.3977 0.12 0.00 0.82 0.00 0.00 0.06
#> TCGA.EP.A3RK.01 3 0.608 0.3456 0.02 0.04 0.50 0.00 0.06 0.38
#> TCGA.DD.A4NR.01 2 0.000 0.6933 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.DD.A4NQ.01 1 0.4875 0.6066 0.72 0.00 0.02 0.02 0.02 0.14 0.08
#> TCGA.CC.A1HT.01 1 0.2769 0.6885 0.86 0.00 0.00 0.04 0.00 0.02 0.08
#> TCGA.BD.A3EP.01 2 0.1363 0.7683 0.00 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.CC.A3M9.01 1 0.2803 0.6604 0.84 0.00 0.06 0.00 0.00 0.00 0.10
#> TCGA.RG.A7D4.01 6 0.3517 0.8155 0.00 0.02 0.28 0.00 0.00 0.70 0.00
#> TCGA.G3.A25W.01 2 0.1718 0.7587 0.00 0.92 0.04 0.00 0.04 0.00 0.00
#> TCGA.K7.A5RG.01 3 0.5134 0.4971 0.02 0.04 0.68 0.00 0.00 0.14 0.12
#> TCGA.DD.AACL.01 2 0.4381 0.2409 0.00 0.58 0.00 0.00 0.36 0.00 0.06
#> TCGA.KR.A7K8.01 7 0.2509 0.0000 0.04 0.00 0.06 0.02 0.00 0.00 0.88
#> TCGA.BW.A5NQ.01 6 0.2906 0.8257 0.00 0.02 0.18 0.00 0.00 0.80 0.00
#> TCGA.BC.4073.01 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.4072.01 5 0.0863 0.0000 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.DD.A1E9.01 3 0.3000 0.5877 0.02 0.06 0.86 0.00 0.00 0.02 0.04
#> TCGA.CC.5262.01 3 0.3994 -0.0281 0.02 0.00 0.50 0.00 0.00 0.00 0.48
#> TCGA.EP.A3RK.01 3 0.2313 0.5777 0.00 0.06 0.88 0.00 0.00 0.06 0.00
#> TCGA.DD.A4NR.01 2 0.0000 0.7826 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.DD.A4NQ.01 8 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CC.A1HT.01 1 0.3690 0.558 0.56 0.00 0.00 0.00 0.00 0.00 0.02 0.42
#> TCGA.BD.A3EP.01 2 0.1874 0.848 0.02 0.92 0.02 0.00 0.02 0.00 0.02 0.00
#> TCGA.CC.A3M9.01 1 0.3873 0.632 0.72 0.00 0.00 0.02 0.00 0.00 0.06 0.20
#> TCGA.RG.A7D4.01 6 0.4464 0.702 0.12 0.02 0.10 0.00 0.00 0.72 0.04 0.00
#> TCGA.G3.A25W.01 2 0.2807 0.837 0.02 0.84 0.10 0.00 0.04 0.00 0.00 0.00
#> TCGA.K7.A5RG.01 3 0.4564 0.578 0.10 0.00 0.72 0.00 0.00 0.08 0.08 0.02
#> TCGA.DD.AACL.01 5 0.6048 0.543 0.14 0.20 0.00 0.00 0.56 0.04 0.04 0.02
#> TCGA.KR.A7K8.01 7 0.2532 0.000 0.02 0.00 0.04 0.00 0.00 0.02 0.88 0.04
#> TCGA.BW.A5NQ.01 6 0.2265 0.698 0.00 0.00 0.08 0.00 0.00 0.88 0.02 0.02
#> TCGA.BC.4073.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.4072.01 5 0.0000 0.539 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A1E9.01 3 0.2532 0.626 0.04 0.04 0.88 0.00 0.00 0.02 0.02 0.00
#> TCGA.CC.5262.01 3 0.4370 0.152 0.08 0.00 0.52 0.00 0.00 0.00 0.40 0.00
#> TCGA.EP.A3RK.01 3 0.1275 0.665 0.04 0.00 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A4NR.01 2 0.0941 0.876 0.00 0.96 0.02 0.00 0.02 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: Node024. Child nodes: Node02121 , Node02122-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221 , Node02222-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02411-leaf , Node02412-leaf , Node02421-leaf , Node02422-leaf , Node02431-leaf , Node02432-leaf , Node02433-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 12 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3037 0.697 0.697
#> 3 3 0.682 0.879 0.900 1.0550 0.621 0.457
#> 4 4 0.909 0.876 0.970 0.0521 0.667 0.333
#> 5 5 0.803 0.840 0.897 0.2010 0.818 0.478
#> 6 6 0.773 0.711 0.888 0.0853 1.000 1.000
#> 7 7 0.773 0.498 0.715 0.0404 0.894 0.462
#> 8 8 0.848 0.458 0.890 0.0303 0.955 0.625
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
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.ES.A2HT.01 2 0 1 0 1
#> TCGA.G3.A7M7.01 2 0 1 0 1
#> TCGA.MR.A8JO.01 2 0 1 0 1
#> TCGA.LG.A9QC.01 1 0 1 1 0
#> TCGA.DD.A3A4.01 2 0 1 0 1
#> TCGA.LG.A9QD.01 2 0 1 0 1
#> TCGA.NI.A8LF.01 2 0 1 0 1
#> TCGA.XR.A8TE.01 1 0 1 1 0
#> TCGA.DD.AAC9.01 2 0 1 0 1
#> TCGA.DD.A1EI.01 2 0 1 0 1
#> TCGA.DD.A1EB.01 2 0 1 0 1
#> TCGA.WX.AA47.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.ES.A2HT.01 2 0.595 0.750 0.00 0.64 0.36
#> TCGA.G3.A7M7.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.MR.A8JO.01 2 0.153 0.671 0.00 0.96 0.04
#> TCGA.LG.A9QC.01 1 0.000 0.977 1.00 0.00 0.00
#> TCGA.DD.A3A4.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.LG.A9QD.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.NI.A8LF.01 2 0.595 0.750 0.00 0.64 0.36
#> TCGA.XR.A8TE.01 1 0.153 0.977 0.96 0.04 0.00
#> TCGA.DD.AAC9.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.DD.A1EI.01 2 0.595 0.750 0.00 0.64 0.36
#> TCGA.DD.A1EB.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.WX.AA47.01 2 0.153 0.671 0.00 0.96 0.04
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.ES.A2HT.01 2 0.0000 0.960 0.00 1.00 0.00 0.00
#> TCGA.G3.A7M7.01 2 0.2647 0.883 0.00 0.88 0.12 0.00
#> TCGA.MR.A8JO.01 2 0.0707 0.946 0.00 0.98 0.00 0.02
#> TCGA.LG.A9QC.01 1 0.0000 0.950 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A4.01 3 0.0707 1.000 0.00 0.02 0.98 0.00
#> TCGA.LG.A9QD.01 2 0.1211 0.951 0.00 0.96 0.04 0.00
#> TCGA.NI.A8LF.01 2 0.0000 0.960 0.00 1.00 0.00 0.00
#> TCGA.XR.A8TE.01 1 0.1913 0.950 0.94 0.00 0.02 0.04
#> TCGA.DD.AAC9.01 2 0.1211 0.951 0.00 0.96 0.04 0.00
#> TCGA.DD.A1EI.01 2 0.0000 0.960 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EB.01 3 0.0707 1.000 0.00 0.02 0.98 0.00
#> TCGA.WX.AA47.01 4 0.1211 0.000 0.00 0.04 0.00 0.96
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.ES.A2HT.01 5 0.3796 0.955 0.00 0.30 0.00 0 0.70
#> TCGA.G3.A7M7.01 2 0.1410 0.894 0.00 0.94 0.06 0 0.00
#> TCGA.MR.A8JO.01 5 0.3424 0.914 0.00 0.24 0.00 0 0.76
#> TCGA.LG.A9QC.01 1 0.0000 0.789 1.00 0.00 0.00 0 0.00
#> TCGA.DD.A3A4.01 3 0.0609 0.977 0.00 0.02 0.98 0 0.00
#> TCGA.LG.A9QD.01 2 0.0609 0.945 0.00 0.98 0.00 0 0.02
#> TCGA.NI.A8LF.01 2 0.0609 0.943 0.00 0.98 0.00 0 0.02
#> TCGA.XR.A8TE.01 1 0.3424 0.789 0.76 0.00 0.00 0 0.24
#> TCGA.DD.AAC9.01 2 0.1043 0.939 0.00 0.96 0.00 0 0.04
#> TCGA.DD.A1EI.01 5 0.3796 0.955 0.00 0.30 0.00 0 0.70
#> TCGA.DD.A1EB.01 3 0.0000 0.977 0.00 0.00 1.00 0 0.00
#> TCGA.WX.AA47.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.ES.A2HT.01 5 0.1814 0.874 0.00 0.10 0.00 0 0.90 0.00
#> TCGA.G3.A7M7.01 2 0.0000 0.832 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.MR.A8JO.01 5 0.2260 0.728 0.00 0.00 0.00 0 0.86 0.14
#> TCGA.LG.A9QC.01 1 0.0000 0.750 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.DD.A3A4.01 3 0.0547 0.825 0.00 0.02 0.98 0 0.00 0.00
#> TCGA.LG.A9QD.01 2 0.0000 0.832 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.NI.A8LF.01 2 0.5265 0.418 0.00 0.50 0.00 0 0.10 0.40
#> TCGA.XR.A8TE.01 1 0.3309 0.750 0.72 0.00 0.00 0 0.00 0.28
#> TCGA.DD.AAC9.01 2 0.0547 0.827 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.DD.A1EI.01 5 0.1814 0.874 0.00 0.10 0.00 0 0.90 0.00
#> TCGA.DD.A1EB.01 3 0.2631 0.825 0.00 0.00 0.82 0 0.00 0.18
#> TCGA.WX.AA47.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.ES.A2HT.01 5 0.352 0.4888 0.00 0.00 0.00 0 0.74 0.22 0.04
#> TCGA.G3.A7M7.01 7 0.000 0.8931 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.MR.A8JO.01 6 0.117 0.0000 0.00 0.00 0.00 0 0.06 0.94 0.00
#> TCGA.LG.A9QC.01 1 0.000 0.7505 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.DD.A3A4.01 3 0.525 0.4299 0.00 0.42 0.42 0 0.00 0.00 0.16
#> TCGA.LG.A9QD.01 7 0.000 0.8931 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.NI.A8LF.01 5 0.511 0.0833 0.00 0.38 0.00 0 0.48 0.00 0.14
#> TCGA.XR.A8TE.01 1 0.414 0.7505 0.72 0.20 0.00 0 0.02 0.06 0.00
#> TCGA.DD.AAC9.01 7 0.226 0.7706 0.00 0.00 0.00 0 0.16 0.00 0.84
#> TCGA.DD.A1EI.01 5 0.352 0.4888 0.00 0.00 0.00 0 0.74 0.22 0.04
#> TCGA.DD.A1EB.01 3 0.000 0.4232 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.WX.AA47.01 4 0.000 0.0000 0.00 0.00 0.00 1 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.ES.A2HT.01 5 0.0808 0.861 0.00 0.0 0.00 0 0.96 0.0 0.04 0.00
#> TCGA.G3.A7M7.01 7 0.1563 0.898 0.00 0.0 0.10 0 0.00 0.0 0.90 0.00
#> TCGA.MR.A8JO.01 6 0.1563 0.000 0.00 0.0 0.00 0 0.10 0.9 0.00 0.00
#> TCGA.LG.A9QC.01 1 0.3073 0.591 0.80 0.1 0.00 0 0.00 0.1 0.00 0.00
#> TCGA.DD.A3A4.01 3 0.0808 0.000 0.00 0.0 0.96 0 0.00 0.0 0.04 0.00
#> TCGA.LG.A9QD.01 7 0.1563 0.898 0.00 0.0 0.10 0 0.00 0.0 0.90 0.00
#> TCGA.NI.A8LF.01 2 0.1887 0.000 0.00 0.9 0.00 0 0.06 0.0 0.04 0.00
#> TCGA.XR.A8TE.01 1 0.3651 0.591 0.76 0.0 0.04 0 0.04 0.0 0.00 0.16
#> TCGA.DD.AAC9.01 7 0.1275 0.799 0.00 0.0 0.00 0 0.04 0.0 0.94 0.02
#> TCGA.DD.A1EI.01 5 0.2404 0.862 0.00 0.0 0.00 0 0.84 0.0 0.14 0.02
#> TCGA.DD.A1EB.01 8 0.2267 0.000 0.00 0.0 0.18 0 0.00 0.0 0.00 0.82
#> TCGA.WX.AA47.01 4 0.0000 0.000 0.00 0.0 0.00 1 0.00 0.0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node024. Child nodes: Node02121 , Node02122-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221 , Node02222-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02314-leaf , Node02411-leaf , Node02412-leaf , Node02421-leaf , Node02422-leaf , Node02431-leaf , Node02432-leaf , Node02433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0243"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 12 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.697 0.936 0.960 0.4419 0.515 0.515
#> 3 3 1.000 1.000 1.000 0.5095 0.576 0.333
#> 4 4 1.000 0.974 0.967 0.1899 0.773 0.400
#> 5 5 0.864 0.710 0.830 0.0601 0.970 0.846
#> 6 6 0.833 0.777 0.880 0.0497 0.909 0.500
#> 7 7 0.848 0.594 0.852 0.0291 0.985 0.857
#> 8 8 0.864 0.404 0.692 0.0220 0.985 0.833
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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.ED.A5KG.01 1 0.000 1.000 1.00 0.00
#> TCGA.HP.A5MZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.2Y.A9GX.01 1 0.000 1.000 1.00 0.00
#> TCGA.DD.A4NB.01 2 0.795 0.789 0.24 0.76
#> TCGA.MI.A75E.01 2 0.795 0.789 0.24 0.76
#> TCGA.DD.AACC.01 1 0.000 1.000 1.00 0.00
#> TCGA.K7.A5RF.01 1 0.000 1.000 1.00 0.00
#> TCGA.DD.A1EC.01 1 0.000 1.000 1.00 0.00
#> TCGA.DD.AADC.01 2 0.000 0.829 0.00 1.00
#> TCGA.DD.A114.01 1 0.000 1.000 1.00 0.00
#> TCGA.G3.AAV7.01 2 0.000 0.829 0.00 1.00
#> TCGA.GJ.A3OU.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.ED.A5KG.01 1 0 1 1 0 0
#> TCGA.HP.A5MZ.01 3 0 1 0 0 1
#> TCGA.2Y.A9GX.01 3 0 1 0 0 1
#> TCGA.DD.A4NB.01 3 0 1 0 0 1
#> TCGA.MI.A75E.01 3 0 1 0 0 1
#> TCGA.DD.AACC.01 1 0 1 1 0 0
#> TCGA.K7.A5RF.01 3 0 1 0 0 1
#> TCGA.DD.A1EC.01 1 0 1 1 0 0
#> TCGA.DD.AADC.01 2 0 1 0 1 0
#> TCGA.DD.A114.01 3 0 1 0 0 1
#> TCGA.G3.AAV7.01 2 0 1 0 1 0
#> TCGA.GJ.A3OU.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.ED.A5KG.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 3 0.000 0.965 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9GX.01 4 0.201 1.000 0.00 0.00 0.08 0.92
#> TCGA.DD.A4NB.01 4 0.201 1.000 0.00 0.00 0.08 0.92
#> TCGA.MI.A75E.01 4 0.201 1.000 0.00 0.00 0.08 0.92
#> TCGA.DD.AACC.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.K7.A5RF.01 3 0.000 0.965 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EC.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AADC.01 2 0.201 0.949 0.00 0.92 0.00 0.08
#> TCGA.DD.A114.01 3 0.000 0.965 0.00 0.00 1.00 0.00
#> TCGA.G3.AAV7.01 2 0.000 0.949 0.00 1.00 0.00 0.00
#> TCGA.GJ.A3OU.01 3 0.201 0.891 0.08 0.00 0.92 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.ED.A5KG.01 1 0.426 1.000 0.56 0.00 0.00 0.00 0.44
#> TCGA.HP.A5MZ.01 3 0.426 0.849 0.44 0.00 0.56 0.00 0.00
#> TCGA.2Y.A9GX.01 4 0.426 0.510 0.00 0.00 0.44 0.56 0.00
#> TCGA.DD.A4NB.01 4 0.000 0.772 0.00 0.00 0.00 1.00 0.00
#> TCGA.MI.A75E.01 4 0.000 0.772 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACC.01 1 0.426 1.000 0.56 0.00 0.00 0.00 0.44
#> TCGA.K7.A5RF.01 3 0.000 0.459 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A1EC.01 5 0.406 0.000 0.36 0.00 0.00 0.00 0.64
#> TCGA.DD.AADC.01 2 0.000 0.730 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A114.01 3 0.426 0.849 0.44 0.00 0.56 0.00 0.00
#> TCGA.G3.AAV7.01 2 0.406 0.730 0.00 0.64 0.00 0.00 0.36
#> TCGA.GJ.A3OU.01 3 0.426 0.849 0.44 0.00 0.56 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.ED.A5KG.01 1 0.0000 0.969 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HP.A5MZ.01 3 0.1807 0.859 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.2Y.A9GX.01 6 0.2048 0.665 0.00 0.00 0.00 0.12 0.00 0.88
#> TCGA.DD.A4NB.01 4 0.0000 0.960 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MI.A75E.01 4 0.0937 0.960 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DD.AACC.01 1 0.0547 0.969 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.K7.A5RF.01 6 0.4566 0.670 0.00 0.00 0.16 0.00 0.14 0.70
#> TCGA.DD.A1EC.01 5 0.3851 0.000 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.DD.AADC.01 2 0.4328 0.769 0.00 0.72 0.00 0.00 0.18 0.10
#> TCGA.DD.A114.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV7.01 2 0.0000 0.769 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GJ.A3OU.01 3 0.2260 0.839 0.00 0.00 0.86 0.00 0.14 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.ED.A5KG.01 1 0.208 0.802 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.HP.A5MZ.01 3 0.328 0.702 0.00 0.00 0.80 0.00 0.00 0.10 0.10
#> TCGA.2Y.A9GX.01 6 0.393 0.704 0.00 0.00 0.00 0.00 0.30 0.66 0.04
#> TCGA.DD.A4NB.01 4 0.000 0.966 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MI.A75E.01 4 0.101 0.966 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.DD.AACC.01 1 0.000 0.802 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K7.A5RF.01 6 0.000 0.704 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A1EC.01 5 0.341 0.000 0.38 0.00 0.00 0.00 0.62 0.00 0.00
#> TCGA.DD.AADC.01 2 0.000 0.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A114.01 3 0.000 0.786 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV7.01 7 0.352 0.000 0.00 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.GJ.A3OU.01 3 0.362 0.700 0.00 0.00 0.76 0.00 0.08 0.00 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.ED.A5KG.01 1 0.569 0.708 0.46 0.06 0.00 0.00 0.32 0.16 0.00 0.00
#> TCGA.HP.A5MZ.01 3 0.490 0.545 0.10 0.06 0.70 0.00 0.00 0.08 0.00 0.06
#> TCGA.2Y.A9GX.01 6 0.276 0.000 0.00 0.00 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.DD.A4NB.01 4 0.180 0.857 0.08 0.02 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.MI.A75E.01 4 0.109 0.853 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.DD.AACC.01 1 0.301 0.708 0.68 0.00 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.K7.A5RF.01 8 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A1EC.01 5 0.000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADC.01 2 0.301 0.000 0.00 0.68 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.DD.A114.01 3 0.000 0.663 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV7.01 7 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GJ.A3OU.01 3 0.505 0.514 0.14 0.18 0.62 0.00 0.00 0.06 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 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["025"]
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 0.808 0.971 0.983 0.4544 0.532 0.532
#> 3 3 0.626 0.781 0.851 0.4447 0.712 0.500
#> 4 4 0.791 0.685 0.838 0.1373 0.899 0.703
#> 5 5 0.783 0.844 0.893 0.0622 0.904 0.639
#> 6 6 0.843 0.778 0.862 0.0271 1.000 1.000
#> 7 7 0.840 0.753 0.876 0.0281 0.990 0.948
#> 8 8 0.781 0.734 0.869 0.0181 0.970 0.836
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.DD.AAW0.01 2 0.000 1.000 0.00 1.00
#> TCGA.ED.A66X.01 2 0.000 1.000 0.00 1.00
#> TCGA.ED.A97K.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAVZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AACD.01 1 0.000 0.945 1.00 0.00
#> TCGA.CC.A5UC.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAVR.01 1 0.634 0.852 0.84 0.16
#> TCGA.2Y.A9H3.01 2 0.000 1.000 0.00 1.00
#> TCGA.G3.A3CH.01 1 0.000 0.945 1.00 0.00
#> TCGA.DD.AAVV.01 2 0.000 1.000 0.00 1.00
#> TCGA.CC.A9FS.01 1 0.000 0.945 1.00 0.00
#> TCGA.CC.A7IE.01 2 0.000 1.000 0.00 1.00
#> TCGA.CC.5258.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAD2.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AACW.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AADK.01 1 0.634 0.852 0.84 0.16
#> TCGA.CC.A8HS.01 2 0.000 1.000 0.00 1.00
#> TCGA.ED.A8O6.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAVW.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.A116.01 1 0.000 0.945 1.00 0.00
#> TCGA.DD.A3A3.01 1 0.000 0.945 1.00 0.00
#> TCGA.CC.A3MC.01 1 0.634 0.852 0.84 0.16
#> TCGA.RC.A6M3.01 2 0.000 1.000 0.00 1.00
#> TCGA.ED.A4XI.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.AAVQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.CC.A7IF.01 1 0.000 0.945 1.00 0.00
#> TCGA.UB.A7ME.01 2 0.000 1.000 0.00 1.00
#> TCGA.DD.A119.01 1 0.000 0.945 1.00 0.00
#> TCGA.DD.AAVP.01 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DD.AAW0.01 3 0.000 0.774 0.00 0.00 1.00
#> TCGA.ED.A66X.01 2 0.604 0.783 0.00 0.62 0.38
#> TCGA.ED.A97K.01 2 0.630 0.643 0.00 0.52 0.48
#> TCGA.DD.AAVZ.01 2 0.000 0.698 0.00 1.00 0.00
#> TCGA.DD.AACD.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.604 0.783 0.00 0.62 0.38
#> TCGA.DD.AAVR.01 3 0.604 0.442 0.38 0.00 0.62
#> TCGA.2Y.A9H3.01 2 0.604 0.783 0.00 0.62 0.38
#> TCGA.G3.A3CH.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DD.AAVV.01 2 0.604 0.783 0.00 0.62 0.38
#> TCGA.CC.A9FS.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.480 0.774 0.00 0.78 0.22
#> TCGA.CC.5258.01 2 0.455 0.770 0.00 0.80 0.20
#> TCGA.DD.AAD2.01 3 0.000 0.774 0.00 0.00 1.00
#> TCGA.DD.AACW.01 2 0.000 0.698 0.00 1.00 0.00
#> TCGA.DD.AADK.01 3 0.604 0.442 0.38 0.00 0.62
#> TCGA.CC.A8HS.01 2 0.000 0.698 0.00 1.00 0.00
#> TCGA.ED.A8O6.01 2 0.000 0.698 0.00 1.00 0.00
#> TCGA.DD.AAVW.01 2 0.604 0.783 0.00 0.62 0.38
#> TCGA.DD.A116.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DD.A3A3.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.CC.A3MC.01 3 0.604 0.442 0.38 0.00 0.62
#> TCGA.RC.A6M3.01 3 0.000 0.774 0.00 0.00 1.00
#> TCGA.ED.A4XI.01 3 0.000 0.774 0.00 0.00 1.00
#> TCGA.DD.AAVQ.01 3 0.000 0.774 0.00 0.00 1.00
#> TCGA.CC.A7IF.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.604 0.783 0.00 0.62 0.38
#> TCGA.DD.A119.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DD.AAVP.01 3 0.000 0.774 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.DD.AAW0.01 3 0.5570 0.544 0.00 0.02 0.54 0.44
#> TCGA.ED.A66X.01 2 0.0000 0.750 0.00 1.00 0.00 0.00
#> TCGA.ED.A97K.01 2 0.4948 0.329 0.00 0.56 0.00 0.44
#> TCGA.DD.AAVZ.01 4 0.4994 0.452 0.00 0.48 0.00 0.52
#> TCGA.DD.AACD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.0000 0.750 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVR.01 3 0.0707 0.797 0.02 0.00 0.98 0.00
#> TCGA.2Y.A9H3.01 2 0.0000 0.750 0.00 1.00 0.00 0.00
#> TCGA.G3.A3CH.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVV.01 2 0.4948 0.329 0.00 0.56 0.00 0.44
#> TCGA.CC.A9FS.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.0000 0.750 0.00 1.00 0.00 0.00
#> TCGA.CC.5258.01 2 0.0000 0.750 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD2.01 3 0.4797 0.689 0.00 0.02 0.72 0.26
#> TCGA.DD.AACW.01 4 0.4994 0.452 0.00 0.48 0.00 0.52
#> TCGA.DD.AADK.01 3 0.0707 0.797 0.02 0.00 0.98 0.00
#> TCGA.CC.A8HS.01 4 0.6554 0.456 0.00 0.40 0.08 0.52
#> TCGA.ED.A8O6.01 2 0.3400 0.416 0.00 0.82 0.00 0.18
#> TCGA.DD.AAVW.01 2 0.2921 0.655 0.00 0.86 0.00 0.14
#> TCGA.DD.A116.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 3 0.0707 0.797 0.02 0.00 0.98 0.00
#> TCGA.RC.A6M3.01 4 0.7581 -0.441 0.00 0.20 0.36 0.44
#> TCGA.ED.A4XI.01 3 0.0707 0.795 0.00 0.02 0.98 0.00
#> TCGA.DD.AAVQ.01 3 0.1211 0.785 0.00 0.04 0.96 0.00
#> TCGA.CC.A7IF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.1211 0.734 0.00 0.96 0.00 0.04
#> TCGA.DD.A119.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 3 0.4994 0.519 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.DD.AAW0.01 5 0.413 0.589 0.00 0.02 0.26 0.00 0.72
#> TCGA.ED.A66X.01 2 0.000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.ED.A97K.01 5 0.368 0.787 0.00 0.28 0.00 0.00 0.72
#> TCGA.DD.AAVZ.01 4 0.311 0.948 0.00 0.20 0.00 0.80 0.00
#> TCGA.DD.AACD.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVR.01 3 0.000 0.905 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H3.01 2 0.000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVV.01 5 0.368 0.787 0.00 0.28 0.00 0.00 0.72
#> TCGA.CC.A9FS.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.122 0.893 0.00 0.96 0.00 0.02 0.02
#> TCGA.CC.5258.01 2 0.122 0.893 0.00 0.96 0.00 0.02 0.02
#> TCGA.DD.AAD2.01 3 0.418 0.204 0.00 0.00 0.60 0.00 0.40
#> TCGA.DD.AACW.01 4 0.311 0.948 0.00 0.20 0.00 0.80 0.00
#> TCGA.DD.AADK.01 3 0.000 0.905 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A8HS.01 4 0.539 0.897 0.00 0.18 0.02 0.70 0.10
#> TCGA.ED.A8O6.01 2 0.385 0.566 0.00 0.76 0.00 0.22 0.02
#> TCGA.DD.AAVW.01 2 0.173 0.846 0.00 0.92 0.00 0.00 0.08
#> TCGA.DD.A116.01 1 0.273 0.880 0.84 0.00 0.00 0.16 0.00
#> TCGA.DD.A3A3.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MC.01 3 0.000 0.905 0.00 0.00 1.00 0.00 0.00
#> TCGA.RC.A6M3.01 5 0.440 0.803 0.00 0.24 0.04 0.00 0.72
#> TCGA.ED.A4XI.01 3 0.000 0.905 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVQ.01 3 0.000 0.905 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A7IF.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.141 0.868 0.00 0.94 0.00 0.00 0.06
#> TCGA.DD.A119.01 1 0.273 0.880 0.84 0.00 0.00 0.16 0.00
#> TCGA.DD.AAVP.01 5 0.363 0.664 0.00 0.02 0.10 0.04 0.84
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DD.AAW0.01 5 0.4806 0.208 0.00 0.00 0.38 0.00 0.56 0.06
#> TCGA.ED.A66X.01 2 0.1556 0.907 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.ED.A97K.01 5 0.2941 0.664 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.DD.AAVZ.01 4 0.1556 0.891 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.DD.AACD.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.1556 0.907 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.DD.AAVR.01 3 0.1480 0.889 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.2Y.A9H3.01 2 0.1556 0.907 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.G3.A3CH.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVV.01 5 0.2941 0.664 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.CC.A9FS.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.0000 0.880 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.5258.01 2 0.0000 0.880 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD2.01 3 0.4247 0.512 0.00 0.00 0.70 0.00 0.24 0.06
#> TCGA.DD.AACW.01 4 0.1556 0.891 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.DD.AADK.01 3 0.0000 0.904 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A8HS.01 4 0.5487 0.770 0.00 0.06 0.02 0.66 0.04 0.22
#> TCGA.ED.A8O6.01 2 0.2941 0.588 0.00 0.78 0.00 0.22 0.00 0.00
#> TCGA.DD.AAVW.01 2 0.2048 0.875 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.DD.A116.01 1 0.3756 0.645 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.DD.A3A3.01 1 0.0937 0.855 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.CC.A3MC.01 3 0.1480 0.889 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.RC.A6M3.01 5 0.2981 0.680 0.00 0.16 0.02 0.00 0.82 0.00
#> TCGA.ED.A4XI.01 3 0.0000 0.904 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 3 0.0000 0.904 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7IF.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.1814 0.895 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.DD.A119.01 1 0.3828 0.611 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.DD.AAVP.01 5 0.5626 0.363 0.00 0.00 0.10 0.02 0.54 0.34
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DD.AAW0.01 5 0.7223 0.353 0.00 0.10 0.14 0.16 0.48 0.00 0.12
#> TCGA.ED.A66X.01 2 0.0000 0.885 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A97K.01 5 0.2422 0.733 0.00 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.DD.AAVZ.01 6 0.0000 0.823 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACD.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.0000 0.885 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVR.01 3 0.0863 0.827 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.2Y.A9H3.01 2 0.1166 0.864 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVV.01 5 0.3052 0.729 0.00 0.20 0.00 0.02 0.78 0.00 0.00
#> TCGA.CC.A9FS.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.2569 0.838 0.00 0.84 0.00 0.14 0.02 0.00 0.00
#> TCGA.CC.5258.01 2 0.2569 0.838 0.00 0.84 0.00 0.14 0.02 0.00 0.00
#> TCGA.DD.AAD2.01 3 0.5977 0.435 0.00 0.00 0.56 0.14 0.18 0.00 0.12
#> TCGA.DD.AACW.01 6 0.0000 0.823 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADK.01 3 0.0000 0.835 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HS.01 6 0.4795 0.610 0.00 0.00 0.00 0.28 0.08 0.62 0.02
#> TCGA.ED.A8O6.01 2 0.4212 0.779 0.00 0.76 0.00 0.14 0.04 0.04 0.02
#> TCGA.DD.AAVW.01 2 0.0504 0.879 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.A116.01 1 0.3221 0.698 0.68 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.DD.A3A3.01 1 0.1363 0.860 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.CC.A3MC.01 3 0.0863 0.827 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.RC.A6M3.01 5 0.3000 0.707 0.00 0.10 0.04 0.02 0.84 0.00 0.00
#> TCGA.ED.A4XI.01 3 0.1006 0.830 0.00 0.00 0.96 0.02 0.02 0.00 0.00
#> TCGA.DD.AAVQ.01 3 0.3052 0.736 0.00 0.00 0.78 0.20 0.02 0.00 0.00
#> TCGA.CC.A7IF.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.1664 0.852 0.00 0.92 0.00 0.06 0.02 0.00 0.00
#> TCGA.DD.A119.01 1 0.3755 0.661 0.64 0.00 0.02 0.34 0.00 0.00 0.00
#> TCGA.DD.AAVP.01 7 0.1433 0.000 0.00 0.00 0.00 0.00 0.08 0.00 0.92
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DD.AAW0.01 5 0.6016 0.237 0.00 0.04 0.22 0.00 0.54 0.00 0.08 0.12
#> TCGA.ED.A66X.01 2 0.1091 0.884 0.00 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.ED.A97K.01 5 0.1804 0.616 0.00 0.02 0.00 0.00 0.90 0.00 0.00 0.08
#> TCGA.DD.AAVZ.01 6 0.3570 0.964 0.00 0.00 0.00 0.36 0.00 0.62 0.02 0.00
#> TCGA.DD.AACD.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A5UC.01 2 0.1091 0.884 0.00 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.DD.AAVR.01 3 0.1804 0.805 0.00 0.00 0.90 0.00 0.00 0.02 0.00 0.08
#> TCGA.2Y.A9H3.01 2 0.1091 0.884 0.00 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.G3.A3CH.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVV.01 5 0.1947 0.554 0.00 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.CC.A9FS.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7IE.01 2 0.0808 0.855 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CC.5258.01 2 0.0808 0.855 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DD.AAD2.01 3 0.5317 0.377 0.00 0.00 0.58 0.00 0.22 0.00 0.08 0.12
#> TCGA.DD.AACW.01 6 0.3142 0.964 0.00 0.00 0.00 0.36 0.00 0.64 0.00 0.00
#> TCGA.DD.AADK.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A8HS.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ED.A8O6.01 2 0.3710 0.671 0.00 0.76 0.00 0.00 0.00 0.10 0.02 0.12
#> TCGA.DD.AAVW.01 2 0.2267 0.818 0.00 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DD.A116.01 8 0.5276 0.929 0.32 0.00 0.00 0.00 0.00 0.32 0.00 0.36
#> TCGA.DD.A3A3.01 1 0.2994 0.712 0.80 0.00 0.00 0.00 0.00 0.00 0.06 0.14
#> TCGA.CC.A3MC.01 3 0.1804 0.805 0.00 0.00 0.90 0.00 0.00 0.02 0.00 0.08
#> TCGA.RC.A6M3.01 5 0.2719 0.554 0.00 0.00 0.00 0.00 0.80 0.02 0.00 0.18
#> TCGA.ED.A4XI.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVQ.01 3 0.2224 0.766 0.00 0.00 0.86 0.00 0.00 0.00 0.02 0.12
#> TCGA.CC.A7IF.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7ME.01 2 0.2267 0.818 0.00 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DD.A119.01 8 0.5246 0.932 0.28 0.00 0.00 0.00 0.00 0.34 0.00 0.38
#> TCGA.DD.AAVP.01 7 0.1563 0.000 0.00 0.00 0.00 0.00 0.10 0.00 0.90 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node025 , Node031-leaf , Node032 , Node041 , Node042 .
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 34 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.998 0.999 0.4515 0.549 0.549
#> 3 3 0.766 0.907 0.932 0.2346 0.898 0.818
#> 4 4 0.714 0.826 0.906 0.2160 0.831 0.643
#> 5 5 0.665 0.680 0.829 0.0527 0.938 0.808
#> 6 6 0.641 0.679 0.854 0.0341 0.980 0.929
#> 7 7 0.665 0.626 0.804 0.0332 0.948 0.812
#> 8 8 0.750 0.648 0.848 0.0237 0.986 0.940
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.KR.A7K7.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAC8.01 2 0.000 0.999 0.00 1.00
#> TCGA.ZP.A9D2.01 1 0.000 0.998 1.00 0.00
#> TCGA.DD.A73B.01 2 0.000 0.999 0.00 1.00
#> TCGA.K7.AAU7.01 2 0.141 0.980 0.02 0.98
#> TCGA.3K.AAZ8.01 2 0.000 0.999 0.00 1.00
#> TCGA.CC.A9FW.01 2 0.000 0.999 0.00 1.00
#> TCGA.T1.A6J8.01 1 0.000 0.998 1.00 0.00
#> TCGA.DD.AACH.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.A7M9.01 1 0.000 0.998 1.00 0.00
#> TCGA.BC.A69H.01 1 0.000 0.998 1.00 0.00
#> TCGA.BC.A5W4.01 2 0.000 0.999 0.00 1.00
#> TCGA.KR.A7K2.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AADM.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AADQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.AAV6.01 1 0.141 0.980 0.98 0.02
#> TCGA.MI.A75C.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAD5.01 1 0.000 0.998 1.00 0.00
#> TCGA.CC.A5UE.01 1 0.000 0.998 1.00 0.00
#> TCGA.DD.A11B.01 2 0.000 0.999 0.00 1.00
#> TCGA.2Y.A9H7.01 2 0.000 0.999 0.00 1.00
#> TCGA.CC.A7II.01 1 0.000 0.998 1.00 0.00
#> TCGA.BC.A10W.01 1 0.000 0.998 1.00 0.00
#> TCGA.FV.A23B.01 2 0.000 0.999 0.00 1.00
#> TCGA.RC.A6M6.01 1 0.000 0.998 1.00 0.00
#> TCGA.DD.AADJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AACG.01 1 0.000 0.998 1.00 0.00
#> TCGA.DD.AAE1.01 2 0.000 0.999 0.00 1.00
#> TCGA.BC.A3KG.01 2 0.000 0.999 0.00 1.00
#> TCGA.BC.A10R.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAVU.01 2 0.000 0.999 0.00 1.00
#> TCGA.O8.A75V.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAEE.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAE6.01 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.KR.A7K7.01 2 0.4551 0.861 0.14 0.84 0.02
#> TCGA.DD.AAC8.01 2 0.4209 0.874 0.12 0.86 0.02
#> TCGA.ZP.A9D2.01 3 0.1529 0.911 0.04 0.00 0.96
#> TCGA.DD.A73B.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.K7.AAU7.01 3 0.4291 0.697 0.00 0.18 0.82
#> TCGA.3K.AAZ8.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.CC.A9FW.01 2 0.4551 0.861 0.14 0.84 0.02
#> TCGA.T1.A6J8.01 3 0.1529 0.883 0.04 0.00 0.96
#> TCGA.DD.AACH.01 2 0.2537 0.888 0.00 0.92 0.08
#> TCGA.G3.A7M9.01 1 0.3686 0.953 0.86 0.00 0.14
#> TCGA.BC.A69H.01 1 0.3686 0.953 0.86 0.00 0.14
#> TCGA.BC.A5W4.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.KR.A7K2.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.DD.AADM.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.DD.AADQ.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.G3.AAV6.01 1 0.2066 0.760 0.94 0.00 0.06
#> TCGA.MI.A75C.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.DD.AAD5.01 3 0.1529 0.911 0.04 0.00 0.96
#> TCGA.CC.A5UE.01 3 0.0000 0.897 0.00 0.00 1.00
#> TCGA.DD.A11B.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.2Y.A9H7.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.CC.A7II.01 1 0.3686 0.953 0.86 0.00 0.14
#> TCGA.BC.A10W.01 3 0.1529 0.911 0.04 0.00 0.96
#> TCGA.FV.A23B.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.RC.A6M6.01 1 0.3686 0.953 0.86 0.00 0.14
#> TCGA.DD.AADJ.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.DD.AACG.01 1 0.3686 0.953 0.86 0.00 0.14
#> TCGA.DD.AAE1.01 2 0.4551 0.861 0.14 0.84 0.02
#> TCGA.BC.A3KG.01 2 0.7164 0.747 0.14 0.72 0.14
#> TCGA.BC.A10R.01 2 0.0892 0.932 0.00 0.98 0.02
#> TCGA.DD.AAVU.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.O8.A75V.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.DD.AAEE.01 2 0.0000 0.945 0.00 1.00 0.00
#> TCGA.DD.AAE6.01 2 0.5667 0.832 0.14 0.80 0.06
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.KR.A7K7.01 4 0.3801 0.8123 0.00 0.22 0.00 0.78
#> TCGA.DD.AAC8.01 2 0.4907 0.0361 0.00 0.58 0.00 0.42
#> TCGA.ZP.A9D2.01 3 0.1913 0.8598 0.04 0.02 0.94 0.00
#> TCGA.DD.A73B.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.K7.AAU7.01 3 0.2011 0.8290 0.00 0.08 0.92 0.00
#> TCGA.3K.AAZ8.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.CC.A9FW.01 4 0.3801 0.8123 0.00 0.22 0.00 0.78
#> TCGA.T1.A6J8.01 3 0.5291 0.7655 0.08 0.00 0.74 0.18
#> TCGA.DD.AACH.01 2 0.6370 0.4164 0.00 0.62 0.28 0.10
#> TCGA.G3.A7M9.01 1 0.0000 0.9896 1.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 1 0.0707 0.9769 0.98 0.00 0.02 0.00
#> TCGA.BC.A5W4.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.KR.A7K2.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.DD.AADM.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.DD.AADQ.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.G3.AAV6.01 4 0.4624 0.3479 0.34 0.00 0.00 0.66
#> TCGA.MI.A75C.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD5.01 3 0.0707 0.8621 0.02 0.00 0.98 0.00
#> TCGA.CC.A5UE.01 3 0.5986 0.7274 0.02 0.06 0.70 0.22
#> TCGA.DD.A11B.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H7.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.CC.A7II.01 1 0.0000 0.9896 1.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.0707 0.8657 0.00 0.02 0.98 0.00
#> TCGA.FV.A23B.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.RC.A6M6.01 1 0.0000 0.9896 1.00 0.00 0.00 0.00
#> TCGA.DD.AADJ.01 2 0.2011 0.8499 0.00 0.92 0.00 0.08
#> TCGA.DD.AACG.01 1 0.0707 0.9795 0.98 0.00 0.00 0.02
#> TCGA.DD.AAE1.01 4 0.3975 0.7979 0.00 0.24 0.00 0.76
#> TCGA.BC.A3KG.01 4 0.4731 0.7225 0.00 0.16 0.06 0.78
#> TCGA.BC.A10R.01 2 0.2647 0.8038 0.00 0.88 0.12 0.00
#> TCGA.DD.AAVU.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.O8.A75V.01 2 0.0000 0.9208 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEE.01 2 0.1211 0.8902 0.00 0.96 0.00 0.04
#> TCGA.DD.AAE6.01 4 0.3037 0.7267 0.00 0.10 0.02 0.88
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.KR.A7K7.01 4 0.2516 0.5562 0.00 0.14 0.00 0.86 0.00
#> TCGA.DD.AAC8.01 4 0.5157 0.2451 0.00 0.44 0.00 0.52 0.04
#> TCGA.ZP.A9D2.01 3 0.0609 0.7973 0.02 0.00 0.98 0.00 0.00
#> TCGA.DD.A73B.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.K7.AAU7.01 3 0.2754 0.6890 0.00 0.08 0.88 0.00 0.04
#> TCGA.3K.AAZ8.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A9FW.01 4 0.2280 0.5326 0.00 0.12 0.00 0.88 0.00
#> TCGA.T1.A6J8.01 3 0.5173 0.0162 0.04 0.00 0.50 0.00 0.46
#> TCGA.DD.AACH.01 2 0.8024 -0.1251 0.00 0.44 0.14 0.20 0.22
#> TCGA.G3.A7M9.01 1 0.0000 0.9644 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 1 0.2675 0.9148 0.90 0.00 0.04 0.04 0.02
#> TCGA.BC.A5W4.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADQ.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV6.01 4 0.6037 0.0123 0.12 0.00 0.02 0.62 0.24
#> TCGA.MI.A75C.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAD5.01 3 0.0609 0.7973 0.02 0.00 0.98 0.00 0.00
#> TCGA.CC.A5UE.01 5 0.5663 -0.2168 0.00 0.02 0.42 0.04 0.52
#> TCGA.DD.A11B.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A7II.01 1 0.0000 0.9644 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.0609 0.7973 0.02 0.00 0.98 0.00 0.00
#> TCGA.FV.A23B.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 1 0.0000 0.9644 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADJ.01 2 0.2280 0.8119 0.00 0.88 0.00 0.12 0.00
#> TCGA.DD.AACG.01 1 0.1648 0.9346 0.94 0.00 0.02 0.00 0.04
#> TCGA.DD.AAE1.01 4 0.2732 0.5514 0.00 0.16 0.00 0.84 0.00
#> TCGA.BC.A3KG.01 5 0.7227 0.2298 0.00 0.10 0.08 0.40 0.42
#> TCGA.BC.A10R.01 2 0.2438 0.8367 0.00 0.90 0.06 0.00 0.04
#> TCGA.DD.AAVU.01 2 0.3421 0.7801 0.00 0.84 0.00 0.08 0.08
#> TCGA.O8.A75V.01 2 0.0000 0.9161 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 2 0.3110 0.8001 0.00 0.86 0.00 0.08 0.06
#> TCGA.DD.AAE6.01 5 0.5173 0.1954 0.00 0.04 0.00 0.46 0.50
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.KR.A7K7.01 4 0.181 0.571 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.DD.AAC8.01 4 0.511 0.266 0.00 0.44 0.00 0.50 0.04 0.02
#> TCGA.ZP.A9D2.01 3 0.000 0.864 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A73B.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.K7.AAU7.01 3 0.296 0.706 0.00 0.12 0.84 0.00 0.04 0.00
#> TCGA.3K.AAZ8.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FW.01 4 0.235 0.548 0.00 0.10 0.00 0.88 0.02 0.00
#> TCGA.T1.A6J8.01 5 0.535 0.330 0.04 0.00 0.24 0.00 0.64 0.08
#> TCGA.DD.AACH.01 2 0.841 -0.235 0.00 0.34 0.12 0.12 0.28 0.14
#> TCGA.G3.A7M9.01 1 0.000 0.919 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 1 0.432 0.779 0.80 0.00 0.04 0.06 0.06 0.04
#> TCGA.BC.A5W4.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADQ.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV6.01 6 0.480 0.000 0.02 0.00 0.02 0.46 0.00 0.50
#> TCGA.MI.A75C.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD5.01 3 0.109 0.859 0.02 0.00 0.96 0.00 0.00 0.02
#> TCGA.CC.A5UE.01 5 0.226 0.442 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.DD.A11B.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7II.01 1 0.000 0.919 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.181 0.830 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.FV.A23B.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 1 0.000 0.919 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADJ.01 2 0.332 0.717 0.00 0.82 0.00 0.14 0.02 0.02
#> TCGA.DD.AACG.01 1 0.235 0.844 0.88 0.00 0.00 0.00 0.10 0.02
#> TCGA.DD.AAE1.01 4 0.311 0.586 0.00 0.12 0.00 0.84 0.02 0.02
#> TCGA.BC.A3KG.01 5 0.709 0.157 0.00 0.10 0.00 0.32 0.40 0.18
#> TCGA.BC.A10R.01 2 0.432 0.667 0.00 0.78 0.12 0.02 0.06 0.02
#> TCGA.DD.AAVU.01 2 0.338 0.759 0.00 0.84 0.00 0.04 0.08 0.04
#> TCGA.O8.A75V.01 2 0.000 0.891 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 2 0.304 0.744 0.00 0.84 0.00 0.10 0.06 0.00
#> TCGA.DD.AAE6.01 5 0.649 0.097 0.00 0.02 0.00 0.30 0.40 0.28
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.KR.A7K7.01 4 0.6372 0.4835 0.00 0.12 0.00 0.42 0.00 0.34 0.12
#> TCGA.DD.AAC8.01 7 0.7169 -0.2179 0.00 0.22 0.00 0.32 0.02 0.12 0.32
#> TCGA.ZP.A9D2.01 3 0.1006 0.7997 0.02 0.02 0.96 0.00 0.00 0.00 0.00
#> TCGA.DD.A73B.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K7.AAU7.01 3 0.4029 0.6138 0.00 0.12 0.78 0.02 0.04 0.00 0.04
#> TCGA.3K.AAZ8.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FW.01 4 0.6391 0.4542 0.00 0.08 0.00 0.40 0.02 0.40 0.10
#> TCGA.T1.A6J8.01 5 0.4005 0.8028 0.02 0.00 0.20 0.02 0.74 0.00 0.02
#> TCGA.DD.AACH.01 7 0.7420 0.1801 0.00 0.26 0.20 0.08 0.08 0.00 0.38
#> TCGA.G3.A7M9.01 1 0.0000 0.8770 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 1 0.3630 0.7489 0.80 0.00 0.06 0.00 0.00 0.10 0.04
#> TCGA.BC.A5W4.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 2 0.0504 0.8756 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DD.AADQ.01 2 0.1363 0.8514 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.G3.AAV6.01 6 0.1166 0.0000 0.06 0.00 0.00 0.00 0.00 0.94 0.00
#> TCGA.MI.A75C.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD5.01 3 0.2163 0.7778 0.02 0.00 0.88 0.00 0.00 0.00 0.10
#> TCGA.CC.A5UE.01 5 0.4589 0.8007 0.00 0.00 0.22 0.04 0.68 0.00 0.06
#> TCGA.DD.A11B.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A7II.01 1 0.0000 0.8770 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.2706 0.7463 0.02 0.00 0.88 0.00 0.04 0.02 0.04
#> TCGA.FV.A23B.01 2 0.0000 0.8836 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 1 0.0504 0.8719 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AADJ.01 2 0.3404 0.7102 0.00 0.82 0.00 0.08 0.00 0.06 0.04
#> TCGA.DD.AACG.01 1 0.3530 0.6971 0.76 0.00 0.00 0.00 0.20 0.02 0.02
#> TCGA.DD.AAE1.01 4 0.6458 0.4030 0.00 0.18 0.00 0.44 0.00 0.28 0.10
#> TCGA.BC.A3KG.01 7 0.5646 -0.0689 0.00 0.02 0.06 0.04 0.10 0.10 0.68
#> TCGA.BC.A10R.01 2 0.5429 0.4962 0.00 0.68 0.12 0.06 0.06 0.00 0.08
#> TCGA.DD.AAVU.01 2 0.5138 0.4748 0.00 0.66 0.00 0.10 0.08 0.00 0.16
#> TCGA.O8.A75V.01 2 0.0504 0.8756 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 2 0.5602 0.2502 0.00 0.58 0.00 0.14 0.02 0.02 0.24
#> TCGA.DD.AAE6.01 4 0.4708 -0.1609 0.00 0.00 0.00 0.64 0.26 0.02 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.KR.A7K7.01 4 0.0471 0.6015 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.DD.AAC8.01 4 0.7022 -0.1619 0.00 0.26 0.00 0.38 0.04 0.02 0.22 0.08
#> TCGA.ZP.A9D2.01 3 0.1275 0.7872 0.00 0.00 0.94 0.00 0.04 0.02 0.00 0.00
#> TCGA.DD.A73B.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.K7.AAU7.01 3 0.3951 0.6349 0.00 0.12 0.76 0.02 0.02 0.00 0.08 0.00
#> TCGA.3K.AAZ8.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A9FW.01 4 0.0941 0.5975 0.00 0.02 0.00 0.96 0.00 0.02 0.00 0.00
#> TCGA.T1.A6J8.01 5 0.2350 0.6755 0.00 0.00 0.10 0.00 0.86 0.00 0.04 0.00
#> TCGA.DD.AACH.01 7 0.8159 0.1456 0.00 0.18 0.04 0.18 0.10 0.02 0.34 0.14
#> TCGA.G3.A7M9.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69H.01 1 0.4075 0.7136 0.76 0.00 0.02 0.00 0.02 0.14 0.04 0.02
#> TCGA.BC.A5W4.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADQ.01 2 0.0941 0.8729 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.G3.AAV6.01 6 0.3170 0.0000 0.00 0.00 0.00 0.20 0.00 0.76 0.00 0.04
#> TCGA.MI.A75C.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAD5.01 3 0.1563 0.7824 0.00 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.CC.A5UE.01 5 0.4870 0.6728 0.00 0.00 0.12 0.00 0.62 0.00 0.22 0.04
#> TCGA.DD.A11B.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 2 0.0808 0.8732 0.00 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.CC.A7II.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10W.01 3 0.2350 0.7426 0.00 0.00 0.86 0.00 0.10 0.00 0.04 0.00
#> TCGA.FV.A23B.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RC.A6M6.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADJ.01 2 0.3337 0.6972 0.00 0.78 0.00 0.16 0.00 0.04 0.02 0.00
#> TCGA.DD.AACG.01 1 0.4295 0.6893 0.74 0.00 0.00 0.00 0.12 0.06 0.06 0.02
#> TCGA.DD.AAE1.01 4 0.3402 0.5525 0.00 0.06 0.00 0.82 0.00 0.06 0.02 0.04
#> TCGA.BC.A3KG.01 7 0.6097 0.0228 0.00 0.00 0.00 0.24 0.12 0.04 0.52 0.08
#> TCGA.BC.A10R.01 2 0.4262 0.6330 0.00 0.74 0.08 0.00 0.04 0.00 0.12 0.02
#> TCGA.DD.AAVU.01 2 0.4662 0.6597 0.00 0.74 0.00 0.02 0.08 0.06 0.06 0.04
#> TCGA.O8.A75V.01 2 0.0000 0.8968 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 2 0.6184 0.1352 0.00 0.52 0.00 0.20 0.04 0.00 0.16 0.08
#> TCGA.DD.AAE6.01 8 0.1804 0.0000 0.00 0.00 0.00 0.08 0.02 0.00 0.00 0.90
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["032"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 8.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5222 0.478 0.478
#> 3 3 0.700 0.879 0.850 0.2295 0.874 0.736
#> 4 4 0.681 0.761 0.796 0.1284 1.000 1.000
#> 5 5 0.767 0.868 0.813 0.1032 0.826 0.506
#> 6 6 0.857 0.927 0.858 0.0501 0.953 0.733
#> 7 7 0.929 0.910 0.908 0.0372 1.000 1.000
#> 8 8 0.943 0.833 0.909 0.0194 0.976 0.818
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.KR.A7K7.01 2 0 1 0 1
#> TCGA.DD.AAC8.01 2 0 1 0 1
#> TCGA.DD.A73B.01 1 0 1 1 0
#> TCGA.K7.AAU7.01 1 0 1 1 0
#> TCGA.3K.AAZ8.01 2 0 1 0 1
#> TCGA.CC.A9FW.01 2 0 1 0 1
#> TCGA.DD.AACH.01 2 0 1 0 1
#> TCGA.BC.A5W4.01 1 0 1 1 0
#> TCGA.KR.A7K2.01 1 0 1 1 0
#> TCGA.DD.AADM.01 2 0 1 0 1
#> TCGA.DD.AADQ.01 2 0 1 0 1
#> TCGA.MI.A75C.01 1 0 1 1 0
#> TCGA.DD.A11B.01 1 0 1 1 0
#> TCGA.2Y.A9H7.01 1 0 1 1 0
#> TCGA.FV.A23B.01 1 0 1 1 0
#> TCGA.DD.AADJ.01 1 0 1 1 0
#> TCGA.DD.AAE1.01 2 0 1 0 1
#> TCGA.BC.A3KG.01 2 0 1 0 1
#> TCGA.BC.A10R.01 1 0 1 1 0
#> TCGA.DD.AAVU.01 2 0 1 0 1
#> TCGA.O8.A75V.01 1 0 1 1 0
#> TCGA.DD.AAEE.01 2 0 1 0 1
#> TCGA.DD.AAE6.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.KR.A7K7.01 2 0.6302 0.889 0.00 0.52 0.48
#> TCGA.DD.AAC8.01 2 0.6045 0.897 0.00 0.62 0.38
#> TCGA.DD.A73B.01 1 0.5706 0.782 0.68 0.32 0.00
#> TCGA.K7.AAU7.01 1 0.0892 0.863 0.98 0.00 0.02
#> TCGA.3K.AAZ8.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CC.A9FW.01 2 0.6302 0.889 0.00 0.52 0.48
#> TCGA.DD.AACH.01 2 0.6302 0.889 0.00 0.52 0.48
#> TCGA.BC.A5W4.01 1 0.5706 0.782 0.68 0.32 0.00
#> TCGA.KR.A7K2.01 1 0.5706 0.782 0.68 0.32 0.00
#> TCGA.DD.AADM.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.DD.AADQ.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.MI.A75C.01 1 0.5706 0.782 0.68 0.32 0.00
#> TCGA.DD.A11B.01 1 0.0000 0.866 1.00 0.00 0.00
#> TCGA.2Y.A9H7.01 1 0.2066 0.854 0.94 0.06 0.00
#> TCGA.FV.A23B.01 1 0.2066 0.854 0.94 0.06 0.00
#> TCGA.DD.AADJ.01 1 0.2066 0.854 0.94 0.06 0.00
#> TCGA.DD.AAE1.01 2 0.6302 0.889 0.00 0.52 0.48
#> TCGA.BC.A3KG.01 2 0.6045 0.897 0.00 0.62 0.38
#> TCGA.BC.A10R.01 1 0.0892 0.863 0.98 0.00 0.02
#> TCGA.DD.AAVU.01 3 0.0892 0.959 0.00 0.02 0.98
#> TCGA.O8.A75V.01 1 0.0000 0.866 1.00 0.00 0.00
#> TCGA.DD.AAEE.01 2 0.6045 0.897 0.00 0.62 0.38
#> TCGA.DD.AAE6.01 2 0.6045 0.897 0.00 0.62 0.38
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.KR.A7K7.01 2 0.201 0.644 0.00 0.92 0.00 0.08
#> TCGA.DD.AAC8.01 2 0.495 0.690 0.00 0.56 0.44 0.00
#> TCGA.DD.A73B.01 1 0.452 0.759 0.68 0.00 0.32 0.00
#> TCGA.K7.AAU7.01 1 0.265 0.774 0.88 0.00 0.00 0.12
#> TCGA.3K.AAZ8.01 4 0.121 0.936 0.00 0.04 0.00 0.96
#> TCGA.CC.A9FW.01 2 0.164 0.657 0.00 0.94 0.00 0.06
#> TCGA.DD.AACH.01 2 0.292 0.582 0.00 0.86 0.00 0.14
#> TCGA.BC.A5W4.01 1 0.452 0.759 0.68 0.00 0.32 0.00
#> TCGA.KR.A7K2.01 1 0.452 0.759 0.68 0.00 0.32 0.00
#> TCGA.DD.AADM.01 4 0.164 0.932 0.00 0.06 0.00 0.94
#> TCGA.DD.AADQ.01 4 0.121 0.936 0.00 0.04 0.00 0.96
#> TCGA.MI.A75C.01 1 0.452 0.759 0.68 0.00 0.32 0.00
#> TCGA.DD.A11B.01 1 0.000 0.813 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H7.01 1 0.353 0.787 0.86 0.00 0.10 0.04
#> TCGA.FV.A23B.01 1 0.353 0.787 0.86 0.00 0.10 0.04
#> TCGA.DD.AADJ.01 1 0.353 0.787 0.86 0.00 0.10 0.04
#> TCGA.DD.AAE1.01 2 0.164 0.657 0.00 0.94 0.00 0.06
#> TCGA.BC.A3KG.01 2 0.495 0.690 0.00 0.56 0.44 0.00
#> TCGA.BC.A10R.01 1 0.265 0.774 0.88 0.00 0.00 0.12
#> TCGA.DD.AAVU.01 4 0.515 0.824 0.00 0.10 0.14 0.76
#> TCGA.O8.A75V.01 1 0.121 0.809 0.96 0.00 0.00 0.04
#> TCGA.DD.AAEE.01 2 0.495 0.690 0.00 0.56 0.44 0.00
#> TCGA.DD.AAE6.01 2 0.495 0.690 0.00 0.56 0.44 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.KR.A7K7.01 2 0.5351 0.992 0.00 0.56 0.00 0.06 0.38
#> TCGA.DD.AAC8.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.A73B.01 3 0.2020 0.994 0.10 0.00 0.90 0.00 0.00
#> TCGA.K7.AAU7.01 1 0.7170 0.628 0.42 0.38 0.16 0.04 0.00
#> TCGA.3K.AAZ8.01 4 0.0609 0.964 0.00 0.00 0.00 0.98 0.02
#> TCGA.CC.A9FW.01 2 0.5351 0.992 0.00 0.56 0.00 0.06 0.38
#> TCGA.DD.AACH.01 2 0.5887 0.977 0.00 0.54 0.02 0.06 0.38
#> TCGA.BC.A5W4.01 3 0.2616 0.982 0.10 0.00 0.88 0.02 0.00
#> TCGA.KR.A7K2.01 3 0.2020 0.994 0.10 0.00 0.90 0.00 0.00
#> TCGA.DD.AADM.01 4 0.0609 0.964 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.AADQ.01 4 0.0609 0.964 0.00 0.00 0.00 0.98 0.02
#> TCGA.MI.A75C.01 3 0.2020 0.994 0.10 0.00 0.90 0.00 0.00
#> TCGA.DD.A11B.01 1 0.6326 0.634 0.46 0.38 0.16 0.00 0.00
#> TCGA.2Y.A9H7.01 1 0.0000 0.581 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A23B.01 1 0.0000 0.581 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADJ.01 1 0.0000 0.581 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAE1.01 2 0.5351 0.992 0.00 0.56 0.00 0.06 0.38
#> TCGA.BC.A3KG.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.BC.A10R.01 1 0.7170 0.628 0.42 0.38 0.16 0.04 0.00
#> TCGA.DD.AAVU.01 4 0.3700 0.888 0.00 0.06 0.08 0.84 0.02
#> TCGA.O8.A75V.01 1 0.6837 0.635 0.44 0.38 0.16 0.02 0.00
#> TCGA.DD.AAEE.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AAE6.01 5 0.0000 1.000 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.KR.A7K7.01 2 0.4503 0.905 0.00 0.68 0.00 0.08 0.24 0.00
#> TCGA.DD.AAC8.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A73B.01 3 0.0000 0.964 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.K7.AAU7.01 1 0.5493 0.927 0.62 0.00 0.06 0.06 0.00 0.26
#> TCGA.3K.AAZ8.01 4 0.0000 0.916 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CC.A9FW.01 2 0.4360 0.905 0.00 0.68 0.00 0.06 0.26 0.00
#> TCGA.DD.AACH.01 2 0.6973 0.778 0.12 0.54 0.00 0.14 0.18 0.02
#> TCGA.BC.A5W4.01 3 0.2260 0.887 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 3 0.0000 0.964 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 4 0.0000 0.916 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADQ.01 4 0.0000 0.916 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MI.A75C.01 3 0.0000 0.964 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A11B.01 1 0.5731 0.826 0.56 0.06 0.06 0.00 0.00 0.32
#> TCGA.2Y.A9H7.01 6 0.0547 1.000 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FV.A23B.01 6 0.0547 1.000 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DD.AADJ.01 6 0.0547 1.000 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DD.AAE1.01 2 0.4864 0.901 0.02 0.66 0.00 0.06 0.26 0.00
#> TCGA.BC.A3KG.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BC.A10R.01 1 0.6593 0.898 0.56 0.06 0.06 0.06 0.00 0.26
#> TCGA.DD.AAVU.01 4 0.4247 0.728 0.24 0.06 0.00 0.70 0.00 0.00
#> TCGA.O8.A75V.01 1 0.5493 0.927 0.62 0.00 0.06 0.06 0.00 0.26
#> TCGA.DD.AAEE.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAE6.01 5 0.0000 1.000 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.KR.A7K7.01 2 0.1433 0.931 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.DD.AAC8.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A73B.01 3 0.0504 0.952 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.K7.AAU7.01 1 0.2422 0.912 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.3K.AAZ8.01 7 0.1006 0.864 0.02 0.00 0.00 0.02 0.00 0.00 0.96
#> TCGA.CC.A9FW.01 2 0.1433 0.931 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.DD.AACH.01 2 0.4774 0.814 0.14 0.70 0.00 0.08 0.08 0.00 0.00
#> TCGA.BC.A5W4.01 3 0.2569 0.874 0.00 0.02 0.84 0.14 0.00 0.00 0.00
#> TCGA.KR.A7K2.01 3 0.0000 0.955 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 7 0.0000 0.874 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DD.AADQ.01 7 0.0000 0.874 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MI.A75C.01 3 0.0000 0.955 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11B.01 1 0.4970 0.751 0.58 0.00 0.00 0.24 0.00 0.18 0.00
#> TCGA.2Y.A9H7.01 6 0.0000 0.974 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FV.A23B.01 6 0.0000 0.974 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AADJ.01 6 0.1363 0.948 0.00 0.02 0.00 0.04 0.00 0.94 0.00
#> TCGA.DD.AAE1.01 2 0.2421 0.919 0.02 0.88 0.00 0.02 0.08 0.00 0.00
#> TCGA.BC.A3KG.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A10R.01 1 0.3386 0.900 0.78 0.02 0.00 0.02 0.00 0.18 0.00
#> TCGA.DD.AAVU.01 7 0.3525 0.608 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.O8.A75V.01 1 0.2422 0.912 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.DD.AAEE.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE6.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.KR.A7K7.01 2 0.0808 0.934 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.DD.AAC8.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A73B.01 3 0.0471 0.936 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.K7.AAU7.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3K.AAZ8.01 7 0.2482 0.860 0.00 0.02 0.00 0.06 0.00 0.02 0.88 0.02
#> TCGA.CC.A9FW.01 2 0.0808 0.934 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.DD.AACH.01 4 0.4105 0.000 0.00 0.42 0.00 0.54 0.02 0.00 0.02 0.00
#> TCGA.BC.A5W4.01 3 0.2725 0.840 0.00 0.00 0.82 0.04 0.00 0.00 0.00 0.14
#> TCGA.KR.A7K2.01 3 0.0000 0.938 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADM.01 7 0.0471 0.932 0.00 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.DD.AADQ.01 7 0.0471 0.932 0.00 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.MI.A75C.01 3 0.0471 0.936 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11B.01 1 0.3785 0.714 0.72 0.00 0.00 0.14 0.00 0.00 0.00 0.14
#> TCGA.2Y.A9H7.01 6 0.1091 0.949 0.06 0.00 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.FV.A23B.01 6 0.1091 0.949 0.06 0.00 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.DD.AADJ.01 6 0.3078 0.895 0.06 0.00 0.00 0.10 0.00 0.82 0.00 0.02
#> TCGA.DD.AAE1.01 2 0.2532 0.866 0.00 0.88 0.00 0.04 0.04 0.02 0.00 0.02
#> TCGA.BC.A3KG.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A10R.01 1 0.1804 0.848 0.90 0.02 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVU.01 8 0.3449 0.000 0.00 0.02 0.00 0.00 0.00 0.00 0.32 0.66
#> TCGA.O8.A75V.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEE.01 5 0.0941 0.962 0.00 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.DD.AAE6.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node025 , Node031-leaf , Node032 , Node041 , Node042 .
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 108 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 0.961 0.963 0.983 0.4820 0.525 0.525
#> 3 3 0.783 0.888 0.945 0.3251 0.706 0.505
#> 4 4 0.715 0.745 0.865 0.1559 0.816 0.544
#> 5 5 0.709 0.535 0.739 0.0697 0.908 0.681
#> 6 6 0.741 0.723 0.811 0.0451 0.889 0.564
#> 7 7 0.763 0.622 0.808 0.0282 0.984 0.907
#> 8 8 0.783 0.650 0.798 0.0180 0.947 0.695
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.FV.A495.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.A4NV.01 1 0.000 0.999 1.00 0.00
#> TCGA.ZP.A9CV.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AACY.01 2 0.000 0.972 0.00 1.00
#> TCGA.CC.A3MB.01 2 0.000 0.972 0.00 1.00
#> TCGA.ED.A459.01 2 0.000 0.972 0.00 1.00
#> TCGA.PD.A5DF.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AAVX.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A3A0.01 2 0.827 0.681 0.26 0.74
#> TCGA.DD.AACM.01 1 0.000 0.999 1.00 0.00
#> TCGA.FV.A3I1.01 1 0.000 0.999 1.00 0.00
#> TCGA.G3.A5SL.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A11A.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A3A2.01 1 0.000 0.999 1.00 0.00
#> TCGA.FV.A2QQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AADP.01 2 0.760 0.741 0.22 0.78
#> TCGA.CC.5259.01 2 0.000 0.972 0.00 1.00
#> TCGA.ES.A2HS.01 2 0.000 0.972 0.00 1.00
#> TCGA.2V.A95S.01 2 0.000 0.972 0.00 1.00
#> TCGA.FV.A4ZP.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAD3.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.A39V.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AACS.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A4NK.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.A4NF.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A3A8.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A4NO.01 2 0.000 0.972 0.00 1.00
#> TCGA.ZS.A9CG.01 2 0.000 0.972 0.00 1.00
#> TCGA.CC.A123.01 2 0.584 0.841 0.14 0.86
#> TCGA.EP.A2KA.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAE7.01 2 0.000 0.972 0.00 1.00
#> TCGA.KR.A7K0.01 2 0.904 0.574 0.32 0.68
#> TCGA.DD.AACX.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAEK.01 1 0.000 0.999 1.00 0.00
#> TCGA.G3.A5SM.01 2 0.000 0.972 0.00 1.00
#> TCGA.G3.AAV1.01 2 0.000 0.972 0.00 1.00
#> TCGA.FV.A4ZQ.01 2 0.000 0.972 0.00 1.00
#> TCGA.WQ.AB4B.01 2 0.000 0.972 0.00 1.00
#> TCGA.BC.A10T.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.A39W.01 2 0.000 0.972 0.00 1.00
#> TCGA.UB.A7MD.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AADE.01 2 0.000 0.972 0.00 1.00
#> TCGA.GJ.A6C0.01 1 0.000 0.999 1.00 0.00
#> TCGA.BC.A69I.01 2 0.000 0.972 0.00 1.00
#> TCGA.K7.A6G5.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.A4NG.01 2 0.000 0.972 0.00 1.00
#> TCGA.UB.A7MC.01 1 0.000 0.999 1.00 0.00
#> TCGA.UB.AA0U.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AACQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.A4NJ.01 1 0.000 0.999 1.00 0.00
#> TCGA.FV.A496.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAE8.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AAEH.01 2 0.000 0.972 0.00 1.00
#> TCGA.2Y.A9GW.01 2 0.000 0.972 0.00 1.00
#> TCGA.NI.A4U2.01 1 0.000 0.999 1.00 0.00
#> TCGA.5C.AAPD.01 1 0.000 0.999 1.00 0.00
#> TCGA.HP.A5N0.01 1 0.000 0.999 1.00 0.00
#> TCGA.YA.A8S7.01 2 0.904 0.574 0.32 0.68
#> TCGA.DD.AACF.01 2 0.000 0.972 0.00 1.00
#> TCGA.G3.AAV5.01 2 0.000 0.972 0.00 1.00
#> TCGA.G3.A5SK.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A3A7.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A73A.01 1 0.000 0.999 1.00 0.00
#> TCGA.G3.AAV3.01 2 0.000 0.972 0.00 1.00
#> TCGA.MI.A75H.01 2 0.000 0.972 0.00 1.00
#> TCGA.BC.A10S.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A73F.01 1 0.000 0.999 1.00 0.00
#> TCGA.ZP.A9D1.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A73C.01 2 0.584 0.841 0.14 0.86
#> TCGA.DD.AADU.01 2 0.000 0.972 0.00 1.00
#> TCGA.UB.A7MB.01 2 0.634 0.819 0.16 0.84
#> TCGA.EP.A12J.01 2 0.000 0.972 0.00 1.00
#> TCGA.ZS.A9CD.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAEI.01 1 0.000 0.999 1.00 0.00
#> TCGA.2Y.A9GV.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AADS.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A39Z.01 2 0.242 0.939 0.04 0.96
#> TCGA.EP.A2KB.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAEA.01 1 0.000 0.999 1.00 0.00
#> TCGA.FV.A3R2.01 2 0.000 0.972 0.00 1.00
#> TCGA.2Y.A9GY.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AACZ.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AAED.01 2 0.000 0.972 0.00 1.00
#> TCGA.EP.A3JL.01 1 0.000 0.999 1.00 0.00
#> TCGA.5R.AA1C.01 2 0.000 0.972 0.00 1.00
#> TCGA.G3.A3CK.01 2 0.000 0.972 0.00 1.00
#> TCGA.G3.A5SJ.01 1 0.000 0.999 1.00 0.00
#> TCGA.5R.AAAM.01 2 0.000 0.972 0.00 1.00
#> TCGA.2Y.A9GS.01 1 0.000 0.999 1.00 0.00
#> TCGA.BD.A3ER.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAVY.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A1EG.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AADN.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AADB.01 1 0.141 0.978 0.98 0.02
#> TCGA.G3.A3CG.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AAW1.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.A4NI.01 2 0.000 0.972 0.00 1.00
#> TCGA.2Y.A9GT.01 1 0.000 0.999 1.00 0.00
#> TCGA.MI.A75I.01 1 0.000 0.999 1.00 0.00
#> TCGA.2Y.A9H1.01 1 0.000 0.999 1.00 0.00
#> TCGA.CC.A8HT.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.AADR.01 2 0.827 0.682 0.26 0.74
#> TCGA.2Y.A9HB.01 2 0.000 0.972 0.00 1.00
#> TCGA.DD.AACI.01 2 0.000 0.972 0.00 1.00
#> TCGA.CC.A5UD.01 2 0.000 0.972 0.00 1.00
#> TCGA.G3.AAV2.01 2 0.000 0.972 0.00 1.00
#> TCGA.ZP.A9CY.01 1 0.000 0.999 1.00 0.00
#> TCGA.DD.A39Y.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.FV.A495.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.A4NV.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.ZP.A9CV.01 1 0.2537 0.841 0.92 0.08 0.00
#> TCGA.DD.AACY.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.CC.A3MB.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.ED.A459.01 2 0.0892 0.931 0.02 0.98 0.00
#> TCGA.PD.A5DF.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.AAVX.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.A3A0.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AACM.01 1 0.5016 0.710 0.76 0.00 0.24
#> TCGA.FV.A3I1.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.G3.A5SL.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.A11A.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.A3A2.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.FV.A2QQ.01 1 0.4002 0.814 0.84 0.00 0.16
#> TCGA.DD.AADP.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.CC.5259.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.ES.A2HS.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.2V.A95S.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.FV.A4ZP.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.AAD3.01 1 0.6302 0.171 0.52 0.00 0.48
#> TCGA.DD.A39V.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AACS.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.A4NK.01 1 0.4002 0.814 0.84 0.00 0.16
#> TCGA.DD.A4NF.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.A3A8.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.A4NO.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.ZS.A9CG.01 2 0.0892 0.931 0.02 0.98 0.00
#> TCGA.CC.A123.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.EP.A2KA.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.AAE7.01 2 0.4796 0.795 0.22 0.78 0.00
#> TCGA.KR.A7K0.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AACX.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.AAEK.01 1 0.4002 0.814 0.84 0.00 0.16
#> TCGA.G3.A5SM.01 2 0.4796 0.795 0.22 0.78 0.00
#> TCGA.G3.AAV1.01 2 0.3340 0.874 0.12 0.88 0.00
#> TCGA.FV.A4ZQ.01 2 0.0892 0.931 0.02 0.98 0.00
#> TCGA.WQ.AB4B.01 1 0.2066 0.865 0.94 0.06 0.00
#> TCGA.BC.A10T.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.A39W.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.UB.A7MD.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.AADE.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.GJ.A6C0.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.BC.A69I.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.K7.A6G5.01 1 0.2066 0.888 0.94 0.00 0.06
#> TCGA.DD.A4NG.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.UB.A7MC.01 1 0.4002 0.814 0.84 0.00 0.16
#> TCGA.UB.AA0U.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AACQ.01 3 0.6192 0.145 0.42 0.00 0.58
#> TCGA.DD.A4NJ.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.FV.A496.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.AAE8.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.AAEH.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.2Y.A9GW.01 2 0.5397 0.716 0.28 0.72 0.00
#> TCGA.NI.A4U2.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.5C.AAPD.01 1 0.6302 0.173 0.52 0.00 0.48
#> TCGA.HP.A5N0.01 1 0.4002 0.814 0.84 0.00 0.16
#> TCGA.YA.A8S7.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AACF.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.G3.AAV5.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.G3.A5SK.01 2 0.4555 0.815 0.20 0.80 0.00
#> TCGA.DD.A3A7.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.A73A.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.G3.AAV3.01 2 0.0892 0.931 0.02 0.98 0.00
#> TCGA.MI.A75H.01 2 0.5216 0.745 0.26 0.74 0.00
#> TCGA.BC.A10S.01 2 0.5397 0.716 0.28 0.72 0.00
#> TCGA.DD.A73F.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.ZP.A9D1.01 2 0.3340 0.874 0.12 0.88 0.00
#> TCGA.DD.A73C.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AADU.01 2 0.0892 0.931 0.02 0.98 0.00
#> TCGA.UB.A7MB.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.EP.A12J.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.ZS.A9CD.01 2 0.0892 0.931 0.02 0.98 0.00
#> TCGA.DD.AAEI.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.2Y.A9GV.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AADS.01 2 0.4796 0.795 0.22 0.78 0.00
#> TCGA.DD.A39Z.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.EP.A2KB.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.AAEA.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.FV.A3R2.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.2Y.A9GY.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.AACZ.01 1 0.4002 0.814 0.84 0.00 0.16
#> TCGA.DD.AAED.01 2 0.4002 0.846 0.16 0.84 0.00
#> TCGA.EP.A3JL.01 1 0.3686 0.831 0.86 0.00 0.14
#> TCGA.5R.AA1C.01 2 0.4796 0.795 0.22 0.78 0.00
#> TCGA.G3.A3CK.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.G3.A5SJ.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.5R.AAAM.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.2Y.A9GS.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.BD.A3ER.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.AAVY.01 2 0.4291 0.832 0.18 0.82 0.00
#> TCGA.DD.A1EG.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.AADN.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.DD.AADB.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.G3.A3CG.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.AAW1.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.DD.A4NI.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.2Y.A9GT.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.MI.A75I.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.2Y.A9H1.01 1 0.4002 0.814 0.84 0.00 0.16
#> TCGA.CC.A8HT.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.AADR.01 1 0.0000 0.922 1.00 0.00 0.00
#> TCGA.2Y.A9HB.01 2 0.4796 0.795 0.22 0.78 0.00
#> TCGA.DD.AACI.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.CC.A5UD.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.G3.AAV2.01 2 0.0000 0.937 0.00 1.00 0.00
#> TCGA.ZP.A9CY.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DD.A39Y.01 3 0.0000 0.974 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.FV.A495.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.A4NV.01 1 0.4406 0.775 0.70 0.00 0.00 0.30
#> TCGA.ZP.A9CV.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.DD.AACY.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.CC.A3MB.01 2 0.4977 0.218 0.00 0.54 0.00 0.46
#> TCGA.ED.A459.01 4 0.5987 0.332 0.04 0.44 0.00 0.52
#> TCGA.PD.A5DF.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.AAVX.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A0.01 1 0.0707 0.847 0.98 0.00 0.00 0.02
#> TCGA.DD.AACM.01 1 0.1211 0.856 0.96 0.00 0.04 0.00
#> TCGA.FV.A3I1.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.G3.A5SL.01 4 0.4134 0.556 0.26 0.00 0.00 0.74
#> TCGA.DD.A11A.01 2 0.4977 0.218 0.00 0.54 0.00 0.46
#> TCGA.DD.A3A2.01 1 0.1211 0.860 0.96 0.00 0.00 0.04
#> TCGA.FV.A2QQ.01 1 0.3525 0.855 0.86 0.00 0.04 0.10
#> TCGA.DD.AADP.01 1 0.4406 0.766 0.70 0.00 0.00 0.30
#> TCGA.CC.5259.01 2 0.4977 0.218 0.00 0.54 0.00 0.46
#> TCGA.ES.A2HS.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.2V.A95S.01 4 0.3172 0.575 0.16 0.00 0.00 0.84
#> TCGA.FV.A4ZP.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.AAD3.01 1 0.1637 0.851 0.94 0.00 0.06 0.00
#> TCGA.DD.A39V.01 1 0.4406 0.775 0.70 0.00 0.00 0.30
#> TCGA.DD.AACS.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NK.01 1 0.1211 0.856 0.96 0.00 0.04 0.00
#> TCGA.DD.A4NF.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.A3A8.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NO.01 2 0.3801 0.598 0.00 0.78 0.00 0.22
#> TCGA.ZS.A9CG.01 4 0.5987 0.332 0.04 0.44 0.00 0.52
#> TCGA.CC.A123.01 1 0.2647 0.780 0.88 0.00 0.00 0.12
#> TCGA.EP.A2KA.01 2 0.4855 0.362 0.00 0.60 0.00 0.40
#> TCGA.DD.AAE7.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.KR.A7K0.01 1 0.0707 0.849 0.98 0.00 0.00 0.02
#> TCGA.DD.AACX.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEK.01 1 0.1211 0.856 0.96 0.00 0.04 0.00
#> TCGA.G3.A5SM.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.G3.AAV1.01 4 0.2345 0.732 0.00 0.10 0.00 0.90
#> TCGA.FV.A4ZQ.01 4 0.5957 0.366 0.04 0.42 0.00 0.54
#> TCGA.WQ.AB4B.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.BC.A10T.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.A39W.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.UB.A7MD.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.AADE.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.GJ.A6C0.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.BC.A69I.01 2 0.4855 0.362 0.00 0.60 0.00 0.40
#> TCGA.K7.A6G5.01 1 0.1211 0.856 0.96 0.00 0.04 0.00
#> TCGA.DD.A4NG.01 4 0.2921 0.608 0.14 0.00 0.00 0.86
#> TCGA.UB.A7MC.01 1 0.2830 0.855 0.90 0.00 0.04 0.06
#> TCGA.UB.AA0U.01 1 0.3400 0.830 0.82 0.00 0.00 0.18
#> TCGA.DD.AACQ.01 1 0.3525 0.830 0.86 0.00 0.10 0.04
#> TCGA.DD.A4NJ.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.FV.A496.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.AAE8.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.AAEH.01 4 0.1211 0.735 0.04 0.00 0.00 0.96
#> TCGA.2Y.A9GW.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.NI.A4U2.01 1 0.0000 0.851 1.00 0.00 0.00 0.00
#> TCGA.5C.AAPD.01 1 0.5327 0.729 0.72 0.00 0.22 0.06
#> TCGA.HP.A5N0.01 1 0.1211 0.856 0.96 0.00 0.04 0.00
#> TCGA.YA.A8S7.01 1 0.4406 0.775 0.70 0.00 0.00 0.30
#> TCGA.DD.AACF.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.G3.AAV5.01 2 0.0707 0.810 0.00 0.98 0.00 0.02
#> TCGA.G3.A5SK.01 4 0.1637 0.754 0.00 0.06 0.00 0.94
#> TCGA.DD.A3A7.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.A73A.01 3 0.0707 0.979 0.02 0.00 0.98 0.00
#> TCGA.G3.AAV3.01 4 0.5987 0.332 0.04 0.44 0.00 0.52
#> TCGA.MI.A75H.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.BC.A10S.01 4 0.2830 0.743 0.06 0.04 0.00 0.90
#> TCGA.DD.A73F.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.ZP.A9D1.01 4 0.1637 0.754 0.00 0.06 0.00 0.94
#> TCGA.DD.A73C.01 1 0.3172 0.733 0.84 0.00 0.00 0.16
#> TCGA.DD.AADU.01 4 0.5987 0.332 0.04 0.44 0.00 0.52
#> TCGA.UB.A7MB.01 1 0.2647 0.780 0.88 0.00 0.00 0.12
#> TCGA.EP.A12J.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.ZS.A9CD.01 4 0.5987 0.332 0.04 0.44 0.00 0.52
#> TCGA.DD.AAEI.01 1 0.4406 0.775 0.70 0.00 0.00 0.30
#> TCGA.2Y.A9GV.01 1 0.0000 0.851 1.00 0.00 0.00 0.00
#> TCGA.DD.AADS.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.DD.A39Z.01 1 0.4277 0.770 0.72 0.00 0.00 0.28
#> TCGA.EP.A2KB.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEA.01 1 0.2345 0.856 0.90 0.00 0.00 0.10
#> TCGA.FV.A3R2.01 1 0.4855 0.606 0.60 0.00 0.00 0.40
#> TCGA.2Y.A9GY.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.AACZ.01 1 0.4406 0.775 0.70 0.00 0.00 0.30
#> TCGA.DD.AAED.01 4 0.6262 0.385 0.06 0.40 0.00 0.54
#> TCGA.EP.A3JL.01 1 0.1913 0.859 0.94 0.00 0.04 0.02
#> TCGA.5R.AA1C.01 4 0.1637 0.754 0.00 0.06 0.00 0.94
#> TCGA.G3.A3CK.01 4 0.4406 0.509 0.00 0.30 0.00 0.70
#> TCGA.G3.A5SJ.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.5R.AAAM.01 4 0.2345 0.727 0.10 0.00 0.00 0.90
#> TCGA.2Y.A9GS.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.BD.A3ER.01 2 0.4790 0.239 0.00 0.62 0.00 0.38
#> TCGA.DD.AAVY.01 4 0.6299 0.350 0.06 0.42 0.00 0.52
#> TCGA.DD.A1EG.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.AADN.01 4 0.2345 0.663 0.10 0.00 0.00 0.90
#> TCGA.DD.AADB.01 1 0.1637 0.860 0.94 0.00 0.00 0.06
#> TCGA.G3.A3CG.01 2 0.4907 0.311 0.00 0.58 0.00 0.42
#> TCGA.DD.AAW1.01 2 0.1211 0.796 0.00 0.96 0.00 0.04
#> TCGA.DD.A4NI.01 4 0.4713 0.399 0.00 0.36 0.00 0.64
#> TCGA.2Y.A9GT.01 1 0.4406 0.775 0.70 0.00 0.00 0.30
#> TCGA.MI.A75I.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9H1.01 1 0.3198 0.857 0.88 0.00 0.04 0.08
#> TCGA.CC.A8HT.01 3 0.0000 0.995 0.00 0.00 1.00 0.00
#> TCGA.DD.AADR.01 1 0.4277 0.770 0.72 0.00 0.00 0.28
#> TCGA.2Y.A9HB.01 4 0.1211 0.758 0.00 0.04 0.00 0.96
#> TCGA.DD.AACI.01 2 0.4790 0.396 0.00 0.62 0.00 0.38
#> TCGA.CC.A5UD.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.G3.AAV2.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9CY.01 3 0.0707 0.979 0.02 0.00 0.98 0.00
#> TCGA.DD.A39Y.01 3 0.1211 0.964 0.00 0.00 0.96 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FV.A495.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A4NV.01 5 0.6047 0.9188 0.40 0.00 0.00 0.12 0.48
#> TCGA.ZP.A9CV.01 4 0.0609 0.6579 0.00 0.00 0.00 0.98 0.02
#> TCGA.DD.AACY.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.CC.A3MB.01 4 0.6275 0.3426 0.00 0.30 0.00 0.52 0.18
#> TCGA.ED.A459.01 4 0.6593 0.4287 0.00 0.22 0.00 0.44 0.34
#> TCGA.PD.A5DF.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVX.01 2 0.0609 0.9181 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.A3A0.01 1 0.4588 0.3478 0.72 0.00 0.00 0.06 0.22
#> TCGA.DD.AACM.01 1 0.1732 0.3896 0.92 0.00 0.00 0.00 0.08
#> TCGA.FV.A3I1.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.G3.A5SL.01 4 0.5425 0.4943 0.08 0.00 0.00 0.60 0.32
#> TCGA.DD.A11A.01 4 0.6275 0.3426 0.00 0.30 0.00 0.52 0.18
#> TCGA.DD.A3A2.01 1 0.0609 0.4247 0.98 0.00 0.00 0.00 0.02
#> TCGA.FV.A2QQ.01 1 0.4262 -0.4450 0.56 0.00 0.00 0.00 0.44
#> TCGA.DD.AADP.01 1 0.6632 -0.6435 0.40 0.00 0.00 0.22 0.38
#> TCGA.CC.5259.01 4 0.6275 0.3426 0.00 0.30 0.00 0.52 0.18
#> TCGA.ES.A2HS.01 2 0.0609 0.9234 0.00 0.98 0.00 0.00 0.02
#> TCGA.2V.A95S.01 4 0.4675 0.0334 0.02 0.00 0.00 0.60 0.38
#> TCGA.FV.A4ZP.01 2 0.1410 0.8930 0.00 0.94 0.00 0.00 0.06
#> TCGA.DD.AAD3.01 1 0.2020 0.3724 0.90 0.00 0.00 0.00 0.10
#> TCGA.DD.A39V.01 5 0.6047 0.9188 0.40 0.00 0.00 0.12 0.48
#> TCGA.DD.AACS.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NK.01 1 0.1732 0.3896 0.92 0.00 0.00 0.00 0.08
#> TCGA.DD.A4NF.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A8.01 2 0.0609 0.9181 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.A4NO.01 2 0.3561 0.5450 0.00 0.74 0.00 0.26 0.00
#> TCGA.ZS.A9CG.01 4 0.6671 0.4007 0.00 0.24 0.00 0.42 0.34
#> TCGA.CC.A123.01 1 0.5156 0.3141 0.62 0.00 0.00 0.06 0.32
#> TCGA.EP.A2KA.01 4 0.5297 0.3496 0.00 0.36 0.00 0.58 0.06
#> TCGA.DD.AAE7.01 4 0.0000 0.6661 0.00 0.00 0.00 1.00 0.00
#> TCGA.KR.A7K0.01 1 0.1732 0.3950 0.92 0.00 0.00 0.08 0.00
#> TCGA.DD.AACX.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 1 0.0000 0.4352 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 4 0.2020 0.6531 0.00 0.00 0.00 0.90 0.10
#> TCGA.G3.AAV1.01 4 0.1410 0.6685 0.00 0.00 0.00 0.94 0.06
#> TCGA.FV.A4ZQ.01 4 0.6593 0.4287 0.00 0.22 0.00 0.44 0.34
#> TCGA.WQ.AB4B.01 4 0.1043 0.6512 0.00 0.00 0.00 0.96 0.04
#> TCGA.BC.A10T.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.A39W.01 2 0.0609 0.9234 0.00 0.98 0.00 0.00 0.02
#> TCGA.UB.A7MD.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADE.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.GJ.A6C0.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.BC.A69I.01 4 0.5351 0.3147 0.00 0.38 0.00 0.56 0.06
#> TCGA.K7.A6G5.01 1 0.0000 0.4352 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.4675 0.0334 0.02 0.00 0.00 0.60 0.38
#> TCGA.UB.A7MC.01 1 0.4287 -0.4556 0.54 0.00 0.00 0.00 0.46
#> TCGA.UB.AA0U.01 5 0.5895 0.8281 0.44 0.00 0.00 0.10 0.46
#> TCGA.DD.AACQ.01 1 0.4798 -0.4281 0.54 0.00 0.02 0.00 0.44
#> TCGA.DD.A4NJ.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.FV.A496.01 2 0.2732 0.8205 0.00 0.84 0.00 0.00 0.16
#> TCGA.DD.AAE8.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEH.01 4 0.0000 0.6661 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9GW.01 4 0.0000 0.6661 0.00 0.00 0.00 1.00 0.00
#> TCGA.NI.A4U2.01 1 0.0000 0.4352 1.00 0.00 0.00 0.00 0.00
#> TCGA.5C.AAPD.01 1 0.6070 -0.5258 0.44 0.00 0.12 0.00 0.44
#> TCGA.HP.A5N0.01 1 0.0000 0.4352 1.00 0.00 0.00 0.00 0.00
#> TCGA.YA.A8S7.01 5 0.6555 0.6660 0.40 0.00 0.00 0.20 0.40
#> TCGA.DD.AACF.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.AAV5.01 2 0.2438 0.8586 0.00 0.90 0.00 0.04 0.06
#> TCGA.G3.A5SK.01 4 0.0000 0.6661 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A3A7.01 2 0.0609 0.9234 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.A73A.01 3 0.3697 0.8176 0.08 0.00 0.82 0.00 0.10
#> TCGA.G3.AAV3.01 4 0.6593 0.4287 0.00 0.22 0.00 0.44 0.34
#> TCGA.MI.A75H.01 4 0.1043 0.6512 0.00 0.00 0.00 0.96 0.04
#> TCGA.BC.A10S.01 4 0.4540 0.5399 0.02 0.00 0.00 0.64 0.34
#> TCGA.DD.A73F.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZP.A9D1.01 4 0.1043 0.6685 0.00 0.00 0.00 0.96 0.04
#> TCGA.DD.A73C.01 1 0.5156 0.3141 0.62 0.00 0.00 0.06 0.32
#> TCGA.DD.AADU.01 4 0.6671 0.4007 0.00 0.24 0.00 0.42 0.34
#> TCGA.UB.A7MB.01 1 0.5156 0.3141 0.62 0.00 0.00 0.06 0.32
#> TCGA.EP.A12J.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 4 0.6593 0.4287 0.00 0.22 0.00 0.44 0.34
#> TCGA.DD.AAEI.01 5 0.6047 0.9188 0.40 0.00 0.00 0.12 0.48
#> TCGA.2Y.A9GV.01 1 0.0000 0.4352 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADS.01 4 0.0000 0.6661 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.A39Z.01 1 0.6619 -0.6362 0.42 0.00 0.00 0.22 0.36
#> TCGA.EP.A2KB.01 2 0.0609 0.9234 0.00 0.98 0.00 0.00 0.02
#> TCGA.DD.AAEA.01 1 0.5095 -0.5074 0.56 0.00 0.00 0.04 0.40
#> TCGA.FV.A3R2.01 1 0.6785 -0.5560 0.36 0.00 0.00 0.28 0.36
#> TCGA.2Y.A9GY.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AACZ.01 5 0.6019 0.8953 0.38 0.00 0.00 0.12 0.50
#> TCGA.DD.AAED.01 4 0.7489 0.4584 0.08 0.14 0.00 0.44 0.34
#> TCGA.EP.A3JL.01 1 0.4262 -0.4450 0.56 0.00 0.00 0.00 0.44
#> TCGA.5R.AA1C.01 4 0.0000 0.6661 0.00 0.00 0.00 1.00 0.00
#> TCGA.G3.A3CK.01 4 0.3641 0.6191 0.00 0.12 0.00 0.82 0.06
#> TCGA.G3.A5SJ.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.5R.AAAM.01 4 0.5156 0.5088 0.06 0.00 0.00 0.62 0.32
#> TCGA.2Y.A9GS.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.BD.A3ER.01 2 0.4726 0.1568 0.00 0.58 0.00 0.40 0.02
#> TCGA.DD.AAVY.01 4 0.7489 0.4584 0.08 0.14 0.00 0.44 0.34
#> TCGA.DD.A1EG.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADN.01 4 0.4182 0.0990 0.00 0.00 0.00 0.60 0.40
#> TCGA.DD.AADB.01 1 0.5351 -0.4683 0.56 0.00 0.00 0.06 0.38
#> TCGA.G3.A3CG.01 4 0.5297 0.3496 0.00 0.36 0.00 0.58 0.06
#> TCGA.DD.AAW1.01 2 0.1043 0.9017 0.00 0.96 0.00 0.04 0.00
#> TCGA.DD.A4NI.01 4 0.3868 0.6061 0.00 0.14 0.00 0.80 0.06
#> TCGA.2Y.A9GT.01 5 0.6047 0.9188 0.40 0.00 0.00 0.12 0.48
#> TCGA.MI.A75I.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.2Y.A9H1.01 1 0.4262 -0.4450 0.56 0.00 0.00 0.00 0.44
#> TCGA.CC.A8HT.01 3 0.0000 0.9726 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADR.01 1 0.6619 -0.6362 0.42 0.00 0.00 0.22 0.36
#> TCGA.2Y.A9HB.01 4 0.0000 0.6661 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACI.01 4 0.5351 0.3147 0.00 0.38 0.00 0.56 0.06
#> TCGA.CC.A5UD.01 2 0.0609 0.9181 0.00 0.98 0.00 0.00 0.02
#> TCGA.G3.AAV2.01 2 0.0000 0.9286 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 3 0.3697 0.8176 0.08 0.00 0.82 0.00 0.10
#> TCGA.DD.A39Y.01 3 0.2280 0.8819 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.FV.A495.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NV.01 5 0.2048 0.7389 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.ZP.A9CV.01 4 0.3076 0.6165 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.DD.AACY.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CC.A3MB.01 4 0.6487 0.5184 0.20 0.18 0.00 0.56 0.02 0.04
#> TCGA.ED.A459.01 6 0.2474 0.8730 0.00 0.08 0.00 0.04 0.00 0.88
#> TCGA.PD.A5DF.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 2 0.2454 0.7624 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.DD.A3A0.01 1 0.3982 0.7180 0.74 0.00 0.00 0.00 0.06 0.20
#> TCGA.DD.AACM.01 1 0.3198 0.8177 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.FV.A3I1.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G3.A5SL.01 6 0.4334 0.6290 0.02 0.00 0.00 0.22 0.04 0.72
#> TCGA.DD.A11A.01 4 0.6156 0.5093 0.20 0.18 0.00 0.58 0.02 0.02
#> TCGA.DD.A3A2.01 1 0.3499 0.7068 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.FV.A2QQ.01 5 0.0547 0.6952 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DD.AADP.01 5 0.4938 0.6508 0.08 0.00 0.00 0.34 0.58 0.00
#> TCGA.CC.5259.01 4 0.6156 0.5093 0.20 0.18 0.00 0.58 0.02 0.02
#> TCGA.ES.A2HS.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2V.A95S.01 5 0.3864 0.4918 0.00 0.00 0.00 0.48 0.52 0.00
#> TCGA.FV.A4ZP.01 2 0.2350 0.8130 0.10 0.88 0.00 0.00 0.00 0.02
#> TCGA.DD.AAD3.01 1 0.3647 0.7221 0.64 0.00 0.00 0.00 0.36 0.00
#> TCGA.DD.A39V.01 5 0.2793 0.7263 0.00 0.00 0.00 0.20 0.80 0.00
#> TCGA.DD.AACS.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NK.01 1 0.3309 0.8027 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.DD.A4NF.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A8.01 2 0.2454 0.7624 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.DD.A4NO.01 2 0.6430 -0.0633 0.12 0.44 0.00 0.06 0.00 0.38
#> TCGA.ZS.A9CG.01 6 0.2474 0.8730 0.00 0.08 0.00 0.04 0.00 0.88
#> TCGA.CC.A123.01 1 0.3578 0.5563 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.EP.A2KA.01 4 0.6713 0.5658 0.14 0.22 0.00 0.52 0.00 0.12
#> TCGA.DD.AAE7.01 4 0.3156 0.6523 0.02 0.00 0.00 0.80 0.00 0.18
#> TCGA.KR.A7K0.01 1 0.3460 0.8116 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.DD.AACX.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 1 0.3198 0.8177 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.G3.A5SM.01 4 0.4713 0.6475 0.12 0.00 0.00 0.72 0.02 0.14
#> TCGA.G3.AAV1.01 4 0.4887 0.6490 0.12 0.00 0.00 0.70 0.02 0.16
#> TCGA.FV.A4ZQ.01 6 0.2474 0.8730 0.00 0.08 0.00 0.04 0.00 0.88
#> TCGA.WQ.AB4B.01 4 0.2260 0.6437 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.BC.A10T.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.A39W.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MD.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADE.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GJ.A6C0.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BC.A69I.01 4 0.6877 0.5300 0.14 0.26 0.00 0.48 0.00 0.12
#> TCGA.K7.A6G5.01 1 0.3198 0.8177 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.DD.A4NG.01 5 0.3864 0.4918 0.00 0.00 0.00 0.48 0.52 0.00
#> TCGA.UB.A7MC.01 5 0.4265 0.5239 0.14 0.00 0.00 0.02 0.76 0.08
#> TCGA.UB.AA0U.01 5 0.2794 0.7227 0.06 0.00 0.00 0.08 0.86 0.00
#> TCGA.DD.AACQ.01 5 0.4265 0.5239 0.14 0.00 0.00 0.02 0.76 0.08
#> TCGA.DD.A4NJ.01 3 0.0937 0.9283 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.FV.A496.01 2 0.4607 0.6873 0.18 0.72 0.00 0.08 0.00 0.02
#> TCGA.DD.AAE8.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEH.01 4 0.3198 0.5954 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.2Y.A9GW.01 4 0.3198 0.5954 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.NI.A4U2.01 1 0.2941 0.8154 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.5C.AAPD.01 5 0.1480 0.6799 0.00 0.00 0.02 0.00 0.94 0.04
#> TCGA.HP.A5N0.01 1 0.3198 0.8177 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.YA.A8S7.01 5 0.4121 0.6972 0.06 0.00 0.00 0.22 0.72 0.00
#> TCGA.DD.AACF.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV5.01 2 0.4903 0.5941 0.14 0.70 0.00 0.14 0.00 0.02
#> TCGA.G3.A5SK.01 4 0.3711 0.6042 0.02 0.00 0.00 0.72 0.00 0.26
#> TCGA.DD.A3A7.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 3 0.3315 0.7871 0.02 0.00 0.78 0.00 0.20 0.00
#> TCGA.G3.AAV3.01 6 0.2474 0.8730 0.00 0.08 0.00 0.04 0.00 0.88
#> TCGA.MI.A75H.01 4 0.2048 0.6377 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.BC.A10S.01 6 0.2454 0.7586 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.DD.A73F.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9D1.01 4 0.3829 0.6576 0.06 0.00 0.00 0.76 0.00 0.18
#> TCGA.DD.A73C.01 1 0.3578 0.5563 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.DD.AADU.01 6 0.2474 0.8730 0.00 0.08 0.00 0.04 0.00 0.88
#> TCGA.UB.A7MB.01 1 0.3578 0.5563 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.EP.A12J.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 6 0.2474 0.8730 0.00 0.08 0.00 0.04 0.00 0.88
#> TCGA.DD.AAEI.01 5 0.1814 0.7334 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.2Y.A9GV.01 1 0.2941 0.8154 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.DD.AADS.01 4 0.3076 0.6165 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.DD.A39Z.01 5 0.5037 0.6081 0.08 0.00 0.00 0.38 0.54 0.00
#> TCGA.EP.A2KB.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEA.01 5 0.3746 0.6703 0.14 0.00 0.00 0.08 0.78 0.00
#> TCGA.FV.A3R2.01 5 0.5037 0.6081 0.08 0.00 0.00 0.38 0.54 0.00
#> TCGA.2Y.A9GY.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACZ.01 5 0.2629 0.6707 0.02 0.00 0.00 0.02 0.88 0.08
#> TCGA.DD.AAED.01 6 0.2345 0.8521 0.02 0.06 0.00 0.02 0.00 0.90
#> TCGA.EP.A3JL.01 5 0.2454 0.5760 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.5R.AA1C.01 4 0.3756 0.3212 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.G3.A3CK.01 4 0.5184 0.6444 0.12 0.02 0.00 0.66 0.00 0.20
#> TCGA.G3.A5SJ.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 6 0.3198 0.6192 0.00 0.00 0.00 0.26 0.00 0.74
#> TCGA.2Y.A9GS.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BD.A3ER.01 6 0.5731 0.4426 0.06 0.32 0.00 0.06 0.00 0.56
#> TCGA.DD.AAVY.01 6 0.2345 0.8521 0.02 0.06 0.00 0.02 0.00 0.90
#> TCGA.DD.A1EG.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADN.01 4 0.3706 -0.1733 0.00 0.00 0.00 0.62 0.38 0.00
#> TCGA.DD.AADB.01 5 0.3679 0.6065 0.20 0.00 0.00 0.04 0.76 0.00
#> TCGA.G3.A3CG.01 4 0.6866 0.5666 0.14 0.22 0.00 0.50 0.00 0.14
#> TCGA.DD.AAW1.01 2 0.4162 0.6827 0.04 0.78 0.00 0.12 0.00 0.06
#> TCGA.DD.A4NI.01 4 0.6767 0.5824 0.14 0.14 0.00 0.52 0.00 0.20
#> TCGA.2Y.A9GT.01 5 0.2048 0.7389 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.MI.A75I.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2Y.A9H1.01 5 0.0547 0.6952 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CC.A8HT.01 3 0.0000 0.9556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AADR.01 5 0.4938 0.6508 0.08 0.00 0.00 0.34 0.58 0.00
#> TCGA.2Y.A9HB.01 4 0.3076 0.6165 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.DD.AACI.01 4 0.6877 0.5300 0.14 0.26 0.00 0.48 0.00 0.12
#> TCGA.CC.A5UD.01 2 0.2454 0.7624 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.G3.AAV2.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 3 0.3460 0.7662 0.02 0.00 0.76 0.00 0.22 0.00
#> TCGA.DD.A39Y.01 3 0.5261 0.6818 0.02 0.00 0.68 0.02 0.20 0.08
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FV.A495.01 3 0.0504 0.9110 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.A4NV.01 5 0.1363 0.5249 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.ZP.A9CV.01 4 0.3370 0.5841 0.00 0.00 0.00 0.78 0.16 0.06 0.00
#> TCGA.DD.AACY.01 2 0.3086 0.7702 0.00 0.80 0.00 0.00 0.00 0.04 0.16
#> TCGA.CC.A3MB.01 4 0.4244 0.5274 0.00 0.04 0.00 0.54 0.00 0.00 0.42
#> TCGA.ED.A459.01 6 0.1433 0.8024 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.PD.A5DF.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 2 0.4629 0.6432 0.00 0.64 0.00 0.00 0.00 0.20 0.16
#> TCGA.DD.A3A0.01 1 0.2159 0.7249 0.90 0.00 0.00 0.00 0.02 0.06 0.02
#> TCGA.DD.AACM.01 1 0.1928 0.8006 0.90 0.00 0.00 0.00 0.08 0.00 0.02
#> TCGA.FV.A3I1.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SL.01 6 0.4003 0.5880 0.00 0.00 0.00 0.32 0.04 0.64 0.00
#> TCGA.DD.A11A.01 4 0.4244 0.5274 0.00 0.04 0.00 0.54 0.00 0.00 0.42
#> TCGA.DD.A3A2.01 1 0.2912 0.7249 0.82 0.00 0.00 0.00 0.14 0.04 0.00
#> TCGA.FV.A2QQ.01 5 0.2906 0.2295 0.02 0.00 0.00 0.00 0.80 0.00 0.18
#> TCGA.DD.AADP.01 5 0.3722 0.5760 0.02 0.00 0.00 0.18 0.76 0.00 0.04
#> TCGA.CC.5259.01 4 0.4244 0.5274 0.00 0.04 0.00 0.54 0.00 0.00 0.42
#> TCGA.ES.A2HS.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2V.A95S.01 5 0.2708 0.5631 0.00 0.00 0.00 0.22 0.78 0.00 0.00
#> TCGA.FV.A4ZP.01 2 0.1433 0.7751 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DD.AAD3.01 1 0.3680 0.6628 0.78 0.00 0.00 0.00 0.14 0.02 0.06
#> TCGA.DD.A39V.01 5 0.0504 0.5321 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AACS.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NK.01 1 0.3000 0.7544 0.84 0.00 0.00 0.00 0.10 0.04 0.02
#> TCGA.DD.A4NF.01 2 0.2745 0.7784 0.00 0.82 0.00 0.00 0.00 0.02 0.16
#> TCGA.DD.A3A8.01 2 0.4030 0.7183 0.00 0.72 0.00 0.00 0.00 0.12 0.16
#> TCGA.DD.A4NO.01 6 0.6661 0.1123 0.00 0.16 0.00 0.30 0.00 0.40 0.14
#> TCGA.ZS.A9CG.01 6 0.2829 0.7784 0.00 0.00 0.00 0.08 0.00 0.84 0.08
#> TCGA.CC.A123.01 1 0.4317 0.3867 0.58 0.00 0.00 0.00 0.02 0.38 0.02
#> TCGA.EP.A2KA.01 4 0.4331 0.6893 0.00 0.04 0.00 0.72 0.00 0.06 0.18
#> TCGA.DD.AAE7.01 4 0.1433 0.6898 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.KR.A7K0.01 1 0.1671 0.8010 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.DD.AACX.01 2 0.2745 0.7784 0.00 0.82 0.00 0.00 0.00 0.02 0.16
#> TCGA.DD.AAEK.01 1 0.1433 0.8117 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.G3.A5SM.01 4 0.2906 0.7112 0.00 0.00 0.00 0.80 0.02 0.00 0.18
#> TCGA.G3.AAV1.01 4 0.3244 0.7154 0.00 0.00 0.00 0.78 0.00 0.04 0.18
#> TCGA.FV.A4ZQ.01 6 0.1433 0.8024 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.WQ.AB4B.01 4 0.2745 0.6128 0.00 0.00 0.00 0.82 0.16 0.02 0.00
#> TCGA.BC.A10T.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MD.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADE.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GJ.A6C0.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69I.01 4 0.4604 0.6772 0.00 0.06 0.00 0.70 0.00 0.06 0.18
#> TCGA.K7.A6G5.01 1 0.1433 0.8117 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.DD.A4NG.01 5 0.2708 0.5631 0.00 0.00 0.00 0.22 0.78 0.00 0.00
#> TCGA.UB.A7MC.01 5 0.6021 -0.9148 0.18 0.00 0.00 0.00 0.40 0.04 0.38
#> TCGA.UB.AA0U.01 5 0.2213 0.5555 0.04 0.00 0.00 0.02 0.90 0.04 0.00
#> TCGA.DD.AACQ.01 7 0.6163 0.0000 0.18 0.00 0.02 0.00 0.38 0.02 0.40
#> TCGA.DD.A4NJ.01 3 0.0863 0.8975 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.FV.A496.01 2 0.4848 0.3846 0.00 0.50 0.00 0.10 0.00 0.00 0.40
#> TCGA.DD.AAE8.01 3 0.0504 0.9110 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DD.AAEH.01 4 0.3670 0.5691 0.00 0.00 0.00 0.76 0.10 0.14 0.00
#> TCGA.2Y.A9GW.01 4 0.3244 0.5875 0.00 0.00 0.00 0.78 0.04 0.18 0.00
#> TCGA.NI.A4U2.01 1 0.1433 0.8117 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.5C.AAPD.01 5 0.3517 -0.0905 0.02 0.00 0.00 0.00 0.70 0.00 0.28
#> TCGA.HP.A5N0.01 1 0.1433 0.8117 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.YA.A8S7.01 5 0.2376 0.5902 0.02 0.00 0.00 0.12 0.86 0.00 0.00
#> TCGA.DD.AACF.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV5.01 2 0.5282 0.1171 0.00 0.48 0.00 0.34 0.00 0.00 0.18
#> TCGA.G3.A5SK.01 4 0.2422 0.6143 0.00 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.DD.A3A7.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 3 0.4812 0.5135 0.02 0.00 0.66 0.00 0.14 0.00 0.18
#> TCGA.G3.AAV3.01 6 0.1433 0.8024 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.MI.A75H.01 4 0.1664 0.6984 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.BC.A10S.01 6 0.3047 0.6656 0.00 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.DD.A73F.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9D1.01 4 0.2572 0.7150 0.00 0.00 0.00 0.86 0.00 0.06 0.08
#> TCGA.DD.A73C.01 1 0.3984 0.5578 0.68 0.00 0.00 0.00 0.02 0.28 0.02
#> TCGA.DD.AADU.01 6 0.2829 0.7784 0.00 0.00 0.00 0.08 0.00 0.84 0.08
#> TCGA.UB.A7MB.01 1 0.3984 0.5578 0.68 0.00 0.00 0.00 0.02 0.28 0.02
#> TCGA.EP.A12J.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 6 0.1433 0.8024 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.DD.AAEI.01 5 0.1664 0.4643 0.02 0.00 0.00 0.00 0.92 0.00 0.06
#> TCGA.2Y.A9GV.01 1 0.1433 0.8117 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.DD.AADS.01 4 0.2569 0.6432 0.00 0.00 0.00 0.84 0.02 0.14 0.00
#> TCGA.DD.A39Z.01 5 0.4663 0.5545 0.02 0.00 0.00 0.20 0.70 0.04 0.04
#> TCGA.EP.A2KB.01 2 0.0000 0.8114 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEA.01 5 0.3689 0.5464 0.06 0.00 0.00 0.04 0.82 0.04 0.04
#> TCGA.FV.A3R2.01 5 0.4663 0.5545 0.02 0.00 0.00 0.20 0.70 0.04 0.04
#> TCGA.2Y.A9GY.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACZ.01 5 0.3927 -0.2364 0.04 0.00 0.00 0.00 0.66 0.00 0.30
#> TCGA.DD.AAED.01 6 0.2509 0.7547 0.06 0.00 0.00 0.04 0.00 0.88 0.02
#> TCGA.EP.A3JL.01 5 0.5477 -0.3957 0.34 0.00 0.00 0.00 0.52 0.04 0.10
#> TCGA.5R.AA1C.01 4 0.3745 0.4496 0.00 0.00 0.00 0.70 0.04 0.26 0.00
#> TCGA.G3.A3CK.01 4 0.3086 0.7147 0.00 0.00 0.00 0.80 0.00 0.04 0.16
#> TCGA.G3.A5SJ.01 3 0.0504 0.9110 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.5R.AAAM.01 6 0.3685 0.5958 0.00 0.00 0.00 0.32 0.02 0.66 0.00
#> TCGA.2Y.A9GS.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A3ER.01 6 0.5286 0.5341 0.00 0.06 0.00 0.22 0.00 0.62 0.10
#> TCGA.DD.AAVY.01 6 0.2509 0.7547 0.06 0.00 0.00 0.04 0.00 0.88 0.02
#> TCGA.DD.A1EG.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADN.01 5 0.3815 0.4027 0.00 0.00 0.00 0.36 0.62 0.00 0.02
#> TCGA.DD.AADB.01 5 0.3186 0.4020 0.22 0.00 0.00 0.00 0.76 0.00 0.02
#> TCGA.G3.A3CG.01 4 0.3902 0.7065 0.00 0.04 0.00 0.76 0.00 0.04 0.16
#> TCGA.DD.AAW1.01 2 0.6459 0.1759 0.00 0.40 0.00 0.34 0.00 0.10 0.16
#> TCGA.DD.A4NI.01 4 0.4092 0.6990 0.00 0.02 0.00 0.74 0.00 0.08 0.16
#> TCGA.2Y.A9GT.01 5 0.1006 0.5154 0.02 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.MI.A75I.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H1.01 5 0.3722 0.1830 0.02 0.00 0.00 0.00 0.76 0.04 0.18
#> TCGA.CC.A8HT.01 3 0.0000 0.9184 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADR.01 5 0.3864 0.5798 0.02 0.00 0.00 0.18 0.76 0.02 0.02
#> TCGA.2Y.A9HB.01 4 0.2912 0.6335 0.00 0.00 0.00 0.82 0.04 0.14 0.00
#> TCGA.DD.AACI.01 4 0.4737 0.6714 0.00 0.06 0.00 0.68 0.00 0.06 0.20
#> TCGA.CC.A5UD.01 2 0.5007 0.5390 0.00 0.56 0.00 0.00 0.00 0.28 0.16
#> TCGA.G3.AAV2.01 2 0.1886 0.7936 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.ZP.A9CY.01 3 0.4812 0.5135 0.02 0.00 0.66 0.00 0.14 0.00 0.18
#> TCGA.DD.A39Y.01 3 0.5635 0.0377 0.02 0.00 0.46 0.00 0.16 0.00 0.36
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FV.A495.01 3 0.1091 0.9313 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DD.A4NV.01 5 0.3002 0.6184 0.04 0.00 0.00 0.00 0.82 0.00 0.12 0.02
#> TCGA.ZP.A9CV.01 4 0.3337 0.6355 0.00 0.00 0.00 0.78 0.16 0.00 0.04 0.02
#> TCGA.DD.AACY.01 2 0.3454 0.7661 0.00 0.80 0.00 0.02 0.00 0.04 0.02 0.12
#> TCGA.CC.A3MB.01 8 0.3142 0.7467 0.00 0.00 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.ED.A459.01 6 0.2025 0.7808 0.00 0.00 0.00 0.10 0.00 0.88 0.02 0.00
#> TCGA.PD.A5DF.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 2 0.5158 0.5299 0.00 0.56 0.00 0.00 0.02 0.30 0.02 0.10
#> TCGA.DD.A3A0.01 1 0.3630 0.6786 0.78 0.00 0.00 0.00 0.00 0.04 0.10 0.08
#> TCGA.DD.AACM.01 1 0.2267 0.6439 0.82 0.00 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.FV.A3I1.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SL.01 6 0.7135 0.2751 0.02 0.00 0.00 0.30 0.16 0.36 0.12 0.04
#> TCGA.DD.A11A.01 8 0.3142 0.7467 0.00 0.00 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.DD.A3A2.01 1 0.3847 0.6408 0.78 0.00 0.00 0.00 0.10 0.02 0.04 0.06
#> TCGA.FV.A2QQ.01 7 0.3992 0.3547 0.04 0.00 0.00 0.00 0.44 0.00 0.52 0.00
#> TCGA.DD.AADP.01 5 0.3637 0.7039 0.02 0.00 0.00 0.06 0.80 0.00 0.08 0.04
#> TCGA.CC.5259.01 8 0.3142 0.7467 0.00 0.00 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.ES.A2HS.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2V.A95S.01 5 0.2025 0.7021 0.00 0.00 0.00 0.10 0.88 0.00 0.00 0.02
#> TCGA.FV.A4ZP.01 2 0.1563 0.7226 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DD.AAD3.01 1 0.2938 0.4776 0.70 0.00 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.DD.A39V.01 5 0.2569 0.6041 0.00 0.00 0.00 0.02 0.82 0.00 0.16 0.00
#> TCGA.DD.AACS.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NK.01 1 0.2224 0.6770 0.86 0.00 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.DD.A4NF.01 2 0.3454 0.7661 0.00 0.80 0.00 0.02 0.00 0.04 0.02 0.12
#> TCGA.DD.A3A8.01 2 0.4898 0.6470 0.00 0.64 0.00 0.02 0.00 0.20 0.02 0.12
#> TCGA.DD.A4NO.01 4 0.6582 -0.1897 0.00 0.14 0.00 0.38 0.00 0.34 0.04 0.10
#> TCGA.ZS.A9CG.01 6 0.2484 0.7793 0.00 0.00 0.00 0.10 0.02 0.86 0.00 0.02
#> TCGA.CC.A123.01 1 0.5599 0.4066 0.50 0.00 0.00 0.00 0.00 0.30 0.12 0.08
#> TCGA.EP.A2KA.01 4 0.2680 0.5627 0.00 0.02 0.00 0.84 0.00 0.00 0.02 0.12
#> TCGA.DD.AAE7.01 4 0.1275 0.7032 0.00 0.00 0.00 0.94 0.04 0.02 0.00 0.00
#> TCGA.KR.A7K0.01 1 0.3185 0.6826 0.82 0.00 0.00 0.00 0.06 0.00 0.08 0.04
#> TCGA.DD.AACX.01 2 0.3454 0.7661 0.00 0.80 0.00 0.02 0.00 0.04 0.02 0.12
#> TCGA.DD.AAEK.01 1 0.0000 0.7466 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 4 0.2404 0.6112 0.00 0.00 0.00 0.84 0.02 0.00 0.00 0.14
#> TCGA.G3.AAV1.01 4 0.2484 0.6481 0.00 0.00 0.00 0.86 0.02 0.02 0.00 0.10
#> TCGA.FV.A4ZQ.01 6 0.2350 0.7755 0.00 0.00 0.00 0.10 0.00 0.86 0.04 0.00
#> TCGA.WQ.AB4B.01 4 0.3337 0.6355 0.00 0.00 0.00 0.78 0.16 0.00 0.04 0.02
#> TCGA.BC.A10T.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39W.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MD.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADE.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GJ.A6C0.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A69I.01 4 0.3178 0.5019 0.00 0.04 0.00 0.80 0.00 0.00 0.02 0.14
#> TCGA.K7.A6G5.01 1 0.0000 0.7466 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 5 0.2680 0.6876 0.00 0.00 0.00 0.12 0.84 0.00 0.02 0.02
#> TCGA.UB.A7MC.01 7 0.4831 0.5500 0.16 0.00 0.00 0.00 0.08 0.02 0.68 0.06
#> TCGA.UB.AA0U.01 5 0.2947 0.7032 0.06 0.00 0.00 0.00 0.84 0.00 0.04 0.06
#> TCGA.DD.AACQ.01 7 0.4471 0.5736 0.16 0.00 0.00 0.00 0.10 0.02 0.70 0.02
#> TCGA.DD.A4NJ.01 3 0.2267 0.7660 0.00 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.FV.A496.01 8 0.3618 0.1849 0.00 0.38 0.00 0.02 0.00 0.00 0.00 0.60
#> TCGA.DD.AAE8.01 3 0.1091 0.9313 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DD.AAEH.01 4 0.4355 0.5972 0.00 0.00 0.00 0.72 0.16 0.04 0.06 0.02
#> TCGA.2Y.A9GW.01 4 0.3270 0.6778 0.00 0.00 0.00 0.80 0.12 0.06 0.02 0.00
#> TCGA.NI.A4U2.01 1 0.0000 0.7466 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.AAPD.01 7 0.3746 0.5149 0.04 0.00 0.00 0.00 0.32 0.00 0.64 0.00
#> TCGA.HP.A5N0.01 1 0.0000 0.7466 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YA.A8S7.01 5 0.2482 0.7049 0.06 0.00 0.00 0.02 0.88 0.00 0.02 0.02
#> TCGA.DD.AACF.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.AAV5.01 2 0.5131 -0.0365 0.00 0.50 0.00 0.34 0.00 0.00 0.02 0.14
#> TCGA.G3.A5SK.01 4 0.1887 0.7007 0.00 0.00 0.00 0.90 0.04 0.06 0.00 0.00
#> TCGA.DD.A3A7.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 7 0.3658 0.3837 0.00 0.00 0.40 0.00 0.02 0.00 0.58 0.00
#> TCGA.G3.AAV3.01 6 0.2025 0.7819 0.00 0.00 0.00 0.10 0.00 0.88 0.00 0.02
#> TCGA.MI.A75H.01 4 0.0808 0.7025 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.BC.A10S.01 6 0.4397 0.6072 0.00 0.00 0.00 0.24 0.04 0.66 0.06 0.00
#> TCGA.DD.A73F.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9D1.01 4 0.1408 0.6946 0.00 0.00 0.00 0.94 0.02 0.02 0.02 0.00
#> TCGA.DD.A73C.01 1 0.5325 0.4948 0.56 0.00 0.00 0.00 0.00 0.26 0.10 0.08
#> TCGA.DD.AADU.01 6 0.2940 0.7703 0.00 0.00 0.00 0.10 0.02 0.84 0.02 0.02
#> TCGA.UB.A7MB.01 1 0.5325 0.4948 0.56 0.00 0.00 0.00 0.00 0.26 0.10 0.08
#> TCGA.EP.A12J.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 6 0.2025 0.7819 0.00 0.00 0.00 0.10 0.00 0.88 0.00 0.02
#> TCGA.DD.AAEI.01 5 0.2888 0.5726 0.04 0.00 0.00 0.00 0.80 0.00 0.16 0.00
#> TCGA.2Y.A9GV.01 1 0.0000 0.7466 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADS.01 4 0.3262 0.6689 0.00 0.00 0.00 0.82 0.10 0.02 0.04 0.02
#> TCGA.DD.A39Z.01 5 0.5564 0.6098 0.02 0.00 0.00 0.10 0.64 0.02 0.12 0.10
#> TCGA.EP.A2KB.01 2 0.0000 0.8081 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEA.01 5 0.4134 0.6756 0.08 0.00 0.00 0.00 0.76 0.02 0.06 0.08
#> TCGA.FV.A3R2.01 5 0.5564 0.6098 0.02 0.00 0.00 0.10 0.64 0.02 0.12 0.10
#> TCGA.2Y.A9GY.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACZ.01 5 0.4770 -0.1256 0.02 0.00 0.00 0.00 0.52 0.02 0.40 0.04
#> TCGA.DD.AAED.01 6 0.3262 0.6959 0.00 0.00 0.00 0.04 0.02 0.82 0.10 0.02
#> TCGA.EP.A3JL.01 1 0.5381 -0.2433 0.42 0.00 0.00 0.00 0.18 0.00 0.38 0.02
#> TCGA.5R.AA1C.01 4 0.4647 0.6057 0.00 0.00 0.00 0.72 0.10 0.08 0.06 0.04
#> TCGA.G3.A3CK.01 4 0.1408 0.6744 0.00 0.00 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.G3.A5SJ.01 3 0.0471 0.9620 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.5R.AAAM.01 6 0.5943 0.3514 0.00 0.00 0.00 0.30 0.14 0.48 0.06 0.02
#> TCGA.2Y.A9GS.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BD.A3ER.01 6 0.5426 0.5413 0.00 0.10 0.00 0.16 0.00 0.62 0.02 0.10
#> TCGA.DD.AAVY.01 6 0.2591 0.7177 0.00 0.00 0.00 0.04 0.02 0.86 0.08 0.00
#> TCGA.DD.A1EG.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADN.01 5 0.3619 0.6322 0.00 0.00 0.00 0.14 0.74 0.00 0.00 0.12
#> TCGA.DD.AADB.01 5 0.4138 0.5989 0.16 0.00 0.00 0.00 0.72 0.00 0.04 0.08
#> TCGA.G3.A3CG.01 4 0.2020 0.6343 0.00 0.02 0.00 0.90 0.00 0.00 0.02 0.06
#> TCGA.DD.AAW1.01 4 0.5968 -0.0847 0.00 0.36 0.00 0.44 0.00 0.04 0.04 0.12
#> TCGA.DD.A4NI.01 4 0.2204 0.6613 0.00 0.02 0.00 0.90 0.00 0.04 0.02 0.02
#> TCGA.2Y.A9GT.01 5 0.3337 0.5633 0.04 0.00 0.00 0.00 0.78 0.00 0.16 0.02
#> TCGA.MI.A75I.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2Y.A9H1.01 7 0.4383 0.3694 0.04 0.00 0.00 0.00 0.42 0.00 0.52 0.02
#> TCGA.CC.A8HT.01 3 0.0000 0.9743 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AADR.01 5 0.3903 0.6961 0.02 0.00 0.00 0.06 0.78 0.00 0.06 0.08
#> TCGA.2Y.A9HB.01 4 0.3320 0.6650 0.00 0.00 0.00 0.80 0.12 0.04 0.04 0.00
#> TCGA.DD.AACI.01 4 0.3178 0.5019 0.00 0.04 0.00 0.80 0.00 0.00 0.02 0.14
#> TCGA.CC.A5UD.01 2 0.5322 0.3673 0.00 0.48 0.00 0.00 0.02 0.38 0.02 0.10
#> TCGA.G3.AAV2.01 2 0.3454 0.7661 0.00 0.80 0.00 0.02 0.00 0.04 0.02 0.12
#> TCGA.ZP.A9CY.01 7 0.3907 0.4315 0.00 0.00 0.38 0.00 0.04 0.00 0.58 0.00
#> TCGA.DD.A39Y.01 7 0.4727 0.6100 0.00 0.00 0.20 0.00 0.10 0.02 0.66 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: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.903 0.978 0.989 0.4302 0.576 0.576
#> 3 3 1.000 0.990 0.996 0.4001 0.684 0.509
#> 4 4 0.781 0.923 0.948 0.2133 0.749 0.448
#> 5 5 0.792 0.747 0.868 0.0734 0.956 0.835
#> 6 6 0.784 0.584 0.778 0.0292 0.938 0.737
#> 7 7 0.764 0.566 0.802 0.0191 0.961 0.804
#> 8 8 0.726 0.607 0.804 0.0217 0.929 0.637
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.FV.A495.01 2 0.584 0.848 0.14 0.86
#> TCGA.DD.A4NV.01 2 0.000 0.986 0.00 1.00
#> TCGA.PD.A5DF.01 1 0.000 0.994 1.00 0.00
#> TCGA.DD.AACM.01 2 0.000 0.986 0.00 1.00
#> TCGA.FV.A3I1.01 1 0.000 0.994 1.00 0.00
#> TCGA.DD.A3A2.01 2 0.000 0.986 0.00 1.00
#> TCGA.FV.A2QQ.01 2 0.529 0.871 0.12 0.88
#> TCGA.DD.AAD3.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.A39V.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.A4NK.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.AAEK.01 2 0.000 0.986 0.00 1.00
#> TCGA.BC.A10T.01 2 0.000 0.986 0.00 1.00
#> TCGA.UB.A7MD.01 2 0.000 0.986 0.00 1.00
#> TCGA.GJ.A6C0.01 1 0.000 0.994 1.00 0.00
#> TCGA.K7.A6G5.01 2 0.000 0.986 0.00 1.00
#> TCGA.UB.A7MC.01 2 0.000 0.986 0.00 1.00
#> TCGA.UB.AA0U.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.AACQ.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.A4NJ.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.AAE8.01 2 0.000 0.986 0.00 1.00
#> TCGA.NI.A4U2.01 2 0.000 0.986 0.00 1.00
#> TCGA.5C.AAPD.01 1 0.327 0.934 0.94 0.06
#> TCGA.HP.A5N0.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.A73A.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.A73F.01 2 0.529 0.871 0.12 0.88
#> TCGA.DD.AAEI.01 2 0.000 0.986 0.00 1.00
#> TCGA.2Y.A9GV.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.AAEA.01 2 0.000 0.986 0.00 1.00
#> TCGA.2Y.A9GY.01 1 0.000 0.994 1.00 0.00
#> TCGA.DD.AACZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.EP.A3JL.01 2 0.000 0.986 0.00 1.00
#> TCGA.G3.A5SJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.2Y.A9GS.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.A1EG.01 1 0.000 0.994 1.00 0.00
#> TCGA.DD.AADB.01 1 0.000 0.994 1.00 0.00
#> TCGA.2Y.A9GT.01 2 0.000 0.986 0.00 1.00
#> TCGA.MI.A75I.01 1 0.000 0.994 1.00 0.00
#> TCGA.2Y.A9H1.01 2 0.000 0.986 0.00 1.00
#> TCGA.CC.A8HT.01 1 0.000 0.994 1.00 0.00
#> TCGA.ZP.A9CY.01 2 0.000 0.986 0.00 1.00
#> TCGA.DD.A39Y.01 1 0.000 0.994 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FV.A495.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.DD.A4NV.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.PD.A5DF.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.DD.AACM.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.FV.A3I1.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.DD.A3A2.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.FV.A2QQ.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.DD.AAD3.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.A39V.01 1 0.1529 0.957 0.96 0.04 0
#> TCGA.DD.A4NK.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.AAEK.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.BC.A10T.01 2 0.0892 0.976 0.02 0.98 0
#> TCGA.UB.A7MD.01 1 0.1529 0.957 0.96 0.04 0
#> TCGA.GJ.A6C0.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.K7.A6G5.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.UB.A7MC.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.UB.AA0U.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.AACQ.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.A4NJ.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.AAE8.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.NI.A4U2.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.5C.AAPD.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.HP.A5N0.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.A73A.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.A73F.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.DD.AAEI.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.2Y.A9GV.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.AAEA.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.2Y.A9GY.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.DD.AACZ.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.EP.A3JL.01 1 0.1529 0.957 0.96 0.04 0
#> TCGA.G3.A5SJ.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.2Y.A9GS.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.DD.A1EG.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.DD.AADB.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.2Y.A9GT.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.MI.A75I.01 1 0.0000 0.985 1.00 0.00 0
#> TCGA.2Y.A9H1.01 1 0.1529 0.957 0.96 0.04 0
#> TCGA.CC.A8HT.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.ZP.A9CY.01 2 0.0000 0.999 0.00 1.00 0
#> TCGA.DD.A39Y.01 3 0.0000 1.000 0.00 0.00 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FV.A495.01 1 0.2647 0.894 0.88 0.00 0 0.12
#> TCGA.DD.A4NV.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.PD.A5DF.01 1 0.0000 0.912 1.00 0.00 0 0.00
#> TCGA.DD.AACM.01 4 0.2921 0.897 0.00 0.14 0 0.86
#> TCGA.FV.A3I1.01 1 0.1637 0.924 0.94 0.00 0 0.06
#> TCGA.DD.A3A2.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.FV.A2QQ.01 4 0.1211 0.879 0.04 0.00 0 0.96
#> TCGA.DD.AAD3.01 4 0.3610 0.847 0.00 0.20 0 0.80
#> TCGA.DD.A39V.01 4 0.0000 0.890 0.00 0.00 0 1.00
#> TCGA.DD.A4NK.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.DD.AAEK.01 4 0.2647 0.905 0.00 0.12 0 0.88
#> TCGA.BC.A10T.01 2 0.5077 0.727 0.08 0.76 0 0.16
#> TCGA.UB.A7MD.01 4 0.0707 0.881 0.02 0.00 0 0.98
#> TCGA.GJ.A6C0.01 1 0.0000 0.912 1.00 0.00 0 0.00
#> TCGA.K7.A6G5.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.UB.A7MC.01 4 0.2647 0.896 0.00 0.12 0 0.88
#> TCGA.UB.AA0U.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.DD.AACQ.01 4 0.2011 0.907 0.00 0.08 0 0.92
#> TCGA.DD.A4NJ.01 4 0.2921 0.897 0.00 0.14 0 0.86
#> TCGA.DD.AAE8.01 4 0.2345 0.908 0.00 0.10 0 0.90
#> TCGA.NI.A4U2.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.5C.AAPD.01 4 0.2921 0.801 0.14 0.00 0 0.86
#> TCGA.HP.A5N0.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.DD.A73A.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.DD.A73F.01 1 0.1211 0.904 0.96 0.00 0 0.04
#> TCGA.DD.AAEI.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.2Y.A9GV.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.DD.AAEA.01 4 0.3172 0.884 0.00 0.16 0 0.84
#> TCGA.2Y.A9GY.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.DD.AACZ.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EP.A3JL.01 4 0.0000 0.890 0.00 0.00 0 1.00
#> TCGA.G3.A5SJ.01 1 0.1637 0.924 0.94 0.00 0 0.06
#> TCGA.2Y.A9GS.01 1 0.4134 0.675 0.74 0.00 0 0.26
#> TCGA.DD.A1EG.01 1 0.1637 0.924 0.94 0.00 0 0.06
#> TCGA.DD.AADB.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.2Y.A9GT.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.MI.A75I.01 1 0.1211 0.924 0.96 0.00 0 0.04
#> TCGA.2Y.A9H1.01 4 0.0000 0.890 0.00 0.00 0 1.00
#> TCGA.CC.A8HT.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.ZP.A9CY.01 2 0.0000 0.980 0.00 1.00 0 0.00
#> TCGA.DD.A39Y.01 3 0.0000 1.000 0.00 0.00 1 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FV.A495.01 1 0.4748 0.518 0.66 0.00 0 0.04 0.30
#> TCGA.DD.A4NV.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.PD.A5DF.01 1 0.2280 0.781 0.88 0.00 0 0.00 0.12
#> TCGA.DD.AACM.01 4 0.0609 0.702 0.00 0.02 0 0.98 0.00
#> TCGA.FV.A3I1.01 1 0.2020 0.807 0.90 0.00 0 0.00 0.10
#> TCGA.DD.A3A2.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.FV.A2QQ.01 4 0.6344 0.155 0.16 0.00 0 0.44 0.40
#> TCGA.DD.AAD3.01 4 0.2020 0.648 0.00 0.10 0 0.90 0.00
#> TCGA.DD.A39V.01 4 0.4613 0.493 0.02 0.00 0 0.62 0.36
#> TCGA.DD.A4NK.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.DD.AAEK.01 4 0.0609 0.702 0.00 0.02 0 0.98 0.00
#> TCGA.BC.A10T.01 5 0.4263 0.600 0.00 0.18 0 0.06 0.76
#> TCGA.UB.A7MD.01 5 0.3852 0.500 0.02 0.00 0 0.22 0.76
#> TCGA.GJ.A6C0.01 1 0.2280 0.748 0.88 0.00 0 0.00 0.12
#> TCGA.K7.A6G5.01 2 0.0609 0.946 0.00 0.98 0 0.02 0.00
#> TCGA.UB.A7MC.01 4 0.5232 0.518 0.00 0.06 0 0.60 0.34
#> TCGA.UB.AA0U.01 2 0.3796 0.557 0.00 0.70 0 0.30 0.00
#> TCGA.DD.AACQ.01 4 0.2331 0.683 0.00 0.02 0 0.90 0.08
#> TCGA.DD.A4NJ.01 4 0.1648 0.702 0.00 0.02 0 0.94 0.04
#> TCGA.DD.AAE8.01 4 0.2012 0.699 0.00 0.02 0 0.92 0.06
#> TCGA.NI.A4U2.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.5C.AAPD.01 4 0.6184 0.265 0.14 0.00 0 0.48 0.38
#> TCGA.HP.A5N0.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.DD.A73A.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.DD.A73F.01 1 0.4726 0.382 0.58 0.00 0 0.02 0.40
#> TCGA.DD.AAEI.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.2Y.A9GV.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.DD.AAEA.01 4 0.1648 0.688 0.00 0.04 0 0.94 0.02
#> TCGA.2Y.A9GY.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DD.AACZ.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EP.A3JL.01 4 0.3796 0.564 0.00 0.00 0 0.70 0.30
#> TCGA.G3.A5SJ.01 1 0.2516 0.784 0.86 0.00 0 0.00 0.14
#> TCGA.2Y.A9GS.01 5 0.4876 0.470 0.22 0.00 0 0.08 0.70
#> TCGA.DD.A1EG.01 1 0.2020 0.807 0.90 0.00 0 0.00 0.10
#> TCGA.DD.AADB.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.2Y.A9GT.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.MI.A75I.01 1 0.0000 0.793 1.00 0.00 0 0.00 0.00
#> TCGA.2Y.A9H1.01 4 0.4675 0.453 0.02 0.00 0 0.60 0.38
#> TCGA.CC.A8HT.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.ZP.A9CY.01 2 0.0000 0.965 0.00 1.00 0 0.00 0.00
#> TCGA.DD.A39Y.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FV.A495.01 1 0.4247 0.3747 0.70 0.00 0.00 0.00 0.24 0.06
#> TCGA.DD.A4NV.01 2 0.0000 0.9332 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.PD.A5DF.01 1 0.5012 -0.0674 0.60 0.00 0.00 0.00 0.10 0.30
#> TCGA.DD.AACM.01 4 0.0547 0.7269 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.FV.A3I1.01 1 0.0547 0.6781 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.A3A2.01 2 0.0000 0.9332 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A2QQ.01 5 0.5963 0.3183 0.32 0.00 0.00 0.24 0.44 0.00
#> TCGA.DD.AAD3.01 4 0.0937 0.7189 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.DD.A39V.01 4 0.5110 -0.0257 0.08 0.00 0.00 0.48 0.44 0.00
#> TCGA.DD.A4NK.01 2 0.0000 0.9332 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 4 0.2020 0.7140 0.00 0.02 0.00 0.92 0.04 0.02
#> TCGA.BC.A10T.01 5 0.6086 -0.1543 0.00 0.20 0.00 0.02 0.52 0.26
#> TCGA.UB.A7MD.01 5 0.5580 0.3204 0.10 0.00 0.00 0.16 0.66 0.08
#> TCGA.GJ.A6C0.01 6 0.3797 -0.0207 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.K7.A6G5.01 2 0.1556 0.8720 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.UB.A7MC.01 4 0.5916 0.0733 0.00 0.06 0.00 0.44 0.44 0.06
#> TCGA.UB.AA0U.01 2 0.3864 0.1452 0.00 0.52 0.00 0.48 0.00 0.00
#> TCGA.DD.AACQ.01 4 0.2794 0.6608 0.00 0.00 0.00 0.86 0.06 0.08
#> TCGA.DD.A4NJ.01 4 0.1092 0.7229 0.00 0.02 0.00 0.96 0.02 0.00
#> TCGA.DD.AAE8.01 4 0.1480 0.7193 0.00 0.02 0.00 0.94 0.04 0.00
#> TCGA.NI.A4U2.01 2 0.0000 0.9332 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5C.AAPD.01 5 0.6070 0.2771 0.32 0.00 0.00 0.28 0.40 0.00
#> TCGA.HP.A5N0.01 2 0.0000 0.9332 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 2 0.0547 0.9230 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DD.A73F.01 6 0.6331 0.2312 0.24 0.00 0.00 0.02 0.28 0.46
#> TCGA.DD.AAEI.01 2 0.0547 0.9230 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.2Y.A9GV.01 2 0.0937 0.9082 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.DD.AAEA.01 4 0.1480 0.7178 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.2Y.A9GY.01 3 0.0000 0.9918 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AACZ.01 3 0.0000 0.9918 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A3JL.01 4 0.4873 0.0822 0.06 0.00 0.00 0.52 0.42 0.00
#> TCGA.G3.A5SJ.01 1 0.1865 0.6355 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.2Y.A9GS.01 5 0.6771 -0.2320 0.18 0.00 0.00 0.08 0.48 0.26
#> TCGA.DD.A1EG.01 1 0.0547 0.6802 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AADB.01 3 0.1092 0.9666 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.2Y.A9GT.01 2 0.0000 0.9332 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MI.A75I.01 1 0.2350 0.5931 0.88 0.00 0.02 0.00 0.00 0.10
#> TCGA.2Y.A9H1.01 5 0.5432 -0.0179 0.12 0.00 0.00 0.40 0.48 0.00
#> TCGA.CC.A8HT.01 3 0.0000 0.9918 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 2 0.0000 0.9332 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Y.01 3 0.0000 0.9918 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FV.A495.01 1 0.4809 0.3582 0.70 0.00 0.00 0.02 0.14 0.02 0.12
#> TCGA.DD.A4NV.01 2 0.0000 0.9270 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PD.A5DF.01 1 0.5535 -0.1855 0.54 0.00 0.00 0.00 0.12 0.30 0.04
#> TCGA.DD.AACM.01 4 0.1718 0.6765 0.00 0.04 0.00 0.92 0.00 0.00 0.04
#> TCGA.FV.A3I1.01 1 0.1166 0.4983 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.DD.A3A2.01 2 0.0000 0.9270 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A2QQ.01 1 0.6354 -0.7346 0.38 0.00 0.00 0.22 0.06 0.00 0.34
#> TCGA.DD.AAD3.01 4 0.1928 0.6671 0.00 0.08 0.00 0.90 0.00 0.02 0.00
#> TCGA.DD.A39V.01 7 0.6166 0.7982 0.26 0.00 0.00 0.28 0.04 0.00 0.42
#> TCGA.DD.A4NK.01 2 0.0000 0.9270 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 4 0.1671 0.6228 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.BC.A10T.01 5 0.2769 0.4656 0.00 0.08 0.00 0.00 0.86 0.02 0.04
#> TCGA.UB.A7MD.01 5 0.7008 -0.1881 0.10 0.00 0.00 0.16 0.44 0.04 0.26
#> TCGA.GJ.A6C0.01 6 0.2945 0.0000 0.26 0.00 0.00 0.00 0.00 0.74 0.00
#> TCGA.K7.A6G5.01 2 0.1928 0.8661 0.00 0.90 0.00 0.08 0.00 0.02 0.00
#> TCGA.UB.A7MC.01 4 0.6459 0.0689 0.00 0.04 0.00 0.44 0.10 0.06 0.36
#> TCGA.UB.AA0U.01 2 0.3909 0.2897 0.00 0.58 0.00 0.40 0.00 0.02 0.00
#> TCGA.DD.AACQ.01 4 0.5058 0.4453 0.00 0.00 0.00 0.62 0.06 0.06 0.26
#> TCGA.DD.A4NJ.01 4 0.3887 0.6552 0.00 0.06 0.00 0.80 0.04 0.02 0.08
#> TCGA.DD.AAE8.01 4 0.4357 0.6230 0.00 0.04 0.00 0.76 0.08 0.02 0.10
#> TCGA.NI.A4U2.01 2 0.0000 0.9270 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.AAPD.01 7 0.5890 0.7101 0.28 0.00 0.00 0.26 0.00 0.02 0.44
#> TCGA.HP.A5N0.01 2 0.0000 0.9270 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 2 0.1860 0.8936 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.DD.A73F.01 5 0.6063 0.0596 0.24 0.00 0.00 0.00 0.50 0.20 0.06
#> TCGA.DD.AAEI.01 2 0.2652 0.8661 0.00 0.88 0.00 0.02 0.02 0.02 0.06
#> TCGA.2Y.A9GV.01 2 0.0000 0.9270 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEA.01 4 0.1363 0.6767 0.00 0.04 0.00 0.94 0.00 0.02 0.00
#> TCGA.2Y.A9GY.01 3 0.0000 0.9527 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACZ.01 3 0.0000 0.9527 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A3JL.01 4 0.5173 -0.5624 0.16 0.00 0.00 0.50 0.00 0.00 0.34
#> TCGA.G3.A5SJ.01 1 0.0504 0.5309 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.2Y.A9GS.01 5 0.2572 0.4995 0.06 0.00 0.00 0.00 0.86 0.00 0.08
#> TCGA.DD.A1EG.01 1 0.0504 0.5322 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AADB.01 3 0.3263 0.8164 0.00 0.00 0.80 0.00 0.00 0.08 0.12
#> TCGA.2Y.A9GT.01 2 0.1006 0.9135 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.MI.A75I.01 1 0.3086 0.3108 0.80 0.00 0.00 0.00 0.04 0.16 0.00
#> TCGA.2Y.A9H1.01 7 0.6677 0.7442 0.20 0.00 0.00 0.28 0.12 0.00 0.40
#> TCGA.CC.A8HT.01 3 0.0000 0.9527 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 2 0.0000 0.9270 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A39Y.01 3 0.0504 0.9465 0.00 0.00 0.98 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FV.A495.01 1 0.4325 0.28565 0.56 0.00 0.00 0.02 0.04 0.00 0.38 0.00
#> TCGA.DD.A4NV.01 2 0.0000 0.92305 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PD.A5DF.01 1 0.4862 0.12428 0.60 0.00 0.00 0.02 0.16 0.22 0.00 0.00
#> TCGA.DD.AACM.01 4 0.1741 0.64493 0.00 0.00 0.00 0.92 0.02 0.00 0.04 0.02
#> TCGA.FV.A3I1.01 1 0.0808 0.61446 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DD.A3A2.01 2 0.0000 0.92305 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FV.A2QQ.01 7 0.3729 0.58965 0.18 0.00 0.00 0.10 0.00 0.00 0.72 0.00
#> TCGA.DD.AAD3.01 4 0.2680 0.56243 0.00 0.12 0.00 0.84 0.00 0.00 0.02 0.02
#> TCGA.DD.A39V.01 7 0.3178 0.58715 0.04 0.00 0.00 0.14 0.02 0.00 0.80 0.00
#> TCGA.DD.A4NK.01 2 0.0000 0.92305 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEK.01 4 0.1765 0.61704 0.00 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.BC.A10T.01 5 0.1874 0.56631 0.00 0.02 0.00 0.02 0.92 0.00 0.02 0.02
#> TCGA.UB.A7MD.01 7 0.5264 0.12273 0.06 0.00 0.00 0.08 0.40 0.00 0.46 0.00
#> TCGA.GJ.A6C0.01 6 0.2756 0.00000 0.26 0.00 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.K7.A6G5.01 2 0.2650 0.65606 0.00 0.76 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.UB.A7MC.01 8 0.7423 0.22700 0.00 0.18 0.00 0.16 0.10 0.00 0.26 0.30
#> TCGA.UB.AA0U.01 4 0.4137 -0.00603 0.00 0.46 0.00 0.50 0.00 0.00 0.02 0.02
#> TCGA.DD.AACQ.01 8 0.4559 0.28457 0.00 0.00 0.00 0.30 0.02 0.00 0.08 0.60
#> TCGA.DD.A4NJ.01 4 0.1804 0.64950 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.DD.AAE8.01 4 0.2407 0.62987 0.00 0.00 0.00 0.86 0.06 0.00 0.08 0.00
#> TCGA.NI.A4U2.01 2 0.0000 0.92305 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5C.AAPD.01 7 0.6497 0.24781 0.04 0.00 0.00 0.16 0.02 0.08 0.52 0.18
#> TCGA.HP.A5N0.01 2 0.0000 0.92305 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A73A.01 2 0.2864 0.82684 0.00 0.84 0.00 0.06 0.08 0.00 0.00 0.02
#> TCGA.DD.A73F.01 5 0.5999 0.23647 0.30 0.00 0.00 0.02 0.50 0.12 0.04 0.02
#> TCGA.DD.AAEI.01 2 0.3452 0.80386 0.00 0.82 0.00 0.06 0.04 0.00 0.04 0.04
#> TCGA.2Y.A9GV.01 2 0.0808 0.90276 0.00 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEA.01 4 0.3817 0.47452 0.00 0.04 0.00 0.76 0.00 0.00 0.08 0.12
#> TCGA.2Y.A9GY.01 3 0.0000 0.92784 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AACZ.01 3 0.0471 0.92685 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EP.A3JL.01 7 0.3570 0.46183 0.00 0.00 0.00 0.36 0.00 0.00 0.62 0.02
#> TCGA.G3.A5SJ.01 1 0.3589 0.57431 0.74 0.00 0.00 0.00 0.00 0.10 0.16 0.00
#> TCGA.2Y.A9GS.01 5 0.3894 0.59535 0.06 0.00 0.00 0.10 0.76 0.00 0.08 0.00
#> TCGA.DD.A1EG.01 1 0.2350 0.61542 0.86 0.00 0.00 0.00 0.00 0.04 0.10 0.00
#> TCGA.DD.AADB.01 3 0.4061 0.73409 0.00 0.00 0.72 0.00 0.00 0.12 0.02 0.14
#> TCGA.2Y.A9GT.01 2 0.0941 0.91001 0.00 0.96 0.00 0.02 0.02 0.00 0.00 0.00
#> TCGA.MI.A75I.01 1 0.2350 0.48089 0.86 0.00 0.00 0.00 0.00 0.10 0.00 0.04
#> TCGA.2Y.A9H1.01 7 0.3619 0.61602 0.12 0.00 0.00 0.14 0.00 0.00 0.74 0.00
#> TCGA.CC.A8HT.01 3 0.0000 0.92784 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZP.A9CY.01 2 0.0471 0.91757 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DD.A39Y.01 3 0.0941 0.92100 0.00 0.00 0.96 0.00 0.00 0.00 0.02 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: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0213-leaf , Node0221 , Node0222 , Node0223-leaf , Node0231 , Node0232-leaf , Node0233-leaf , Node0241 , Node0242 , Node0243 , Node0251-leaf , Node0252-leaf , Node0321-leaf , Node0322-leaf , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0424-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 67 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 0.938 0.955 0.977 0.5007 0.493 0.493
#> 3 3 0.811 0.887 0.941 0.2988 0.640 0.401
#> 4 4 0.977 0.958 0.980 0.1658 0.848 0.591
#> 5 5 0.786 0.837 0.897 0.0583 0.877 0.562
#> 6 6 0.759 0.702 0.771 0.0384 0.962 0.808
#> 7 7 0.798 0.796 0.863 0.0277 0.937 0.646
#> 8 8 0.797 0.752 0.834 0.0135 0.991 0.939
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.ZP.A9CV.01 1 0.327 0.916 0.94 0.06
#> TCGA.DD.AACY.01 2 0.000 0.999 0.00 1.00
#> TCGA.CC.A3MB.01 2 0.000 0.999 0.00 1.00
#> TCGA.ED.A459.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAVX.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.A3A0.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.A5SL.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.A11A.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AADP.01 2 0.000 0.999 0.00 1.00
#> TCGA.CC.5259.01 2 0.000 0.999 0.00 1.00
#> TCGA.ES.A2HS.01 1 0.000 0.950 1.00 0.00
#> TCGA.2V.A95S.01 2 0.000 0.999 0.00 1.00
#> TCGA.FV.A4ZP.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AACS.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.A4NF.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.A3A8.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.A4NO.01 2 0.000 0.999 0.00 1.00
#> TCGA.ZS.A9CG.01 1 0.000 0.950 1.00 0.00
#> TCGA.CC.A123.01 2 0.000 0.999 0.00 1.00
#> TCGA.EP.A2KA.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAE7.01 1 0.760 0.762 0.78 0.22
#> TCGA.KR.A7K0.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.AACX.01 1 0.000 0.950 1.00 0.00
#> TCGA.G3.A5SM.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.AAV1.01 2 0.000 0.999 0.00 1.00
#> TCGA.FV.A4ZQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.WQ.AB4B.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.A39W.01 2 0.242 0.955 0.04 0.96
#> TCGA.DD.AADE.01 1 0.000 0.950 1.00 0.00
#> TCGA.BC.A69I.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.A4NG.01 1 0.141 0.941 0.98 0.02
#> TCGA.FV.A496.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAEH.01 1 0.000 0.950 1.00 0.00
#> TCGA.2Y.A9GW.01 2 0.000 0.999 0.00 1.00
#> TCGA.YA.A8S7.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AACF.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.AAV5.01 1 0.000 0.950 1.00 0.00
#> TCGA.G3.A5SK.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.A3A7.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.AAV3.01 2 0.000 0.999 0.00 1.00
#> TCGA.MI.A75H.01 1 0.000 0.950 1.00 0.00
#> TCGA.BC.A10S.01 1 0.000 0.950 1.00 0.00
#> TCGA.ZP.A9D1.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.A73C.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AADU.01 1 0.000 0.950 1.00 0.00
#> TCGA.UB.A7MB.01 2 0.000 0.999 0.00 1.00
#> TCGA.EP.A12J.01 1 0.000 0.950 1.00 0.00
#> TCGA.ZS.A9CD.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AADS.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.A39Z.01 1 0.827 0.710 0.74 0.26
#> TCGA.EP.A2KB.01 2 0.000 0.999 0.00 1.00
#> TCGA.FV.A3R2.01 1 0.469 0.885 0.90 0.10
#> TCGA.DD.AAED.01 2 0.000 0.999 0.00 1.00
#> TCGA.5R.AA1C.01 1 0.000 0.950 1.00 0.00
#> TCGA.G3.A3CK.01 1 0.000 0.950 1.00 0.00
#> TCGA.5R.AAAM.01 1 0.327 0.916 0.94 0.06
#> TCGA.BD.A3ER.01 2 0.000 0.999 0.00 1.00
#> TCGA.DD.AAVY.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.AADN.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.A3CG.01 1 0.827 0.710 0.74 0.26
#> TCGA.DD.AAW1.01 1 0.000 0.950 1.00 0.00
#> TCGA.DD.A4NI.01 1 0.141 0.941 0.98 0.02
#> TCGA.DD.AADR.01 1 0.827 0.710 0.74 0.26
#> TCGA.2Y.A9HB.01 1 0.827 0.710 0.74 0.26
#> TCGA.DD.AACI.01 2 0.000 0.999 0.00 1.00
#> TCGA.CC.A5UD.01 2 0.000 0.999 0.00 1.00
#> TCGA.G3.AAV2.01 1 0.000 0.950 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.ZP.A9CV.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.AACY.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.CC.A3MB.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.ED.A459.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.DD.AAVX.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.DD.A3A0.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.G3.A5SL.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.DD.A11A.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.DD.AADP.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.CC.5259.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.ES.A2HS.01 1 0.628 0.0957 0.54 0.00 0.46
#> TCGA.2V.A95S.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.FV.A4ZP.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.DD.AACS.01 3 0.540 0.7334 0.00 0.28 0.72
#> TCGA.DD.A4NF.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.DD.A3A8.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.DD.A4NO.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.ZS.A9CG.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.CC.A123.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.EP.A2KA.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.AAE7.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.KR.A7K0.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.DD.AACX.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.G3.A5SM.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.G3.AAV1.01 3 0.613 0.5340 0.00 0.40 0.60
#> TCGA.FV.A4ZQ.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.WQ.AB4B.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.A39W.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.DD.AADE.01 1 0.502 0.6523 0.76 0.00 0.24
#> TCGA.BC.A69I.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.DD.A4NG.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.FV.A496.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.DD.AAEH.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.2Y.A9GW.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.YA.A8S7.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.DD.AACF.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.G3.AAV5.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.G3.A5SK.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.A3A7.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.G3.AAV3.01 3 0.624 0.4423 0.00 0.44 0.56
#> TCGA.MI.A75H.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.BC.A10S.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.ZP.A9D1.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.A73C.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.DD.AADU.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.UB.A7MB.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.EP.A12J.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.ZS.A9CD.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.DD.AADS.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.A39Z.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.EP.A2KB.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.FV.A3R2.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.AAED.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.5R.AA1C.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.G3.A3CK.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.5R.AAAM.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.BD.A3ER.01 3 0.502 0.7799 0.00 0.24 0.76
#> TCGA.DD.AAVY.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.DD.AADN.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.G3.A3CG.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.AAW1.01 1 0.000 0.9524 1.00 0.00 0.00
#> TCGA.DD.A4NI.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.AADR.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.2Y.A9HB.01 3 0.000 0.8804 0.00 0.00 1.00
#> TCGA.DD.AACI.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.CC.A5UD.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.G3.AAV2.01 1 0.000 0.9524 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.ZP.A9CV.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.DD.AACY.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.CC.A3MB.01 2 0.0707 0.987 0.00 0.98 0.02 0.00
#> TCGA.ED.A459.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.DD.AAVX.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.DD.A3A0.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.G3.A5SL.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 2 0.0707 0.987 0.00 0.98 0.02 0.00
#> TCGA.DD.AADP.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.CC.5259.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.ES.A2HS.01 3 0.0707 0.970 0.00 0.00 0.98 0.02
#> TCGA.2V.A95S.01 4 0.3606 0.817 0.00 0.14 0.02 0.84
#> TCGA.FV.A4ZP.01 2 0.0707 0.987 0.00 0.98 0.02 0.00
#> TCGA.DD.AACS.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.DD.A4NF.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.DD.A3A8.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NO.01 3 0.0707 0.963 0.00 0.02 0.98 0.00
#> TCGA.ZS.A9CG.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.CC.A123.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EP.A2KA.01 4 0.0707 0.967 0.00 0.00 0.02 0.98
#> TCGA.DD.AAE7.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.KR.A7K0.01 1 0.4948 0.248 0.56 0.00 0.44 0.00
#> TCGA.DD.AACX.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 3 0.2830 0.910 0.00 0.04 0.90 0.06
#> TCGA.G3.AAV1.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.FV.A4ZQ.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.DD.A39W.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.DD.AADE.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.BC.A69I.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.FV.A496.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.DD.AAEH.01 3 0.0707 0.970 0.00 0.00 0.98 0.02
#> TCGA.2Y.A9GW.01 3 0.2830 0.910 0.00 0.04 0.90 0.06
#> TCGA.YA.A8S7.01 2 0.0707 0.987 0.00 0.98 0.02 0.00
#> TCGA.DD.AACF.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.G3.AAV5.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.G3.A5SK.01 3 0.0707 0.970 0.00 0.00 0.98 0.02
#> TCGA.DD.A3A7.01 2 0.0707 0.987 0.00 0.98 0.02 0.00
#> TCGA.G3.AAV3.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.MI.A75H.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.BC.A10S.01 3 0.0707 0.970 0.00 0.00 0.98 0.02
#> TCGA.ZP.A9D1.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.DD.A73C.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.DD.AADU.01 1 0.2011 0.900 0.92 0.00 0.08 0.00
#> TCGA.UB.A7MB.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EP.A12J.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.ZS.A9CD.01 3 0.0000 0.975 0.00 0.00 1.00 0.00
#> TCGA.DD.AADS.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.DD.A39Z.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.EP.A2KB.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.FV.A3R2.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.DD.AAED.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.5R.AA1C.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 3 0.0707 0.970 0.00 0.00 0.98 0.02
#> TCGA.BD.A3ER.01 3 0.2830 0.910 0.00 0.04 0.90 0.06
#> TCGA.DD.AAVY.01 1 0.2011 0.900 0.92 0.00 0.08 0.00
#> TCGA.DD.AADN.01 2 0.0707 0.987 0.00 0.98 0.02 0.00
#> TCGA.G3.A3CG.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.DD.AAW1.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 3 0.0707 0.970 0.00 0.00 0.98 0.02
#> TCGA.DD.AADR.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.2Y.A9HB.01 4 0.0000 0.987 0.00 0.00 0.00 1.00
#> TCGA.DD.AACI.01 2 0.0707 0.987 0.00 0.98 0.02 0.00
#> TCGA.CC.A5UD.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.G3.AAV2.01 1 0.0000 0.958 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.ZP.A9CV.01 4 0.0000 0.91688 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACY.01 4 0.2516 0.82797 0.00 0.00 0.00 0.86 0.14
#> TCGA.CC.A3MB.01 5 0.3109 0.83959 0.00 0.20 0.00 0.00 0.80
#> TCGA.ED.A459.01 2 0.0000 0.97822 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 3 0.0609 0.80779 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.A3A0.01 2 0.0609 0.96156 0.00 0.98 0.02 0.00 0.00
#> TCGA.G3.A5SL.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 5 0.2929 0.86012 0.00 0.18 0.00 0.00 0.82
#> TCGA.DD.AADP.01 4 0.3274 0.73860 0.00 0.00 0.00 0.78 0.22
#> TCGA.CC.5259.01 2 0.1410 0.92088 0.00 0.94 0.00 0.00 0.06
#> TCGA.ES.A2HS.01 3 0.3110 0.79664 0.00 0.00 0.86 0.08 0.06
#> TCGA.2V.A95S.01 5 0.3291 0.81067 0.00 0.04 0.00 0.12 0.84
#> TCGA.FV.A4ZP.01 5 0.2929 0.86012 0.00 0.18 0.00 0.00 0.82
#> TCGA.DD.AACS.01 3 0.1043 0.79796 0.00 0.00 0.96 0.00 0.04
#> TCGA.DD.A4NF.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A8.01 1 0.2020 0.93598 0.90 0.00 0.00 0.00 0.10
#> TCGA.DD.A4NO.01 3 0.4726 0.18250 0.00 0.00 0.58 0.02 0.40
#> TCGA.ZS.A9CG.01 1 0.2020 0.93598 0.90 0.00 0.00 0.00 0.10
#> TCGA.CC.A123.01 2 0.0000 0.97822 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A2KA.01 5 0.2929 0.74057 0.00 0.00 0.00 0.18 0.82
#> TCGA.DD.AAE7.01 4 0.1410 0.87981 0.00 0.00 0.00 0.94 0.06
#> TCGA.KR.A7K0.01 3 0.5326 0.74905 0.10 0.00 0.74 0.08 0.08
#> TCGA.DD.AACX.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 5 0.3106 0.79950 0.00 0.00 0.14 0.02 0.84
#> TCGA.G3.AAV1.01 3 0.0609 0.80779 0.00 0.00 0.98 0.00 0.02
#> TCGA.FV.A4ZQ.01 2 0.0000 0.97822 0.00 1.00 0.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.2929 0.79409 0.00 0.00 0.00 0.82 0.18
#> TCGA.DD.A39W.01 3 0.0000 0.81082 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADE.01 3 0.1043 0.80072 0.00 0.00 0.96 0.00 0.04
#> TCGA.BC.A69I.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.0000 0.91688 0.00 0.00 0.00 1.00 0.00
#> TCGA.FV.A496.01 2 0.0000 0.97822 0.00 1.00 0.00 0.00 0.00
#> TCGA.DD.AAEH.01 3 0.4588 0.71409 0.00 0.00 0.72 0.22 0.06
#> TCGA.2Y.A9GW.01 5 0.3999 0.69206 0.00 0.00 0.24 0.02 0.74
#> TCGA.YA.A8S7.01 5 0.2732 0.87060 0.00 0.16 0.00 0.00 0.84
#> TCGA.DD.AACF.01 3 0.1732 0.77675 0.00 0.00 0.92 0.00 0.08
#> TCGA.G3.AAV5.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SK.01 3 0.4075 0.76928 0.00 0.00 0.78 0.16 0.06
#> TCGA.DD.A3A7.01 5 0.2732 0.87060 0.00 0.16 0.00 0.00 0.84
#> TCGA.G3.AAV3.01 3 0.0000 0.81082 0.00 0.00 1.00 0.00 0.00
#> TCGA.MI.A75H.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.01 3 0.4075 0.76928 0.00 0.00 0.78 0.16 0.06
#> TCGA.ZP.A9D1.01 4 0.2929 0.79409 0.00 0.00 0.00 0.82 0.18
#> TCGA.DD.A73C.01 3 0.0000 0.81082 0.00 0.00 1.00 0.00 0.00
#> TCGA.DD.AADU.01 3 0.5895 -0.00459 0.44 0.00 0.46 0.00 0.10
#> TCGA.UB.A7MB.01 2 0.0000 0.97822 0.00 1.00 0.00 0.00 0.00
#> TCGA.EP.A12J.01 1 0.2020 0.93598 0.90 0.00 0.00 0.00 0.10
#> TCGA.ZS.A9CD.01 3 0.0609 0.80779 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AADS.01 4 0.1410 0.87981 0.00 0.00 0.00 0.94 0.06
#> TCGA.DD.A39Z.01 4 0.0000 0.91688 0.00 0.00 0.00 1.00 0.00
#> TCGA.EP.A2KB.01 2 0.0000 0.97822 0.00 1.00 0.00 0.00 0.00
#> TCGA.FV.A3R2.01 4 0.0000 0.91688 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAED.01 2 0.0000 0.97822 0.00 1.00 0.00 0.00 0.00
#> TCGA.5R.AA1C.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 3 0.4075 0.76928 0.00 0.00 0.78 0.16 0.06
#> TCGA.BD.A3ER.01 5 0.3999 0.69206 0.00 0.00 0.24 0.02 0.74
#> TCGA.DD.AAVY.01 3 0.5884 0.06944 0.42 0.00 0.48 0.00 0.10
#> TCGA.DD.AADN.01 5 0.2732 0.87060 0.00 0.16 0.00 0.00 0.84
#> TCGA.G3.A3CG.01 4 0.0000 0.91688 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AAW1.01 1 0.0000 0.97222 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 3 0.4075 0.76928 0.00 0.00 0.78 0.16 0.06
#> TCGA.DD.AADR.01 4 0.0000 0.91688 0.00 0.00 0.00 1.00 0.00
#> TCGA.2Y.A9HB.01 4 0.0000 0.91688 0.00 0.00 0.00 1.00 0.00
#> TCGA.DD.AACI.01 5 0.2732 0.87060 0.00 0.16 0.00 0.00 0.84
#> TCGA.CC.A5UD.01 2 0.1732 0.89833 0.00 0.92 0.08 0.00 0.00
#> TCGA.G3.AAV2.01 1 0.2020 0.93598 0.90 0.00 0.00 0.00 0.10
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.ZP.A9CV.01 4 0.1556 0.8142 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.DD.AACY.01 4 0.1267 0.7878 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.CC.A3MB.01 5 0.2631 0.7516 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.ED.A459.01 2 0.0547 0.9095 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DD.AAVX.01 3 0.3499 0.5952 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.DD.A3A0.01 2 0.2350 0.8344 0.00 0.88 0.10 0.00 0.02 0.00
#> TCGA.G3.A5SL.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 5 0.2981 0.7712 0.00 0.16 0.02 0.00 0.82 0.00
#> TCGA.DD.AADP.01 4 0.3679 0.6094 0.00 0.00 0.04 0.76 0.20 0.00
#> TCGA.CC.5259.01 2 0.2941 0.6706 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.ES.A2HS.01 6 0.2794 0.8419 0.00 0.00 0.08 0.06 0.00 0.86
#> TCGA.2V.A95S.01 5 0.3688 0.7367 0.00 0.04 0.02 0.14 0.80 0.00
#> TCGA.FV.A4ZP.01 5 0.2454 0.7692 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.DD.AACS.01 3 0.4764 0.5408 0.00 0.00 0.54 0.02 0.02 0.42
#> TCGA.DD.A4NF.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A8.01 1 0.5835 0.6897 0.64 0.00 0.14 0.00 0.10 0.12
#> TCGA.DD.A4NO.01 3 0.6807 0.3501 0.00 0.00 0.42 0.06 0.20 0.32
#> TCGA.ZS.A9CG.01 1 0.6610 0.6093 0.54 0.00 0.20 0.00 0.14 0.12
#> TCGA.CC.A123.01 2 0.0000 0.9149 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KA.01 5 0.3315 0.6760 0.00 0.00 0.02 0.20 0.78 0.00
#> TCGA.DD.AAE7.01 4 0.3706 0.3927 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.KR.A7K0.01 6 0.3600 0.7584 0.02 0.00 0.08 0.08 0.00 0.82
#> TCGA.DD.AACX.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 5 0.4495 0.6485 0.00 0.00 0.20 0.06 0.72 0.02
#> TCGA.G3.AAV1.01 3 0.3309 0.5946 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.FV.A4ZQ.01 2 0.0000 0.9149 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.2981 0.6889 0.00 0.00 0.02 0.82 0.16 0.00
#> TCGA.DD.A39W.01 3 0.3409 0.5857 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.DD.AADE.01 3 0.5195 0.3569 0.00 0.00 0.54 0.00 0.10 0.36
#> TCGA.BC.A69I.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.1267 0.8197 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.FV.A496.01 2 0.0000 0.9149 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEH.01 6 0.2454 0.8710 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.2Y.A9GW.01 5 0.6807 0.0994 0.00 0.00 0.32 0.06 0.42 0.20
#> TCGA.YA.A8S7.01 5 0.3846 0.7614 0.00 0.08 0.10 0.02 0.80 0.00
#> TCGA.DD.AACF.01 3 0.5020 0.5349 0.00 0.00 0.56 0.02 0.04 0.38
#> TCGA.G3.AAV5.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SK.01 6 0.2048 0.9140 0.00 0.00 0.00 0.12 0.00 0.88
#> TCGA.DD.A3A7.01 5 0.2790 0.7760 0.00 0.14 0.00 0.02 0.84 0.00
#> TCGA.G3.AAV3.01 3 0.3409 0.5987 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.MI.A75H.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.01 6 0.2048 0.9140 0.00 0.00 0.00 0.12 0.00 0.88
#> TCGA.ZP.A9D1.01 4 0.2981 0.6889 0.00 0.00 0.02 0.82 0.16 0.00
#> TCGA.DD.A73C.01 3 0.4328 0.5122 0.00 0.00 0.52 0.00 0.02 0.46
#> TCGA.DD.AADU.01 3 0.7333 -0.1230 0.20 0.00 0.40 0.00 0.14 0.26
#> TCGA.UB.A7MB.01 2 0.1092 0.8997 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.EP.A12J.01 1 0.5615 0.7024 0.66 0.00 0.14 0.00 0.08 0.12
#> TCGA.ZS.A9CD.01 3 0.4764 0.5408 0.00 0.00 0.54 0.02 0.02 0.42
#> TCGA.DD.AADS.01 4 0.3578 0.4900 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.DD.A39Z.01 4 0.0547 0.8202 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EP.A2KB.01 2 0.0547 0.9056 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.FV.A3R2.01 4 0.1814 0.8052 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.DD.AAED.01 2 0.0000 0.9149 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1C.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 6 0.2048 0.9140 0.00 0.00 0.00 0.12 0.00 0.88
#> TCGA.BD.A3ER.01 5 0.6900 -0.0254 0.00 0.00 0.34 0.06 0.38 0.22
#> TCGA.DD.AAVY.01 3 0.7143 -0.0668 0.16 0.00 0.44 0.00 0.14 0.26
#> TCGA.DD.AADN.01 5 0.2454 0.7692 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.G3.A3CG.01 4 0.0547 0.8202 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DD.AAW1.01 1 0.0000 0.8748 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 6 0.2474 0.8794 0.00 0.00 0.04 0.08 0.00 0.88
#> TCGA.DD.AADR.01 4 0.1267 0.8197 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.2Y.A9HB.01 4 0.1814 0.8052 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.DD.AACI.01 5 0.3318 0.7752 0.00 0.14 0.02 0.02 0.82 0.00
#> TCGA.CC.A5UD.01 2 0.3076 0.7118 0.00 0.76 0.24 0.00 0.00 0.00
#> TCGA.G3.AAV2.01 1 0.6610 0.6093 0.54 0.00 0.20 0.00 0.14 0.12
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.ZP.A9CV.01 4 0.1928 0.862 0.00 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.DD.AACY.01 4 0.0863 0.856 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.CC.A3MB.01 5 0.0504 0.892 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.ED.A459.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAVX.01 3 0.1886 0.798 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.DD.A3A0.01 2 0.2654 0.812 0.00 0.86 0.10 0.00 0.00 0.02 0.02
#> TCGA.G3.A5SL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 5 0.1363 0.873 0.00 0.02 0.00 0.00 0.94 0.04 0.00
#> TCGA.DD.AADP.01 4 0.2376 0.782 0.00 0.00 0.02 0.86 0.12 0.00 0.00
#> TCGA.CC.5259.01 2 0.3413 0.426 0.00 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.ES.A2HS.01 6 0.2159 0.793 0.00 0.00 0.06 0.02 0.00 0.90 0.02
#> TCGA.2V.A95S.01 5 0.2376 0.851 0.00 0.00 0.02 0.12 0.86 0.00 0.00
#> TCGA.FV.A4ZP.01 5 0.0504 0.892 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DD.AACS.01 3 0.2422 0.801 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.DD.A4NF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A8.01 7 0.3558 0.453 0.48 0.00 0.00 0.00 0.00 0.00 0.52
#> TCGA.DD.A4NO.01 3 0.5036 0.729 0.00 0.00 0.68 0.08 0.04 0.18 0.02
#> TCGA.ZS.A9CG.01 7 0.3517 0.691 0.28 0.00 0.00 0.00 0.00 0.02 0.70
#> TCGA.CC.A123.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KA.01 5 0.3052 0.786 0.00 0.00 0.02 0.20 0.78 0.00 0.00
#> TCGA.DD.AAE7.01 6 0.3909 0.358 0.00 0.00 0.00 0.40 0.00 0.58 0.02
#> TCGA.KR.A7K0.01 6 0.3142 0.746 0.02 0.00 0.02 0.02 0.00 0.84 0.10
#> TCGA.DD.AACX.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 5 0.4841 0.612 0.00 0.00 0.24 0.06 0.66 0.02 0.02
#> TCGA.G3.AAV1.01 3 0.3011 0.764 0.00 0.00 0.82 0.00 0.00 0.12 0.06
#> TCGA.FV.A4ZQ.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WQ.AB4B.01 4 0.1928 0.823 0.00 0.00 0.02 0.90 0.08 0.00 0.00
#> TCGA.DD.A39W.01 3 0.2803 0.772 0.00 0.00 0.84 0.00 0.00 0.10 0.06
#> TCGA.DD.AADE.01 3 0.4538 0.489 0.00 0.00 0.62 0.00 0.00 0.10 0.28
#> TCGA.BC.A69I.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.1928 0.862 0.00 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.FV.A496.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.AAEH.01 6 0.2512 0.810 0.00 0.00 0.04 0.10 0.00 0.86 0.00
#> TCGA.2Y.A9GW.01 3 0.6026 0.563 0.00 0.00 0.58 0.08 0.20 0.12 0.02
#> TCGA.YA.A8S7.01 5 0.3488 0.852 0.00 0.04 0.06 0.02 0.84 0.02 0.02
#> TCGA.DD.AACF.01 3 0.2422 0.801 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.G3.AAV5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SK.01 6 0.2016 0.816 0.00 0.00 0.06 0.04 0.00 0.90 0.00
#> TCGA.DD.A3A7.01 5 0.0504 0.890 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.G3.AAV3.01 3 0.2163 0.792 0.00 0.00 0.88 0.00 0.00 0.10 0.02
#> TCGA.MI.A75H.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.01 6 0.2016 0.824 0.00 0.00 0.04 0.06 0.00 0.90 0.00
#> TCGA.ZP.A9D1.01 4 0.1664 0.837 0.00 0.00 0.02 0.92 0.06 0.00 0.00
#> TCGA.DD.A73C.01 3 0.3052 0.783 0.00 0.00 0.78 0.00 0.00 0.20 0.02
#> TCGA.DD.AADU.01 7 0.2159 0.670 0.02 0.00 0.02 0.00 0.00 0.06 0.90
#> TCGA.UB.A7MB.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A12J.01 7 0.3562 0.408 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.ZS.A9CD.01 3 0.3052 0.780 0.00 0.00 0.78 0.00 0.00 0.20 0.02
#> TCGA.DD.AADS.01 6 0.3943 0.279 0.00 0.00 0.00 0.42 0.00 0.56 0.02
#> TCGA.DD.A39Z.01 4 0.0863 0.880 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EP.A2KB.01 2 0.1433 0.857 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.FV.A3R2.01 4 0.3052 0.714 0.00 0.00 0.00 0.78 0.00 0.20 0.02
#> TCGA.DD.AAED.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AA1C.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 6 0.2016 0.824 0.00 0.00 0.04 0.06 0.00 0.90 0.00
#> TCGA.BD.A3ER.01 3 0.5937 0.615 0.00 0.00 0.60 0.08 0.16 0.14 0.02
#> TCGA.DD.AAVY.01 7 0.1664 0.652 0.00 0.00 0.02 0.00 0.00 0.06 0.92
#> TCGA.DD.AADN.01 5 0.0504 0.892 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.G3.A3CG.01 4 0.0863 0.880 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.DD.AAW1.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 6 0.1928 0.796 0.00 0.00 0.08 0.02 0.00 0.90 0.00
#> TCGA.DD.AADR.01 4 0.1363 0.878 0.00 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.2Y.A9HB.01 4 0.2376 0.827 0.00 0.00 0.00 0.86 0.00 0.12 0.02
#> TCGA.DD.AACI.01 5 0.2213 0.881 0.00 0.04 0.02 0.04 0.90 0.00 0.00
#> TCGA.CC.A5UD.01 2 0.4001 0.706 0.00 0.74 0.18 0.00 0.02 0.00 0.06
#> TCGA.G3.AAV2.01 7 0.3244 0.721 0.18 0.00 0.00 0.00 0.00 0.04 0.78
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.ZP.A9CV.01 4 0.2350 0.755 0.00 0.00 0.00 0.86 0.04 0.10 0.00 0.00
#> TCGA.DD.AACY.01 4 0.1741 0.759 0.00 0.00 0.02 0.92 0.02 0.00 0.00 0.04
#> TCGA.CC.A3MB.01 8 0.1607 0.773 0.00 0.04 0.00 0.00 0.04 0.00 0.00 0.92
#> TCGA.ED.A459.01 2 0.0941 0.845 0.00 0.96 0.02 0.00 0.00 0.02 0.00 0.00
#> TCGA.DD.AAVX.01 3 0.3619 0.729 0.00 0.00 0.74 0.00 0.14 0.12 0.00 0.00
#> TCGA.DD.A3A0.01 2 0.3873 0.641 0.00 0.72 0.20 0.00 0.06 0.02 0.00 0.00
#> TCGA.G3.A5SL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A11A.01 8 0.3586 0.711 0.00 0.04 0.06 0.00 0.12 0.00 0.00 0.78
#> TCGA.DD.AADP.01 4 0.4397 0.481 0.00 0.00 0.06 0.66 0.04 0.00 0.00 0.24
#> TCGA.CC.5259.01 2 0.3514 0.501 0.00 0.64 0.00 0.00 0.02 0.00 0.00 0.34
#> TCGA.ES.A2HS.01 6 0.2407 0.833 0.00 0.00 0.06 0.00 0.08 0.86 0.00 0.00
#> TCGA.2V.A95S.01 8 0.3218 0.760 0.00 0.00 0.06 0.06 0.06 0.00 0.00 0.82
#> TCGA.FV.A4ZP.01 8 0.1607 0.773 0.00 0.04 0.00 0.00 0.04 0.00 0.00 0.92
#> TCGA.DD.AACS.01 3 0.3154 0.747 0.00 0.00 0.78 0.00 0.06 0.16 0.00 0.00
#> TCGA.DD.A4NF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A3A8.01 7 0.3015 0.782 0.32 0.00 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.DD.A4NO.01 3 0.3794 0.721 0.00 0.00 0.74 0.00 0.04 0.18 0.00 0.04
#> TCGA.ZS.A9CG.01 7 0.2650 0.835 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.CC.A123.01 2 0.0471 0.858 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EP.A2KA.01 8 0.4544 0.600 0.00 0.00 0.06 0.22 0.06 0.00 0.00 0.66
#> TCGA.DD.AAE7.01 6 0.3198 0.544 0.00 0.00 0.00 0.26 0.02 0.72 0.00 0.00
#> TCGA.KR.A7K0.01 6 0.1563 0.837 0.00 0.00 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.DD.AACX.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SM.01 8 0.4174 0.387 0.00 0.00 0.40 0.00 0.06 0.00 0.00 0.54
#> TCGA.G3.AAV1.01 3 0.3675 0.650 0.00 0.00 0.66 0.00 0.30 0.04 0.00 0.00
#> TCGA.FV.A4ZQ.01 2 0.0471 0.858 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.WQ.AB4B.01 4 0.3601 0.632 0.00 0.00 0.06 0.76 0.02 0.00 0.00 0.16
#> TCGA.DD.A39W.01 3 0.4401 0.616 0.00 0.00 0.62 0.00 0.30 0.04 0.04 0.00
#> TCGA.DD.AADE.01 3 0.5918 0.241 0.00 0.00 0.38 0.00 0.16 0.08 0.38 0.00
#> TCGA.BC.A69I.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NG.01 4 0.2165 0.770 0.00 0.00 0.00 0.88 0.06 0.06 0.00 0.00
#> TCGA.FV.A496.01 2 0.0471 0.858 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DD.AAEH.01 6 0.1275 0.878 0.00 0.00 0.02 0.04 0.00 0.94 0.00 0.00
#> TCGA.2Y.A9GW.01 3 0.4893 0.510 0.00 0.00 0.64 0.00 0.06 0.12 0.00 0.18
#> TCGA.YA.A8S7.01 8 0.4406 0.627 0.00 0.02 0.26 0.00 0.08 0.00 0.00 0.64
#> TCGA.DD.AACF.01 3 0.3036 0.743 0.00 0.00 0.78 0.00 0.04 0.18 0.00 0.00
#> TCGA.G3.AAV5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A5SK.01 6 0.0941 0.893 0.00 0.00 0.02 0.00 0.02 0.96 0.00 0.00
#> TCGA.DD.A3A7.01 8 0.0000 0.795 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G3.AAV3.01 3 0.3102 0.738 0.00 0.00 0.82 0.00 0.08 0.08 0.02 0.00
#> TCGA.MI.A75H.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BC.A10S.01 6 0.0471 0.895 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.ZP.A9D1.01 4 0.3913 0.610 0.00 0.00 0.06 0.74 0.04 0.00 0.00 0.16
#> TCGA.DD.A73C.01 3 0.3808 0.662 0.00 0.00 0.66 0.00 0.02 0.30 0.02 0.00
#> TCGA.DD.AADU.01 7 0.1607 0.748 0.04 0.00 0.00 0.00 0.04 0.00 0.92 0.00
#> TCGA.UB.A7MB.01 2 0.1741 0.833 0.00 0.92 0.02 0.00 0.04 0.02 0.00 0.00
#> TCGA.EP.A12J.01 7 0.3015 0.782 0.32 0.00 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.ZS.A9CD.01 3 0.2856 0.733 0.00 0.00 0.78 0.00 0.02 0.20 0.00 0.00
#> TCGA.DD.AADS.01 4 0.4004 0.089 0.00 0.00 0.00 0.50 0.04 0.46 0.00 0.00
#> TCGA.DD.A39Z.01 4 0.0000 0.786 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EP.A2KB.01 2 0.1557 0.835 0.00 0.92 0.00 0.00 0.02 0.00 0.00 0.06
#> TCGA.FV.A3R2.01 4 0.3299 0.685 0.00 0.00 0.00 0.76 0.06 0.18 0.00 0.00
#> TCGA.DD.AAED.01 2 0.0471 0.858 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.5R.AA1C.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G3.A3CK.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5R.AAAM.01 6 0.0471 0.895 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.BD.A3ER.01 3 0.4620 0.579 0.00 0.00 0.68 0.00 0.06 0.12 0.00 0.14
#> TCGA.DD.AAVY.01 7 0.0471 0.708 0.00 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.DD.AADN.01 8 0.0808 0.791 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.G3.A3CG.01 4 0.0471 0.788 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DD.AAW1.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DD.A4NI.01 6 0.0941 0.893 0.00 0.00 0.02 0.00 0.02 0.96 0.00 0.00
#> TCGA.DD.AADR.01 4 0.0471 0.788 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.2Y.A9HB.01 4 0.3036 0.694 0.00 0.00 0.00 0.78 0.04 0.18 0.00 0.00
#> TCGA.DD.AACI.01 8 0.2807 0.770 0.00 0.02 0.10 0.00 0.04 0.00 0.00 0.84
#> TCGA.CC.A5UD.01 2 0.5062 0.458 0.00 0.48 0.12 0.00 0.38 0.00 0.02 0.00
#> TCGA.G3.AAV2.01 7 0.2650 0.835 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6