Date: 2021-07-22 18:42:07 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 375953 rows and 478 columns.
#> Performed in total 106400 partitions.
#> There are 51 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, 478 cols
#> |-- 01, 72 cols, 13145 signatures
#> | |-- 011, 27 cols, 4241 signatures
#> | | |-- 0111, 10 cols (b)
#> | | `-- 0112, 17 cols, 385 signatures (c)
#> | |-- 012, 18 cols, 1380 signatures
#> | | |-- 0121, 4 cols (b)
#> | | |-- 0122, 6 cols (b)
#> | | |-- 0123, 3 cols (b)
#> | | `-- 0124, 5 cols (b)
#> | `-- 013, 27 cols, 1887 signatures
#> | |-- 0131, 21 cols, 91 signatures (c)
#> | `-- 0132, 6 cols (b)
#> |-- 02, 189 cols, 13545 signatures
#> | |-- 021, 50 cols, 2280 signatures
#> | | |-- 0211, 24 cols, 3255 signatures
#> | | | |-- 02111, 9 cols (b)
#> | | | |-- 02112, 11 cols (b)
#> | | | `-- 02113, 4 cols (b)
#> | | `-- 0212, 26 cols, 1196 signatures
#> | | |-- 02121, 10 cols (b)
#> | | `-- 02122, 16 cols, 629 signatures (c)
#> | |-- 022, 51 cols, 14295 signatures
#> | | |-- 0221, 9 cols (b)
#> | | |-- 0222, 36 cols, 245 signatures (c)
#> | | `-- 0223, 6 cols (b)
#> | |-- 023, 48 cols, 20159 signatures
#> | | |-- 0231, 10 cols (b)
#> | | |-- 0232, 17 cols, 1073 signatures
#> | | | |-- 02321, 11 cols (b)
#> | | | |-- 02322, 4 cols (b)
#> | | | `-- 02323, 2 cols (b)
#> | | |-- 0233, 9 cols (b)
#> | | `-- 0234, 12 cols, 1046 signatures
#> | | |-- 02341, 10 cols (b)
#> | | `-- 02342, 2 cols (b)
#> | `-- 024, 40 cols, 13519 signatures
#> | |-- 0241, 10 cols (b)
#> | |-- 0242, 11 cols (b)
#> | |-- 0243, 8 cols (b)
#> | `-- 0244, 11 cols (b)
#> |-- 03, 52 cols, 25163 signatures
#> | |-- 031, 9 cols (b)
#> | |-- 032, 8 cols (b)
#> | |-- 033, 11 cols (b)
#> | |-- 034, 11 cols (b)
#> | |-- 035, 7 cols (b)
#> | `-- 036, 6 cols (b)
#> |-- 04, 99 cols, 10682 signatures
#> | |-- 041, 34 cols, 4163 signatures
#> | | |-- 0411, 27 cols, 1939 signatures
#> | | | |-- 04111, 21 cols, 141 signatures (c)
#> | | | `-- 04112, 6 cols (b)
#> | | `-- 0412, 7 cols (b)
#> | |-- 042, 27 cols, 6449 signatures
#> | | |-- 0421, 10 cols (b)
#> | | |-- 0422, 11 cols (b)
#> | | `-- 0423, 6 cols (b)
#> | `-- 043, 38 cols, 3423 signatures
#> | |-- 0431, 27 cols, 3793 signatures
#> | | |-- 04311, 12 cols, 628 signatures (c)
#> | | |-- 04312, 10 cols (b)
#> | | `-- 04313, 5 cols (b)
#> | `-- 0432, 11 cols (b)
#> `-- 05, 66 cols, 5406 signatures
#> |-- 051, 37 cols, 7025 signatures
#> | |-- 0511, 13 cols, 1170 signatures
#> | | |-- 05111, 5 cols (b)
#> | | |-- 05112, 6 cols (b)
#> | | `-- 05113, 2 cols (b)
#> | |-- 0512, 14 cols, 131 signatures (c)
#> | `-- 0513, 10 cols (b)
#> `-- 052, 29 cols, 9922 signatures
#> |-- 0521, 11 cols (b)
#> |-- 0522, 8 cols (b)
#> `-- 0523, 10 cols (b)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375953 478
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" "012" "0121" "0122" "0123" "0124" "013" "0131"
#> [13] "0132" "02" "021" "0211" "02111" "02112" "02113" "0212" "02121" "02122" "022" "0221"
#> [25] "0222" "0223" "023" "0231" "0232" "02321" "02322" "02323" "0233" "0234" "02341" "02342"
#> [37] "024" "0241" "0242" "0243" "0244" "03" "031" "032" "033" "034" "035" "036"
#> [49] "04" "041" "0411" "04111" "04112" "0412" "042" "0421" "0422" "0423" "043" "0431"
#> [61] "04311" "04312" "04313" "0432" "05" "051" "0511" "05111" "05112" "05113" "0512" "0513"
#> [73] "052" "0521" "0522" "0523"
all_leaves(res_rh)
#> [1] "0111" "0112" "0121" "0122" "0123" "0124" "0131" "0132" "02111" "02112" "02113" "02121"
#> [13] "02122" "0221" "0222" "0223" "0231" "02321" "02322" "02323" "0233" "02341" "02342" "0241"
#> [25] "0242" "0243" "0244" "031" "032" "033" "034" "035" "036" "04111" "04112" "0412"
#> [37] "0421" "0422" "0423" "04311" "04312" "04313" "0432" "05111" "05112" "05113" "0512" "0513"
#> [49] "0521" "0522" "0523"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 5 478 59276 0.157669 FALSE
#> 2 01 ATC:kmeans 2 3 72 13145 0.034964 FALSE
#> 3 011 ATC:kmeans 3 2 27 4241 0.011281 FALSE
#> 4 0111 not applied 4 NA 10 NA NA TRUE
#> 5 0112 SD:kmeans 4 2 17 385 0.001024 TRUE
#> 6 012 ATC:kmeans 3 4 18 1380 0.003671 FALSE
#> 7 0121 not applied 4 NA 4 NA NA TRUE
#> 8 0122 not applied 4 NA 6 NA NA TRUE
#> 9 0123 not applied 4 NA 3 NA NA TRUE
#> 10 0124 not applied 4 NA 5 NA NA TRUE
#> 11 013 ATC:kmeans 3 2 27 1887 0.005019 FALSE
#> 12 0131 ATC:skmeans 4 2 21 91 0.000242 TRUE
#> 13 0132 not applied 4 NA 6 NA NA TRUE
#> 14 02 ATC:kmeans 2 4 189 13545 0.036028 FALSE
#> 15 021 ATC:kmeans 3 2 50 2280 0.006065 FALSE
#> 16 0211 ATC:kmeans 4 3 24 3255 0.008658 FALSE
#> 17 02111 not applied 5 NA 9 NA NA TRUE
#> 18 02112 not applied 5 NA 11 NA NA TRUE
#> 19 02113 not applied 5 NA 4 NA NA TRUE
#> 20 0212 ATC:skmeans 4 2 26 1196 0.003181 FALSE
#> 21 02121 not applied 5 NA 10 NA NA TRUE
#> 22 02122 ATC:skmeans 5 3 16 629 0.001673 TRUE
#> 23 022 ATC:skmeans 3 3 51 14295 0.038023 FALSE
#> 24 0221 not applied 4 NA 9 NA NA TRUE
#> 25 0222 ATC:skmeans 4 2 36 245 0.000652 TRUE
#> 26 0223 not applied 4 NA 6 NA NA TRUE
#> 27 023 ATC:kmeans 3 4 48 20159 0.053621 FALSE
#> 28 0231 not applied 4 NA 10 NA NA TRUE
#> 29 0232 ATC:skmeans 4 3 17 1073 0.002854 FALSE
#> 30 02321 not applied 5 NA 11 NA NA TRUE
#> 31 02322 not applied 5 NA 4 NA NA TRUE
#> 32 02323 not applied 5 NA 2 NA NA TRUE
#> 33 0233 not applied 4 NA 9 NA NA TRUE
#> 34 0234 ATC:kmeans 4 2 12 1046 0.002782 FALSE
#> 35 02341 not applied 5 NA 10 NA NA TRUE
#> 36 02342 not applied 5 NA 2 NA NA TRUE
#> 37 024 ATC:skmeans 3 4 40 13519 0.035959 FALSE
#> 38 0241 not applied 4 NA 10 NA NA TRUE
#> 39 0242 not applied 4 NA 11 NA NA TRUE
#> 40 0243 not applied 4 NA 8 NA NA TRUE
#> 41 0244 not applied 4 NA 11 NA NA TRUE
#> 42 03 ATC:skmeans 2 6 52 25163 0.066931 FALSE
#> 43 031 not applied 3 NA 9 NA NA TRUE
#> 44 032 not applied 3 NA 8 NA NA TRUE
#> 45 033 not applied 3 NA 11 NA NA TRUE
#> 46 034 not applied 3 NA 11 NA NA TRUE
#> 47 035 not applied 3 NA 7 NA NA TRUE
#> 48 036 not applied 3 NA 6 NA NA TRUE
#> 49 04 ATC:kmeans 2 3 99 10682 0.028413 FALSE
#> 50 041 ATC:kmeans 3 2 34 4163 0.011073 FALSE
#> 51 0411 ATC:kmeans 4 2 27 1939 0.005158 FALSE
#> 52 04111 SD:kmeans 5 2 21 141 0.000375 TRUE
#> 53 04112 not applied 5 NA 6 NA NA TRUE
#> 54 0412 not applied 4 NA 7 NA NA TRUE
#> 55 042 ATC:kmeans 3 3 27 6449 0.017154 FALSE
#> 56 0421 not applied 4 NA 10 NA NA TRUE
#> 57 0422 not applied 4 NA 11 NA NA TRUE
#> 58 0423 not applied 4 NA 6 NA NA TRUE
#> 59 043 ATC:kmeans 3 2 38 3423 0.009105 FALSE
#> 60 0431 ATC:skmeans 4 3 27 3793 0.010089 FALSE
#> 61 04311 ATC:kmeans 5 2 12 628 0.001670 TRUE
#> 62 04312 not applied 5 NA 10 NA NA TRUE
#> 63 04313 not applied 5 NA 5 NA NA TRUE
#> 64 0432 not applied 4 NA 11 NA NA TRUE
#> 65 05 ATC:kmeans 2 2 66 5406 0.014379 FALSE
#> 66 051 ATC:kmeans 3 3 37 7025 0.018686 FALSE
#> 67 0511 ATC:skmeans 4 3 13 1170 0.003112 FALSE
#> 68 05111 not applied 5 NA 5 NA NA TRUE
#> 69 05112 not applied 5 NA 6 NA NA TRUE
#> 70 05113 not applied 5 NA 2 NA NA TRUE
#> 71 0512 ATC:kmeans 4 3 14 131 0.000348 TRUE
#> 72 0513 not applied 4 NA 10 NA NA TRUE
#> 73 052 ATC:kmeans 3 3 29 9922 0.026392 FALSE
#> 74 0521 not applied 4 NA 11 NA NA TRUE
#> 75 0522 not applied 4 NA 8 NA NA TRUE
#> 76 0523 not applied 4 NA 10 NA NA TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:skmeans | 7 | 0.97 | 0.91 | 0.96 | 478 | ** | |
| Node01 | ATC:kmeans | 3 | 0.97 | 0.98 | 0.99 | 72 | ** | |
| Node011 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 27 | ** | |
| Node0111-leaf | not applied | ✓ (b) | 10 | |||||
| Node0112-leaf | SD:kmeans | ✓ (c) | 2 | 0.88 | 0.99 | 0.99 | 17 | |
| Node012 | ATC:kmeans | 4 | 0.95 | 0.96 | 0.97 | 18 | ** | |
| Node0121-leaf | not applied | ✓ (b) | 4 | |||||
| Node0122-leaf | not applied | ✓ (b) | 6 | |||||
| Node0123-leaf | not applied | ✓ (b) | 3 | |||||
| Node0124-leaf | not applied | ✓ (b) | 5 | |||||
| Node013 | ATC:kmeans | 2 | 1.00 | 0.99 | 1.00 | 27 | ** | |
| Node0131-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 21 | ** |
| Node0132-leaf | not applied | ✓ (b) | 6 | |||||
| Node02 | ATC:kmeans | 4 | 0.99 | 0.96 | 0.98 | 189 | ** | |
| Node021 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 50 | ** | |
| Node0211 | ATC:kmeans | 8 | 0.91 | 0.66 | 0.83 | 24 | * | |
| Node02111-leaf | not applied | ✓ (b) | 9 | |||||
| Node02112-leaf | not applied | ✓ (b) | 11 | |||||
| Node02113-leaf | not applied | ✓ (b) | 4 | |||||
| Node0212 | ATC:skmeans | 4 | 0.94 | 0.86 | 0.94 | 26 | * | |
| Node02121-leaf | not applied | ✓ (b) | 10 | |||||
| Node02122-leaf | ATC:skmeans | ✓ (c) | 8 | 0.91 | 0.60 | 0.88 | 16 | * |
| Node022 | ATC:skmeans | 3 | 0.99 | 0.95 | 0.98 | 51 | ** | |
| Node0221-leaf | not applied | ✓ (b) | 9 | |||||
| Node0222-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.97 | 0.99 | 36 | ** |
| Node0223-leaf | not applied | ✓ (b) | 6 | |||||
| Node023 | ATC:kmeans | 2 | 1.00 | 0.99 | 0.99 | 48 | ** | |
| Node0231-leaf | not applied | ✓ (b) | 10 | |||||
| Node0232 | ATC:skmeans | 4 | 0.93 | 0.88 | 0.96 | 17 | * | |
| Node02321-leaf | not applied | ✓ (b) | 11 | |||||
| Node02322-leaf | not applied | ✓ (b) | 4 | |||||
| Node02323-leaf | not applied | ✓ (b) | 2 | |||||
| Node0233-leaf | not applied | ✓ (b) | 9 | |||||
| Node0234 | ATC:kmeans | 7 | 0.91 | 0.65 | 0.89 | 12 | * | |
| Node02341-leaf | not applied | ✓ (b) | 10 | |||||
| Node02342-leaf | not applied | ✓ (b) | 2 | |||||
| Node024 | ATC:skmeans | 5 | 0.93 | 0.94 | 0.95 | 40 | * | |
| Node0241-leaf | not applied | ✓ (b) | 10 | |||||
| Node0242-leaf | not applied | ✓ (b) | 11 | |||||
| Node0243-leaf | not applied | ✓ (b) | 8 | |||||
| Node0244-leaf | not applied | ✓ (b) | 11 | |||||
| Node03 | ATC:skmeans | 6 | 1.00 | 1.00 | 1.00 | 52 | ** | |
| Node031-leaf | not applied | ✓ (b) | 9 | |||||
| Node032-leaf | not applied | ✓ (b) | 8 | |||||
| Node033-leaf | not applied | ✓ (b) | 11 | |||||
| Node034-leaf | not applied | ✓ (b) | 11 | |||||
| Node035-leaf | not applied | ✓ (b) | 7 | |||||
| Node036-leaf | not applied | ✓ (b) | 6 | |||||
| Node04 | ATC:kmeans | 3 | 1.00 | 0.96 | 0.98 | 99 | ** | |
| Node041 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 34 | ** | |
| Node0411 | ATC:kmeans | 5 | 0.90 | 0.85 | 0.94 | 27 | * | |
| Node04111-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.97 | 0.99 | 21 | ** |
| Node04112-leaf | not applied | ✓ (b) | 6 | |||||
| Node0412-leaf | not applied | ✓ (b) | 7 | |||||
| Node042 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.98 | 27 | ** | |
| Node0421-leaf | not applied | ✓ (b) | 10 | |||||
| Node0422-leaf | not applied | ✓ (b) | 11 | |||||
| Node0423-leaf | not applied | ✓ (b) | 6 | |||||
| Node043 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 38 | ** | |
| Node0431 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 27 | ** | |
| Node04311-leaf | ATC:kmeans | ✓ (c) | 8 | 0.91 | 0.19 | 0.80 | 12 | * |
| Node04312-leaf | not applied | ✓ (b) | 10 | |||||
| Node04313-leaf | not applied | ✓ (b) | 5 | |||||
| Node0432-leaf | not applied | ✓ (b) | 11 | |||||
| Node05 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 66 | ** | |
| Node051 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 37 | ** | |
| Node0511 | ATC:skmeans | 7 | 0.91 | 0.76 | 0.93 | 13 | * | |
| Node05111-leaf | not applied | ✓ (b) | 5 | |||||
| Node05112-leaf | not applied | ✓ (b) | 6 | |||||
| Node05113-leaf | not applied | ✓ (b) | 2 | |||||
| Node0512-leaf | ATC:kmeans | ✓ (c) | 4 | 1.00 | 0.93 | 1.00 | 14 | ** |
| Node0513-leaf | not applied | ✓ (b) | 10 | |||||
| Node052 | ATC:kmeans | 4 | 0.92 | 0.78 | 0.92 | 29 | * | |
| Node0521-leaf | not applied | ✓ (b) | 11 | |||||
| Node0522-leaf | not applied | ✓ (b) | 8 | |||||
| Node0523-leaf | not applied | ✓ (b) | 10 |
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 = 1046))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1073))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1170))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1196))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1380))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1887))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1939))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2280))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3255))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3423))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3793))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4163))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4241))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5406))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6449))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7025))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9922))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10682))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13145))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13519))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13545))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14295))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20159))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 25163))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 59276))
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 = 1046))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04111" "0521" "0513" "0112" "02121" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "02341" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "02321" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "05112" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "02122" "04313" "0222" "0131" "0124"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "0123" "04111" "02321" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "02121" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "0131" "02112" "0512" "0222" "04111" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02122" "04111" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "0131" "0222" "036" "02321" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "0124" "04111" "0244" "04311" "02121"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "0131" "0412" "0521" "0222" "0423" "0131"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "02322" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "02322" "0523" "0131" "0512" "0233" "02122"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "02341" "02122" "0513" "05112" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "0131" "02113" "02323"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "02341" "02112" "036" "0242" "04112"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04111" "02113" "02112" "0523" "02341" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "0121" "04111"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "02341" "0422" "04112" "02321"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "02321" "0243" "02321"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "0131"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "05113" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "0121" "0111" "02112" "05113" "0122" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "02122" "04311" "0123"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "0131" "0242" "0244" "0513" "02321" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "04111" "0522" "0432" "05112"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "02323" "02122" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "04112" "0243" "0131" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05112" "0421" "0121" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "0131" "0222" "0222" "0123" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "0122"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "0132" "0523" "02112" "04111"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "0122" "0231" "02111" "0521" "02122" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "0124" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "0132" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "0131" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "02341" "0112" "0222" "04111" "02341"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "02122" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04111" "0231" "05111" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "02321" "0522" "0112" "02122" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "02122" "02111" "0132"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "02341" "05111" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "02322" "0242" "02122" "0132" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "04112" "04312" "0131" "0131"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "0132" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02121" "02121" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "0121" "05111" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "0122" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "0131" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "02322" "04312" "02122" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "0131" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "02321" "0222" "0223" "035" "05111" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "02122" "02122" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "0124" "0131" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "0131" "036" "04111" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "02321" "02121" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "0131" "0111" "0242" "0131"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "04111" "04111" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "04111" "0243" "05112" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04111" "031" "0111" "0512" "0124" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04111" "0512" "0111" "0112" "0432" "02342"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "04112" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "02121" "02122" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04111" "0521" "0422" "02321" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "02342" "0222" "04111" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04111" "04313" "0523" "04111" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02121" "0412" "0122" "05112" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02121" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04112" "02121" "032" "0112" "0222" "02341"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "0122" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "02341" "05111" "031" "0241" "0132" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "02122" "0131" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1073))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04111" "0521" "0513" "0112" "02121" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "02321" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "05112" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "02122" "04313" "0222" "0131" "0124"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "0123" "04111" "02321" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "02121" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "0131" "02112" "0512" "0222" "04111" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02122" "04111" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "0131" "0222" "036" "02321" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "0124" "04111" "0244" "04311" "02121"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "0131" "0412" "0521" "0222" "0423" "0131"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "02322" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "02322" "0523" "0131" "0512" "0233" "02122"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "02122" "0513" "05112" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "0131" "02113" "02323"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "02112" "036" "0242" "04112"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04111" "02113" "02112" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "0121" "04111"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "04112" "02321"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "02321" "0243" "02321"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "0131"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "05113" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "0121" "0111" "02112" "05113" "0122" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "02122" "04311" "0123"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "0131" "0242" "0244" "0513" "02321" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "04111" "0522" "0432" "05112"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "02323" "02122" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "04112" "0243" "0131" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05112" "0421" "0121" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "0131" "0222" "0222" "0123" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "0122"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "0132" "0523" "02112" "04111"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "0122" "0231" "02111" "0521" "02122" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "0124" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "0132" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "0131" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "04111" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "02122" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04111" "0231" "05111" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "02321" "0522" "0112" "02122" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "02122" "02111" "0132"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "0234" "05111" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "02322" "0242" "02122" "0132" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "04112" "04312" "0131" "0131"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "0132" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02121" "02121" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "0121" "05111" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "0122" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "0131" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "02322" "04312" "02122" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "0131" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "02321" "0222" "0223" "035" "05111" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "02122" "02122" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "0124" "0131" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "0131" "036" "04111" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "02321" "02121" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "0131" "0111" "0242" "0131"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "04111" "04111" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "04111" "0243" "05112" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04111" "031" "0111" "0512" "0124" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04111" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "04112" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "02121" "02122" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04111" "0521" "0422" "02321" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04111" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04111" "04313" "0523" "04111" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02121" "0412" "0122" "05112" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02121" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04112" "02121" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "0122" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05111" "031" "0241" "0132" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "02122" "0131" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1170))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04111" "0521" "0513" "0112" "02121" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "05112" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "02122" "04313" "0222" "0131" "0124"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "0123" "04111" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "02121" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "0131" "02112" "0512" "0222" "04111" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02122" "04111" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "0131" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "0124" "04111" "0244" "04311" "02121"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "0131" "0412" "0521" "0222" "0423" "0131"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "0131" "0512" "0233" "02122"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "02122" "0513" "05112" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "0131" "02113" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "02112" "036" "0242" "04112"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04111" "02113" "02112" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "0121" "04111"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "04112" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "0131"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "05113" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "0121" "0111" "02112" "05113" "0122" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "02122" "04311" "0123"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "0131" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "04111" "0522" "0432" "05112"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "0232" "02122" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "04112" "0243" "0131" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05112" "0421" "0121" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "0131" "0222" "0222" "0123" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "0122"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "0132" "0523" "02112" "04111"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "0122" "0231" "02111" "0521" "02122" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "0124" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "0132" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "0131" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "04111" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "02122" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04111" "0231" "05111" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "02122" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "02122" "02111" "0132"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "0234" "05111" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "02122" "0132" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "04112" "04312" "0131" "0131"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "0132" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02121" "02121" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "0121" "05111" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "0122" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "0131" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "02122" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "0131" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05111" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "02122" "02122" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "0124" "0131" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "0131" "036" "04111" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "02121" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "0131" "0111" "0242" "0131"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "04111" "04111" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "04111" "0243" "05112" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04111" "031" "0111" "0512" "0124" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04111" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "04112" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "02121" "02122" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04111" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04111" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04111" "04313" "0523" "04111" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02121" "0412" "0122" "05112" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02121" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04112" "02121" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "0122" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05111" "031" "0241" "0132" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "02122" "0131" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1196))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04111" "0521" "0513" "0112" "02121" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "02122" "04313" "0222" "0131" "0124"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "0123" "04111" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "02121" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "0131" "02112" "0512" "0222" "04111" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02122" "04111" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "0131" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "0124" "04111" "0244" "04311" "02121"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "0131" "0412" "0521" "0222" "0423" "0131"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "0131" "0512" "0233" "02122"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "02122" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "0131" "02113" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "02112" "036" "0242" "04112"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04111" "02113" "02112" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "0121" "04111"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "04112" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "0131"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "0121" "0111" "02112" "0511" "0122" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "02122" "04311" "0123"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "0131" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "04111" "0522" "0432" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "0232" "02122" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "04112" "0243" "0131" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "0121" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "0131" "0222" "0222" "0123" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "0122"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "0132" "0523" "02112" "04111"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "0122" "0231" "02111" "0521" "02122" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "0124" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "0132" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "0131" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "04111" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "02122" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04111" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "02122" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "02122" "02111" "0132"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "02122" "0132" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "04112" "04312" "0131" "0131"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "0132" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02121" "02121" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "0121" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "0122" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "0131" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "02122" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "0131" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "02122" "02122" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "0124" "0131" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "0131" "036" "04111" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "02121" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "0131" "0111" "0242" "0131"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "04111" "04111" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "04111" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04111" "031" "0111" "0512" "0124" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04111" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "04112" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "02121" "02122" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04111" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04111" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04111" "04313" "0523" "04111" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02121" "0412" "0122" "0511" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02121" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04112" "02121" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "0122" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "0132" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "02122" "0131" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1380))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04111" "0521" "0513" "0112" "0212" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "0212" "04313" "0222" "0131" "0124"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "0123" "04111" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "0212" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "0131" "02112" "0512" "0222" "04111" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "0212" "04111" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "0131" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "0124" "04111" "0244" "04311" "0212"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "0131" "0412" "0521" "0222" "0423" "0131"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "0131" "0512" "0233" "0212"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "0212" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "0131" "02113" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "02112" "036" "0242" "04112"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04111" "02113" "02112" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "0121" "04111"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "04112" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "0131"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "0121" "0111" "02112" "0511" "0122" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "0212" "04311" "0123"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "0131" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "04111" "0522" "0432" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "0232" "0212" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "04112" "0243" "0131" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "0121" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "0131" "0222" "0222" "0123" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "0122"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "0132" "0523" "02112" "04111"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "0122" "0231" "02111" "0521" "0212" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "0124" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "0132" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "0131" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "04111" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "0212" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04111" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "0212" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "0212" "02111" "0132"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "0212" "0132" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "04112" "04312" "0131" "0131"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "0132" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "0212" "0212" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "0121" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "0122" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "0131" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "0212" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "0131" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "0212" "0212" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "0124" "0131" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "0131" "036" "04111" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "0212" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "0131" "0111" "0242" "0131"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "04111" "04111" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "04111" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04111" "031" "0111" "0512" "0124" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04111" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "04112" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "0212" "0212" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04111" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04111" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04111" "04313" "0523" "04111" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "0212" "0412" "0122" "0511" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "0212" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04112" "0212" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "0122" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "0132" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "0212" "0131" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1887))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04111" "0521" "0513" "0112" "0212" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "0212" "04313" "0222" "0131" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "04111" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "0212" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "0131" "02112" "0512" "0222" "04111" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "0212" "04111" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "0131" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "04111" "0244" "04311" "0212"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "0131" "0412" "0521" "0222" "0423" "0131"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "0131" "0512" "0233" "0212"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "0212" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "0131" "02113" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "02112" "036" "0242" "04112"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04111" "02113" "02112" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "012" "04111"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "04112" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "0131"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "02112" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "0212" "04311" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "0131" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "04111" "0522" "0432" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "0232" "0212" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "04112" "0243" "0131" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "0131" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "0132" "0523" "02112" "04111"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "02111" "0521" "0212" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "012" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "0132" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "0131" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "04111" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "0212" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04111" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "0212" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "0212" "02111" "0132"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "0212" "0132" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "04112" "04312" "0131" "0131"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "0132" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "0212" "0212" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "0131" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "0212" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "0131" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "0212" "0212" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "0131" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "0131" "036" "04111" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "0212" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "0131" "0111" "0242" "0131"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "04111" "04111" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "04111" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04111" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04111" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "04112" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "0212" "0212" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04111" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04111" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04111" "04313" "0523" "04111" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "0212" "0412" "012" "0511" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "0212" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04112" "0212" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "012" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "0132" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "0212" "0131" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1939))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04111" "0521" "0513" "0112" "0212" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "0212" "04313" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "04111" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "0212" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "02112" "0512" "0222" "04111" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "0212" "04111" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "04111" "0244" "04311" "0212"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "0412" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "0212"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "0212" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "02113" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "02112" "036" "0242" "04112"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04111" "02113" "02112" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "012" "04111"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "04112" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "02112" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "0212" "04311" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "04111" "0522" "0432" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "0232" "0212" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "04112" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "013" "0523" "02112" "04111"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "02111" "0521" "0212" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "012" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "04111" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "0212" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04111" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "0212" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "0212" "02111" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "0212" "013" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "04112" "04312" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "013" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "0212" "0212" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "0212" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "0212" "0212" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "04111" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "0212" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "013" "0111" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "04111" "04111" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "04111" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04111" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04111" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "04112" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "0212" "0212" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04111" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04111" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04111" "04313" "0523" "04111" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "0212" "0412" "012" "0511" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "0212" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04112" "0212" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "012" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "0212" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2280))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "0411" "0521" "0513" "0112" "0212" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02111" "0212" "04313" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "0411" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "0212" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "02112" "0512" "0222" "0411" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "0212" "0411" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "0411" "0244" "04311" "0212"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "0412" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "0212"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "0212" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "02113" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "02112" "036" "0242" "0411"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "0411" "02113" "02112" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "012" "0411"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "0411" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "02112" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02111" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "02112" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "0212" "04311" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "02113" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "0411" "0522" "0432" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "02112" "0232" "0212" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "0411" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "013" "0523" "02112" "0411"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "02111" "0521" "0212" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "012" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "0432" "02111" "02111" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "02112" "0244" "0112" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "0411" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "0212" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "0411" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "0212" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "0212" "02111" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "02111" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "0212" "013" "0242" "02111"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "0411" "04312" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "013" "0222" "02113" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "0212" "0212" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "0212" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "0212" "0212" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "0411" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "0212" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "013" "0111" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "0411" "0411" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02112" "0512" "0411" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "0411" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "0411" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "0411" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "0212" "0212" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "0411" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "0411" "0421" "0222" "02112"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "0411" "04313" "0523" "0411" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "0212" "0412" "012" "0511" "0512" "02112"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "02111"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "0212" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "0411" "0212" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "012" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "0212" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3255))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "0411" "0521" "0513" "0112" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "04313" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "0411" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "0512" "0222" "0411" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "0411" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "0411" "0244" "04311" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "0412" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "0411"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "0411" "021" "021" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "012" "0411"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "0411" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "021" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "021" "04311" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "0411" "0522" "0432" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "021" "0232" "021" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "0411" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "013" "0523" "021" "0411"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "0521" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "012" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "0432" "021" "021" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "0112" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "0411" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "021" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "0411" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "0411" "04312" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "013" "0222" "021" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "0411" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "021" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "013" "0111" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "0411" "0411" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "0512" "0411" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "0411" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "0411" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "0411" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "021" "021" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "0411" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "0411" "0421" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "0411" "04313" "0523" "0411" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "0412" "012" "0511" "0512" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "0411" "021" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "012" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3423))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "0411" "0521" "0513" "0112" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "04312" "04312"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "04311" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "04313" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "0411" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "0512" "0222" "0411" "04311"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "0411" "031" "034" "0432" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "0411" "0244" "04311" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "0412" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "0411"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "0411" "021" "021" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "0432" "0221" "0421" "0223" "012" "0411"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04313" "0233" "0234" "0422" "0411" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "0432" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04312" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "021" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04312" "0521" "0221" "021" "04311" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "0411" "0522" "0432" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "021" "0232" "021" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04311" "0112" "0411" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "0432" "0432"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "013" "0523" "021" "0411"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "0521" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04311" "012" "04311" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "0432" "021" "021" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "0112" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04311" "0234" "0112" "0222" "0411" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "0432" "0244" "032" "0423" "021" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "04311" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "0411" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "0432" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "04311" "0411" "04312" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04311" "013" "0222" "021" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "04311"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04312" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "0411" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04313" "0232" "021" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04312" "013" "0111" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "0411" "0411" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "0512" "0411" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "0411" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "0411" "0512" "0111" "0112" "0432" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "0411" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04312" "04313" "021" "021" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "0411" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "0411" "0421" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "0411" "04313" "0523" "0411" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "0412" "012" "0511" "0512" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "0432" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "0411" "021" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "012" "0223" "0423" "04312" "04312"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3793))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "0411" "0521" "0513" "0112" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "043" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "0411" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "0512" "0222" "0411" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "0411" "031" "034" "043" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "0411" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "0412" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "0411"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "0411" "021" "021" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "0421" "0223" "012" "0411"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "0422" "0411" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "021" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "0521" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "0411" "0522" "043" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "021" "0232" "021" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "0112" "0411" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "013" "0523" "021" "0411"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "0521" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "0112" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "0112" "0222" "0411" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "0423" "021" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "0411" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "043" "0411" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "0411" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "0111" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "0411" "0411" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "0512" "0411" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "0411" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "0411" "0512" "0111" "0112" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "0411" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "0411" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "0411" "0421" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "0411" "043" "0523" "0411" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "0412" "012" "0511" "0512" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "0411" "021" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "012" "0223" "0423" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4163))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "0411" "0521" "0513" "0112" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "043" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "0411" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "0512" "0222" "0411" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "0411" "031" "034" "043" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "0411" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "0412" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "0411"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "0411" "021" "021" "0523" "0234" "0412"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "0421" "0223" "012" "0411"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "0412" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "0422" "0411" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "021" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "0521" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "0411" "0522" "043" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "021" "0232" "021" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "0112" "0411" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "013" "0523" "021" "0411"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "0521" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "0112" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "0112" "0222" "0411" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "0423" "021" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "0411" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "043" "0411" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "0412" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "0412" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "0411" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "0111" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "0411" "0411" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "0512" "0411" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "0411" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "0411" "0512" "0111" "0112" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "0411" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "0411" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "0411" "0421" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "0411" "043" "0523" "0411" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "0412" "012" "0511" "0512" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "0411" "021" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "0412" "012" "0223" "0423" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4241))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "041" "0521" "0513" "0112" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "0112" "0112" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "0112" "0512" "043" "0111"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "041" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "0512" "0222" "041" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "041" "031" "034" "043" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "041" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "041" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "0111" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "041"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "041" "021" "021" "0523" "0234" "041"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "0421" "0223" "012" "041"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "041" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "0422" "041" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "0112" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "0111" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "0111" "021" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "0521" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "0111" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "0112"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "041" "0522" "043" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "0111" "021" "0232" "021" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "0112" "041" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "0112" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "0111" "0512" "013" "0523" "021" "041"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "0521" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "0112" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "0112" "0222" "041" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "0423" "021" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "041" "0231" "0511" "0112"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "0112" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "0112" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "043" "041" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "041" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "041" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "041" "0112"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "0111" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "0112" "0422" "034" "041" "041" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "0512" "041" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "041" "031" "0111" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "041" "0512" "0111" "0112" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "041" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "041" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "041" "0421" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "041" "043" "0523" "041" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "041" "012" "0511" "0512" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "041" "021" "032" "0112" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "041" "012" "0223" "0423" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5406))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "041" "0521" "0513" "011" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "0522" "011" "011" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "011" "0512" "043" "011"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "0521" "0511" "0513" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "0512" "012" "041" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "0512" "0222" "041" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "041" "031" "034" "043" "0523"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "041" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "041" "0521" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "011" "0222" "0523" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "0523" "013" "0512" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "0513" "0511" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "041"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "041" "021" "021" "0523" "0234" "041"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "0421" "0223" "012" "041"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "041" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "0422" "041" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "011" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "0522" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "0513" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "011" "0243" "0511" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "011" "021" "0511" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "0521" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "0523" "011" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "0513" "0232" "011"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "0512" "0522" "041" "0522" "043" "0511"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "011" "021" "0232" "021" "0513"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "011" "041" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "0511" "0421" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "011" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "011" "0512" "013" "0523" "021" "041"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "0521" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "0521"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "0523"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "011" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "011" "0222" "041" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "0423" "021" "0513"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "041" "0231" "0511" "011"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "0522" "011" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "0522" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "0511" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "011" "0241" "033" "0521" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "0512" "043" "041" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "0522"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "041" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "0511" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "0513" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "0512"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "041" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "0511" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "0512" "034" "0522" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "041" "011"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "011" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "011" "0422" "034" "041" "041" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "0512" "041" "0243" "0511" "0523"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "041" "031" "011" "0512" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "041" "0512" "011" "011" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "0521" "041" "0521" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "041" "0521" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "041" "0421" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "041" "043" "0523" "041" "0422" "0521"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "041" "012" "0511" "0512" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "0523" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "0513"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "041" "021" "032" "011" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "041" "012" "0223" "0423" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "0511" "031" "0241" "013" "0513"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "0512"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6449))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "041" "05" "05" "011" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "05" "011" "011" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "011" "05" "043" "011"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "0422" "0222" "05" "05" "05" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "012" "041" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "0423" "0244" "0421" "0422"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "05" "0222" "041" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "041" "031" "034" "043" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "041" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "041" "05" "0222" "0423" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "0421" "0232" "011" "0222" "05" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "05" "013" "05" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "05" "05" "0421"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "0422" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "041"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "041" "021" "021" "05" "0234" "041"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "0421" "0223" "012" "041"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "041" "0221" "0222" "032" "031" "0422"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "0422" "041" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "011" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "05" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "05" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "011" "0243" "05" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "011" "021" "05" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "05" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "05" "011" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "05" "0232" "011"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "041" "05" "043" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "011" "021" "0232" "021" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "011" "041" "0243" "013" "0423"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "0421" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "0421" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "0421" "011" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "011" "05" "013" "05" "021" "041"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "05" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "011" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "011" "0222" "041" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "0423" "021" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "0422" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "041" "0231" "05" "011"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "05" "011" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "05" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "05" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "011" "0241" "033" "05" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "043" "041" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "041" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "0422" "012" "05" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "0421" "035" "012" "05" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "0421" "041" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "041" "011"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "0422" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "011" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "011" "0422" "034" "041" "041" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "05" "041" "0243" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "041" "031" "011" "05" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "041" "05" "011" "011" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "05" "041" "05" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "0423"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "041" "05" "0422" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "041" "0421" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "041" "043" "05" "041" "0422" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "041" "012" "05" "05" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "041" "021" "032" "011" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "041" "012" "0223" "0423" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05" "031" "0241" "013" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7025))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "041" "05" "05" "011" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "05" "011" "011" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "011" "05" "043" "011"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "042" "0222" "05" "05" "05" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "012" "041" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "042" "0244" "042" "042"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "05" "0222" "041" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "041" "031" "034" "043" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "041" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "041" "05" "0222" "042" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "042" "0232" "011" "0222" "05" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "05" "013" "05" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "05" "05" "042"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "042" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "041"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "041" "021" "021" "05" "0234" "041"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "042" "0223" "012" "041"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "041" "0221" "0222" "032" "031" "042"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "042" "041" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "011" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "05" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "05" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "011" "0243" "05" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "011" "021" "05" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "05" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "05" "011" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "05" "0232" "011"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "041" "05" "043" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "011" "021" "0232" "021" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "011" "041" "0243" "013" "042"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "042" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "042" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "042" "011" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "011" "05" "013" "05" "021" "041"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "05" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "011" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "011" "0222" "041" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "042" "021" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "042" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "041" "0231" "05" "011"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "05" "011" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "05" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "05" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "011" "0241" "033" "05" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "043" "041" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "041" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "042" "012" "05" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "042" "035" "012" "05" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "042" "041" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "041" "011"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "042" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "011" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "011" "042" "034" "041" "041" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "05" "041" "0243" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "041" "031" "011" "05" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "041" "05" "011" "011" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "05" "041" "05" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "042"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "041" "05" "042" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "041" "042" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "041" "043" "05" "041" "042" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "041" "012" "05" "05" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "041" "021" "032" "011" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "041" "012" "0223" "042" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05" "031" "0241" "013" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9922))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "041" "05" "05" "011" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "05" "011" "011" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "011" "05" "043" "011"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "042" "0222" "05" "05" "05" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "012" "041" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "042" "0244" "042" "042"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "05" "0222" "041" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "041" "031" "034" "043" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "041" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "041" "05" "0222" "042" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "042" "0232" "011" "0222" "05" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "05" "013" "05" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "05" "05" "042"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "042" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "041"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "041" "021" "021" "05" "0234" "041"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "042" "0223" "012" "041"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "041" "0221" "0222" "032" "031" "042"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "042" "041" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "011" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "05" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "05" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "011" "0243" "05" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "011" "021" "05" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "05" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "05" "011" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "05" "0232" "011"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "041" "05" "043" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "011" "021" "0232" "021" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "011" "041" "0243" "013" "042"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "042" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "042" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "042" "011" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "011" "05" "013" "05" "021" "041"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "05" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "011" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "011" "0222" "041" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "042" "021" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "042" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "041" "0231" "05" "011"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "05" "011" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "05" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "05" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "011" "0241" "033" "05" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "043" "041" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "041" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "042" "012" "05" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "042" "035" "012" "05" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "042" "041" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "041" "011"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "042" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "011" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "011" "042" "034" "041" "041" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "05" "041" "0243" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "041" "031" "011" "05" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "041" "05" "011" "011" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "05" "041" "05" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "042"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "041" "05" "042" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "041" "042" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "041" "043" "05" "041" "042" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "041" "012" "05" "05" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "041" "021" "032" "011" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "041" "012" "0223" "042" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05" "031" "0241" "013" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10682))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "041" "05" "05" "011" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "05" "011" "011" "043" "043"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "011" "05" "043" "011"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "042" "0222" "05" "05" "05" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "043" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "012" "041" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "042" "0244" "042" "042"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "05" "0222" "041" "043"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "041" "031" "034" "043" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "041" "0244" "043" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "041" "05" "0222" "042" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "042" "0232" "011" "0222" "05" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "05" "013" "05" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "05" "05" "042"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "042" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "041"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "041" "021" "021" "05" "0234" "041"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "043" "0221" "042" "0223" "012" "041"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "041" "0221" "0222" "032" "031" "042"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "043" "0233" "0234" "042" "041" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "043" "0221" "011" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "05" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "043" "05" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "011" "0243" "05" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "011" "021" "05" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "043" "05" "0221" "021" "043" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "05" "011" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "05" "0232" "011"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "041" "05" "043" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "011" "021" "0232" "021" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "043" "011" "041" "0243" "013" "042"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "042" "012" "0231" "043" "043"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "042" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "042" "011" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "011" "05" "013" "05" "021" "041"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "05" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "043" "012" "043" "0242" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "043" "021" "021" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "011" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "043" "0234" "011" "0222" "041" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "043" "0244" "032" "042" "021" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "042" "0222" "043" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "041" "0231" "05" "011"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "05" "011" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "05" "043" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "05" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "011" "0241" "033" "05" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "043" "041" "043" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "043" "013" "0222" "021" "0222" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "041" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "042" "012" "05" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "042" "035" "012" "05" "043"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "043" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "042" "041" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "041" "011"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "043" "0232" "021" "0242" "042" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "043" "013" "011" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "011" "042" "034" "041" "041" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "05" "041" "0243" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "041" "031" "011" "05" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "041" "05" "011" "011" "043" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "05" "041" "05" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "043" "043" "021" "021" "042"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "041" "05" "042" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "041" "042" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "041" "043" "05" "041" "042" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "041" "012" "05" "05" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "043" "034" "032" "0233" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "041" "021" "032" "011" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "041" "012" "0223" "042" "043" "043"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05" "031" "0241" "013" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13145))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04" "05" "05" "011" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "05" "011" "011" "04" "04"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "011" "05" "04" "011"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "04" "0222" "05" "05" "05" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "04" "0222" "013" "012"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "012" "04" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "04" "0244" "04" "04"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "013" "021" "05" "0222" "04" "04"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "04" "031" "034" "04" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "013" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "012" "04" "0244" "04" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "013" "04" "05" "0222" "04" "013"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "04" "0232" "011" "0222" "05" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "05" "013" "05" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "05" "05" "04"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "04" "0231" "013" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "04"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04" "021" "021" "05" "0234" "04"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "04" "0221" "04" "0223" "012" "04"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "04" "0221" "0222" "032" "031" "04"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04" "0233" "0234" "04" "04" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "04" "0221" "011" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "05" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04" "05" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "013"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "011" "0243" "05" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "012" "011" "021" "05" "012" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04" "05" "0221" "021" "04" "012"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "05" "011" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "013" "0242" "0244" "05" "0232" "011"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "04" "05" "04" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "011" "021" "0232" "021" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04" "011" "04" "0243" "013" "04"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "04" "012" "0231" "04" "04"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "04" "013" "0222" "0222" "012" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "04" "011" "0231" "0241" "012"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "011" "05" "013" "05" "021" "04"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "012" "0231" "021" "05" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04" "012" "04" "0242" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "013" "0241" "04" "021" "021" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "011" "013" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04" "0234" "011" "0222" "04" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "04" "0244" "032" "04" "021" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "04" "0222" "04" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04" "0231" "05" "011"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "05" "011" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "05" "04" "021" "021" "013"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "05" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "011" "0241" "033" "05" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "013" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "04" "04" "04" "013" "013"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04" "013" "0222" "021" "0222" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "04" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "04" "012" "05" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "04" "035" "012" "05" "04"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "013" "035" "0231" "0243" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "04" "04" "034" "013" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "012" "013" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "013" "036" "04" "011"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04" "0232" "021" "0242" "04" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04" "013" "011" "0242" "013"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "011" "04" "034" "04" "04" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "05" "04" "0243" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04" "031" "011" "05" "012" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04" "05" "011" "011" "04" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "05" "04" "05" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04" "04" "021" "021" "04"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04" "05" "04" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04" "04" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04" "04" "05" "04" "04" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "04" "012" "05" "05" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "04" "034" "032" "0233" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04" "021" "032" "011" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "04" "012" "0223" "04" "04" "04"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05" "031" "0241" "013" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "013" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13519))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04" "05" "05" "01" "021" "0243"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "05" "01" "01" "04" "04"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "0243" "01" "05" "04" "01"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "04" "0222" "05" "05" "05" "0244"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "04" "0222" "01" "01"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "01" "04" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "04" "0244" "04" "04"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "01" "021" "05" "0222" "04" "04"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "04" "031" "034" "04" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "01" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "01" "04" "0244" "04" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "01" "04" "05" "0222" "04" "01"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "04" "0232" "01" "0222" "05" "0244"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "05" "01" "05" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "05" "05" "04"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "04" "0231" "01" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "0242" "0234" "021" "036" "0242" "04"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04" "021" "021" "05" "0234" "04"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "04" "0221" "04" "0223" "01" "04"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "04" "0221" "0222" "032" "031" "04"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04" "0233" "0234" "04" "04" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "04" "0221" "01" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "05" "0223" "0232" "0243" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04" "05" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "0244" "0221" "0244" "01"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "01" "0243" "05" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "01" "01" "021" "05" "01" "0241"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04" "05" "0221" "021" "04" "01"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "05" "01" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "01" "0242" "0244" "05" "0232" "01"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "04" "05" "04" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "01" "021" "0232" "021" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04" "01" "04" "0243" "01" "04"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "04" "01" "0231" "04" "04"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "04" "01" "0222" "0222" "01" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "0244" "04" "01" "0231" "0241" "01"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "01" "05" "01" "05" "021" "04"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "01" "0231" "021" "05" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04" "01" "04" "0242" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "01" "0241" "04" "021" "021" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "0241" "021" "0244" "01" "01" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04" "0234" "01" "0222" "04" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "04" "0244" "032" "04" "021" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "04" "0222" "04" "036" "0242" "0241"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "0241" "04" "0231" "05" "01"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "05" "01" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "05" "04" "021" "021" "01"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "05" "0244"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "01" "0241" "033" "05" "032" "0243"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "0242" "021" "01" "0242" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "04" "04" "04" "01" "01"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04" "01" "0222" "021" "0222" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "04" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "04" "01" "05" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "04" "035" "01" "05" "04"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "0242" "01" "035" "0231" "0243" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "04" "04" "034" "01" "0241"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "01" "01" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "01" "036" "04" "01"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04" "0232" "021" "0242" "04" "0242"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04" "01" "01" "0242" "01"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "01" "04" "034" "04" "04" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "05" "04" "0243" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04" "031" "01" "05" "01" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04" "05" "01" "01" "04" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "05" "04" "05" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04" "04" "021" "021" "04"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "0241" "04" "05" "04" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04" "04" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04" "04" "05" "04" "04" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "04" "01" "05" "05" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "04" "034" "032" "0233" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04" "021" "032" "01" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "04" "01" "0223" "04" "04" "04"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05" "031" "0241" "01" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "01" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13545))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04" "05" "05" "01" "021" "024"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "0234" "05" "01" "01" "04" "04"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "0232" "024" "01" "05" "04" "01"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "04" "0222" "05" "05" "05" "024"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "021" "021" "04" "0222" "01" "01"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "01" "04" "0232" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "0222" "021" "04" "024" "04" "04"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "01" "021" "05" "0222" "04" "04"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "021" "04" "031" "034" "04" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "01" "0222" "036" "0232" "031" "0223"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "01" "04" "024" "04" "021"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "01" "04" "05" "0222" "04" "01"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "04" "0232" "01" "0222" "05" "024"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "0232" "05" "01" "05" "0233" "021"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "0234" "021" "05" "05" "04"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "04" "0231" "01" "021" "0232"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "024" "0234" "021" "036" "024" "04"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04" "021" "021" "05" "0234" "04"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "04" "0221" "04" "0223" "01" "04"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "04" "0221" "0222" "032" "031" "04"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04" "0233" "0234" "04" "04" "0232"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "0233" "021" "04" "0221" "01" "0222"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "0231" "05" "0223" "0232" "024" "0232"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04" "05" "035" "0231" "035" "0222"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "0222" "0222" "024" "0221" "024" "01"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "021" "01" "024" "05" "0231" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "01" "01" "021" "05" "01" "024"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04" "05" "0221" "021" "04" "01"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "0221" "05" "01" "0222" "021" "0233"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "01" "024" "024" "05" "0232" "01"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "04" "05" "04" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "01" "021" "0232" "021" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04" "01" "04" "024" "01" "04"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "04" "01" "0231" "04" "04"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "04" "01" "0222" "0222" "01" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "024" "04" "01" "0231" "024" "01"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "01" "05" "01" "05" "021" "04"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "01" "0231" "021" "05" "021" "0222"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "0222" "04" "01" "04" "024" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "01" "024" "04" "021" "021" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "024" "021" "024" "01" "01" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04" "0234" "01" "0222" "04" "0234"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "04" "024" "032" "04" "021" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "04" "0222" "04" "036" "024" "024"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "0222" "024" "04" "0231" "05" "01"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "0232" "05" "01" "021" "0221" "0233"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "0223" "05" "04" "021" "021" "01"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "0233" "0221" "021" "0234" "05" "024"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "01" "024" "033" "05" "032" "024"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "0232" "024" "021" "01" "024" "021"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "04" "04" "04" "01" "01"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04" "01" "0222" "021" "0222" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "021" "021" "04" "034" "033" "0222"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "04" "01" "05" "033" "0222" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "0222" "04" "035" "01" "05" "04"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "024" "01" "035" "0231" "024" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "0232" "04" "021" "0222" "036" "0222"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "0222" "04" "04" "034" "01" "024"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "0232" "0222" "0223" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "0222" "021" "021" "031" "036" "0233"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "01" "01" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "0222" "0231" "01" "036" "04" "01"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04" "0232" "021" "024" "04" "024"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04" "01" "01" "024" "01"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "01" "04" "034" "04" "04" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "021" "05" "04" "024" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04" "031" "01" "05" "01" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04" "05" "01" "01" "04" "0234"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "0233" "0222" "05" "04" "05" "0221"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04" "04" "021" "021" "04"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "024" "04" "05" "04" "0232" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "0234" "0222" "04" "04" "0222" "021"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04" "04" "05" "04" "04" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "021" "04" "01" "05" "05" "021"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "0222" "032" "021"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "021" "04" "034" "032" "0233" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04" "021" "032" "01" "0222" "0234"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "04" "01" "0223" "04" "04" "04"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "0234" "05" "031" "024" "01" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "021" "01" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14295))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04" "05" "05" "01" "02" "02"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "02" "05" "01" "01" "04" "04"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "02" "02" "01" "05" "04" "01"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "04" "02" "05" "05" "05" "02"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02" "02" "04" "02" "01" "01"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "01" "04" "02" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "02" "02" "04" "02" "04" "04"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "01" "02" "05" "02" "04" "04"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02" "04" "031" "034" "04" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "01" "02" "036" "02" "031" "02"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "01" "04" "02" "04" "02"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "01" "04" "05" "02" "04" "01"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "04" "02" "01" "02" "05" "02"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "02" "05" "01" "05" "02" "02"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "02" "02" "05" "05" "04"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "04" "02" "01" "02" "02"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "02" "02" "02" "036" "02" "04"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04" "02" "02" "05" "02" "04"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "04" "02" "04" "02" "01" "04"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "04" "02" "02" "032" "031" "04"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04" "02" "02" "04" "04" "02"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "02" "05" "02" "02" "02" "02"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04" "05" "035" "02" "035" "02"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02" "01" "02" "05" "02" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "01" "01" "02" "05" "01" "02"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "01" "02" "02" "05" "02" "01"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "04" "05" "04" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "01" "02" "02" "02" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04" "01" "04" "02" "01" "04"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "04" "01" "02" "04" "04"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "04" "01" "02" "02" "01" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "02" "04" "01" "02" "02" "01"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "01" "05" "01" "05" "02" "04"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "02" "04" "01" "04" "02" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "01" "02" "04" "02" "02" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "02" "02" "02" "01" "01" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04" "02" "01" "02" "04" "02"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "04" "02" "032" "04" "02" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "04" "02" "04" "036" "02" "02"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "02" "02" "04" "02" "05" "01"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "02" "05" "04" "02" "02" "01"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "01" "02" "033" "05" "032" "02"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "04" "04" "04" "01" "01"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04" "01" "02" "02" "02" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02" "02" "04" "034" "033" "02"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "04" "01" "05" "033" "02" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "02" "04" "035" "01" "05" "04"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "02" "01" "035" "02" "02" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "02" "04" "02" "02" "036" "02"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "02" "04" "04" "034" "01" "02"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "02" "02" "02" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "02" "02" "02" "031" "036" "02"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "01" "01" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "02" "02" "01" "036" "04" "01"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04" "02" "02" "02" "04" "02"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04" "01" "01" "02" "01"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "01" "04" "034" "04" "04" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02" "05" "04" "02" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04" "031" "01" "05" "01" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04" "05" "01" "01" "04" "02"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "02" "02" "05" "04" "05" "02"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04" "04" "02" "02" "04"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "02" "04" "05" "04" "02" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "02" "02" "04" "04" "02" "02"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04" "04" "05" "04" "04" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02" "04" "01" "05" "05" "02"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "02" "032" "02"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02" "04" "034" "032" "02" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04" "02" "032" "01" "02" "02"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "04" "01" "02" "04" "04" "04"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "02" "05" "031" "02" "01" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "02" "01" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20159))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04" "05" "05" "01" "02" "02"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "02" "05" "01" "01" "04" "04"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "02" "02" "01" "05" "04" "01"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "04" "02" "05" "05" "05" "02"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02" "02" "04" "02" "01" "01"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "01" "04" "02" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "02" "02" "04" "02" "04" "04"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "01" "02" "05" "02" "04" "04"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02" "04" "031" "034" "04" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "01" "02" "036" "02" "031" "02"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "01" "04" "02" "04" "02"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "01" "04" "05" "02" "04" "01"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "04" "02" "01" "02" "05" "02"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "02" "05" "01" "05" "02" "02"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "02" "02" "05" "05" "04"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "04" "02" "01" "02" "02"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "02" "02" "02" "036" "02" "04"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04" "02" "02" "05" "02" "04"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "04" "02" "04" "02" "01" "04"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "04" "02" "02" "032" "031" "04"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04" "02" "02" "04" "04" "02"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "02" "05" "02" "02" "02" "02"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04" "05" "035" "02" "035" "02"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02" "01" "02" "05" "02" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "01" "01" "02" "05" "01" "02"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "01" "02" "02" "05" "02" "01"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "04" "05" "04" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "01" "02" "02" "02" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04" "01" "04" "02" "01" "04"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "04" "01" "02" "04" "04"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "04" "01" "02" "02" "01" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "02" "04" "01" "02" "02" "01"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "01" "05" "01" "05" "02" "04"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "02" "04" "01" "04" "02" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "01" "02" "04" "02" "02" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "02" "02" "02" "01" "01" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04" "02" "01" "02" "04" "02"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "04" "02" "032" "04" "02" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "04" "02" "04" "036" "02" "02"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "02" "02" "04" "02" "05" "01"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "02" "05" "04" "02" "02" "01"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "01" "02" "033" "05" "032" "02"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "04" "04" "04" "01" "01"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04" "01" "02" "02" "02" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02" "02" "04" "034" "033" "02"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "04" "01" "05" "033" "02" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "02" "04" "035" "01" "05" "04"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "02" "01" "035" "02" "02" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "02" "04" "02" "02" "036" "02"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "02" "04" "04" "034" "01" "02"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "02" "02" "02" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "02" "02" "02" "031" "036" "02"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "01" "01" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "02" "02" "01" "036" "04" "01"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04" "02" "02" "02" "04" "02"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04" "01" "01" "02" "01"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "01" "04" "034" "04" "04" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02" "05" "04" "02" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04" "031" "01" "05" "01" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04" "05" "01" "01" "04" "02"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "02" "02" "05" "04" "05" "02"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04" "04" "02" "02" "04"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "02" "04" "05" "04" "02" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "02" "02" "04" "04" "02" "02"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04" "04" "05" "04" "04" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02" "04" "01" "05" "05" "02"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "02" "032" "02"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02" "04" "034" "032" "02" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04" "02" "032" "01" "02" "02"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "04" "01" "02" "04" "04" "04"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "02" "05" "031" "02" "01" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "02" "01" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 25163))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04" "05" "05" "01" "02" "02"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "02" "05" "01" "01" "04" "04"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "02" "02" "01" "05" "04" "01"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "04" "02" "05" "05" "05" "02"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02" "02" "04" "02" "01" "01"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "034" "05" "01" "04" "02" "033"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "02" "02" "04" "02" "04" "04"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "01" "02" "05" "02" "04" "04"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02" "04" "031" "034" "04" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "01" "02" "036" "02" "031" "02"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "033" "01" "04" "02" "04" "02"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "01" "04" "05" "02" "04" "01"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "04" "02" "01" "02" "05" "02"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "02" "05" "01" "05" "02" "02"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "033" "02" "02" "05" "05" "04"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "033" "04" "02" "01" "02" "02"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "02" "02" "02" "036" "02" "04"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04" "02" "02" "05" "02" "04"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "04" "02" "04" "02" "01" "04"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "04" "02" "02" "032" "031" "04"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04" "02" "02" "04" "04" "02"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "02" "05" "02" "02" "02" "02"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04" "05" "035" "02" "035" "02"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02" "01" "02" "05" "02" "034"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "01" "01" "02" "05" "01" "02"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "01" "02" "02" "05" "02" "01"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "04" "05" "04" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "032" "01" "02" "02" "02" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04" "01" "04" "02" "01" "04"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "04" "01" "02" "04" "04"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "04" "01" "02" "02" "01" "033"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "02" "04" "01" "02" "02" "01"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "01" "05" "01" "05" "02" "04"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "02" "04" "01" "04" "02" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "01" "02" "04" "02" "02" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "02" "02" "02" "01" "01" "033"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04" "02" "01" "02" "04" "02"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "04" "02" "032" "04" "02" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "04" "02" "04" "036" "02" "02"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "02" "02" "04" "02" "05" "01"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "02" "05" "04" "02" "02" "01"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "01" "02" "033" "05" "032" "02"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "04" "04" "04" "01" "01"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04" "01" "02" "02" "02" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02" "02" "04" "034" "033" "02"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "04" "01" "05" "033" "02" "031"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "02" "04" "035" "01" "05" "04"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "02" "01" "035" "02" "02" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "02" "04" "02" "02" "036" "02"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "02" "04" "04" "034" "01" "02"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "02" "02" "02" "035" "05" "034"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "02" "02" "02" "031" "036" "02"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "034" "05" "01" "01" "033"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "02" "02" "01" "036" "04" "01"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04" "02" "02" "02" "04" "02"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "031" "04" "01" "01" "02" "01"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "01" "04" "034" "04" "04" "031"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02" "05" "04" "02" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04" "031" "01" "05" "01" "035"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04" "05" "01" "01" "04" "02"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "02" "02" "05" "04" "05" "02"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "034" "04" "04" "02" "02" "04"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "02" "04" "05" "04" "02" "034"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "02" "02" "04" "04" "02" "02"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04" "04" "05" "04" "04" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02" "04" "01" "05" "05" "02"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "035" "033" "05" "02" "032" "02"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02" "04" "034" "032" "02" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04" "02" "032" "01" "02" "02"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "04" "01" "02" "04" "04" "04"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "02" "05" "031" "02" "01" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "032" "02" "01" "05"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 59276))
#> TCGA.D1.A0ZV.01 TCGA.B5.A5OE.01 TCGA.AP.A3K1.01 TCGA.B5.A0K8.01 TCGA.AP.A1DO.01 TCGA.AX.A2H7.01
#> "04" "05" "05" "01" "02" "02"
#> TCGA.EC.A24G.01 TCGA.D1.A0ZZ.01 TCGA.AX.A1CR.01 TCGA.BG.A3PP.01 TCGA.A5.A3LO.01 TCGA.AP.A0LM.01
#> "02" "05" "01" "01" "04" "04"
#> TCGA.BG.A2AD.01 TCGA.AX.A3FW.01 TCGA.PG.A5BC.01 TCGA.AP.A5FX.01 TCGA.D1.A101.01 TCGA.B5.A1MY.01
#> "02" "02" "01" "05" "04" "01"
#> TCGA.A5.A1OF.01 TCGA.D1.A16R.01 TCGA.AX.A3FZ.01 TCGA.DI.A1NN.01 TCGA.AX.A2HK.01 TCGA.B5.A11L.01
#> "04" "02" "05" "05" "05" "02"
#> TCGA.B5.A11Z.01 TCGA.A5.A2K7.01 TCGA.FI.A2D0.01 TCGA.B5.A3FC.01 TCGA.D1.A16I.01 TCGA.EY.A3L3.01
#> "02" "02" "04" "02" "01" "01"
#> TCGA.AX.A2H5.11 TCGA.D1.A17K.01 TCGA.E6.A8L9.01 TCGA.BG.A18A.01 TCGA.EO.A3KX.01 TCGA.FL.A1YU.11
#> "03" "05" "01" "04" "02" "03"
#> TCGA.AX.A1CJ.01 TCGA.EY.A5W2.01 TCGA.PG.A6IB.01 TCGA.D1.A17T.01 TCGA.BG.A221.01 TCGA.EO.A22T.01
#> "02" "02" "04" "02" "04" "04"
#> TCGA.B5.A1MU.01 TCGA.EY.A1GQ.01 TCGA.DI.A0WH.01 TCGA.D1.A103.01 TCGA.D1.A17N.01 TCGA.D1.A1NS.01
#> "01" "02" "05" "02" "04" "04"
#> TCGA.EO.A22R.01 TCGA.D1.A16O.01 TCGA.BK.A6W4.01 TCGA.AX.A2H8.11 TCGA.AX.A1C5.01 TCGA.D1.A1NW.01
#> "02" "04" "03" "03" "04" "05"
#> TCGA.A5.A1OH.01 TCGA.D1.A16Q.01 TCGA.AX.A2HC.11 TCGA.AP.A05O.01 TCGA.FL.A1YV.11 TCGA.AJ.A3BI.01
#> "01" "02" "03" "02" "03" "02"
#> TCGA.FL.A1YF.11 TCGA.D1.A3JQ.01 TCGA.BS.A0V7.01 TCGA.B5.A11W.01 TCGA.AX.A0IZ.01 TCGA.D1.A17M.01
#> "03" "01" "04" "02" "04" "02"
#> TCGA.AJ.A3BF.01 TCGA.B5.A11H.01 TCGA.AJ.A3QS.01 TCGA.EY.A1GE.01 TCGA.FI.A2D6.01 TCGA.B5.A1N2.01
#> "01" "04" "05" "02" "04" "01"
#> TCGA.AX.A3FT.01 TCGA.BG.A0MK.01 TCGA.DI.A2QT.01 TCGA.D1.A161.01 TCGA.EY.A2OQ.01 TCGA.PG.A916.01
#> "04" "02" "01" "02" "05" "02"
#> TCGA.EY.A1H0.01 TCGA.A5.A7WK.01 TCGA.AX.A1CA.01 TCGA.BS.A0U9.01 TCGA.BK.A13C.01 TCGA.EO.A3AU.01
#> "02" "05" "01" "05" "02" "02"
#> TCGA.FL.A1YM.11 TCGA.EY.A1GI.01 TCGA.FI.A2D4.01 TCGA.A5.A2K2.01 TCGA.EY.A1GJ.01 TCGA.B5.A1MR.01
#> "03" "02" "02" "05" "05" "04"
#> TCGA.FL.A1YQ.11 TCGA.D1.A15X.01 TCGA.D1.A0ZO.01 TCGA.QS.A8F1.01 TCGA.EY.A215.01 TCGA.AX.A1CK.01
#> "03" "04" "02" "01" "02" "02"
#> TCGA.B5.A11S.01 TCGA.EY.A1GL.01 TCGA.AP.A1DM.01 TCGA.BG.A3EW.11 TCGA.BG.A186.01 TCGA.QF.A5YS.01
#> "02" "02" "02" "03" "02" "04"
#> TCGA.BK.A0CA.01 TCGA.AJ.A8CW.01 TCGA.D1.A1NZ.01 TCGA.D1.A3DG.01 TCGA.D1.A17U.01 TCGA.D1.A16F.01
#> "04" "02" "02" "05" "02" "04"
#> TCGA.EY.A3QX.01 TCGA.AX.A06D.01 TCGA.EY.A1GS.01 TCGA.AJ.A3EL.01 TCGA.EO.A1Y5.01 TCGA.D1.A16X.01
#> "04" "02" "04" "02" "01" "04"
#> TCGA.B5.A1MV.01 TCGA.EY.A2OM.01 TCGA.D1.A175.01 TCGA.FI.A2CX.01 TCGA.FL.A1YL.11 TCGA.A5.A0G1.01
#> "04" "02" "02" "03" "03" "04"
#> TCGA.B5.A3FA.01 TCGA.AJ.A2QL.01 TCGA.AP.A1DH.01 TCGA.AJ.A3OJ.01 TCGA.AJ.A8CT.01 TCGA.BG.A0VZ.01
#> "04" "02" "02" "04" "04" "02"
#> TCGA.EO.A22Y.01 TCGA.D1.A17A.01 TCGA.BG.A2AE.01 TCGA.EO.A3B0.01 TCGA.AX.A2IO.01 TCGA.BS.A0WQ.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.AX.A3G9.01 TCGA.EY.A1GC.01 TCGA.D1.A1O0.01 TCGA.AP.A0LS.01 TCGA.EY.A1GW.01 TCGA.D1.A167.01
#> "02" "05" "02" "02" "02" "02"
#> TCGA.D1.A2G6.01 TCGA.FI.A2F8.01 TCGA.BG.A2L7.11 TCGA.DF.A2KU.01 TCGA.AX.A1CI.11 TCGA.D1.A0ZU.01
#> "04" "05" "03" "02" "03" "02"
#> TCGA.B5.A11F.01 TCGA.SJ.A6ZJ.01 TCGA.EO.A3AY.01 TCGA.BG.A220.01 TCGA.BG.A0VW.01 TCGA.BK.A26L.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.FI.A2F4.01 TCGA.AX.A1C8.01 TCGA.AJ.A3BK.01 TCGA.BG.A0YV.01 TCGA.B5.A1MX.01 TCGA.AX.A05Y.11
#> "02" "01" "02" "05" "02" "03"
#> TCGA.AX.A2H5.01 TCGA.JU.AAVI.01 TCGA.D1.A0ZN.01 TCGA.D1.A16S.01 TCGA.FI.A2D2.01 TCGA.D1.A3DA.01
#> "01" "01" "02" "05" "01" "02"
#> TCGA.B5.A11N.01 TCGA.E6.A1LZ.01 TCGA.QS.A744.01 TCGA.BS.A0VI.01 TCGA.BS.A0UA.01 TCGA.KP.A3VZ.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.D1.A168.01 TCGA.H5.A2HR.01 TCGA.D1.A0ZP.01 TCGA.D1.A17F.01 TCGA.AP.A1E1.01 TCGA.EC.A1NJ.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.KP.A3W3.01 TCGA.EY.A549.01 TCGA.BK.A6W3.01 TCGA.FI.A3PV.01 TCGA.B5.A11J.01 TCGA.EO.A2CG.01
#> "01" "02" "02" "05" "02" "01"
#> TCGA.BG.A18C.01 TCGA.EY.A1GP.01 TCGA.BS.A0V6.01 TCGA.DI.A2QU.01 TCGA.AJ.A3NE.01 TCGA.2E.A9G8.01
#> "05" "05" "04" "05" "04" "05"
#> TCGA.AX.A1CJ.11 TCGA.FI.A2EW.01 TCGA.D1.A176.01 TCGA.D1.A17R.01 TCGA.EO.A22S.01 TCGA.FI.A2EX.01
#> "03" "01" "02" "02" "02" "05"
#> TCGA.D1.A17B.01 TCGA.KP.A3W4.01 TCGA.A5.AB3J.01 TCGA.PG.A917.01 TCGA.BK.A0CC.01 TCGA.DF.A2KN.01
#> "04" "01" "04" "02" "01" "04"
#> TCGA.D1.A1NU.01 TCGA.B5.A5OC.01 TCGA.SL.A6J9.01 TCGA.D1.A1NY.01 TCGA.BK.A139.02 TCGA.BK.A139.01
#> "05" "04" "01" "02" "04" "04"
#> TCGA.D1.A16G.01 TCGA.B5.A1MS.01 TCGA.BG.A0W2.01 TCGA.BS.A0U5.01 TCGA.DI.A1NO.01 TCGA.FL.A1YH.11
#> "04" "01" "02" "02" "01" "03"
#> TCGA.D1.A15W.01 TCGA.AJ.A3BH.01 TCGA.AJ.A3EJ.01 TCGA.D1.A174.01 TCGA.AX.A2HD.01 TCGA.FI.A2CY.01
#> "02" "04" "01" "02" "02" "01"
#> TCGA.A5.A2K4.01 TCGA.B5.A11U.01 TCGA.AJ.A2QM.01 TCGA.AJ.A3BD.01 TCGA.AX.A3GB.01 TCGA.AX.A06L.01
#> "01" "05" "01" "05" "02" "04"
#> TCGA.KJ.A3U4.01 TCGA.A5.A2K5.01 TCGA.D1.A160.01 TCGA.AX.A3FV.01 TCGA.BG.A3EW.01 TCGA.BG.A0MA.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.BK.A4ZD.01 TCGA.AX.A06H.01 TCGA.EO.A3KU.01 TCGA.A5.A0GQ.01 TCGA.D1.A17L.01 TCGA.EO.A3B1.01
#> "02" "04" "01" "04" "02" "05"
#> TCGA.AX.A1C7.01 TCGA.AX.A3G8.01 TCGA.B5.A11X.01 TCGA.B5.A11Q.01 TCGA.E6.A2P9.01 TCGA.EO.A2CH.01
#> "01" "02" "04" "02" "02" "05"
#> TCGA.EO.A22X.01 TCGA.EY.A1GU.01 TCGA.EY.A1GH.01 TCGA.AP.A1DQ.01 TCGA.AX.A3G4.01 TCGA.FL.A3WE.11
#> "02" "02" "02" "01" "01" "03"
#> TCGA.D1.A16E.01 TCGA.B5.A0JU.01 TCGA.FI.A2F9.01 TCGA.EO.A1Y7.01 TCGA.BG.A0VV.01 TCGA.AJ.A8CV.01
#> "04" "02" "01" "02" "04" "02"
#> TCGA.EY.A1G7.01 TCGA.BK.A56F.01 TCGA.EY.A1GV.01 TCGA.DF.A2KY.01 TCGA.AJ.A3OL.01 TCGA.AP.A0LF.01
#> "04" "02" "03" "04" "02" "05"
#> TCGA.AX.A2H4.01 TCGA.D1.A102.01 TCGA.DF.A2KZ.01 TCGA.BG.A2AE.11 TCGA.D1.A165.01 TCGA.AX.A2HH.01
#> "04" "02" "04" "03" "02" "02"
#> TCGA.D1.A17S.01 TCGA.E6.A1LX.01 TCGA.AP.A1E3.01 TCGA.BS.A0V4.01 TCGA.5B.A90C.01 TCGA.AJ.A3IA.01
#> "02" "02" "04" "02" "05" "01"
#> TCGA.D1.A1O7.01 TCGA.AW.A1PO.01 TCGA.K6.A3WQ.01 TCGA.AP.A1E0.01 TCGA.DF.A2KS.01 TCGA.BG.A2L7.01
#> "02" "05" "01" "02" "02" "02"
#> TCGA.EY.A548.01 TCGA.B5.A3FD.01 TCGA.D1.A0ZS.01 TCGA.BG.A222.01 TCGA.AX.A1CI.01 TCGA.AX.A2H2.01
#> "02" "05" "04" "02" "02" "01"
#> TCGA.D1.A16V.01 TCGA.AX.A3FS.01 TCGA.EY.A1GF.01 TCGA.BG.A18B.01 TCGA.AJ.A3TW.01 TCGA.DI.A1BY.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.AX.A1CP.01 TCGA.SL.A6JA.01 TCGA.FL.A1YI.11 TCGA.EY.A4KR.01 TCGA.AX.A1CK.11 TCGA.EY.A547.01
#> "01" "02" "03" "05" "03" "02"
#> TCGA.B5.A11G.01 TCGA.A5.A1OK.01 TCGA.EY.A2OO.01 TCGA.EY.A1GR.01 TCGA.B5.A1MZ.01 TCGA.AX.A0IS.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.BS.A0V8.01 TCGA.EC.A1QX.01 TCGA.4E.A92E.01 TCGA.BS.A0UL.01 TCGA.B5.A11I.01 TCGA.A5.A1OG.01
#> "05" "04" "04" "04" "01" "01"
#> TCGA.B5.A11O.01 TCGA.FI.A2EU.01 TCGA.AJ.A3I9.01 TCGA.5S.A9Q8.01 TCGA.B5.A0JT.01 TCGA.BG.A0YU.01
#> "04" "01" "02" "02" "02" "05"
#> TCGA.AJ.A2QO.01 TCGA.AX.A2HC.01 TCGA.AJ.A3NG.01 TCGA.DI.A2QU.11 TCGA.AJ.A3NE.11 TCGA.BG.A0MH.01
#> "02" "02" "04" "03" "03" "02"
#> TCGA.AX.A2HG.01 TCGA.D1.A179.01 TCGA.D1.A15V.01 TCGA.FL.A1YN.11 TCGA.AJ.A5DW.01 TCGA.EO.A22S.11
#> "04" "01" "05" "03" "02" "03"
#> TCGA.AX.A0J0.01 TCGA.D1.A16J.01 TCGA.AX.A2HA.11 TCGA.AX.A1CF.01 TCGA.FI.A3PX.01 TCGA.QS.A5YR.01
#> "02" "04" "03" "01" "05" "04"
#> TCGA.AJ.A3NC.01 TCGA.DI.A2QY.01 TCGA.AJ.A3NH.11 TCGA.AP.A1DV.01 TCGA.B5.A11P.01 TCGA.AX.A3G6.01
#> "02" "01" "03" "02" "02" "05"
#> TCGA.A5.A0VO.01 TCGA.EO.A3L0.01 TCGA.EO.A22U.01 TCGA.QS.A5YQ.01 TCGA.BG.A2AD.11 TCGA.E6.A1M0.01
#> "02" "04" "02" "02" "03" "02"
#> TCGA.D1.A17H.01 TCGA.DI.A1BU.01 TCGA.BS.A0T9.01 TCGA.DI.A1NO.11 TCGA.D1.A1NX.01 TCGA.AX.A1C9.01
#> "02" "04" "04" "03" "01" "02"
#> TCGA.B5.A0JX.01 TCGA.B5.A11V.01 TCGA.B5.A1MW.01 TCGA.AX.A2HD.11 TCGA.EY.A2ON.01 TCGA.AX.A2H7.11
#> "02" "02" "02" "03" "05" "03"
#> TCGA.AX.A3FX.01 TCGA.EY.A2OP.01 TCGA.AJ.A3BG.01 TCGA.BG.A3PP.11 TCGA.BG.A0MA.11 TCGA.D1.A2G5.01
#> "02" "02" "02" "03" "03" "02"
#> TCGA.EY.A214.01 TCGA.BK.A4ZD.11 TCGA.EY.A1GO.01 TCGA.PG.A915.01 TCGA.AJ.A23M.01 TCGA.FL.A1YT.11
#> "05" "03" "05" "01" "01" "03"
#> TCGA.D1.A1O5.01 TCGA.D1.A0ZQ.01 TCGA.KP.A3W0.01 TCGA.DI.A1NN.11 TCGA.B5.A3F9.01 TCGA.B5.A5OD.01
#> "02" "02" "01" "03" "04" "01"
#> TCGA.DF.A2KR.01 TCGA.EY.A1GK.01 TCGA.AP.A1DR.01 TCGA.D1.A0ZR.01 TCGA.SJ.A6ZI.01 TCGA.BG.A0VT.01
#> "04" "02" "02" "02" "04" "02"
#> TCGA.FL.A1YG.11 TCGA.DF.A2KV.01 TCGA.AP.A1E4.01 TCGA.A5.A3LP.01 TCGA.B5.A3FH.01 TCGA.AX.A2HF.01
#> "03" "04" "01" "01" "02" "01"
#> TCGA.D1.A2G7.01 TCGA.A5.A2K3.01 TCGA.AX.A2H4.11 TCGA.BG.A0VX.01 TCGA.A5.A0GG.01 TCGA.EO.A22T.11
#> "01" "04" "03" "04" "04" "03"
#> TCGA.AP.A1DP.01 TCGA.AX.A3G1.01 TCGA.A5.A1OJ.01 TCGA.AX.A2HJ.01 TCGA.AX.A3GI.01 TCGA.PG.A7D5.01
#> "02" "05" "04" "02" "05" "05"
#> TCGA.B5.A121.01 TCGA.EO.A22R.11 TCGA.EY.A54A.01 TCGA.AX.A2H8.01 TCGA.EY.A212.01 TCGA.AX.A1CC.01
#> "04" "03" "01" "05" "01" "03"
#> TCGA.B5.A11M.01 TCGA.B5.A3FB.01 TCGA.EY.A210.01 TCGA.AJ.A23N.01 TCGA.B5.A3S1.01 TCGA.AX.A1CE.01
#> "04" "05" "01" "01" "04" "02"
#> TCGA.EY.A1GX.01 TCGA.QF.A5YT.01 TCGA.KP.A3W1.01 TCGA.AJ.A3OK.01 TCGA.B5.A0KB.01 TCGA.EY.A72D.01
#> "02" "02" "05" "04" "05" "02"
#> TCGA.AX.A0IZ.11 TCGA.B5.A11Y.01 TCGA.EO.A3AS.01 TCGA.AX.A1C4.01 TCGA.EY.A1GT.01 TCGA.D1.A2G0.01
#> "03" "04" "04" "02" "02" "04"
#> TCGA.EY.A1G8.01 TCGA.D1.A17C.01 TCGA.A5.A0GR.01 TCGA.EO.A3AV.01 TCGA.AJ.A5DV.01 TCGA.BK.A13C.11
#> "02" "04" "05" "04" "02" "03"
#> TCGA.B5.A11E.01 TCGA.D1.A17Q.01 TCGA.D1.A16D.01 TCGA.EO.A3AZ.01 TCGA.D1.A15Z.01 TCGA.D1.A17D.01
#> "02" "02" "04" "04" "02" "02"
#> TCGA.D1.A169.01 TCGA.AJ.A6NU.01 TCGA.AX.A3G7.01 TCGA.D1.A16B.01 TCGA.AP.A059.01 TCGA.D1.A3JP.01
#> "04" "04" "05" "04" "04" "05"
#> TCGA.D1.A177.01 TCGA.AJ.A2QK.01 TCGA.AP.A1DK.01 TCGA.EO.A3KW.01 TCGA.AJ.A2QN.01 TCGA.BK.A13B.01
#> "02" "04" "01" "05" "05" "02"
#> TCGA.AJ.A3NF.01 TCGA.AX.A0J0.11 TCGA.D1.A3DH.01 TCGA.EY.A1GD.01 TCGA.AX.A1CF.11 TCGA.BG.A0W1.01
#> "03" "03" "05" "02" "03" "02"
#> TCGA.AJ.A3EK.01 TCGA.D1.A1O8.01 TCGA.AJ.A3NC.11 TCGA.DI.A2QY.11 TCGA.B5.A11R.01 TCGA.AJ.A3NH.01
#> "02" "04" "03" "03" "02" "05"
#> TCGA.D1.A162.01 TCGA.A5.A7WJ.01 TCGA.AJ.A2QL.11 TCGA.DI.A1C3.01 TCGA.DF.A2L0.01 TCGA.BG.A187.01
#> "04" "02" "03" "01" "02" "02"
#> TCGA.FI.A2D5.01 TCGA.PG.A914.01 TCGA.D1.A16N.01 TCGA.E6.A2P8.01 TCGA.AX.A2IN.01 TCGA.AJ.A23O.01
#> "04" "01" "02" "04" "04" "04"
#> TCGA.D1.A163.01 TCGA.AX.A1CN.01 TCGA.E6.A1M0.11 TCGA.D1.A16Y.01 TCGA.EY.A1GM.01 TCGA.EO.A1Y8.01
#> "02" "05" "03" "02" "01" "05"
#> TCGA.AX.A3G3.01 TCGA.AX.A2HA.01 TCGA.FI.A2EY.01 TCGA.AJ.A3EM.01
#> "03" "02" "01" "05"
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 = 1046),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1046),
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 = 1073),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1073),
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 = 1170),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1170),
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 = 1196),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1196),
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 = 1380),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1380),
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 = 1887),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1887),
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 = 1939),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1939),
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 = 2280),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2280),
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 = 3255),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3255),
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 = 3423),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3423),
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 = 3793),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3793),
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 = 4163),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4163),
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 = 4241),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4241),
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 = 5406),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5406),
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 = 6449),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6449),
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 = 7025),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7025),
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 = 9922),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9922),
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 = 10682),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10682),
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 = 13145),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 13145),
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 = 13519),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 13519),
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 = 13545),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 13545),
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 = 14295),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 14295),
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 = 20159),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 20159),
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 = 25163),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 25163),
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 = 59276),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 59276),
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 = 1046))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1073))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1170))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1196))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1380))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1887))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1939))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2280))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3255))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3423))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3793))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4163))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4241))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5406))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6449))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7025))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9922))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10682))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 13145))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 13519))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 13545))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 14295))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 20159))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 25163))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 59276))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 , Node04 , Node05 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 478 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 0.995 0.998 0.4453 0.555 0.555
#> 3 3 1.000 0.987 0.995 0.1879 0.870 0.775
#> 4 4 1.000 0.979 0.991 0.2710 0.820 0.632
#> 5 5 0.992 0.954 0.982 0.1141 0.852 0.594
#> 6 6 0.973 0.942 0.977 0.0586 0.924 0.715
#> 7 7 0.966 0.915 0.964 0.0188 0.971 0.865
#> 8 8 0.873 0.708 0.841 0.0214 0.974 0.871
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.D1.A0ZV.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A5OE.01 1 0.634 0.810 0.84 0.16
#> TCGA.AP.A3K1.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A0K8.01 1 0.000 0.997 1.00 0.00
#> TCGA.AP.A1DO.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2H7.01 2 0.000 0.999 0.00 1.00
#> TCGA.EC.A24G.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A0ZZ.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A1CR.01 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A3PP.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A3LO.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A0LM.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A2AD.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3FW.01 2 0.000 0.999 0.00 1.00
#> TCGA.PG.A5BC.01 1 0.000 0.997 1.00 0.00
#> TCGA.AP.A5FX.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A101.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A1MY.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A1OF.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A16R.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3FZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.DI.A1NN.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A2HK.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A11L.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11Z.01 2 0.000 0.999 0.00 1.00
#> TCGA.A5.A2K7.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2D0.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A3FC.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A16I.01 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A3L3.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A2H5.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A17K.01 1 0.141 0.977 0.98 0.02
#> TCGA.E6.A8L9.01 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A18A.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3KX.01 2 0.000 0.999 0.00 1.00
#> TCGA.FL.A1YU.11 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A1CJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A5W2.01 2 0.000 0.999 0.00 1.00
#> TCGA.PG.A6IB.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17T.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A221.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22T.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A1MU.01 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A1GQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.DI.A0WH.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A103.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17N.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A1NS.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22R.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A16O.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A6W4.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A2H8.11 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A1C5.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A1NW.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A1OH.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A16Q.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2HC.11 1 0.000 0.997 1.00 0.00
#> TCGA.AP.A05O.01 2 0.000 0.999 0.00 1.00
#> TCGA.FL.A1YV.11 1 0.000 0.997 1.00 0.00
#> TCGA.AJ.A3BI.01 2 0.000 0.999 0.00 1.00
#> TCGA.FL.A1YF.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A3JQ.01 1 0.000 0.997 1.00 0.00
#> TCGA.BS.A0V7.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11W.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A0IZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17M.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3BF.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A11H.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3QS.01 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A1GE.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2D6.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A1N2.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A3FT.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A0MK.01 2 0.000 0.999 0.00 1.00
#> TCGA.DI.A2QT.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A161.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A2OQ.01 2 0.680 0.780 0.18 0.82
#> TCGA.PG.A916.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1H0.01 2 0.000 0.999 0.00 1.00
#> TCGA.A5.A7WK.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CA.01 1 0.000 0.997 1.00 0.00
#> TCGA.BS.A0U9.01 1 0.000 0.997 1.00 0.00
#> TCGA.BK.A13C.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3AU.01 2 0.000 0.999 0.00 1.00
#> TCGA.FL.A1YM.11 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A1GI.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2D4.01 2 0.000 0.999 0.00 1.00
#> TCGA.A5.A2K2.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GJ.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A1MR.01 1 0.242 0.956 0.96 0.04
#> TCGA.FL.A1YQ.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A15X.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A0ZO.01 2 0.000 0.999 0.00 1.00
#> TCGA.QS.A8F1.01 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A215.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CK.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11S.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GL.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1DM.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A3EW.11 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A186.01 2 0.000 0.999 0.00 1.00
#> TCGA.QF.A5YS.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A0CA.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A8CW.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A1NZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A3DG.01 2 0.141 0.978 0.02 0.98
#> TCGA.D1.A17U.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A16F.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A3QX.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A06D.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GS.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3EL.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A1Y5.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A16X.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A1MV.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A2OM.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A175.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2CX.01 1 0.000 0.997 1.00 0.00
#> TCGA.FL.A1YL.11 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A0G1.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A3FA.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A2QL.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1DH.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3OJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A8CT.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A0VZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22Y.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17A.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A2AE.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3B0.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2IO.01 1 0.000 0.997 1.00 0.00
#> TCGA.BS.A0WQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3G9.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GC.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A1O0.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A0LS.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GW.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A167.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A2G6.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2F8.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A2L7.11 1 0.000 0.997 1.00 0.00
#> TCGA.DF.A2KU.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CI.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A0ZU.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11F.01 2 0.000 0.999 0.00 1.00
#> TCGA.SJ.A6ZJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3AY.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A220.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A0VW.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A26L.01 1 0.000 0.997 1.00 0.00
#> TCGA.FI.A2F4.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1C8.01 1 0.000 0.997 1.00 0.00
#> TCGA.AJ.A3BK.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A0YV.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A1MX.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A05Y.11 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A2H5.01 1 0.000 0.997 1.00 0.00
#> TCGA.JU.AAVI.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A0ZN.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A16S.01 1 0.000 0.997 1.00 0.00
#> TCGA.FI.A2D2.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A3DA.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11N.01 2 0.000 0.999 0.00 1.00
#> TCGA.E6.A1LZ.01 1 0.000 0.997 1.00 0.00
#> TCGA.QS.A744.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0VI.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0UA.01 2 0.000 0.999 0.00 1.00
#> TCGA.KP.A3VZ.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A168.01 2 0.000 0.999 0.00 1.00
#> TCGA.H5.A2HR.01 1 0.881 0.572 0.70 0.30
#> TCGA.D1.A0ZP.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A17F.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1E1.01 2 0.000 0.999 0.00 1.00
#> TCGA.EC.A1NJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.KP.A3W3.01 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A549.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A6W3.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A3PV.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11J.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A2CG.01 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A18C.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GP.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0V6.01 2 0.000 0.999 0.00 1.00
#> TCGA.DI.A2QU.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3NE.01 2 0.000 0.999 0.00 1.00
#> TCGA.2E.A9G8.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A1CJ.11 1 0.000 0.997 1.00 0.00
#> TCGA.FI.A2EW.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A176.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17R.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22S.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2EX.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A17B.01 2 0.000 0.999 0.00 1.00
#> TCGA.KP.A3W4.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.AB3J.01 2 0.000 0.999 0.00 1.00
#> TCGA.PG.A917.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A0CC.01 1 0.000 0.997 1.00 0.00
#> TCGA.DF.A2KN.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A1NU.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A5OC.01 2 0.000 0.999 0.00 1.00
#> TCGA.SL.A6J9.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A1NY.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A139.02 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A139.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A16G.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A1MS.01 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A0W2.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0U5.01 2 0.000 0.999 0.00 1.00
#> TCGA.DI.A1NO.01 1 0.000 0.997 1.00 0.00
#> TCGA.FL.A1YH.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A15W.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3BH.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3EJ.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A174.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2HD.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2CY.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A2K4.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A11U.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A2QM.01 1 0.000 0.997 1.00 0.00
#> TCGA.AJ.A3BD.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3GB.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A06L.01 2 0.000 0.999 0.00 1.00
#> TCGA.KJ.A3U4.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A2K5.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A160.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3FV.01 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A3EW.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A0MA.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A4ZD.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A06H.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3KU.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A0GQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17L.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3B1.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A1C7.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A3G8.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11X.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11Q.01 2 0.000 0.999 0.00 1.00
#> TCGA.E6.A2P9.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A2CH.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22X.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GU.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GH.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1DQ.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A3G4.01 1 0.000 0.997 1.00 0.00
#> TCGA.FL.A3WE.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A16E.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A0JU.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2F9.01 1 0.000 0.997 1.00 0.00
#> TCGA.EO.A1Y7.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A0VV.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A8CV.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1G7.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A56F.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GV.01 1 0.000 0.997 1.00 0.00
#> TCGA.DF.A2KY.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3OL.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A0LF.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2H4.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A102.01 2 0.000 0.999 0.00 1.00
#> TCGA.DF.A2KZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A2AE.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A165.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2HH.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17S.01 2 0.000 0.999 0.00 1.00
#> TCGA.E6.A1LX.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1E3.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0V4.01 2 0.000 0.999 0.00 1.00
#> TCGA.5B.A90C.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3IA.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A1O7.01 2 0.000 0.999 0.00 1.00
#> TCGA.AW.A1PO.01 2 0.000 0.999 0.00 1.00
#> TCGA.K6.A3WQ.01 1 0.000 0.997 1.00 0.00
#> TCGA.AP.A1E0.01 2 0.000 0.999 0.00 1.00
#> TCGA.DF.A2KS.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A2L7.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A548.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A3FD.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A0ZS.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A222.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CI.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2H2.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A16V.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3FS.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GF.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A18B.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3TW.01 1 0.000 0.997 1.00 0.00
#> TCGA.DI.A1BY.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CP.01 1 0.000 0.997 1.00 0.00
#> TCGA.SL.A6JA.01 2 0.000 0.999 0.00 1.00
#> TCGA.FL.A1YI.11 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A4KR.01 1 0.000 0.997 1.00 0.00
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#> TCGA.EY.A547.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11G.01 2 0.000 0.999 0.00 1.00
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#> TCGA.EY.A1GR.01 1 0.000 0.997 1.00 0.00
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#> TCGA.AX.A0IS.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0V8.01 2 0.000 0.999 0.00 1.00
#> TCGA.EC.A1QX.01 2 0.000 0.999 0.00 1.00
#> TCGA.4E.A92E.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0UL.01 2 0.000 0.999 0.00 1.00
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#> TCGA.B5.A0JT.01 2 0.000 0.999 0.00 1.00
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#> TCGA.D1.A179.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A15V.01 2 0.000 0.999 0.00 1.00
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#> TCGA.AJ.A5DW.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22S.11 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A0J0.01 2 0.000 0.999 0.00 1.00
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#> TCGA.AX.A2HA.11 1 0.000 0.997 1.00 0.00
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#> TCGA.FI.A3PX.01 1 0.000 0.997 1.00 0.00
#> TCGA.QS.A5YR.01 2 0.000 0.999 0.00 1.00
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#> TCGA.DI.A2QY.01 1 0.000 0.997 1.00 0.00
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#> TCGA.AP.A1DV.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11P.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3G6.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A0VO.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3L0.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22U.01 2 0.000 0.999 0.00 1.00
#> TCGA.QS.A5YQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A2AD.11 1 0.000 0.997 1.00 0.00
#> TCGA.E6.A1M0.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17H.01 2 0.000 0.999 0.00 1.00
#> TCGA.DI.A1BU.01 2 0.000 0.999 0.00 1.00
#> TCGA.BS.A0T9.01 2 0.000 0.999 0.00 1.00
#> TCGA.DI.A1NO.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A1NX.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A1C9.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A0JX.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A11V.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A1MW.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2HD.11 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A2ON.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2H7.11 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A3FX.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A2OP.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3BG.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A3PP.11 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A0MA.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A2G5.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A214.01 1 0.000 0.997 1.00 0.00
#> TCGA.BK.A4ZD.11 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A1GO.01 2 0.000 0.999 0.00 1.00
#> TCGA.PG.A915.01 1 0.000 0.997 1.00 0.00
#> TCGA.AJ.A23M.01 1 0.000 0.997 1.00 0.00
#> TCGA.FL.A1YT.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A1O5.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A0ZQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.KP.A3W0.01 1 0.000 0.997 1.00 0.00
#> TCGA.DI.A1NN.11 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A3F9.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A5OD.01 1 0.000 0.997 1.00 0.00
#> TCGA.DF.A2KR.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GK.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1DR.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A0ZR.01 2 0.000 0.999 0.00 1.00
#> TCGA.SJ.A6ZI.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A0VT.01 2 0.000 0.999 0.00 1.00
#> TCGA.FL.A1YG.11 1 0.000 0.997 1.00 0.00
#> TCGA.DF.A2KV.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1E4.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A3LP.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A3FH.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2HF.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A2G7.01 1 0.000 0.997 1.00 0.00
#> TCGA.A5.A2K3.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2H4.11 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A0VX.01 2 0.000 0.999 0.00 1.00
#> TCGA.A5.A0GG.01 1 0.000 0.997 1.00 0.00
#> TCGA.EO.A22T.11 1 0.000 0.997 1.00 0.00
#> TCGA.AP.A1DP.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3G1.01 2 0.000 0.999 0.00 1.00
#> TCGA.A5.A1OJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2HJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A3GI.01 1 0.000 0.997 1.00 0.00
#> TCGA.PG.A7D5.01 2 0.827 0.648 0.26 0.74
#> TCGA.B5.A121.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A22R.11 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A54A.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A2H8.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A212.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A1CC.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A11M.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A3FB.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A210.01 1 0.000 0.997 1.00 0.00
#> TCGA.AJ.A23N.01 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A3S1.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CE.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GX.01 2 0.000 0.999 0.00 1.00
#> TCGA.QF.A5YT.01 2 0.000 0.999 0.00 1.00
#> TCGA.KP.A3W1.01 1 0.000 0.997 1.00 0.00
#> TCGA.AJ.A3OK.01 2 0.000 0.999 0.00 1.00
#> TCGA.B5.A0KB.01 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A72D.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A0IZ.11 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A11Y.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3AS.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1C4.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GT.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A2G0.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1G8.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17C.01 2 0.000 0.999 0.00 1.00
#> TCGA.A5.A0GR.01 1 0.000 0.997 1.00 0.00
#> TCGA.EO.A3AV.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A5DV.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A13C.11 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A11E.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17Q.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A16D.01 2 0.000 0.999 0.00 1.00
#> TCGA.EO.A3AZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A15Z.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A17D.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A169.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A6NU.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A3G7.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A16B.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A059.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A3JP.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A177.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A2QK.01 2 0.000 0.999 0.00 1.00
#> TCGA.AP.A1DK.01 1 0.000 0.997 1.00 0.00
#> TCGA.EO.A3KW.01 1 0.141 0.977 0.98 0.02
#> TCGA.AJ.A2QN.01 2 0.000 0.999 0.00 1.00
#> TCGA.BK.A13B.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3NF.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A0J0.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A3DH.01 1 0.000 0.997 1.00 0.00
#> TCGA.EY.A1GD.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CF.11 1 0.000 0.997 1.00 0.00
#> TCGA.BG.A0W1.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3EK.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A1O8.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3NC.11 1 0.000 0.997 1.00 0.00
#> TCGA.DI.A2QY.11 1 0.000 0.997 1.00 0.00
#> TCGA.B5.A11R.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A3NH.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A162.01 2 0.000 0.999 0.00 1.00
#> TCGA.A5.A7WJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A2QL.11 1 0.000 0.997 1.00 0.00
#> TCGA.DI.A1C3.01 1 0.000 0.997 1.00 0.00
#> TCGA.DF.A2L0.01 2 0.000 0.999 0.00 1.00
#> TCGA.BG.A187.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2D5.01 2 0.000 0.999 0.00 1.00
#> TCGA.PG.A914.01 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A16N.01 2 0.000 0.999 0.00 1.00
#> TCGA.E6.A2P8.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A2IN.01 2 0.000 0.999 0.00 1.00
#> TCGA.AJ.A23O.01 2 0.000 0.999 0.00 1.00
#> TCGA.D1.A163.01 2 0.000 0.999 0.00 1.00
#> TCGA.AX.A1CN.01 2 0.000 0.999 0.00 1.00
#> TCGA.E6.A1M0.11 1 0.000 0.997 1.00 0.00
#> TCGA.D1.A16Y.01 2 0.000 0.999 0.00 1.00
#> TCGA.EY.A1GM.01 1 0.000 0.997 1.00 0.00
#> TCGA.EO.A1Y8.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A3G3.01 1 0.000 0.997 1.00 0.00
#> TCGA.AX.A2HA.01 2 0.000 0.999 0.00 1.00
#> TCGA.FI.A2EY.01 1 0.000 0.997 1.00 0.00
#> TCGA.AJ.A3EM.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.D1.A0ZV.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A5OE.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AP.A3K1.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.B5.A0K8.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AP.A1DO.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A2H7.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EC.A24G.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A0ZZ.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AX.A1CR.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.BG.A3PP.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.A5.A3LO.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AP.A0LM.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A2AD.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A3FW.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.PG.A5BC.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AP.A5FX.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A101.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A1MY.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.A5.A1OF.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A16R.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A3FZ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.DI.A1NN.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AX.A2HK.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.B5.A11L.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A11Z.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A5.A2K7.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FI.A2D0.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A3FC.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A16I.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EY.A3L3.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AX.A2H5.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D1.A17K.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.E6.A8L9.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.BG.A18A.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A3KX.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FL.A1YU.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AX.A1CJ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A5W2.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.PG.A6IB.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A17T.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A221.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A22T.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A1MU.01 1 0.6045 0.385 0.62 0.00 0.38
#> TCGA.EY.A1GQ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.DI.A0WH.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A103.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A17N.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A1NS.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A22R.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A16O.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BK.A6W4.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AX.A2H8.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AX.A1C5.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A1NW.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.A5.A1OH.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A2HC.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AP.A05O.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FL.A1YV.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AJ.A3BI.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FL.A1YF.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D1.A3JQ.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.BS.A0V7.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A11W.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A0IZ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A17M.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A3BF.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.B5.A11H.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A3QS.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FI.A2D6.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A1N2.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AX.A3FT.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A0MK.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.DI.A2QT.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A2OQ.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.PG.A916.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1H0.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A5.A7WK.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A1CA.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.BS.A0U9.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.BK.A13C.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A3AU.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FL.A1YM.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EY.A1GI.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FI.A2D4.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A5.A2K2.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EY.A1GJ.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.B5.A1MR.01 2 0.2537 0.905 0.08 0.92 0.00
#> TCGA.FL.A1YQ.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D1.A15X.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A0ZO.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.QS.A8F1.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EY.A215.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A1CK.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1GL.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AP.A1DM.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A3EW.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BG.A186.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.QF.A5YS.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BK.A0CA.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A8CW.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A1NZ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A3DG.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A17U.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A16F.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A3QX.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A06D.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1GS.01 1 0.0892 0.955 0.98 0.02 0.00
#> TCGA.AJ.A3EL.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A1Y5.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A16X.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A1MV.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A2OM.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A175.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FI.A2CX.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FL.A1YL.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.A5.A0G1.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A3FA.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A2QL.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AP.A1DH.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A3OJ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A8CT.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A0VZ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A22Y.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A17A.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A2AE.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A3B0.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A2IO.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.BS.A0WQ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A3G9.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1GC.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A1O0.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AP.A0LS.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1GW.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A167.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A2G6.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FI.A2F8.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.BG.A2L7.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DF.A2KU.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A1CI.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D1.A0ZU.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A3AY.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A220.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A0VW.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BK.A26L.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.FI.A2F4.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A1C8.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AJ.A3BK.01 2 0.0000 0.998 0.00 1.00 0.00
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#> TCGA.B5.A0KB.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EY.A72D.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A0IZ.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.B5.A11Y.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A3AS.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A1C4.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1GT.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A2G0.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1G8.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A17C.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A5.A0GR.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EO.A3AV.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A5DV.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BK.A13C.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.B5.A11E.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A17Q.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A16D.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EO.A3AZ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A15Z.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A17D.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A169.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A6NU.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AX.A3G7.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A16B.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AP.A059.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A3JP.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A177.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A2QK.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AP.A1DK.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EO.A3KW.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AJ.A2QN.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BK.A13B.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A3NF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AX.A0J0.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D1.A3DH.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EY.A1GD.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A1CF.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BG.A0W1.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A3EK.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A1O8.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A3NC.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DI.A2QY.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.B5.A11R.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A3NH.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A162.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A5.A7WJ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A2QL.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DI.A1C3.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.DF.A2L0.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BG.A187.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FI.A2D5.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.PG.A914.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.D1.A16N.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.E6.A2P8.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A2IN.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AJ.A23O.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D1.A163.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AX.A1CN.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.E6.A1M0.11 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D1.A16Y.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EY.A1GM.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.EO.A1Y8.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AX.A3G3.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AX.A2HA.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.FI.A2EY.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.AJ.A3EM.01 2 0.5016 0.678 0.24 0.76 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D1.A0ZV.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.B5.A5OE.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AP.A3K1.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.B5.A0K8.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AP.A1DO.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A2H7.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EC.A24G.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A0ZZ.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CR.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.BG.A3PP.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.A5.A3LO.01 2 0.3400 0.782 0.00 0.82 0.00 0.18
#> TCGA.AP.A0LM.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.BG.A2AD.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FW.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.PG.A5BC.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AP.A5FX.01 1 0.1211 0.951 0.96 0.00 0.00 0.04
#> TCGA.D1.A101.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.B5.A1MY.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.A5.A1OF.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A16R.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FZ.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.DI.A1NN.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HK.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.B5.A11L.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.B5.A11Z.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FI.A2D0.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.B5.A3FC.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A16I.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.EY.A3L3.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H5.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A17K.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.E6.A8L9.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.BG.A18A.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KX.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FL.A1YU.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A1CJ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A5W2.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.PG.A6IB.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A17T.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BG.A221.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.EO.A22T.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.B5.A1MU.01 1 0.0707 0.974 0.98 0.00 0.02 0.00
#> TCGA.EY.A1GQ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.DI.A0WH.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A103.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A17N.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A1NS.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A22R.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A16O.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.BK.A6W4.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A2H8.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A1C5.01 2 0.0707 0.971 0.00 0.98 0.00 0.02
#> TCGA.D1.A1NW.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.A5.A1OH.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A2HC.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AP.A05O.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FL.A1YV.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3BI.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FL.A1YF.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A3JQ.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.BS.A0V7.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.B5.A11W.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A0IZ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A17M.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3BF.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.B5.A11H.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3QS.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FI.A2D6.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.B5.A1N2.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.BG.A0MK.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.DI.A2QT.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A2OQ.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.PG.A916.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A1H0.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.A5.A7WK.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AX.A1CA.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.BS.A0U9.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.BK.A13C.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A3AU.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FL.A1YM.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GI.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.A5.A2K2.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.EY.A1GJ.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MR.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.FL.A1YQ.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A15X.01 2 0.4134 0.656 0.00 0.74 0.00 0.26
#> TCGA.D1.A0ZO.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.QS.A8F1.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.EY.A215.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CK.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GL.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AP.A1DM.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BG.A3EW.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BG.A186.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.QF.A5YS.01 4 0.1211 0.931 0.00 0.04 0.00 0.96
#> TCGA.BK.A0CA.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A8CW.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A1NZ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A3DG.01 4 0.4134 0.651 0.26 0.00 0.00 0.74
#> TCGA.D1.A17U.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A16F.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A3QX.01 2 0.1211 0.951 0.00 0.96 0.00 0.04
#> TCGA.AX.A06D.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GS.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3EL.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A1Y5.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A16X.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.B5.A1MV.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A2OM.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A175.01 4 0.4522 0.486 0.00 0.32 0.00 0.68
#> TCGA.FI.A2CX.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FL.A1YL.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.A5.A0G1.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.B5.A3FA.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AJ.A2QL.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AP.A1DH.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3OJ.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AJ.A8CT.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.BG.A0VZ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A22Y.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A17A.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BG.A2AE.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A3B0.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A2IO.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.BS.A0WQ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A3G9.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GC.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A1O0.01 2 0.3610 0.751 0.00 0.80 0.00 0.20
#> TCGA.AP.A0LS.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GW.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A167.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A2G6.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FI.A2F8.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.BG.A2L7.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DF.A2KU.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CI.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A0ZU.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A3AY.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BG.A220.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BG.A0VW.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BK.A26L.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.FI.A2F4.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BG.A0YV.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.B5.A1MX.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A05Y.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A2H5.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.JU.AAVI.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZN.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A16S.01 1 0.4624 0.482 0.66 0.00 0.00 0.34
#> TCGA.FI.A2D2.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A3DA.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.B5.A11N.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.E6.A1LZ.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.QS.A744.01 2 0.0707 0.971 0.00 0.98 0.00 0.02
#> TCGA.BS.A0VI.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BS.A0UA.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.KP.A3VZ.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A168.01 4 0.0707 0.958 0.00 0.02 0.00 0.98
#> TCGA.H5.A2HR.01 4 0.2345 0.876 0.10 0.00 0.00 0.90
#> TCGA.D1.A0ZP.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A17F.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AP.A1E1.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EC.A1NJ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.KP.A3W3.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.EY.A549.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BK.A6W3.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FI.A3PV.01 4 0.1211 0.944 0.04 0.00 0.00 0.96
#> TCGA.B5.A11J.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A2CG.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
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#> TCGA.D1.A165.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A2HH.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
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#> TCGA.E6.A1LX.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
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#> TCGA.DI.A1BY.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
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#> TCGA.B5.A11Y.01 4 0.1211 0.931 0.00 0.04 0.00 0.96
#> TCGA.EO.A3AS.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AX.A1C4.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GT.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A2G0.01 2 0.0707 0.971 0.00 0.98 0.00 0.02
#> TCGA.EY.A1G8.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A17C.01 2 0.3801 0.723 0.00 0.78 0.00 0.22
#> TCGA.A5.A0GR.01 4 0.3975 0.686 0.24 0.00 0.00 0.76
#> TCGA.EO.A3AV.01 4 0.1211 0.931 0.00 0.04 0.00 0.96
#> TCGA.AJ.A5DV.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BK.A13C.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.B5.A11E.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A16D.01 4 0.0707 0.958 0.00 0.02 0.00 0.98
#> TCGA.EO.A3AZ.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A15Z.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A17D.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A169.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A6NU.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AX.A3G7.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A16B.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AP.A059.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A3JP.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A177.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QK.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AP.A1DK.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.EO.A3KW.01 1 0.1211 0.950 0.96 0.00 0.00 0.04
#> TCGA.AJ.A2QN.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.BK.A13B.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NF.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A0J0.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A3DH.01 1 0.2345 0.880 0.90 0.00 0.00 0.10
#> TCGA.EY.A1GD.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CF.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BG.A0W1.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3EK.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A1O8.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3NC.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DI.A2QY.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.B5.A11R.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NH.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.D1.A162.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.A5.A7WJ.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QL.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DI.A1C3.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.DF.A2L0.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.BG.A187.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FI.A2D5.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.PG.A914.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.D1.A16N.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.E6.A2P8.01 2 0.3400 0.783 0.00 0.82 0.00 0.18
#> TCGA.AX.A2IN.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AJ.A23O.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.D1.A163.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CN.01 4 0.0000 0.982 0.00 0.00 0.00 1.00
#> TCGA.E6.A1M0.11 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A16Y.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GM.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AX.A3G3.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A2HA.01 2 0.0000 0.990 0.00 1.00 0.00 0.00
#> TCGA.FI.A2EY.01 1 0.0000 0.993 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EM.01 4 0.0000 0.982 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.D1.A0ZV.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A5OE.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.AP.A3K1.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.B5.A0K8.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AP.A1DO.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A2H7.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EC.A24G.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A0ZZ.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.AX.A1CR.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.BG.A3PP.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.A5.A3LO.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AP.A0LM.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.BG.A2AD.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A3FW.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.PG.A5BC.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AP.A5FX.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.D1.A101.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A1MY.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.A5.A1OF.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A16R.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A3FZ.01 5 0.0609 0.9449 0.00 0.00 0.0 0.02 0.98
#> TCGA.DI.A1NN.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.AX.A2HK.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.B5.A11L.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.B5.A11Z.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FI.A2D0.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A3FC.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A16I.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.EY.A3L3.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AX.A2H5.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.D1.A17K.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.E6.A8L9.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.BG.A18A.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EO.A3KX.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FL.A1YU.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AX.A1CJ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A5W2.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.PG.A6IB.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A17T.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BG.A221.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EO.A22T.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A1MU.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.DI.A0WH.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.D1.A103.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A17N.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A1NS.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EO.A22R.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A16O.01 4 0.1043 0.9301 0.00 0.00 0.0 0.96 0.04
#> TCGA.BK.A6W4.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AX.A2H8.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AX.A1C5.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A1NW.01 5 0.4182 0.3088 0.40 0.00 0.0 0.00 0.60
#> TCGA.A5.A1OH.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A2HC.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AP.A05O.01 2 0.2929 0.7799 0.00 0.82 0.0 0.18 0.00
#> TCGA.FL.A1YV.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AJ.A3BI.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FL.A1YF.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.D1.A3JQ.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.BS.A0V7.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A11W.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A0IZ.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A17M.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AJ.A3BF.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.B5.A11H.01 4 0.0609 0.9418 0.00 0.02 0.0 0.98 0.00
#> TCGA.AJ.A3QS.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.EY.A1GE.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FI.A2D6.01 4 0.0609 0.9415 0.00 0.02 0.0 0.98 0.00
#> TCGA.B5.A1N2.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AX.A3FT.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.BG.A0MK.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.DI.A2QT.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A2OQ.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.PG.A916.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1H0.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.A5.A7WK.01 5 0.3424 0.6570 0.00 0.00 0.0 0.24 0.76
#> TCGA.AX.A1CA.01 1 0.3796 0.5752 0.70 0.00 0.0 0.00 0.30
#> TCGA.BS.A0U9.01 5 0.4126 0.3694 0.38 0.00 0.0 0.00 0.62
#> TCGA.BK.A13C.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EO.A3AU.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FL.A1YM.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.EY.A1GI.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.A5.A2K2.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.EY.A1GJ.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.B5.A1MR.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.FL.A1YQ.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.D1.A15X.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A0ZO.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.QS.A8F1.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.EY.A215.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A1CK.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1GL.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AP.A1DM.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BG.A3EW.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.BG.A186.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.QF.A5YS.01 4 0.0609 0.9417 0.00 0.02 0.0 0.98 0.00
#> TCGA.BK.A0CA.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AJ.A8CW.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A1NZ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A3DG.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.D1.A17U.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A16F.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EY.A3QX.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AX.A06D.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1GS.01 4 0.2929 0.7772 0.00 0.00 0.0 0.82 0.18
#> TCGA.AJ.A3EL.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EO.A1Y5.01 1 0.2280 0.8451 0.88 0.00 0.0 0.00 0.12
#> TCGA.D1.A16X.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A1MV.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EY.A2OM.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A175.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FI.A2CX.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.FL.A1YL.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.A5.A0G1.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A3FA.01 4 0.3561 0.6636 0.00 0.00 0.0 0.74 0.26
#> TCGA.AJ.A2QL.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AP.A1DH.01 2 0.2020 0.8835 0.00 0.90 0.0 0.10 0.00
#> TCGA.AJ.A3OJ.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AJ.A8CT.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.BG.A0VZ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EO.A22Y.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A17A.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BG.A2AE.01 4 0.0609 0.9415 0.00 0.02 0.0 0.98 0.00
#> TCGA.EO.A3B0.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A2IO.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.BS.A0WQ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A3G9.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1GC.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.D1.A1O0.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AP.A0LS.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1GW.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A167.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.FI.A2F8.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.BG.A2L7.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.DF.A2KU.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A1CI.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.D1.A0ZU.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EO.A3AY.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BG.A220.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BG.A0VW.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BK.A26L.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.FI.A2F4.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AJ.A3BK.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BG.A0YV.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.B5.A1MX.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A05Y.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AX.A2H5.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.JU.AAVI.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
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#> TCGA.B5.A3F9.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A5OD.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.DF.A2KR.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EY.A1GK.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AP.A1DR.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A0ZR.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.SJ.A6ZI.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.BG.A0VT.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FL.A1YG.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.DF.A2KV.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AP.A1E4.01 1 0.3983 0.4932 0.66 0.00 0.0 0.00 0.34
#> TCGA.A5.A3LP.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.B5.A3FH.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A2HF.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.D1.A2G7.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.A5.A2K3.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AX.A2H4.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.BG.A0VX.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.A5.A0GG.01 4 0.3895 0.5398 0.00 0.00 0.0 0.68 0.32
#> TCGA.EO.A22T.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AP.A1DP.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A3G1.01 5 0.1410 0.9024 0.00 0.00 0.0 0.06 0.94
#> TCGA.A5.A1OJ.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AX.A2HJ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A3GI.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.PG.A7D5.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.B5.A121.01 4 0.3561 0.6640 0.00 0.00 0.0 0.74 0.26
#> TCGA.EO.A22R.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.EY.A54A.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AX.A2H8.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.EY.A212.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AX.A1CC.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.B5.A11M.01 4 0.3561 0.6565 0.00 0.00 0.0 0.74 0.26
#> TCGA.B5.A3FB.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.EY.A210.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AJ.A23N.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.B5.A3S1.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AX.A1CE.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1GX.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.QF.A5YT.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.KP.A3W1.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.AJ.A3OK.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A0KB.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.EY.A72D.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A0IZ.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.B5.A11Y.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EO.A3AS.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AX.A1C4.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1GT.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A2G0.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EY.A1G8.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A17C.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.A5.A0GR.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.EO.A3AV.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AJ.A5DV.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BK.A13C.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.B5.A11E.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A16D.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.EO.A3AZ.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A15Z.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A17D.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A169.01 4 0.1410 0.8940 0.00 0.06 0.0 0.94 0.00
#> TCGA.AJ.A6NU.01 4 0.4227 0.2957 0.00 0.00 0.0 0.58 0.42
#> TCGA.AX.A3G7.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.D1.A16B.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AP.A059.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A3JP.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.D1.A177.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AJ.A2QK.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AP.A1DK.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.EO.A3KW.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.AJ.A2QN.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.BK.A13B.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AJ.A3NF.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.AX.A0J0.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.D1.A3DH.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.EY.A1GD.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A1CF.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.BG.A0W1.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AJ.A3EK.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.D1.A1O8.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AJ.A3NC.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.DI.A2QY.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.B5.A11R.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AJ.A3NH.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.D1.A162.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.A5.A7WJ.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AJ.A2QL.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.DI.A1C3.01 1 0.4227 0.2875 0.58 0.00 0.0 0.00 0.42
#> TCGA.DF.A2L0.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.BG.A187.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FI.A2D5.01 4 0.0609 0.9419 0.00 0.02 0.0 0.98 0.00
#> TCGA.PG.A914.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.D1.A16N.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.E6.A2P8.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AX.A2IN.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.AJ.A23O.01 4 0.0000 0.9616 0.00 0.00 0.0 1.00 0.00
#> TCGA.D1.A163.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.AX.A1CN.01 5 0.0000 0.9641 0.00 0.00 0.0 0.00 1.00
#> TCGA.E6.A1M0.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00
#> TCGA.D1.A16Y.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1GM.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.EO.A1Y8.01 5 0.4182 0.3098 0.40 0.00 0.0 0.00 0.60
#> TCGA.AX.A3G3.01 3 0.2020 0.8881 0.10 0.00 0.9 0.00 0.00
#> TCGA.AX.A2HA.01 2 0.0000 0.9958 0.00 1.00 0.0 0.00 0.00
#> TCGA.FI.A2EY.01 1 0.0000 0.9653 1.00 0.00 0.0 0.00 0.00
#> TCGA.AJ.A3EM.01 5 0.0000 0.9641 0.00 0.00 0.0 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.D1.A0ZV.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A5OE.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AP.A3K1.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.B5.A0K8.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A1DO.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2H7.01 2 0.3409 0.5617 0.00 0.70 0.0 0.00 0.00 0.30
#> TCGA.EC.A24G.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A0ZZ.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A1CR.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A3PP.01 1 0.3198 0.6848 0.74 0.00 0.0 0.00 0.26 0.00
#> TCGA.A5.A3LO.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AP.A0LM.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BG.A2AD.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3FW.01 2 0.2631 0.7679 0.00 0.82 0.0 0.00 0.00 0.18
#> TCGA.PG.A5BC.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A5FX.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A101.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A1MY.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A1OF.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A16R.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AX.A3FZ.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.DI.A1NN.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A2HK.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.B5.A11L.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11Z.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2D0.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16I.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A3L3.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2H5.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A17K.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.E6.A8L9.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A18A.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EO.A3KX.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FL.A1YU.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A1CJ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A5W2.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.PG.A6IB.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A17T.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A221.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EO.A22T.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A1MU.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DI.A0WH.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.D1.A103.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A17N.01 4 0.0547 0.9373 0.00 0.00 0.0 0.98 0.00 0.02
#> TCGA.D1.A1NS.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EO.A22R.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16O.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BK.A6W4.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A2H8.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A1C5.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A1NW.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.A5.A1OH.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2HC.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AP.A05O.01 2 0.1814 0.8744 0.00 0.90 0.0 0.10 0.00 0.00
#> TCGA.FL.A1YV.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AJ.A3BI.01 6 0.0547 0.9463 0.00 0.02 0.0 0.00 0.00 0.98
#> TCGA.FL.A1YF.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A3JQ.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.BS.A0V7.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A11W.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A0IZ.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A17M.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3BF.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11H.01 4 0.2454 0.7602 0.00 0.16 0.0 0.84 0.00 0.00
#> TCGA.AJ.A3QS.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2D6.01 4 0.0547 0.9331 0.00 0.02 0.0 0.98 0.00 0.00
#> TCGA.B5.A1N2.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BG.A0MK.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DI.A2QT.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A2OQ.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.PG.A916.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1H0.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A7WK.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AX.A1CA.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.BS.A0U9.01 5 0.2454 0.8016 0.16 0.00 0.0 0.00 0.84 0.00
#> TCGA.BK.A13C.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A3AU.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FL.A1YM.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A2K2.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.EY.A1GJ.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.B5.A1MR.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.FL.A1YQ.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A15X.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A0ZO.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.QS.A8F1.01 1 0.3198 0.6849 0.74 0.00 0.0 0.00 0.26 0.00
#> TCGA.EY.A215.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1CK.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GL.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A1DM.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A3EW.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BG.A186.01 6 0.2793 0.7155 0.00 0.20 0.0 0.00 0.00 0.80
#> TCGA.QF.A5YS.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BK.A0CA.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A8CW.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A17U.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16F.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EY.A3QX.01 6 0.2793 0.7408 0.00 0.00 0.0 0.20 0.00 0.80
#> TCGA.AX.A06D.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GS.01 4 0.2793 0.7247 0.00 0.00 0.0 0.80 0.20 0.00
#> TCGA.AJ.A3EL.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A1Y5.01 5 0.2260 0.8291 0.14 0.00 0.0 0.00 0.86 0.00
#> TCGA.D1.A16X.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A1MV.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EY.A2OM.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.D1.A175.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.FI.A2CX.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.FL.A1YL.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.A5.A0G1.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A3FA.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AJ.A2QL.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A1DH.01 2 0.0547 0.9621 0.00 0.98 0.0 0.02 0.00 0.00
#> TCGA.AJ.A3OJ.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A8CT.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BG.A0VZ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A22Y.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A17A.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A2AE.01 4 0.2454 0.7599 0.00 0.16 0.0 0.84 0.00 0.00
#> TCGA.EO.A3B0.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2IO.01 1 0.2048 0.8644 0.88 0.00 0.0 0.00 0.12 0.00
#> TCGA.BS.A0WQ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3G9.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GC.01 5 0.3198 0.6544 0.00 0.00 0.0 0.00 0.74 0.26
#> TCGA.D1.A1O0.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AP.A0LS.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GW.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A167.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.FI.A2F8.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.BG.A2L7.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.DF.A2KU.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1CI.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A0ZU.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.B5.A11F.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A3AY.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A220.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BG.A0VW.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BK.A26L.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2F4.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A0YV.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.B5.A1MX.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A05Y.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A2H5.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.JU.AAVI.01 1 0.2260 0.8441 0.86 0.00 0.0 0.00 0.14 0.00
#> TCGA.D1.A0ZN.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16S.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.FI.A2D2.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A3DA.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11N.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.E6.A1LZ.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.QS.A744.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BS.A0VI.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 2 0.3756 0.3091 0.00 0.60 0.0 0.40 0.00 0.00
#> TCGA.KP.A3VZ.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A168.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.H5.A2HR.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A0ZP.01 1 0.2260 0.8441 0.86 0.00 0.0 0.00 0.14 0.00
#> TCGA.D1.A17F.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A1E1.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.KP.A3W3.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A549.01 6 0.0937 0.9248 0.00 0.04 0.0 0.00 0.00 0.96
#> TCGA.BK.A6W3.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A3PV.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.B5.A11J.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A2CG.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A18C.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.EY.A1GP.01 5 0.0547 0.9594 0.00 0.00 0.0 0.00 0.98 0.02
#> TCGA.BS.A0V6.01 2 0.3869 -0.0373 0.00 0.50 0.0 0.50 0.00 0.00
#> TCGA.DI.A2QU.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AJ.A3NE.01 4 0.2793 0.7242 0.00 0.00 0.0 0.80 0.00 0.20
#> TCGA.2E.A9G8.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A1CJ.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.FI.A2EW.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A176.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A17R.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A22S.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A17B.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.KP.A3W4.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.A5.AB3J.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.PG.A917.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.DF.A2KN.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A1NU.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.B5.A5OC.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.SL.A6J9.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A1NY.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BK.A139.02 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BK.A139.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A16G.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A1MS.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A0W2.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BS.A0U5.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DI.A1NO.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.FL.A1YH.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A15W.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3BH.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A3EJ.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A174.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2HD.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2CY.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A2K4.01 1 0.2048 0.8644 0.88 0.00 0.0 0.00 0.12 0.00
#> TCGA.B5.A11U.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AJ.A2QM.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3BD.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A3GB.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A06L.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.KJ.A3U4.01 1 0.2454 0.8079 0.84 0.00 0.0 0.00 0.16 0.00
#> TCGA.A5.A2K5.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A160.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3FV.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.BG.A3EW.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A0MA.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BK.A4ZD.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A06H.01 4 0.3409 0.5610 0.00 0.30 0.0 0.70 0.00 0.00
#> TCGA.EO.A3KU.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A0GQ.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A17L.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A3B1.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A1C7.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3G8.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11X.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A11Q.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A2CH.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.EO.A22X.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A1DQ.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3G4.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.FL.A3WE.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A16E.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A0JU.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2F9.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A1Y7.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A0VV.01 4 0.3864 0.0935 0.00 0.48 0.0 0.52 0.00 0.00
#> TCGA.AJ.A8CV.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1G7.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BK.A56F.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GV.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.DF.A2KY.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A0LF.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A2H4.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A102.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DF.A2KZ.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BG.A2AE.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A165.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2HH.01 2 0.3828 0.1955 0.00 0.56 0.0 0.00 0.00 0.44
#> TCGA.D1.A17S.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.E6.A1LX.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A1E3.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BS.A0V4.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.5B.A90C.01 5 0.1814 0.8791 0.00 0.00 0.0 0.00 0.90 0.10
#> TCGA.AJ.A3IA.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A1O7.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.K6.A3WQ.01 1 0.3851 0.2178 0.54 0.00 0.0 0.00 0.46 0.00
#> TCGA.AP.A1E0.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A2L7.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A548.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.B5.A3FD.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A0ZS.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BG.A222.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1CI.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2H2.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16V.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3FS.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A18B.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3TW.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.DI.A1BY.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1CP.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.SL.A6JA.01 6 0.0547 0.9463 0.00 0.02 0.0 0.00 0.00 0.98
#> TCGA.FL.A1YI.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A1CK.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.EY.A547.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11G.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A1OK.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A1MZ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A0IS.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BS.A0V8.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.EC.A1QX.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.4E.A92E.01 6 0.4863 0.6009 0.00 0.00 0.0 0.20 0.14 0.66
#> TCGA.BS.A0UL.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.B5.A11I.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.A5.A1OG.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11O.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.FI.A2EU.01 1 0.3647 0.4925 0.64 0.00 0.0 0.00 0.36 0.00
#> TCGA.AJ.A3I9.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A0YU.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AJ.A2QO.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3NG.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.DI.A2QU.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AJ.A3NE.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.3851 0.1324 0.00 0.54 0.0 0.00 0.00 0.46
#> TCGA.AX.A2HG.01 4 0.2260 0.7868 0.00 0.14 0.0 0.86 0.00 0.00
#> TCGA.D1.A179.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A15V.01 6 0.0937 0.9320 0.00 0.00 0.0 0.00 0.04 0.96
#> TCGA.FL.A1YN.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AJ.A5DW.01 6 0.1814 0.8513 0.00 0.10 0.0 0.00 0.00 0.90
#> TCGA.EO.A22S.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16J.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AX.A2HA.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A1CF.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A3PX.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.QS.A5YR.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A3NC.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AJ.A3NH.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AP.A1DV.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11P.01 6 0.3198 0.6274 0.00 0.26 0.0 0.00 0.00 0.74
#> TCGA.AX.A3G6.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.A5.A0VO.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A3L0.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EO.A22U.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A2AD.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.E6.A1M0.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.D1.A17H.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DI.A1BU.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BS.A0T9.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.DI.A1NO.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A1NX.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1C9.01 2 0.0547 0.9622 0.00 0.98 0.0 0.02 0.00 0.00
#> TCGA.B5.A0JX.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A11V.01 6 0.2793 0.7144 0.00 0.20 0.0 0.00 0.00 0.80
#> TCGA.B5.A1MW.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2HD.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.EY.A2ON.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A2H7.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A3FX.01 6 0.0547 0.9463 0.00 0.02 0.0 0.00 0.00 0.98
#> TCGA.EY.A2OP.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BG.A3PP.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BG.A0MA.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A2G5.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A214.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.BK.A4ZD.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.PG.A915.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A23M.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.FL.A1YT.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A1O5.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.KP.A3W0.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.DI.A1NN.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.B5.A3F9.01 6 0.0547 0.9482 0.00 0.00 0.0 0.02 0.00 0.98
#> TCGA.B5.A5OD.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.DF.A2KR.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.EY.A1GK.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AP.A1DR.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A0ZR.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.BG.A0VT.01 2 0.3851 0.1306 0.00 0.54 0.0 0.00 0.00 0.46
#> TCGA.FL.A1YG.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.DF.A2KV.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AP.A1E4.01 5 0.2048 0.8481 0.12 0.00 0.0 0.00 0.88 0.00
#> TCGA.A5.A3LP.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.B5.A3FH.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A2G7.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.A5.A2K3.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AX.A2H4.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BG.A0VX.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.A5.A0GG.01 4 0.3578 0.4664 0.00 0.00 0.0 0.66 0.34 0.00
#> TCGA.EO.A22T.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AP.A1DP.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3G1.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.A5.A1OJ.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AX.A2HJ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A3GI.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.PG.A7D5.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.B5.A121.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.EO.A22R.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.EY.A54A.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A2H8.01 5 0.0547 0.9587 0.00 0.00 0.0 0.00 0.98 0.02
#> TCGA.EY.A212.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1CC.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.B5.A11M.01 4 0.3499 0.5107 0.00 0.00 0.0 0.68 0.32 0.00
#> TCGA.B5.A3FB.01 6 0.1267 0.9133 0.00 0.00 0.0 0.00 0.06 0.94
#> TCGA.EY.A210.01 1 0.2260 0.8441 0.86 0.00 0.0 0.00 0.14 0.00
#> TCGA.AJ.A23N.01 1 0.2454 0.8217 0.84 0.00 0.0 0.00 0.16 0.00
#> TCGA.B5.A3S1.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AX.A1CE.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GX.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.QF.A5YT.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.KP.A3W1.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AJ.A3OK.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.B5.A0KB.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.EY.A72D.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A0IZ.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.B5.A11Y.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EO.A3AS.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AX.A1C4.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A2G0.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EY.A1G8.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A17C.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.A5.A0GR.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.EO.A3AV.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A5DV.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BK.A13C.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.B5.A11E.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16D.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.EO.A3AZ.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A15Z.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A17D.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A169.01 4 0.3706 0.4000 0.00 0.38 0.0 0.62 0.00 0.00
#> TCGA.AJ.A6NU.01 5 0.3797 0.2762 0.00 0.00 0.0 0.42 0.58 0.00
#> TCGA.AX.A3G7.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A16B.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AP.A059.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A3JP.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.D1.A177.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A2QK.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.AP.A1DK.01 1 0.1267 0.9169 0.94 0.00 0.0 0.00 0.06 0.00
#> TCGA.EO.A3KW.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AJ.A2QN.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.BK.A13B.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3NF.01 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.AX.A0J0.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A3DH.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.EY.A1GD.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1CF.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BG.A0W1.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A1O8.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A3NC.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.DI.A2QY.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.B5.A11R.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3NH.01 6 0.1267 0.9135 0.00 0.00 0.0 0.00 0.06 0.94
#> TCGA.D1.A162.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.A5.A7WJ.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A2QL.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.DI.A1C3.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.DF.A2L0.01 6 0.0547 0.9463 0.00 0.02 0.0 0.00 0.00 0.98
#> TCGA.BG.A187.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2D5.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.PG.A914.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.D1.A16N.01 6 0.1556 0.8776 0.00 0.08 0.0 0.00 0.00 0.92
#> TCGA.E6.A2P8.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.AJ.A23O.01 4 0.0000 0.9547 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.D1.A163.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.AX.A1CN.01 6 0.0000 0.9632 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.E6.A1M0.11 3 0.0000 0.9980 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D1.A16Y.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EY.A1GM.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 5 0.0000 0.9756 0.00 0.00 0.0 0.00 1.00 0.00
#> TCGA.AX.A3G3.01 3 0.1814 0.8869 0.10 0.00 0.9 0.00 0.00 0.00
#> TCGA.AX.A2HA.01 2 0.0000 0.9820 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 1 0.0000 0.9622 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.AJ.A3EM.01 5 0.1814 0.8801 0.00 0.00 0.0 0.00 0.90 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D1.A0ZV.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A5OE.01 7 0.2422 0.75961 0.00 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.AP.A3K1.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A0K8.01 1 0.0504 0.96112 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AP.A1DO.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H7.01 2 0.3413 0.36000 0.00 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.EC.A24G.01 2 0.0504 0.96472 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D1.A0ZZ.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CR.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3PP.01 7 0.2745 0.77852 0.16 0.00 0.00 0.00 0.02 0.00 0.82
#> TCGA.A5.A3LO.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A0LM.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A2AD.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FW.01 2 0.2708 0.70279 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.PG.A5BC.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A5FX.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A101.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MY.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A1OF.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A16R.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A3FZ.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DI.A1NN.01 5 0.3221 0.51920 0.00 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.AX.A2HK.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11L.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11Z.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D0.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16I.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A3L3.01 1 0.0504 0.96313 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AX.A2H5.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17K.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E6.A8L9.01 1 0.0504 0.96313 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BG.A18A.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3KX.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YU.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CJ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A5W2.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A6IB.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17T.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A221.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A22T.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MU.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A0WH.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A103.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17N.01 4 0.3388 0.73864 0.00 0.00 0.00 0.76 0.00 0.04 0.20
#> TCGA.D1.A1NS.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A22R.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16O.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BK.A6W4.01 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H8.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C5.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NW.01 7 0.2259 0.77853 0.00 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.A5.A1OH.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A05O.01 2 0.3558 0.09108 0.00 0.52 0.00 0.48 0.00 0.00 0.00
#> TCGA.FL.A1YV.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BI.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FL.A1YF.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3JQ.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0V7.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11W.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0IZ.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17M.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BF.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11H.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3QS.01 7 0.1166 0.83391 0.00 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.EY.A1GE.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D6.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1N2.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0MK.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QT.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OQ.01 7 0.1433 0.82572 0.00 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.PG.A916.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1H0.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A7WK.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A1CA.01 7 0.2912 0.78619 0.04 0.00 0.00 0.00 0.14 0.00 0.82
#> TCGA.BS.A0U9.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BK.A13C.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AU.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YM.11 7 0.0504 0.83913 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.EY.A1GI.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K2.01 5 0.0504 0.87161 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EY.A1GJ.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A1MR.01 4 0.2259 0.83482 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.FL.A1YQ.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A15X.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZO.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A8F1.01 7 0.4597 0.44619 0.36 0.00 0.00 0.00 0.08 0.00 0.56
#> TCGA.EY.A215.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CK.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GL.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DM.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3EW.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A186.01 6 0.2832 0.59095 0.00 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.QF.A5YS.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BK.A0CA.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A8CW.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A17U.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16F.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A3QX.01 6 0.3139 0.54263 0.00 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.AX.A06D.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GS.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3EL.01 2 0.2259 0.79570 0.00 0.84 0.00 0.16 0.00 0.00 0.00
#> TCGA.EO.A1Y5.01 5 0.1671 0.79278 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.D1.A16X.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MV.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A2OM.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A175.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FI.A2CX.01 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YL.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A0G1.01 4 0.2259 0.83482 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.B5.A3FA.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A2QL.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DH.01 2 0.3139 0.57936 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.AJ.A3OJ.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A8CT.01 4 0.2081 0.85604 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.BG.A0VZ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22Y.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17A.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A2AE.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3B0.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2IO.01 7 0.1671 0.81917 0.10 0.00 0.00 0.00 0.00 0.00 0.90
#> TCGA.BS.A0WQ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G9.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GC.01 6 0.5534 -0.14122 0.00 0.00 0.00 0.00 0.36 0.40 0.24
#> TCGA.D1.A1O0.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AP.A0LS.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GW.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A167.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2F8.01 5 0.3294 0.50187 0.00 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.BG.A2L7.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KU.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CI.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZU.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AY.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A220.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BG.A0VW.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A26L.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2F4.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0YV.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A1MX.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A05Y.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H5.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JU.AAVI.01 7 0.0504 0.84381 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.D1.A0ZN.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 7 0.3546 0.17125 0.00 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.FI.A2D2.01 1 0.0504 0.96313 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D1.A3DA.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11N.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E6.A1LZ.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.QS.A744.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BS.A0VI.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 4 0.0863 0.92798 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.KP.A3VZ.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A168.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.H5.A2HR.01 5 0.2259 0.75524 0.00 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.D1.A0ZP.01 7 0.2422 0.76859 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.D1.A17F.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1E1.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W3.01 1 0.1433 0.90953 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.EY.A549.01 6 0.0504 0.88965 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BK.A6W3.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A3PV.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11J.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A2CG.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18C.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GP.01 5 0.1006 0.86307 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.BS.A0V6.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DI.A2QU.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NE.01 4 0.1433 0.89828 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.2E.A9G8.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CJ.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EW.01 5 0.3459 0.27469 0.00 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.D1.A176.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22S.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 5 0.3496 0.23245 0.00 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.D1.A17B.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.AB3J.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.PG.A917.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KN.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NU.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A5OC.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.SL.A6J9.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NY.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A139.02 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BK.A139.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A16G.01 4 0.2422 0.81117 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.B5.A1MS.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0W2.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BS.A0U5.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A1NO.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YH.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A15W.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BH.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EJ.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A174.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HD.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2CY.01 1 0.0863 0.94944 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.A5.A2K4.01 7 0.1671 0.81917 0.10 0.00 0.00 0.00 0.00 0.00 0.90
#> TCGA.B5.A11U.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A2QM.01 1 0.1671 0.88987 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.AJ.A3BD.01 7 0.3815 0.43072 0.00 0.00 0.00 0.00 0.36 0.02 0.62
#> TCGA.AX.A3GB.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.KJ.A3U4.01 1 0.2422 0.78919 0.82 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.A5.A2K5.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A160.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FV.01 7 0.2832 0.69114 0.00 0.00 0.00 0.00 0.24 0.00 0.76
#> TCGA.BG.A3EW.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BK.A4ZD.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06H.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3KU.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A0GQ.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17L.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3B1.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A1C7.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G8.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11X.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11Q.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A2CH.01 5 0.3558 0.00956 0.00 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.EO.A22X.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DQ.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G4.01 1 0.0504 0.96313 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FL.A3WE.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16E.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A0JU.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2F9.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y7.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VV.01 4 0.0863 0.92815 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.AJ.A8CV.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1G7.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BK.A56F.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GV.01 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KY.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A0LF.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A2H4.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A102.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KZ.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A2AE.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A165.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HH.01 2 0.3558 0.02896 0.00 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.D1.A17S.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E6.A1LX.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1E3.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BS.A0V4.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5B.A90C.01 5 0.0504 0.86848 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.AJ.A3IA.01 7 0.3139 0.63023 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.D1.A1O7.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.K6.A3WQ.01 7 0.3617 0.74979 0.16 0.00 0.00 0.00 0.08 0.00 0.76
#> TCGA.AP.A1E0.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A2L7.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A548.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A3FD.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A0ZS.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A222.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CI.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H2.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16V.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FS.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3TW.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DI.A1BY.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CP.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SL.A6JA.01 6 0.0504 0.88965 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.FL.A1YI.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A1CK.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A547.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11G.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A1OK.01 2 0.1671 0.87400 0.00 0.90 0.00 0.10 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 1 0.0504 0.96313 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B5.A1MZ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0IS.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0V8.01 6 0.3221 0.50064 0.00 0.00 0.00 0.00 0.32 0.68 0.00
#> TCGA.EC.A1QX.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4E.A92E.01 7 0.3517 0.52398 0.00 0.00 0.00 0.02 0.00 0.28 0.70
#> TCGA.BS.A0UL.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11I.01 7 0.2912 0.78619 0.04 0.00 0.00 0.00 0.14 0.00 0.82
#> TCGA.A5.A1OG.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11O.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2EU.01 7 0.4243 0.66527 0.22 0.00 0.00 0.00 0.10 0.00 0.68
#> TCGA.AJ.A3I9.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0YU.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A2QO.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NG.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DI.A2QU.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NE.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 6 0.3459 0.36042 0.00 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.AX.A2HG.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A179.01 1 0.0863 0.94737 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.D1.A15V.01 6 0.3459 0.31944 0.00 0.00 0.00 0.00 0.40 0.60 0.00
#> TCGA.FL.A1YN.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A5DW.01 6 0.2081 0.73482 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.EO.A22S.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0504 0.96518 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D1.A16J.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HA.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CF.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A3PX.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QS.A5YR.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3NC.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 7 0.2745 0.77537 0.02 0.00 0.00 0.00 0.16 0.00 0.82
#> TCGA.AJ.A3NH.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DV.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11P.01 6 0.3139 0.50110 0.00 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.AX.A3G6.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A0VO.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3L0.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A22U.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A2AD.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1M0.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A17H.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A1BU.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BS.A0T9.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DI.A1NO.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NX.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C9.01 2 0.1166 0.92155 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.B5.A0JX.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11V.01 6 0.2708 0.61901 0.00 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.B5.A1MW.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HD.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2ON.01 5 0.1664 0.83463 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.AX.A2H7.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FX.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EY.A2OP.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3PP.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G5.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A214.01 7 0.2832 0.62866 0.00 0.00 0.00 0.00 0.24 0.00 0.76
#> TCGA.BK.A4ZD.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.PG.A915.01 1 0.0504 0.96313 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AJ.A23M.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YT.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O5.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W0.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A1NN.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3F9.01 6 0.1433 0.83320 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.B5.A5OD.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KR.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GK.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DR.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZR.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0VT.01 6 0.3459 0.35890 0.00 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.FL.A1YG.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KV.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A1E4.01 5 0.2945 0.60949 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.A5.A3LP.01 1 0.3558 -0.09596 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.B5.A3FH.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G7.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K3.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VX.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A5.A0GG.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EO.A22T.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DP.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G1.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A5.A1OJ.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HJ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3GI.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.PG.A7D5.01 7 0.1433 0.82572 0.00 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.B5.A121.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EO.A22R.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A54A.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H8.01 5 0.4348 0.61555 0.00 0.00 0.00 0.00 0.68 0.14 0.18
#> TCGA.EY.A212.01 1 0.1433 0.90953 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.AX.A1CC.01 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11M.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B5.A3FB.01 6 0.2572 0.70287 0.00 0.00 0.00 0.00 0.20 0.80 0.00
#> TCGA.EY.A210.01 7 0.2422 0.76859 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.AJ.A23N.01 7 0.2422 0.76859 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.B5.A3S1.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A1CE.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GX.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QF.A5YT.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W1.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3OK.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A0KB.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EY.A72D.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0IZ.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11Y.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3AS.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A1C4.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G0.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1G8.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17C.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A5.A0GR.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EO.A3AV.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A5DV.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A13C.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11E.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16D.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3AZ.01 4 0.2259 0.83482 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.D1.A15Z.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17D.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A169.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A3G7.01 7 0.2259 0.77853 0.00 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.D1.A16B.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AP.A059.01 4 0.2081 0.85604 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.D1.A3JP.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D1.A177.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QK.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AP.A1DK.01 7 0.0504 0.84381 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.EO.A3KW.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QN.01 6 0.2259 0.75738 0.00 0.00 0.00 0.00 0.16 0.84 0.00
#> TCGA.BK.A13B.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NF.01 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DH.01 5 0.3413 0.36397 0.00 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.EY.A1GD.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CF.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0W1.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O8.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3NC.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11R.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NH.01 6 0.2569 0.75913 0.00 0.00 0.00 0.00 0.14 0.84 0.02
#> TCGA.D1.A162.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A5.A7WJ.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QL.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A1C3.01 7 0.0000 0.84827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DF.A2L0.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BG.A187.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D5.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.PG.A914.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16N.01 6 0.0504 0.88959 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.E6.A2P8.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A23O.01 4 0.0000 0.98151 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A163.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CN.01 6 0.0000 0.90988 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E6.A1M0.11 3 0.0000 0.99772 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16Y.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GM.01 1 0.0000 0.97457 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 5 0.0000 0.88267 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A3G3.01 3 0.1671 0.87888 0.10 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HA.01 2 0.0000 0.98519 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 1 0.1433 0.90953 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.AJ.A3EM.01 5 0.1006 0.86307 0.00 0.00 0.00 0.00 0.96 0.02 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D1.A0ZV.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.B5.A5OE.01 8 0.3729 -0.04272 0.00 0.00 0.00 0.00 0.02 0.00 0.46 0.52
#> TCGA.AP.A3K1.01 5 0.3333 0.77740 0.00 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.B5.A0K8.01 1 0.1341 0.89574 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.AP.A1DO.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H7.01 2 0.3618 0.34753 0.00 0.60 0.00 0.00 0.02 0.38 0.00 0.00
#> TCGA.EC.A24G.01 2 0.3318 0.27760 0.00 0.54 0.00 0.46 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZZ.01 5 0.3333 0.78689 0.00 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.AX.A1CR.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3PP.01 8 0.4813 -0.12785 0.14 0.00 0.00 0.00 0.00 0.00 0.42 0.44
#> TCGA.A5.A3LO.01 4 0.1091 0.77824 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.AP.A0LM.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.BG.A2AD.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FW.01 2 0.3291 0.56994 0.00 0.70 0.00 0.00 0.02 0.28 0.00 0.00
#> TCGA.PG.A5BC.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A5FX.01 5 0.3329 0.77313 0.00 0.00 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.D1.A101.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.B5.A1MY.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A1OF.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.D1.A16R.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.AX.A3FZ.01 6 0.1091 0.85257 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.DI.A1NN.01 8 0.4943 -0.20709 0.00 0.00 0.00 0.00 0.34 0.00 0.18 0.48
#> TCGA.AX.A2HK.01 8 0.3329 -0.79821 0.00 0.00 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.B5.A11L.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.B5.A11Z.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D0.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.B5.A3FC.01 2 0.0471 0.91539 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.D1.A16I.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A3L3.01 1 0.2623 0.87170 0.84 0.00 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.AX.A2H5.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17K.01 5 0.3318 0.75970 0.00 0.00 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.E6.A8L9.01 1 0.2623 0.87170 0.84 0.00 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.BG.A18A.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3KX.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YU.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.AX.A1CJ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A5W2.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A6IB.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17T.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A221.01 4 0.3272 0.48323 0.00 0.00 0.00 0.58 0.00 0.00 0.42 0.00
#> TCGA.EO.A22T.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MU.01 1 0.1563 0.84937 0.90 0.00 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A0WH.01 6 0.1563 0.83296 0.00 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.D1.A103.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17N.01 7 0.3618 -0.09975 0.00 0.00 0.00 0.38 0.00 0.02 0.60 0.00
#> TCGA.D1.A1NS.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22R.01 2 0.2938 0.61339 0.00 0.70 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.D1.A16O.01 6 0.0000 0.86211 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BK.A6W4.01 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.AX.A2H8.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C5.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NW.01 8 0.3272 0.03845 0.00 0.00 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.A5.A1OH.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.AX.A2HC.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A05O.01 4 0.2756 0.46360 0.00 0.26 0.00 0.74 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YV.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BI.01 6 0.0941 0.84798 0.00 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.FL.A1YF.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.D1.A3JQ.01 1 0.2350 0.88168 0.86 0.00 0.00 0.00 0.04 0.00 0.00 0.10
#> TCGA.BS.A0V7.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.B5.A11W.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0IZ.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17M.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BF.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11H.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3QS.01 7 0.3299 0.24168 0.00 0.00 0.00 0.00 0.00 0.00 0.56 0.44
#> TCGA.EY.A1GE.01 2 0.1275 0.88994 0.00 0.94 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.FI.A2D6.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1N2.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 4 0.3237 0.51518 0.00 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.BG.A0MK.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QT.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OQ.01 7 0.4224 0.08107 0.00 0.00 0.00 0.00 0.06 0.00 0.48 0.46
#> TCGA.PG.A916.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1H0.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A7WK.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.AX.A1CA.01 8 0.3272 0.03845 0.00 0.00 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.BS.A0U9.01 8 0.3333 -0.74023 0.00 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.BK.A13C.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AU.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YM.11 7 0.4904 0.16327 0.00 0.00 0.00 0.00 0.32 0.00 0.50 0.18
#> TCGA.EY.A1GI.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K2.01 5 0.3299 0.80924 0.00 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.EY.A1GJ.01 5 0.3329 0.74074 0.00 0.00 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.B5.A1MR.01 7 0.3272 -0.17540 0.00 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.FL.A1YQ.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.D1.A15X.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZO.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A8F1.01 8 0.5755 0.04457 0.24 0.00 0.00 0.00 0.04 0.00 0.30 0.42
#> TCGA.EY.A215.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CK.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GL.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DM.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3EW.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A186.01 6 0.3291 0.51291 0.00 0.28 0.00 0.00 0.02 0.70 0.00 0.00
#> TCGA.QF.A5YS.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.BK.A0CA.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A8CW.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 5 0.3237 0.78626 0.00 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.D1.A17U.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16F.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A3QX.01 4 0.3449 0.38791 0.00 0.00 0.00 0.66 0.02 0.32 0.00 0.00
#> TCGA.AX.A06D.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.EY.A1GS.01 7 0.1563 0.33574 0.00 0.00 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.AJ.A3EL.01 4 0.3237 0.19517 0.00 0.40 0.00 0.60 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y5.01 8 0.4199 -0.62141 0.06 0.00 0.00 0.00 0.42 0.00 0.00 0.52
#> TCGA.D1.A16X.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MV.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OM.01 6 0.1275 0.83694 0.00 0.00 0.00 0.04 0.02 0.94 0.00 0.00
#> TCGA.D1.A175.01 6 0.0000 0.86211 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FI.A2CX.01 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.FL.A1YL.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.A5.A0G1.01 7 0.3272 -0.17540 0.00 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.B5.A3FA.01 6 0.0808 0.85962 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.AJ.A2QL.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DH.01 4 0.3015 0.38446 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3OJ.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A8CT.01 7 0.3272 -0.17540 0.00 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.BG.A0VZ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22Y.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17A.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.BG.A2AE.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3B0.01 2 0.0471 0.91656 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.AX.A2IO.01 7 0.4537 0.19945 0.10 0.00 0.00 0.00 0.00 0.00 0.50 0.40
#> TCGA.BS.A0WQ.01 2 0.0471 0.91656 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.AX.A3G9.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GC.01 6 0.5477 0.12128 0.00 0.00 0.00 0.00 0.32 0.48 0.04 0.16
#> TCGA.D1.A1O0.01 6 0.0000 0.86211 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AP.A0LS.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GW.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A167.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2F8.01 5 0.4849 0.42374 0.00 0.00 0.00 0.00 0.54 0.00 0.24 0.22
#> TCGA.BG.A2L7.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KU.01 2 0.0471 0.91539 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CI.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZU.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AY.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A220.01 6 0.0808 0.85962 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BG.A0VW.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A26L.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2F4.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.BG.A0YV.01 6 0.1765 0.81970 0.00 0.00 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.B5.A1MX.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A05Y.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H5.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JU.AAVI.01 7 0.3943 0.26116 0.04 0.00 0.00 0.00 0.00 0.00 0.56 0.40
#> TCGA.D1.A0ZN.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 8 0.5030 0.29457 0.00 0.00 0.00 0.00 0.20 0.00 0.34 0.46
#> TCGA.FI.A2D2.01 1 0.2818 0.86265 0.82 0.00 0.00 0.00 0.06 0.00 0.00 0.12
#> TCGA.D1.A3DA.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11N.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1LZ.01 7 0.3193 0.30311 0.00 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.QS.A744.01 6 0.0808 0.85962 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BS.A0VI.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 4 0.0808 0.76514 0.00 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.KP.A3VZ.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A168.01 6 0.0808 0.85962 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.H5.A2HR.01 5 0.4914 0.44778 0.00 0.00 0.00 0.00 0.42 0.00 0.16 0.42
#> TCGA.D1.A0ZP.01 7 0.4999 0.10012 0.18 0.00 0.00 0.00 0.00 0.00 0.42 0.40
#> TCGA.D1.A17F.01 2 0.4040 0.43323 0.00 0.58 0.00 0.38 0.02 0.02 0.00 0.00
#> TCGA.AP.A1E1.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W3.01 1 0.2818 0.85715 0.82 0.00 0.00 0.00 0.06 0.00 0.00 0.12
#> TCGA.EY.A549.01 6 0.1557 0.81117 0.00 0.06 0.00 0.00 0.02 0.92 0.00 0.00
#> TCGA.BK.A6W3.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A3PV.01 5 0.3299 0.80924 0.00 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.B5.A11J.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A2CG.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18C.01 5 0.3272 0.79608 0.00 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.EY.A1GP.01 5 0.3618 0.76703 0.00 0.00 0.00 0.00 0.60 0.02 0.00 0.38
#> TCGA.BS.A0V6.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QU.01 5 0.3299 0.80924 0.00 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.AJ.A3NE.01 4 0.2025 0.70035 0.00 0.00 0.00 0.88 0.02 0.10 0.00 0.00
#> TCGA.2E.A9G8.01 8 0.3329 -0.73380 0.00 0.00 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.AX.A1CJ.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.FI.A2EW.01 8 0.4069 0.18914 0.00 0.00 0.00 0.00 0.14 0.00 0.18 0.68
#> TCGA.D1.A176.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22S.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 8 0.4560 0.12075 0.00 0.00 0.00 0.00 0.22 0.00 0.18 0.60
#> TCGA.D1.A17B.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.KP.A3W4.01 1 0.0808 0.89911 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.A5.AB3J.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.PG.A917.01 2 0.2114 0.79405 0.00 0.84 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KN.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NU.01 5 0.3299 0.80924 0.00 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.B5.A5OC.01 4 0.1765 0.74605 0.00 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.SL.A6J9.01 1 0.1887 0.89836 0.90 0.00 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.D1.A1NY.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A139.02 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A139.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16G.01 7 0.3272 -0.17540 0.00 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.B5.A1MS.01 1 0.1091 0.90830 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.BG.A0W2.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.BS.A0U5.01 2 0.2025 0.83421 0.00 0.88 0.00 0.00 0.02 0.10 0.00 0.00
#> TCGA.DI.A1NO.01 1 0.1887 0.90057 0.90 0.00 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.FL.A1YH.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.D1.A15W.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BH.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.AJ.A3EJ.01 1 0.0471 0.91133 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D1.A174.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HD.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.FI.A2CY.01 1 0.3299 0.81091 0.76 0.00 0.00 0.00 0.06 0.00 0.00 0.18
#> TCGA.A5.A2K4.01 7 0.4804 0.14985 0.14 0.00 0.00 0.00 0.00 0.00 0.46 0.40
#> TCGA.B5.A11U.01 6 0.1341 0.84386 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.AJ.A2QM.01 1 0.2994 0.84070 0.80 0.00 0.00 0.00 0.06 0.00 0.00 0.14
#> TCGA.AJ.A3BD.01 8 0.5203 0.23303 0.00 0.00 0.00 0.00 0.28 0.00 0.30 0.42
#> TCGA.AX.A3GB.01 2 0.3015 0.58242 0.00 0.68 0.00 0.32 0.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.KJ.A3U4.01 1 0.4247 0.60906 0.62 0.00 0.00 0.00 0.10 0.00 0.00 0.28
#> TCGA.A5.A2K5.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A160.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FV.01 8 0.4255 0.15317 0.00 0.00 0.00 0.00 0.08 0.00 0.34 0.58
#> TCGA.BG.A3EW.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.BK.A4ZD.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06H.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3KU.01 1 0.2350 0.88168 0.86 0.00 0.00 0.00 0.04 0.00 0.00 0.10
#> TCGA.A5.A0GQ.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.D1.A17L.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3B1.01 7 0.3237 0.28649 0.00 0.00 0.00 0.00 0.00 0.00 0.60 0.40
#> TCGA.AX.A1C7.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G8.01 2 0.1408 0.89557 0.00 0.94 0.00 0.02 0.02 0.02 0.00 0.00
#> TCGA.B5.A11X.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.B5.A11Q.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A2CH.01 5 0.5203 -0.04521 0.00 0.00 0.00 0.00 0.42 0.00 0.30 0.28
#> TCGA.EO.A22X.01 2 0.3618 0.45668 0.00 0.60 0.00 0.38 0.02 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DQ.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G4.01 1 0.2623 0.87170 0.84 0.00 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.FL.A3WE.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.D1.A16E.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A0JU.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2F9.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y7.01 2 0.1275 0.88994 0.00 0.94 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.BG.A0VV.01 4 0.1275 0.75869 0.00 0.00 0.00 0.94 0.02 0.04 0.00 0.00
#> TCGA.AJ.A8CV.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.EY.A1G7.01 6 0.2569 0.71863 0.00 0.00 0.00 0.16 0.02 0.82 0.00 0.00
#> TCGA.BK.A56F.01 2 0.2224 0.81214 0.00 0.86 0.00 0.00 0.02 0.12 0.00 0.00
#> TCGA.EY.A1GV.01 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.DF.A2KY.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A0LF.01 7 0.2938 0.31947 0.00 0.00 0.00 0.00 0.00 0.00 0.70 0.30
#> TCGA.AX.A2H4.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A102.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.DF.A2KZ.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A2AE.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A165.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HH.01 2 0.3737 0.01922 0.00 0.50 0.00 0.00 0.02 0.48 0.00 0.00
#> TCGA.D1.A17S.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.E6.A1LX.01 2 0.2680 0.81442 0.00 0.84 0.00 0.12 0.02 0.02 0.00 0.00
#> TCGA.AP.A1E3.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.BS.A0V4.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5B.A90C.01 5 0.3690 0.79859 0.00 0.00 0.00 0.00 0.56 0.02 0.00 0.42
#> TCGA.AJ.A3IA.01 8 0.6461 0.00256 0.30 0.00 0.00 0.00 0.24 0.00 0.14 0.32
#> TCGA.D1.A1O7.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 6 0.1091 0.85257 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.K6.A3WQ.01 8 0.4370 -0.02984 0.08 0.00 0.00 0.00 0.00 0.00 0.40 0.52
#> TCGA.AP.A1E0.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 2 0.3843 0.65442 0.00 0.70 0.00 0.24 0.02 0.04 0.00 0.00
#> TCGA.BG.A2L7.01 2 0.0471 0.91539 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EY.A548.01 6 0.0000 0.86211 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A3FD.01 5 0.3318 0.80601 0.00 0.00 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.D1.A0ZS.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A222.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CI.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H2.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16V.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FS.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3TW.01 7 0.3318 0.23080 0.00 0.00 0.00 0.00 0.00 0.00 0.54 0.46
#> TCGA.DI.A1BY.01 2 0.3537 0.67357 0.00 0.72 0.00 0.24 0.02 0.02 0.00 0.00
#> TCGA.AX.A1CP.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SL.A6JA.01 6 0.0941 0.84798 0.00 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.FL.A1YI.11 3 0.2756 0.80808 0.00 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 7 0.3193 0.30311 0.00 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.AX.A1CK.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A547.01 2 0.1275 0.88994 0.00 0.94 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.B5.A11G.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A1OK.01 4 0.3299 0.05475 0.00 0.44 0.00 0.56 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 1 0.2623 0.87170 0.84 0.00 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.B5.A1MZ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0IS.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0V8.01 6 0.4059 0.49984 0.00 0.00 0.00 0.00 0.28 0.64 0.00 0.08
#> TCGA.EC.A1QX.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4E.A92E.01 7 0.2025 0.25250 0.00 0.00 0.00 0.00 0.02 0.10 0.88 0.00
#> TCGA.BS.A0UL.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.B5.A11I.01 8 0.3943 0.03490 0.00 0.00 0.00 0.00 0.04 0.00 0.40 0.56
#> TCGA.A5.A1OG.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11O.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.FI.A2EU.01 8 0.4971 0.01732 0.18 0.00 0.00 0.00 0.00 0.00 0.36 0.46
#> TCGA.AJ.A3I9.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.5S.A9Q8.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0YU.01 6 0.0808 0.85962 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.AJ.A2QO.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NG.01 6 0.0808 0.85945 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.DI.A2QU.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NE.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.3737 0.01826 0.00 0.50 0.00 0.00 0.02 0.48 0.00 0.00
#> TCGA.AX.A2HG.01 4 0.0941 0.77449 0.00 0.00 0.00 0.96 0.02 0.02 0.00 0.00
#> TCGA.D1.A179.01 1 0.2818 0.85715 0.82 0.00 0.00 0.00 0.06 0.00 0.00 0.12
#> TCGA.D1.A15V.01 6 0.3991 0.45779 0.00 0.00 0.00 0.00 0.32 0.62 0.00 0.06
#> TCGA.FL.A1YN.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.AJ.A5DW.01 6 0.2856 0.62721 0.00 0.20 0.00 0.00 0.02 0.78 0.00 0.00
#> TCGA.EO.A22S.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.1804 0.85441 0.00 0.90 0.00 0.00 0.02 0.08 0.00 0.00
#> TCGA.D1.A16J.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HA.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CF.01 1 0.2547 0.87616 0.84 0.00 0.00 0.00 0.04 0.00 0.00 0.12
#> TCGA.FI.A3PX.01 8 0.3329 -0.78293 0.00 0.00 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.QS.A5YR.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NC.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 8 0.3272 0.03845 0.00 0.00 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.AJ.A3NH.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DV.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11P.01 6 0.3637 0.52374 0.00 0.26 0.00 0.02 0.02 0.70 0.00 0.00
#> TCGA.AX.A3G6.01 5 0.3329 0.74074 0.00 0.00 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.A5.A0VO.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3L0.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22U.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.1275 0.88994 0.00 0.94 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.BG.A2AD.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1M0.01 6 0.0000 0.86211 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A17H.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.DI.A1BU.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0T9.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.DI.A1NO.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NX.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C9.01 4 0.4586 0.07563 0.00 0.40 0.00 0.52 0.02 0.06 0.00 0.00
#> TCGA.B5.A0JX.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.B5.A11V.01 6 0.3514 0.42911 0.00 0.34 0.00 0.00 0.02 0.64 0.00 0.00
#> TCGA.B5.A1MW.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.AX.A2HD.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2ON.01 5 0.3690 0.79780 0.00 0.00 0.00 0.00 0.56 0.00 0.02 0.42
#> TCGA.AX.A2H7.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FX.01 6 0.0941 0.84798 0.00 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.EY.A2OP.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3PP.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G5.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A214.01 8 0.4804 0.05057 0.00 0.00 0.00 0.00 0.14 0.00 0.40 0.46
#> TCGA.BK.A4ZD.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 6 0.1563 0.83334 0.00 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.PG.A915.01 1 0.2623 0.87170 0.84 0.00 0.00 0.00 0.06 0.00 0.00 0.10
#> TCGA.AJ.A23M.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YT.11 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.D1.A1O5.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W0.01 1 0.1275 0.90989 0.94 0.00 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.DI.A1NN.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3F9.01 6 0.3690 0.28122 0.00 0.00 0.00 0.42 0.02 0.56 0.00 0.00
#> TCGA.B5.A5OD.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KR.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.EY.A1GK.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DR.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZR.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VT.01 6 0.3737 0.03522 0.00 0.48 0.00 0.00 0.02 0.50 0.00 0.00
#> TCGA.FL.A1YG.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KV.01 4 0.3015 0.59595 0.00 0.00 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.AP.A1E4.01 8 0.5402 -0.29184 0.24 0.00 0.00 0.00 0.26 0.00 0.02 0.48
#> TCGA.A5.A3LP.01 1 0.4059 0.36962 0.64 0.00 0.00 0.00 0.00 0.00 0.08 0.28
#> TCGA.B5.A3FH.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 1 0.2350 0.88168 0.86 0.00 0.00 0.00 0.04 0.00 0.00 0.10
#> TCGA.D1.A2G7.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K3.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.AX.A2H4.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VX.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.A5.A0GG.01 7 0.1341 0.33197 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.EO.A22T.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DP.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G1.01 6 0.1765 0.81970 0.00 0.00 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.A5.A1OJ.01 4 0.2267 0.70657 0.00 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.AX.A2HJ.01 2 0.2650 0.69825 0.00 0.76 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.AX.A3GI.01 5 0.3333 0.75809 0.00 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.PG.A7D5.01 7 0.4004 0.16146 0.00 0.00 0.00 0.00 0.04 0.00 0.50 0.46
#> TCGA.B5.A121.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.EO.A22R.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A54A.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H8.01 5 0.5718 0.43977 0.00 0.00 0.00 0.00 0.54 0.16 0.12 0.18
#> TCGA.EY.A212.01 1 0.2818 0.85715 0.82 0.00 0.00 0.00 0.06 0.00 0.00 0.12
#> TCGA.AX.A1CC.01 3 0.3015 0.78558 0.00 0.00 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.B5.A11M.01 7 0.0471 0.31439 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.B5.A3FB.01 6 0.3170 0.69606 0.00 0.00 0.00 0.00 0.20 0.76 0.00 0.04
#> TCGA.EY.A210.01 7 0.4999 0.10012 0.18 0.00 0.00 0.00 0.00 0.00 0.42 0.40
#> TCGA.AJ.A23N.01 7 0.4999 0.10012 0.18 0.00 0.00 0.00 0.00 0.00 0.42 0.40
#> TCGA.B5.A3S1.01 6 0.1563 0.83334 0.00 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.AX.A1CE.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GX.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QF.A5YT.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W1.01 7 0.3193 0.30311 0.00 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.AJ.A3OK.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.B5.A0KB.01 7 0.1947 0.33809 0.00 0.00 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.EY.A72D.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.AX.A0IZ.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11Y.01 4 0.1947 0.73339 0.00 0.00 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.EO.A3AS.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.AX.A1C4.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 2 0.1091 0.88634 0.00 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G0.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1G8.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.D1.A17C.01 4 0.1765 0.74605 0.00 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.A5.A0GR.01 7 0.3193 0.30311 0.00 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.EO.A3AV.01 4 0.3083 0.57884 0.00 0.00 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.AJ.A5DV.01 2 0.1765 0.83341 0.00 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.BK.A13C.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11E.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.0471 0.91656 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.D1.A16D.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AZ.01 7 0.3272 -0.17540 0.00 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.D1.A15Z.01 2 0.0471 0.91656 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.D1.A17D.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A169.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 7 0.1765 0.33809 0.00 0.00 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.AX.A3G7.01 8 0.3272 0.03845 0.00 0.00 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.D1.A16B.01 6 0.0471 0.86263 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.AP.A059.01 7 0.3299 -0.22557 0.00 0.00 0.00 0.44 0.00 0.00 0.56 0.00
#> TCGA.D1.A3JP.01 7 0.3193 0.30311 0.00 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.D1.A177.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QK.01 6 0.0808 0.85962 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.AP.A1DK.01 7 0.3907 0.27933 0.04 0.00 0.00 0.00 0.00 0.00 0.58 0.38
#> TCGA.EO.A3KW.01 8 0.3333 -0.80400 0.00 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.AJ.A2QN.01 6 0.3293 0.67058 0.00 0.00 0.00 0.00 0.22 0.74 0.00 0.04
#> TCGA.BK.A13B.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NF.01 3 0.4380 0.69139 0.10 0.00 0.58 0.00 0.32 0.00 0.00 0.00
#> TCGA.AX.A0J0.11 3 0.2938 0.79341 0.00 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.D1.A3DH.01 8 0.4952 -0.09546 0.00 0.00 0.00 0.00 0.30 0.00 0.20 0.50
#> TCGA.EY.A1GD.01 2 0.0941 0.90411 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.AX.A1CF.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0W1.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 2 0.3193 0.47648 0.00 0.62 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O8.01 4 0.3193 0.54291 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.AJ.A3NC.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11R.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NH.01 6 0.3299 0.71201 0.00 0.00 0.00 0.00 0.18 0.76 0.00 0.06
#> TCGA.D1.A162.01 6 0.0471 0.85776 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.A5.A7WJ.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QL.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A1C3.01 7 0.3193 0.30311 0.00 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.DF.A2L0.01 6 0.0941 0.84976 0.00 0.00 0.00 0.02 0.02 0.96 0.00 0.00
#> TCGA.BG.A187.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D5.01 6 0.3514 0.46662 0.00 0.00 0.00 0.34 0.02 0.64 0.00 0.00
#> TCGA.PG.A914.01 1 0.1275 0.90989 0.94 0.00 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.D1.A16N.01 6 0.1804 0.78927 0.00 0.08 0.00 0.00 0.02 0.90 0.00 0.00
#> TCGA.E6.A2P8.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A23O.01 4 0.0000 0.80543 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A163.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CN.01 6 0.1765 0.81970 0.00 0.00 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.E6.A1M0.11 3 0.0000 0.89382 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16Y.01 2 0.3514 0.53265 0.00 0.64 0.00 0.34 0.02 0.00 0.00 0.00
#> TCGA.EY.A1GM.01 1 0.0000 0.92187 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 5 0.3333 0.71756 0.00 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.AX.A3G3.01 3 0.4904 0.58879 0.18 0.00 0.50 0.00 0.32 0.00 0.00 0.00
#> TCGA.AX.A2HA.01 2 0.0000 0.92770 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 1 0.2818 0.85715 0.82 0.00 0.00 0.00 0.06 0.00 0.00 0.12
#> TCGA.AJ.A3EM.01 5 0.3299 0.80924 0.00 0.00 0.00 0.00 0.56 0.00 0.00 0.44
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node035-leaf , Node036-leaf , Node041 , Node042 , Node043 , Node051 , Node052 .
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 72 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.971 0.936 0.975 0.4969 0.503 0.503
#> 3 3 0.969 0.975 0.988 0.3374 0.689 0.459
#> 4 4 0.726 0.632 0.821 0.1125 0.871 0.646
#> 5 5 0.730 0.657 0.716 0.0716 0.846 0.496
#> 6 6 0.753 0.660 0.805 0.0314 0.927 0.672
#> 7 7 0.790 0.673 0.818 0.0276 0.949 0.747
#> 8 8 0.801 0.571 0.758 0.0187 0.960 0.785
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.B5.A0K8.01 1 0.000 0.973 1.00 0.00
#> TCGA.AX.A1CR.01 1 0.000 0.973 1.00 0.00
#> TCGA.BG.A3PP.01 1 0.000 0.973 1.00 0.00
#> TCGA.PG.A5BC.01 1 0.000 0.973 1.00 0.00
#> TCGA.B5.A1MY.01 1 0.000 0.973 1.00 0.00
#> TCGA.D1.A16I.01 1 0.000 0.973 1.00 0.00
#> TCGA.EY.A3L3.01 2 0.000 0.973 0.00 1.00
#> TCGA.E6.A8L9.01 2 0.000 0.973 0.00 1.00
#> TCGA.B5.A1MU.01 1 0.634 0.794 0.84 0.16
#> TCGA.A5.A1OH.01 2 0.000 0.973 0.00 1.00
#> TCGA.D1.A3JQ.01 2 0.000 0.973 0.00 1.00
#> TCGA.AJ.A3BF.01 2 0.402 0.906 0.08 0.92
#> TCGA.B5.A1N2.01 1 0.981 0.266 0.58 0.42
#> TCGA.DI.A2QT.01 1 0.000 0.973 1.00 0.00
#> TCGA.AX.A1CA.01 2 0.327 0.924 0.06 0.94
#> TCGA.QS.A8F1.01 1 0.981 0.266 0.58 0.42
#> TCGA.EO.A1Y5.01 2 0.000 0.973 0.00 1.00
#> TCGA.AX.A2IO.01 1 0.000 0.973 1.00 0.00
#> TCGA.BK.A26L.01 2 0.469 0.884 0.10 0.90
#> TCGA.AX.A1C8.01 1 0.000 0.973 1.00 0.00
#> TCGA.AX.A2H5.01 2 0.000 0.973 0.00 1.00
#> TCGA.JU.AAVI.01 1 0.000 0.973 1.00 0.00
#> TCGA.FI.A2D2.01 2 0.000 0.973 0.00 1.00
#> TCGA.KP.A3VZ.01 2 0.000 0.973 0.00 1.00
#> TCGA.D1.A0ZP.01 1 0.000 0.973 1.00 0.00
#> TCGA.KP.A3W3.01 2 0.000 0.973 0.00 1.00
#> TCGA.EO.A2CG.01 1 0.000 0.973 1.00 0.00
#> TCGA.FI.A2EW.01 1 0.000 0.973 1.00 0.00
#> TCGA.KP.A3W4.01 1 0.000 0.973 1.00 0.00
#> TCGA.BK.A0CC.01 1 0.000 0.973 1.00 0.00
#> TCGA.SL.A6J9.01 2 0.000 0.973 0.00 1.00
#> TCGA.B5.A1MS.01 1 0.000 0.973 1.00 0.00
#> TCGA.DI.A1NO.01 2 0.000 0.973 0.00 1.00
#> TCGA.AJ.A3EJ.01 1 0.000 0.973 1.00 0.00
#> TCGA.FI.A2CY.01 2 0.000 0.973 0.00 1.00
#> TCGA.A5.A2K4.01 1 0.000 0.973 1.00 0.00
#> TCGA.AJ.A2QM.01 1 0.000 0.973 1.00 0.00
#> TCGA.KJ.A3U4.01 2 0.000 0.973 0.00 1.00
#> TCGA.EO.A3KU.01 2 0.000 0.973 0.00 1.00
#> TCGA.AX.A1C7.01 2 0.000 0.973 0.00 1.00
#> TCGA.AP.A1DQ.01 1 0.000 0.973 1.00 0.00
#> TCGA.AX.A3G4.01 2 0.000 0.973 0.00 1.00
#> TCGA.FI.A2F9.01 1 0.000 0.973 1.00 0.00
#> TCGA.AJ.A3IA.01 1 0.000 0.973 1.00 0.00
#> TCGA.K6.A3WQ.01 1 0.000 0.973 1.00 0.00
#> TCGA.AX.A2H2.01 1 0.242 0.935 0.96 0.04
#> TCGA.AX.A1CP.01 1 0.000 0.973 1.00 0.00
#> TCGA.EY.A1GR.01 2 0.402 0.906 0.08 0.92
#> TCGA.B5.A11I.01 2 0.990 0.195 0.44 0.56
#> TCGA.A5.A1OG.01 1 0.000 0.973 1.00 0.00
#> TCGA.FI.A2EU.01 1 0.000 0.973 1.00 0.00
#> TCGA.D1.A179.01 2 0.000 0.973 0.00 1.00
#> TCGA.AX.A1CF.01 2 0.000 0.973 0.00 1.00
#> TCGA.DI.A2QY.01 1 0.000 0.973 1.00 0.00
#> TCGA.D1.A1NX.01 2 0.000 0.973 0.00 1.00
#> TCGA.PG.A915.01 2 0.000 0.973 0.00 1.00
#> TCGA.AJ.A23M.01 1 0.000 0.973 1.00 0.00
#> TCGA.KP.A3W0.01 2 0.000 0.973 0.00 1.00
#> TCGA.B5.A5OD.01 1 0.000 0.973 1.00 0.00
#> TCGA.AP.A1E4.01 1 0.000 0.973 1.00 0.00
#> TCGA.A5.A3LP.01 1 0.000 0.973 1.00 0.00
#> TCGA.AX.A2HF.01 2 0.000 0.973 0.00 1.00
#> TCGA.D1.A2G7.01 1 0.000 0.973 1.00 0.00
#> TCGA.EY.A54A.01 1 0.000 0.973 1.00 0.00
#> TCGA.EY.A212.01 2 0.000 0.973 0.00 1.00
#> TCGA.EY.A210.01 1 0.000 0.973 1.00 0.00
#> TCGA.AJ.A23N.01 1 0.000 0.973 1.00 0.00
#> TCGA.AP.A1DK.01 2 0.000 0.973 0.00 1.00
#> TCGA.DI.A1C3.01 1 0.000 0.973 1.00 0.00
#> TCGA.PG.A914.01 2 0.000 0.973 0.00 1.00
#> TCGA.EY.A1GM.01 1 0.000 0.973 1.00 0.00
#> TCGA.FI.A2EY.01 2 0.000 0.973 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B5.A0K8.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AX.A1CR.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BG.A3PP.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.PG.A5BC.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B5.A1MY.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D1.A16I.01 3 0.1529 0.944 0.04 0.00 0.96
#> TCGA.EY.A3L3.01 2 0.1529 0.959 0.00 0.96 0.04
#> TCGA.E6.A8L9.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.B5.A1MU.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.A5.A1OH.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.D1.A3JQ.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.AJ.A3BF.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.B5.A1N2.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.DI.A2QT.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AX.A1CA.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.QS.A8F1.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.EO.A1Y5.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.AX.A2IO.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BK.A26L.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.AX.A1C8.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AX.A2H5.01 2 0.1529 0.959 0.00 0.96 0.04
#> TCGA.JU.AAVI.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FI.A2D2.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.KP.A3VZ.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.D1.A0ZP.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.KP.A3W3.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.EO.A2CG.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FI.A2EW.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.KP.A3W4.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BK.A0CC.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.SL.A6J9.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.B5.A1MS.01 3 0.3340 0.867 0.12 0.00 0.88
#> TCGA.DI.A1NO.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.AJ.A3EJ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FI.A2CY.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.A5.A2K4.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AJ.A2QM.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.KJ.A3U4.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.EO.A3KU.01 2 0.2959 0.906 0.00 0.90 0.10
#> TCGA.AX.A1C7.01 3 0.0892 0.959 0.00 0.02 0.98
#> TCGA.AP.A1DQ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AX.A3G4.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.FI.A2F9.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AJ.A3IA.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.K6.A3WQ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AX.A2H2.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.AX.A1CP.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EY.A1GR.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.B5.A11I.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.A5.A1OG.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.FI.A2EU.01 3 0.0892 0.960 0.02 0.00 0.98
#> TCGA.D1.A179.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.AX.A1CF.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.DI.A2QY.01 3 0.4555 0.769 0.20 0.00 0.80
#> TCGA.D1.A1NX.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.PG.A915.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.AJ.A23M.01 3 0.3340 0.867 0.12 0.00 0.88
#> TCGA.KP.A3W0.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.B5.A5OD.01 1 0.0892 0.978 0.98 0.00 0.02
#> TCGA.AP.A1E4.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.A5.A3LP.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AX.A2HF.01 3 0.2537 0.902 0.00 0.08 0.92
#> TCGA.D1.A2G7.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EY.A54A.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EY.A212.01 2 0.2959 0.906 0.00 0.90 0.10
#> TCGA.EY.A210.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AJ.A23N.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AP.A1DK.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.DI.A1C3.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.PG.A914.01 2 0.0000 0.984 0.00 1.00 0.00
#> TCGA.EY.A1GM.01 3 0.0000 0.974 0.00 0.00 1.00
#> TCGA.FI.A2EY.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.B5.A0K8.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.AX.A1CR.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.BG.A3PP.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.PG.A5BC.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.B5.A1MY.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.D1.A16I.01 4 0.1913 0.710 0.02 0.00 0.04 0.94
#> TCGA.EY.A3L3.01 3 0.5000 -0.162 0.00 0.50 0.50 0.00
#> TCGA.E6.A8L9.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.B5.A1MU.01 4 0.5000 -0.223 0.00 0.00 0.50 0.50
#> TCGA.A5.A1OH.01 3 0.2647 0.616 0.00 0.00 0.88 0.12
#> TCGA.D1.A3JQ.01 2 0.0707 0.962 0.00 0.98 0.02 0.00
#> TCGA.AJ.A3BF.01 3 0.4907 0.363 0.00 0.00 0.58 0.42
#> TCGA.B5.A1N2.01 3 0.4948 0.330 0.00 0.00 0.56 0.44
#> TCGA.DI.A2QT.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CA.01 3 0.4713 0.438 0.00 0.00 0.64 0.36
#> TCGA.QS.A8F1.01 3 0.4994 0.253 0.00 0.00 0.52 0.48
#> TCGA.EO.A1Y5.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.AX.A2IO.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.BK.A26L.01 3 0.4907 0.363 0.00 0.00 0.58 0.42
#> TCGA.AX.A1C8.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H5.01 3 0.5000 -0.162 0.00 0.50 0.50 0.00
#> TCGA.JU.AAVI.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.FI.A2D2.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.KP.A3VZ.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.D1.A0ZP.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.KP.A3W3.01 3 0.2647 0.616 0.00 0.00 0.88 0.12
#> TCGA.EO.A2CG.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.FI.A2EW.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 4 0.4277 0.460 0.00 0.00 0.28 0.72
#> TCGA.SL.A6J9.01 2 0.4134 0.666 0.00 0.74 0.26 0.00
#> TCGA.B5.A1MS.01 4 0.1913 0.711 0.02 0.00 0.04 0.94
#> TCGA.DI.A1NO.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3EJ.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.FI.A2CY.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.A5.A2K4.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.AJ.A2QM.01 3 0.4948 0.131 0.00 0.00 0.56 0.44
#> TCGA.KJ.A3U4.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KU.01 3 0.4472 0.495 0.00 0.22 0.76 0.02
#> TCGA.AX.A1C7.01 3 0.1637 0.528 0.00 0.00 0.94 0.06
#> TCGA.AP.A1DQ.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.AX.A3G4.01 3 0.2647 0.616 0.00 0.00 0.88 0.12
#> TCGA.FI.A2F9.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3IA.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.K6.A3WQ.01 1 0.2011 0.773 0.92 0.00 0.00 0.08
#> TCGA.AX.A2H2.01 3 0.4624 0.325 0.00 0.00 0.66 0.34
#> TCGA.AX.A1CP.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.EY.A1GR.01 3 0.4994 0.246 0.00 0.00 0.52 0.48
#> TCGA.B5.A11I.01 3 0.4994 0.239 0.00 0.00 0.52 0.48
#> TCGA.A5.A1OG.01 4 0.4790 0.181 0.00 0.00 0.38 0.62
#> TCGA.FI.A2EU.01 4 0.1913 0.710 0.02 0.00 0.04 0.94
#> TCGA.D1.A179.01 2 0.0707 0.962 0.00 0.98 0.02 0.00
#> TCGA.AX.A1CF.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.DI.A2QY.01 4 0.1913 0.711 0.02 0.00 0.04 0.94
#> TCGA.D1.A1NX.01 3 0.2647 0.616 0.00 0.00 0.88 0.12
#> TCGA.PG.A915.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.AJ.A23M.01 4 0.1913 0.711 0.02 0.00 0.04 0.94
#> TCGA.KP.A3W0.01 3 0.2647 0.616 0.00 0.00 0.88 0.12
#> TCGA.B5.A5OD.01 4 0.3400 0.482 0.18 0.00 0.00 0.82
#> TCGA.AP.A1E4.01 4 0.2345 0.695 0.00 0.00 0.10 0.90
#> TCGA.A5.A3LP.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 3 0.2647 0.616 0.00 0.00 0.88 0.12
#> TCGA.D1.A2G7.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.EY.A54A.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.EY.A212.01 3 0.3975 0.482 0.00 0.24 0.76 0.00
#> TCGA.EY.A210.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.AJ.A23N.01 1 0.0000 0.800 1.00 0.00 0.00 0.00
#> TCGA.AP.A1DK.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.DI.A1C3.01 1 0.4948 0.590 0.56 0.00 0.00 0.44
#> TCGA.PG.A914.01 2 0.0000 0.976 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GM.01 4 0.4948 0.208 0.00 0.00 0.44 0.56
#> TCGA.FI.A2EY.01 3 0.2647 0.616 0.00 0.00 0.88 0.12
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.B5.A0K8.01 5 0.2280 0.852 0.12 0.00 0.00 0.00 0.88
#> TCGA.AX.A1CR.01 5 0.3109 0.850 0.20 0.00 0.00 0.00 0.80
#> TCGA.BG.A3PP.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A5BC.01 5 0.2732 0.869 0.16 0.00 0.00 0.00 0.84
#> TCGA.B5.A1MY.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16I.01 4 0.4767 0.359 0.00 0.00 0.02 0.56 0.42
#> TCGA.EY.A3L3.01 3 0.3903 0.521 0.00 0.16 0.80 0.02 0.02
#> TCGA.E6.A8L9.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MU.01 4 0.6070 0.250 0.00 0.00 0.44 0.44 0.12
#> TCGA.A5.A1OH.01 3 0.2020 0.582 0.00 0.00 0.90 0.10 0.00
#> TCGA.D1.A3JQ.01 2 0.3684 0.684 0.00 0.72 0.28 0.00 0.00
#> TCGA.AJ.A3BF.01 4 0.6070 0.250 0.00 0.00 0.44 0.44 0.12
#> TCGA.B5.A1N2.01 3 0.5895 -0.320 0.00 0.00 0.46 0.44 0.10
#> TCGA.DI.A2QT.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CA.01 3 0.5895 -0.320 0.00 0.00 0.46 0.44 0.10
#> TCGA.QS.A8F1.01 4 0.5788 0.519 0.00 0.00 0.30 0.58 0.12
#> TCGA.EO.A1Y5.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2IO.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.BK.A26L.01 3 0.5895 -0.320 0.00 0.00 0.46 0.44 0.10
#> TCGA.AX.A1C8.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.AX.A2H5.01 3 0.3903 0.521 0.00 0.16 0.80 0.02 0.02
#> TCGA.JU.AAVI.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D2.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.KP.A3VZ.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZP.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.KP.A3W3.01 3 0.2732 0.543 0.00 0.00 0.84 0.16 0.00
#> TCGA.EO.A2CG.01 5 0.2732 0.869 0.16 0.00 0.00 0.00 0.84
#> TCGA.FI.A2EW.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 4 0.6054 0.561 0.00 0.00 0.16 0.56 0.28
#> TCGA.SL.A6J9.01 3 0.4818 -0.244 0.00 0.46 0.52 0.02 0.00
#> TCGA.B5.A1MS.01 5 0.1043 0.763 0.00 0.00 0.00 0.04 0.96
#> TCGA.DI.A1NO.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EJ.01 5 0.3109 0.850 0.20 0.00 0.00 0.00 0.80
#> TCGA.FI.A2CY.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.A5.A2K4.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.AJ.A2QM.01 4 0.2077 0.559 0.00 0.00 0.04 0.92 0.04
#> TCGA.KJ.A3U4.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3KU.01 3 0.1216 0.603 0.00 0.02 0.96 0.02 0.00
#> TCGA.AX.A1C7.01 3 0.3424 0.455 0.00 0.00 0.76 0.24 0.00
#> TCGA.AP.A1DQ.01 5 0.2732 0.869 0.16 0.00 0.00 0.00 0.84
#> TCGA.AX.A3G4.01 3 0.3424 0.441 0.00 0.00 0.76 0.24 0.00
#> TCGA.FI.A2F9.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3IA.01 5 0.2929 0.862 0.18 0.00 0.00 0.00 0.82
#> TCGA.K6.A3WQ.01 1 0.4302 -0.168 0.52 0.00 0.00 0.00 0.48
#> TCGA.AX.A2H2.01 4 0.2280 0.535 0.00 0.00 0.12 0.88 0.00
#> TCGA.AX.A1CP.01 5 0.2732 0.869 0.16 0.00 0.00 0.00 0.84
#> TCGA.EY.A1GR.01 4 0.4075 0.562 0.00 0.00 0.16 0.78 0.06
#> TCGA.B5.A11I.01 4 0.6219 0.285 0.00 0.00 0.42 0.44 0.14
#> TCGA.A5.A1OG.01 4 0.6265 0.556 0.00 0.00 0.24 0.54 0.22
#> TCGA.FI.A2EU.01 4 0.4767 0.359 0.00 0.00 0.02 0.56 0.42
#> TCGA.D1.A179.01 2 0.3895 0.633 0.00 0.68 0.32 0.00 0.00
#> TCGA.AX.A1CF.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 5 0.1043 0.763 0.00 0.00 0.00 0.04 0.96
#> TCGA.D1.A1NX.01 3 0.0000 0.609 0.00 0.00 1.00 0.00 0.00
#> TCGA.PG.A915.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A23M.01 5 0.1043 0.763 0.00 0.00 0.00 0.04 0.96
#> TCGA.KP.A3W0.01 3 0.2732 0.543 0.00 0.00 0.84 0.16 0.00
#> TCGA.B5.A5OD.01 5 0.0609 0.763 0.00 0.00 0.00 0.02 0.98
#> TCGA.AP.A1E4.01 5 0.4767 -0.265 0.00 0.00 0.02 0.42 0.56
#> TCGA.A5.A3LP.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.AX.A2HF.01 3 0.0000 0.609 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A2G7.01 5 0.2929 0.862 0.18 0.00 0.00 0.00 0.82
#> TCGA.EY.A54A.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A212.01 3 0.0609 0.607 0.00 0.02 0.98 0.00 0.00
#> TCGA.EY.A210.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.AJ.A23N.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DK.01 2 0.3424 0.727 0.00 0.76 0.24 0.00 0.00
#> TCGA.DI.A1C3.01 5 0.2929 0.862 0.18 0.00 0.00 0.00 0.82
#> TCGA.PG.A914.01 2 0.0000 0.926 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GM.01 4 0.2077 0.559 0.00 0.00 0.04 0.92 0.04
#> TCGA.FI.A2EY.01 3 0.4360 0.293 0.00 0.00 0.68 0.30 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.B5.A0K8.01 5 0.1556 0.8270 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.AX.A1CR.01 5 0.4502 0.7727 0.10 0.00 0.00 0.02 0.74 0.14
#> TCGA.BG.A3PP.01 1 0.1480 0.9496 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.PG.A5BC.01 5 0.2350 0.8267 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.B5.A1MY.01 1 0.1092 0.9605 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.D1.A16I.01 4 0.6791 0.4622 0.00 0.00 0.10 0.42 0.36 0.12
#> TCGA.EY.A3L3.01 6 0.3997 0.7525 0.00 0.14 0.06 0.02 0.00 0.78
#> TCGA.E6.A8L9.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MU.01 3 0.4380 0.4865 0.00 0.00 0.70 0.22 0.08 0.00
#> TCGA.A5.A1OH.01 3 0.3156 0.4369 0.00 0.00 0.80 0.02 0.00 0.18
#> TCGA.D1.A3JQ.01 2 0.4758 0.2531 0.00 0.58 0.06 0.00 0.00 0.36
#> TCGA.AJ.A3BF.01 3 0.4503 0.4718 0.00 0.00 0.68 0.24 0.08 0.00
#> TCGA.B5.A1N2.01 3 0.3746 0.5219 0.00 0.00 0.78 0.14 0.08 0.00
#> TCGA.DI.A2QT.01 1 0.1807 0.9363 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.AX.A1CA.01 3 0.3045 0.5276 0.00 0.00 0.84 0.10 0.06 0.00
#> TCGA.QS.A8F1.01 3 0.4834 0.4243 0.00 0.00 0.64 0.26 0.10 0.00
#> TCGA.EO.A1Y5.01 2 0.0547 0.8733 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AX.A2IO.01 1 0.0547 0.9712 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BK.A26L.01 3 0.4380 0.4906 0.00 0.00 0.70 0.22 0.08 0.00
#> TCGA.AX.A1C8.01 1 0.0547 0.9712 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AX.A2H5.01 6 0.3985 0.7580 0.00 0.14 0.10 0.00 0.00 0.76
#> TCGA.JU.AAVI.01 1 0.1807 0.9363 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.FI.A2D2.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3VZ.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZP.01 1 0.0547 0.9712 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.KP.A3W3.01 3 0.3523 0.4937 0.00 0.00 0.78 0.04 0.00 0.18
#> TCGA.EO.A2CG.01 5 0.1556 0.8270 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.FI.A2EW.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 3 0.6113 0.2118 0.00 0.00 0.56 0.22 0.18 0.04
#> TCGA.SL.A6J9.01 6 0.4613 0.6181 0.00 0.26 0.08 0.00 0.00 0.66
#> TCGA.B5.A1MS.01 5 0.0000 0.7670 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DI.A1NO.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EJ.01 5 0.4066 0.7979 0.12 0.00 0.00 0.02 0.78 0.08
#> TCGA.FI.A2CY.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K4.01 1 0.0547 0.9712 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AJ.A2QM.01 4 0.2728 0.5450 0.00 0.00 0.10 0.86 0.04 0.00
#> TCGA.KJ.A3U4.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3KU.01 6 0.3309 0.5890 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.AX.A1C7.01 6 0.5783 0.4971 0.00 0.00 0.22 0.28 0.00 0.50
#> TCGA.AP.A1DQ.01 5 0.1814 0.8291 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.AX.A3G4.01 3 0.2350 0.5309 0.00 0.00 0.88 0.02 0.00 0.10
#> TCGA.FI.A2F9.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3IA.01 5 0.3572 0.8066 0.10 0.00 0.00 0.02 0.82 0.06
#> TCGA.K6.A3WQ.01 5 0.4844 0.5416 0.32 0.00 0.00 0.02 0.62 0.04
#> TCGA.AX.A2H2.01 4 0.4873 0.2751 0.00 0.00 0.42 0.52 0.00 0.06
#> TCGA.AX.A1CP.01 5 0.1814 0.8291 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.EY.A1GR.01 4 0.5248 0.1974 0.00 0.00 0.34 0.58 0.04 0.04
#> TCGA.B5.A11I.01 3 0.4727 0.4463 0.00 0.00 0.66 0.24 0.10 0.00
#> TCGA.A5.A1OG.01 3 0.6129 0.2860 0.00 0.00 0.56 0.26 0.12 0.06
#> TCGA.FI.A2EU.01 4 0.6791 0.4622 0.00 0.00 0.10 0.42 0.36 0.12
#> TCGA.D1.A179.01 2 0.4631 0.3609 0.00 0.62 0.06 0.00 0.00 0.32
#> TCGA.AX.A1CF.01 2 0.0547 0.8733 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DI.A2QY.01 5 0.0000 0.7670 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A1NX.01 3 0.3309 0.2857 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.PG.A915.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A23M.01 5 0.2794 0.6247 0.00 0.00 0.00 0.08 0.86 0.06
#> TCGA.KP.A3W0.01 3 0.2790 0.4927 0.00 0.00 0.84 0.02 0.00 0.14
#> TCGA.B5.A5OD.01 5 0.0937 0.7498 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.AP.A1E4.01 5 0.7107 -0.4793 0.00 0.00 0.30 0.24 0.38 0.08
#> TCGA.A5.A3LP.01 1 0.1480 0.9617 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.AX.A2HF.01 3 0.3756 -0.0617 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.D1.A2G7.01 5 0.1814 0.8291 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.EY.A54A.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A212.01 3 0.3851 -0.2918 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.EY.A210.01 1 0.0547 0.9712 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AJ.A23N.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DK.01 2 0.4360 0.4910 0.00 0.68 0.06 0.00 0.00 0.26
#> TCGA.DI.A1C3.01 5 0.3258 0.8157 0.10 0.00 0.00 0.02 0.84 0.04
#> TCGA.PG.A914.01 2 0.0000 0.8826 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GM.01 4 0.2190 0.5533 0.00 0.00 0.06 0.90 0.04 0.00
#> TCGA.FI.A2EY.01 3 0.1865 0.5415 0.00 0.00 0.92 0.04 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.B5.A0K8.01 5 0.0504 0.86562 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.AX.A1CR.01 5 0.6084 0.36936 0.16 0.06 0.00 0.32 0.46 0.00 0.00
#> TCGA.BG.A3PP.01 1 0.1363 0.88582 0.94 0.04 0.00 0.02 0.00 0.00 0.00
#> TCGA.PG.A5BC.01 5 0.3000 0.81912 0.02 0.04 0.00 0.10 0.84 0.00 0.00
#> TCGA.B5.A1MY.01 1 0.1505 0.89221 0.94 0.02 0.00 0.02 0.00 0.02 0.00
#> TCGA.D1.A16I.01 4 0.4478 0.60269 0.00 0.00 0.20 0.66 0.14 0.00 0.00
#> TCGA.EY.A3L3.01 6 0.3685 0.51510 0.00 0.32 0.00 0.00 0.00 0.66 0.02
#> TCGA.E6.A8L9.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B5.A1MU.01 3 0.1006 0.68360 0.00 0.00 0.96 0.02 0.02 0.00 0.00
#> TCGA.A5.A1OH.01 6 0.4977 0.28657 0.00 0.04 0.42 0.04 0.00 0.50 0.00
#> TCGA.D1.A3JQ.01 7 0.3994 0.26481 0.00 0.02 0.00 0.00 0.00 0.48 0.50
#> TCGA.AJ.A3BF.01 3 0.3257 0.63712 0.00 0.02 0.84 0.08 0.02 0.04 0.00
#> TCGA.B5.A1N2.01 3 0.1860 0.67796 0.00 0.00 0.92 0.04 0.02 0.02 0.00
#> TCGA.DI.A2QT.01 1 0.2803 0.80327 0.84 0.06 0.00 0.10 0.00 0.00 0.00
#> TCGA.AX.A1CA.01 3 0.0000 0.68273 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A8F1.01 3 0.2421 0.63974 0.00 0.02 0.88 0.08 0.02 0.00 0.00
#> TCGA.EO.A1Y5.01 7 0.1166 0.84333 0.00 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.AX.A2IO.01 1 0.2512 0.88412 0.86 0.10 0.00 0.04 0.00 0.00 0.00
#> TCGA.BK.A26L.01 3 0.0000 0.68273 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.2512 0.88412 0.86 0.10 0.00 0.04 0.00 0.00 0.00
#> TCGA.AX.A2H5.01 6 0.3417 0.52573 0.00 0.26 0.00 0.00 0.00 0.72 0.02
#> TCGA.JU.AAVI.01 1 0.2572 0.82409 0.86 0.06 0.00 0.08 0.00 0.00 0.00
#> TCGA.FI.A2D2.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.KP.A3VZ.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D1.A0ZP.01 1 0.2512 0.88412 0.86 0.10 0.00 0.04 0.00 0.00 0.00
#> TCGA.KP.A3W3.01 6 0.5438 0.25403 0.00 0.12 0.42 0.02 0.00 0.44 0.00
#> TCGA.EO.A2CG.01 5 0.0504 0.86562 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.FI.A2EW.01 1 0.0504 0.90160 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 1 0.0000 0.90401 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 3 0.1886 0.60103 0.00 0.00 0.88 0.12 0.00 0.00 0.00
#> TCGA.SL.A6J9.01 6 0.3449 0.51148 0.00 0.08 0.00 0.00 0.00 0.78 0.14
#> TCGA.B5.A1MS.01 5 0.0000 0.85560 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DI.A1NO.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3EJ.01 5 0.5091 0.66828 0.16 0.06 0.00 0.12 0.66 0.00 0.00
#> TCGA.FI.A2CY.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A5.A2K4.01 1 0.2512 0.88412 0.86 0.10 0.00 0.04 0.00 0.00 0.00
#> TCGA.AJ.A2QM.01 4 0.5338 0.60400 0.00 0.32 0.20 0.48 0.00 0.00 0.00
#> TCGA.KJ.A3U4.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EO.A3KU.01 6 0.3086 0.58154 0.00 0.16 0.04 0.00 0.00 0.80 0.00
#> TCGA.AX.A1C7.01 6 0.3745 0.51469 0.00 0.26 0.00 0.04 0.00 0.70 0.00
#> TCGA.AP.A1DQ.01 5 0.0504 0.86562 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.AX.A3G4.01 3 0.3984 0.29001 0.00 0.02 0.68 0.02 0.00 0.28 0.00
#> TCGA.FI.A2F9.01 1 0.1006 0.89575 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.AJ.A3IA.01 5 0.3000 0.81912 0.02 0.04 0.00 0.10 0.84 0.00 0.00
#> TCGA.K6.A3WQ.01 5 0.4654 0.70271 0.16 0.04 0.00 0.06 0.72 0.02 0.00
#> TCGA.AX.A2H2.01 4 0.5180 0.47351 0.00 0.10 0.34 0.54 0.00 0.02 0.00
#> TCGA.AX.A1CP.01 5 0.0504 0.86562 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.EY.A1GR.01 3 0.6022 -0.41367 0.00 0.32 0.36 0.30 0.00 0.02 0.00
#> TCGA.B5.A11I.01 3 0.2911 0.64518 0.00 0.02 0.86 0.08 0.02 0.02 0.00
#> TCGA.A5.A1OG.01 3 0.2016 0.64546 0.00 0.00 0.90 0.06 0.04 0.00 0.00
#> TCGA.FI.A2EU.01 4 0.4478 0.60269 0.00 0.00 0.20 0.66 0.14 0.00 0.00
#> TCGA.D1.A179.01 7 0.3546 0.36206 0.00 0.00 0.00 0.00 0.00 0.46 0.54
#> TCGA.AX.A1CF.01 7 0.0863 0.85386 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.DI.A2QY.01 5 0.0000 0.85560 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A1NX.01 6 0.4832 0.43152 0.00 0.04 0.34 0.04 0.00 0.58 0.00
#> TCGA.PG.A915.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A23M.01 5 0.1928 0.78957 0.00 0.00 0.02 0.08 0.90 0.00 0.00
#> TCGA.KP.A3W0.01 3 0.4701 -0.24442 0.00 0.04 0.50 0.02 0.00 0.44 0.00
#> TCGA.B5.A5OD.01 5 0.0504 0.85062 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.AP.A1E4.01 3 0.5806 0.00668 0.00 0.04 0.50 0.16 0.30 0.00 0.00
#> TCGA.A5.A3LP.01 1 0.2722 0.88536 0.84 0.12 0.00 0.04 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 6 0.4305 0.51760 0.00 0.04 0.28 0.02 0.00 0.66 0.00
#> TCGA.D1.A2G7.01 5 0.0504 0.86562 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.EY.A54A.01 1 0.0000 0.90401 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A212.01 6 0.2906 0.60329 0.00 0.00 0.18 0.02 0.00 0.80 0.00
#> TCGA.EY.A210.01 1 0.2512 0.88412 0.86 0.10 0.00 0.04 0.00 0.00 0.00
#> TCGA.AJ.A23N.01 1 0.0504 0.90160 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DK.01 7 0.3909 0.42051 0.00 0.02 0.00 0.00 0.00 0.40 0.58
#> TCGA.DI.A1C3.01 5 0.3630 0.79695 0.06 0.04 0.00 0.10 0.80 0.00 0.00
#> TCGA.PG.A914.01 7 0.0000 0.86902 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EY.A1GM.01 4 0.5190 0.61623 0.00 0.30 0.18 0.52 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 3 0.2906 0.51629 0.00 0.00 0.80 0.02 0.00 0.18 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.B5.A0K8.01 5 0.0000 0.839 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CR.01 5 0.5693 0.376 0.16 0.00 0.32 0.00 0.46 0.00 0.00 0.06
#> TCGA.BG.A3PP.01 1 0.1563 0.808 0.90 0.00 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A5BC.01 5 0.2114 0.784 0.00 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.B5.A1MY.01 1 0.1804 0.811 0.90 0.00 0.08 0.00 0.00 0.00 0.00 0.02
#> TCGA.D1.A16I.01 4 0.7402 0.480 0.00 0.18 0.24 0.32 0.16 0.00 0.00 0.10
#> TCGA.EY.A3L3.01 6 0.3729 0.460 0.00 0.00 0.18 0.00 0.00 0.72 0.00 0.10
#> TCGA.E6.A8L9.01 7 0.0000 0.929 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A1MU.01 2 0.1563 0.549 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.A5.A1OH.01 2 0.4832 -0.450 0.00 0.54 0.00 0.00 0.00 0.20 0.00 0.26
#> TCGA.D1.A3JQ.01 6 0.3658 0.249 0.00 0.00 0.00 0.02 0.00 0.58 0.40 0.00
#> TCGA.AJ.A3BF.01 2 0.3291 0.448 0.00 0.70 0.00 0.02 0.00 0.00 0.00 0.28
#> TCGA.B5.A1N2.01 2 0.1563 0.545 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DI.A2QT.01 1 0.3537 0.663 0.72 0.00 0.24 0.00 0.02 0.00 0.00 0.02
#> TCGA.AX.A1CA.01 2 0.0000 0.561 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A8F1.01 2 0.2725 0.510 0.00 0.82 0.00 0.04 0.00 0.00 0.00 0.14
#> TCGA.EO.A1Y5.01 7 0.1804 0.858 0.00 0.00 0.00 0.02 0.00 0.08 0.90 0.00
#> TCGA.AX.A2IO.01 1 0.2534 0.806 0.78 0.00 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A26L.01 2 0.0000 0.561 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.2534 0.806 0.78 0.00 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H5.01 6 0.3551 0.472 0.00 0.00 0.22 0.00 0.00 0.72 0.00 0.06
#> TCGA.JU.AAVI.01 1 0.3095 0.687 0.74 0.00 0.24 0.00 0.00 0.00 0.00 0.02
#> TCGA.FI.A2D2.01 7 0.0471 0.920 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.KP.A3VZ.01 7 0.0000 0.929 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A0ZP.01 1 0.2534 0.806 0.78 0.00 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W3.01 2 0.4971 -0.416 0.00 0.46 0.00 0.00 0.00 0.18 0.00 0.36
#> TCGA.EO.A2CG.01 5 0.0000 0.839 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2EW.01 1 0.0941 0.836 0.96 0.00 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.KP.A3W4.01 1 0.0000 0.839 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CC.01 2 0.2071 0.541 0.00 0.90 0.04 0.00 0.02 0.00 0.00 0.04
#> TCGA.SL.A6J9.01 6 0.2224 0.505 0.00 0.00 0.00 0.02 0.00 0.86 0.12 0.00
#> TCGA.B5.A1MS.01 5 0.0471 0.834 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DI.A1NO.01 7 0.0000 0.929 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3EJ.01 5 0.4757 0.552 0.20 0.00 0.24 0.00 0.56 0.00 0.00 0.00
#> TCGA.FI.A2CY.01 7 0.0000 0.929 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A5.A2K4.01 1 0.2534 0.806 0.78 0.00 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QM.01 4 0.0808 0.540 0.00 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.KJ.A3U4.01 7 0.0000 0.929 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EO.A3KU.01 6 0.2265 0.444 0.00 0.02 0.02 0.00 0.00 0.88 0.00 0.08
#> TCGA.AX.A1C7.01 6 0.5583 0.285 0.00 0.00 0.14 0.06 0.00 0.48 0.00 0.32
#> TCGA.AP.A1DQ.01 5 0.0000 0.839 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3G4.01 2 0.4412 -0.187 0.00 0.60 0.00 0.00 0.00 0.12 0.00 0.28
#> TCGA.FI.A2F9.01 1 0.0471 0.837 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AJ.A3IA.01 5 0.2534 0.753 0.00 0.00 0.22 0.00 0.78 0.00 0.00 0.00
#> TCGA.K6.A3WQ.01 5 0.4467 0.650 0.12 0.00 0.20 0.00 0.66 0.00 0.00 0.02
#> TCGA.AX.A2H2.01 4 0.5991 0.303 0.00 0.30 0.10 0.44 0.00 0.00 0.00 0.16
#> TCGA.AX.A1CP.01 5 0.0000 0.839 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 4 0.4760 0.428 0.00 0.16 0.02 0.62 0.00 0.00 0.00 0.20
#> TCGA.B5.A11I.01 2 0.4028 0.434 0.00 0.66 0.04 0.02 0.00 0.00 0.00 0.28
#> TCGA.A5.A1OG.01 2 0.1804 0.559 0.00 0.90 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.FI.A2EU.01 4 0.7520 0.489 0.00 0.18 0.20 0.32 0.14 0.00 0.00 0.16
#> TCGA.D1.A179.01 6 0.4471 0.368 0.00 0.00 0.02 0.00 0.00 0.58 0.34 0.06
#> TCGA.AX.A1CF.01 7 0.0941 0.907 0.00 0.00 0.00 0.02 0.00 0.02 0.96 0.00
#> TCGA.DI.A2QY.01 5 0.0471 0.834 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A1NX.01 8 0.5281 0.000 0.00 0.34 0.00 0.00 0.00 0.32 0.00 0.34
#> TCGA.PG.A915.01 7 0.0000 0.929 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A23M.01 5 0.1557 0.806 0.00 0.00 0.06 0.00 0.92 0.00 0.00 0.02
#> TCGA.KP.A3W0.01 2 0.4686 -0.341 0.00 0.56 0.00 0.00 0.00 0.16 0.00 0.28
#> TCGA.B5.A5OD.01 5 0.1275 0.816 0.00 0.00 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.AP.A1E4.01 2 0.5986 0.123 0.00 0.50 0.06 0.02 0.18 0.00 0.00 0.24
#> TCGA.A5.A3LP.01 1 0.2938 0.791 0.70 0.00 0.30 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 6 0.5211 -0.808 0.00 0.26 0.00 0.00 0.00 0.40 0.00 0.34
#> TCGA.D1.A2G7.01 5 0.0000 0.839 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A54A.01 1 0.0941 0.836 0.96 0.00 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.EY.A212.01 6 0.4406 0.144 0.00 0.08 0.02 0.00 0.00 0.64 0.00 0.26
#> TCGA.EY.A210.01 1 0.2534 0.806 0.78 0.00 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A23N.01 1 0.0000 0.839 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DK.01 7 0.3714 0.052 0.00 0.00 0.00 0.02 0.00 0.44 0.54 0.00
#> TCGA.DI.A1C3.01 5 0.3735 0.714 0.04 0.00 0.22 0.00 0.72 0.00 0.00 0.02
#> TCGA.PG.A914.01 7 0.0000 0.929 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GM.01 4 0.0471 0.541 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 2 0.3170 0.231 0.00 0.76 0.00 0.00 0.00 0.04 0.00 0.20
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 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["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 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4848 0.516 0.516
#> 3 3 0.871 0.915 0.949 0.3965 0.746 0.529
#> 4 4 0.737 0.799 0.755 0.0967 0.906 0.708
#> 5 5 0.703 0.743 0.863 0.0540 0.966 0.860
#> 6 6 0.760 0.579 0.832 0.0386 0.900 0.611
#> 7 7 0.790 0.692 0.836 0.0351 0.952 0.767
#> 8 8 0.757 0.583 0.807 0.0161 0.994 0.966
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.B5.A0K8.01 2 0 1 0 1
#> TCGA.AX.A1CR.01 2 0 1 0 1
#> TCGA.BG.A3PP.01 2 0 1 0 1
#> TCGA.PG.A5BC.01 2 0 1 0 1
#> TCGA.B5.A1MY.01 1 0 1 1 0
#> TCGA.DI.A2QT.01 1 0 1 1 0
#> TCGA.AX.A2IO.01 2 0 1 0 1
#> TCGA.AX.A1C8.01 1 0 1 1 0
#> TCGA.JU.AAVI.01 1 0 1 1 0
#> TCGA.D1.A0ZP.01 1 0 1 1 0
#> TCGA.EO.A2CG.01 2 0 1 0 1
#> TCGA.FI.A2EW.01 1 0 1 1 0
#> TCGA.KP.A3W4.01 2 0 1 0 1
#> TCGA.AJ.A3EJ.01 2 0 1 0 1
#> TCGA.A5.A2K4.01 1 0 1 1 0
#> TCGA.AP.A1DQ.01 2 0 1 0 1
#> TCGA.FI.A2F9.01 2 0 1 0 1
#> TCGA.AJ.A3IA.01 2 0 1 0 1
#> TCGA.K6.A3WQ.01 2 0 1 0 1
#> TCGA.AX.A1CP.01 2 0 1 0 1
#> TCGA.B5.A5OD.01 2 0 1 0 1
#> TCGA.A5.A3LP.01 1 0 1 1 0
#> TCGA.D1.A2G7.01 2 0 1 0 1
#> TCGA.EY.A54A.01 1 0 1 1 0
#> TCGA.EY.A210.01 1 0 1 1 0
#> TCGA.AJ.A23N.01 2 0 1 0 1
#> TCGA.DI.A1C3.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B5.A0K8.01 3 0.595 0.643 0 0.36 0.64
#> TCGA.AX.A1CR.01 3 0.000 0.808 0 0.00 1.00
#> TCGA.BG.A3PP.01 3 0.000 0.808 0 0.00 1.00
#> TCGA.PG.A5BC.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B5.A1MY.01 3 0.000 0.808 0 0.00 1.00
#> TCGA.DI.A2QT.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AX.A2IO.01 3 0.583 0.673 0 0.34 0.66
#> TCGA.AX.A1C8.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.JU.AAVI.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D1.A0ZP.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.EO.A2CG.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.FI.A2EW.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.KP.A3W4.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AJ.A3EJ.01 3 0.000 0.808 0 0.00 1.00
#> TCGA.A5.A2K4.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AP.A1DQ.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.FI.A2F9.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AJ.A3IA.01 3 0.583 0.673 0 0.34 0.66
#> TCGA.K6.A3WQ.01 3 0.583 0.673 0 0.34 0.66
#> TCGA.AX.A1CP.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B5.A5OD.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A5.A3LP.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D1.A2G7.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.EY.A54A.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.EY.A210.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AJ.A23N.01 3 0.000 0.808 0 0.00 1.00
#> TCGA.DI.A1C3.01 2 0.000 1.000 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B5.A0K8.01 3 0.694 0.818 0.00 0.12 0.52 0.36
#> TCGA.AX.A1CR.01 4 0.000 0.838 0.00 0.00 0.00 1.00
#> TCGA.BG.A3PP.01 4 0.000 0.838 0.00 0.00 0.00 1.00
#> TCGA.PG.A5BC.01 2 0.317 0.810 0.00 0.84 0.16 0.00
#> TCGA.B5.A1MY.01 4 0.452 0.591 0.00 0.00 0.32 0.68
#> TCGA.DI.A2QT.01 1 0.000 0.917 1.00 0.00 0.00 0.00
#> TCGA.AX.A2IO.01 3 0.694 0.818 0.00 0.12 0.52 0.36
#> TCGA.AX.A1C8.01 1 0.201 0.900 0.92 0.00 0.08 0.00
#> TCGA.JU.AAVI.01 1 0.000 0.917 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZP.01 1 0.485 0.643 0.60 0.00 0.40 0.00
#> TCGA.EO.A2CG.01 2 0.000 0.888 0.00 1.00 0.00 0.00
#> TCGA.FI.A2EW.01 1 0.000 0.917 1.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 2 0.317 0.810 0.00 0.84 0.16 0.00
#> TCGA.AJ.A3EJ.01 3 0.500 0.539 0.00 0.00 0.50 0.50
#> TCGA.A5.A2K4.01 1 0.201 0.900 0.92 0.00 0.08 0.00
#> TCGA.AP.A1DQ.01 2 0.000 0.888 0.00 1.00 0.00 0.00
#> TCGA.FI.A2F9.01 2 0.201 0.836 0.00 0.92 0.08 0.00
#> TCGA.AJ.A3IA.01 3 0.694 0.818 0.00 0.12 0.52 0.36
#> TCGA.K6.A3WQ.01 3 0.694 0.818 0.00 0.12 0.52 0.36
#> TCGA.AX.A1CP.01 2 0.000 0.888 0.00 1.00 0.00 0.00
#> TCGA.B5.A5OD.01 2 0.380 0.727 0.00 0.78 0.22 0.00
#> TCGA.A5.A3LP.01 1 0.000 0.917 1.00 0.00 0.00 0.00
#> TCGA.D1.A2G7.01 2 0.000 0.888 0.00 1.00 0.00 0.00
#> TCGA.EY.A54A.01 1 0.398 0.802 0.76 0.00 0.24 0.00
#> TCGA.EY.A210.01 1 0.000 0.917 1.00 0.00 0.00 0.00
#> TCGA.AJ.A23N.01 4 0.000 0.838 0.00 0.00 0.00 1.00
#> TCGA.DI.A1C3.01 3 0.559 0.104 0.00 0.46 0.52 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.B5.A0K8.01 3 0.1216 0.875 0.00 0.02 0.96 0.02 0.00
#> TCGA.AX.A1CR.01 4 0.5895 1.000 0.00 0.00 0.10 0.46 0.44
#> TCGA.BG.A3PP.01 4 0.5895 1.000 0.00 0.00 0.10 0.46 0.44
#> TCGA.PG.A5BC.01 2 0.4060 0.583 0.00 0.64 0.36 0.00 0.00
#> TCGA.B5.A1MY.01 5 0.0000 -0.104 0.00 0.00 0.00 0.00 1.00
#> TCGA.DI.A2QT.01 1 0.0000 0.892 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2IO.01 3 0.0609 0.874 0.00 0.02 0.98 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.2280 0.846 0.88 0.00 0.00 0.12 0.00
#> TCGA.JU.AAVI.01 1 0.0000 0.892 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZP.01 5 0.5864 0.151 0.32 0.00 0.00 0.12 0.56
#> TCGA.EO.A2CG.01 2 0.0609 0.788 0.00 0.98 0.02 0.00 0.00
#> TCGA.FI.A2EW.01 1 0.0000 0.892 1.00 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 2 0.4060 0.583 0.00 0.64 0.36 0.00 0.00
#> TCGA.AJ.A3EJ.01 3 0.3319 0.776 0.00 0.00 0.82 0.16 0.02
#> TCGA.A5.A2K4.01 1 0.2280 0.846 0.88 0.00 0.00 0.12 0.00
#> TCGA.AP.A1DQ.01 2 0.0609 0.788 0.00 0.98 0.02 0.00 0.00
#> TCGA.FI.A2F9.01 2 0.2929 0.666 0.00 0.82 0.00 0.18 0.00
#> TCGA.AJ.A3IA.01 3 0.3106 0.819 0.00 0.02 0.84 0.14 0.00
#> TCGA.K6.A3WQ.01 3 0.1216 0.875 0.00 0.02 0.96 0.02 0.00
#> TCGA.AX.A1CP.01 2 0.0609 0.788 0.00 0.98 0.02 0.00 0.00
#> TCGA.B5.A5OD.01 2 0.4726 0.483 0.00 0.58 0.40 0.02 0.00
#> TCGA.A5.A3LP.01 1 0.0000 0.892 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G7.01 2 0.0609 0.788 0.00 0.98 0.02 0.00 0.00
#> TCGA.EY.A54A.01 1 0.5050 0.586 0.70 0.00 0.00 0.12 0.18
#> TCGA.EY.A210.01 1 0.2331 0.828 0.90 0.00 0.02 0.08 0.00
#> TCGA.AJ.A23N.01 4 0.5895 1.000 0.00 0.00 0.10 0.46 0.44
#> TCGA.DI.A1C3.01 3 0.2929 0.667 0.00 0.18 0.82 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.B5.A0K8.01 3 0.0000 0.396 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CR.01 4 0.1480 0.962 0.00 0.00 0.02 0.94 0.00 0.04
#> TCGA.BG.A3PP.01 4 0.0547 0.981 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.PG.A5BC.01 3 0.4246 0.440 0.00 0.40 0.58 0.00 0.00 0.02
#> TCGA.B5.A1MY.01 5 0.5144 0.107 0.00 0.00 0.00 0.34 0.56 0.10
#> TCGA.DI.A2QT.01 1 0.0937 0.834 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.AX.A2IO.01 3 0.0547 0.376 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.AX.A1C8.01 1 0.3506 0.769 0.80 0.00 0.00 0.02 0.16 0.02
#> TCGA.JU.AAVI.01 1 0.0000 0.835 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZP.01 5 0.3198 0.253 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.EO.A2CG.01 2 0.0000 0.918 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EW.01 1 0.0937 0.834 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.KP.A3W4.01 3 0.4246 0.440 0.00 0.40 0.58 0.00 0.00 0.02
#> TCGA.AJ.A3EJ.01 6 0.3864 0.000 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.A5.A2K4.01 1 0.3506 0.769 0.80 0.00 0.00 0.02 0.16 0.02
#> TCGA.AP.A1DQ.01 2 0.0000 0.918 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2F9.01 2 0.5027 0.625 0.00 0.64 0.00 0.00 0.20 0.16
#> TCGA.AJ.A3IA.01 3 0.3851 -0.901 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.K6.A3WQ.01 3 0.1807 0.308 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.AX.A1CP.01 2 0.0000 0.918 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A5OD.01 3 0.4078 0.499 0.00 0.34 0.64 0.00 0.00 0.02
#> TCGA.A5.A3LP.01 1 0.0000 0.835 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G7.01 2 0.0000 0.918 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A54A.01 1 0.4689 0.405 0.58 0.00 0.00 0.02 0.38 0.02
#> TCGA.EY.A210.01 1 0.2260 0.759 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.AJ.A23N.01 4 0.0547 0.981 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.DI.A1C3.01 3 0.2350 0.467 0.00 0.10 0.88 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.B5.A0K8.01 3 0.136 0.7142 0.00 0.02 0.94 0.00 0.04 0.00 0.00
#> TCGA.AX.A1CR.01 4 0.251 0.8971 0.00 0.06 0.00 0.88 0.02 0.04 0.00
#> TCGA.BG.A3PP.01 4 0.000 0.9494 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.PG.A5BC.01 3 0.283 0.7359 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.B5.A1MY.01 5 0.539 0.2744 0.00 0.18 0.00 0.14 0.62 0.06 0.00
#> TCGA.DI.A2QT.01 1 0.136 0.7595 0.94 0.04 0.00 0.00 0.00 0.02 0.00
#> TCGA.AX.A2IO.01 3 0.186 0.7004 0.00 0.02 0.92 0.00 0.04 0.02 0.00
#> TCGA.AX.A1C8.01 1 0.537 0.3693 0.56 0.10 0.00 0.00 0.30 0.04 0.00
#> TCGA.JU.AAVI.01 1 0.000 0.7630 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZP.01 5 0.117 0.5068 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.EO.A2CG.01 7 0.000 0.9017 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FI.A2EW.01 1 0.136 0.7595 0.94 0.04 0.00 0.00 0.00 0.02 0.00
#> TCGA.KP.A3W4.01 3 0.283 0.7359 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.AJ.A3EJ.01 6 0.257 0.8296 0.00 0.00 0.20 0.00 0.00 0.80 0.00
#> TCGA.A5.A2K4.01 1 0.537 0.3693 0.56 0.10 0.00 0.00 0.30 0.04 0.00
#> TCGA.AP.A1DQ.01 7 0.000 0.9017 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FI.A2F9.01 7 0.350 0.5253 0.00 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.AJ.A3IA.01 6 0.322 0.8221 0.00 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.K6.A3WQ.01 3 0.373 0.5840 0.00 0.14 0.78 0.00 0.04 0.04 0.00
#> TCGA.AX.A1CP.01 7 0.000 0.9017 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B5.A5OD.01 3 0.257 0.7492 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.A5.A3LP.01 1 0.000 0.7630 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G7.01 7 0.000 0.9017 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EY.A54A.01 5 0.464 -0.0945 0.38 0.08 0.00 0.00 0.54 0.00 0.00
#> TCGA.EY.A210.01 1 0.306 0.6630 0.82 0.08 0.00 0.00 0.00 0.10 0.00
#> TCGA.AJ.A23N.01 4 0.000 0.9494 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DI.A1C3.01 3 0.143 0.7510 0.00 0.00 0.92 0.00 0.00 0.00 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.B5.A0K8.01 3 0.4034 0.55226 0.00 0.06 0.76 0.12 0.04 0.02 0.00 0.00
#> TCGA.AX.A1CR.01 8 0.2674 0.84189 0.00 0.04 0.00 0.06 0.00 0.04 0.00 0.86
#> TCGA.BG.A3PP.01 8 0.0000 0.92295 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.PG.A5BC.01 3 0.2406 0.65427 0.00 0.00 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.B5.A1MY.01 2 0.2856 0.00000 0.00 0.78 0.00 0.00 0.00 0.02 0.00 0.20
#> TCGA.DI.A2QT.01 1 0.0941 0.70257 0.96 0.02 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.AX.A2IO.01 3 0.3580 0.53405 0.00 0.04 0.80 0.10 0.02 0.04 0.00 0.00
#> TCGA.AX.A1C8.01 1 0.3237 0.17801 0.60 0.00 0.00 0.00 0.40 0.00 0.00 0.00
#> TCGA.JU.AAVI.01 1 0.0000 0.70510 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZP.01 5 0.5832 0.18469 0.10 0.36 0.00 0.04 0.46 0.04 0.00 0.00
#> TCGA.EO.A2CG.01 7 0.0000 0.88596 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FI.A2EW.01 1 0.0941 0.70257 0.96 0.02 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W4.01 3 0.2406 0.65427 0.00 0.00 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.AJ.A3EJ.01 6 0.1947 0.77920 0.00 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.A5.A2K4.01 1 0.3237 0.17801 0.60 0.00 0.00 0.00 0.40 0.00 0.00 0.00
#> TCGA.AP.A1DQ.01 7 0.0000 0.88596 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FI.A2F9.01 7 0.3329 0.40985 0.00 0.00 0.00 0.48 0.00 0.00 0.52 0.00
#> TCGA.AJ.A3IA.01 6 0.3291 0.78975 0.00 0.00 0.28 0.02 0.00 0.70 0.00 0.00
#> TCGA.K6.A3WQ.01 3 0.5982 -0.00824 0.00 0.04 0.42 0.12 0.38 0.04 0.00 0.00
#> TCGA.AX.A1CP.01 7 0.0000 0.88596 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A5OD.01 3 0.4363 0.63102 0.00 0.04 0.70 0.04 0.02 0.00 0.20 0.00
#> TCGA.A5.A3LP.01 1 0.0000 0.70510 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G7.01 7 0.0000 0.88596 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EY.A54A.01 5 0.4860 0.14999 0.40 0.06 0.00 0.00 0.50 0.04 0.00 0.00
#> TCGA.EY.A210.01 1 0.5024 0.38292 0.64 0.04 0.00 0.20 0.10 0.02 0.00 0.00
#> TCGA.AJ.A23N.01 8 0.0000 0.92295 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DI.A1C3.01 3 0.0471 0.63214 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["012"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 18 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.497 0.933 0.946 0.3857 0.634 0.634
#> 3 3 0.641 0.846 0.900 0.7142 0.706 0.536
#> 4 4 0.954 0.962 0.968 0.1675 0.804 0.483
#> 5 5 0.824 0.675 0.852 0.0654 0.954 0.811
#> 6 6 0.824 0.705 0.806 0.0355 0.863 0.432
#> 7 7 0.830 0.829 0.901 0.0351 0.954 0.682
#> 8 8 0.902 0.759 0.886 0.0215 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
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.EY.A3L3.01 2 0.000 0.916 0.00 1.00
#> TCGA.E6.A8L9.01 2 0.000 0.916 0.00 1.00
#> TCGA.D1.A3JQ.01 2 0.584 0.912 0.14 0.86
#> TCGA.EO.A1Y5.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A2H5.01 1 0.000 1.000 1.00 0.00
#> TCGA.FI.A2D2.01 2 0.584 0.912 0.14 0.86
#> TCGA.KP.A3VZ.01 2 0.000 0.916 0.00 1.00
#> TCGA.SL.A6J9.01 1 0.000 1.000 1.00 0.00
#> TCGA.DI.A1NO.01 2 0.000 0.916 0.00 1.00
#> TCGA.FI.A2CY.01 2 0.584 0.912 0.14 0.86
#> TCGA.KJ.A3U4.01 2 0.584 0.912 0.14 0.86
#> TCGA.EO.A3KU.01 2 0.584 0.912 0.14 0.86
#> TCGA.D1.A179.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A1CF.01 2 0.584 0.912 0.14 0.86
#> TCGA.PG.A915.01 2 0.000 0.916 0.00 1.00
#> TCGA.EY.A212.01 2 0.584 0.912 0.14 0.86
#> TCGA.AP.A1DK.01 2 0.000 0.916 0.00 1.00
#> TCGA.PG.A914.01 2 0.000 0.916 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EY.A3L3.01 3 0.334 0.635 0 0.12 0.88
#> TCGA.E6.A8L9.01 3 0.502 0.829 0 0.24 0.76
#> TCGA.D1.A3JQ.01 2 0.502 0.800 0 0.76 0.24
#> TCGA.EO.A1Y5.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AX.A2H5.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.FI.A2D2.01 2 0.502 0.800 0 0.76 0.24
#> TCGA.KP.A3VZ.01 3 0.502 0.829 0 0.24 0.76
#> TCGA.SL.A6J9.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.DI.A1NO.01 3 0.502 0.829 0 0.24 0.76
#> TCGA.FI.A2CY.01 2 0.000 0.838 0 1.00 0.00
#> TCGA.KJ.A3U4.01 2 0.000 0.838 0 1.00 0.00
#> TCGA.EO.A3KU.01 2 0.502 0.800 0 0.76 0.24
#> TCGA.D1.A179.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AX.A1CF.01 2 0.000 0.838 0 1.00 0.00
#> TCGA.PG.A915.01 3 0.000 0.718 0 0.00 1.00
#> TCGA.EY.A212.01 2 0.502 0.800 0 0.76 0.24
#> TCGA.AP.A1DK.01 2 0.000 0.838 0 1.00 0.00
#> TCGA.PG.A914.01 2 0.000 0.838 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EY.A3L3.01 4 0.121 0.920 0.00 0.00 0.04 0.96
#> TCGA.E6.A8L9.01 3 0.121 1.000 0.00 0.04 0.96 0.00
#> TCGA.D1.A3JQ.01 4 0.121 0.940 0.00 0.04 0.00 0.96
#> TCGA.EO.A1Y5.01 1 0.000 0.980 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H5.01 1 0.000 0.980 1.00 0.00 0.00 0.00
#> TCGA.FI.A2D2.01 2 0.121 0.948 0.00 0.96 0.00 0.04
#> TCGA.KP.A3VZ.01 3 0.121 1.000 0.00 0.04 0.96 0.00
#> TCGA.SL.A6J9.01 1 0.000 0.980 1.00 0.00 0.00 0.00
#> TCGA.DI.A1NO.01 3 0.121 1.000 0.00 0.04 0.96 0.00
#> TCGA.FI.A2CY.01 2 0.000 0.990 0.00 1.00 0.00 0.00
#> TCGA.KJ.A3U4.01 2 0.000 0.990 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KU.01 4 0.121 0.940 0.00 0.04 0.00 0.96
#> TCGA.D1.A179.01 1 0.241 0.938 0.92 0.00 0.04 0.04
#> TCGA.AX.A1CF.01 2 0.000 0.990 0.00 1.00 0.00 0.00
#> TCGA.PG.A915.01 4 0.340 0.797 0.00 0.00 0.18 0.82
#> TCGA.EY.A212.01 4 0.121 0.940 0.00 0.04 0.00 0.96
#> TCGA.AP.A1DK.01 2 0.000 0.990 0.00 1.00 0.00 0.00
#> TCGA.PG.A914.01 2 0.000 0.990 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.EY.A3L3.01 4 0.4227 0.445 0.00 0.00 0.42 0.58 0.00
#> TCGA.E6.A8L9.01 3 0.4227 0.711 0.42 0.00 0.58 0.00 0.00
#> TCGA.D1.A3JQ.01 4 0.0000 0.846 0.00 0.00 0.00 1.00 0.00
#> TCGA.EO.A1Y5.01 5 0.0000 0.932 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A2H5.01 5 0.0000 0.932 0.00 0.00 0.00 0.00 1.00
#> TCGA.FI.A2D2.01 2 0.4227 0.251 0.00 0.58 0.00 0.42 0.00
#> TCGA.KP.A3VZ.01 3 0.4227 0.711 0.42 0.00 0.58 0.00 0.00
#> TCGA.SL.A6J9.01 5 0.0000 0.932 0.00 0.00 0.00 0.00 1.00
#> TCGA.DI.A1NO.01 3 0.4227 0.711 0.42 0.00 0.58 0.00 0.00
#> TCGA.FI.A2CY.01 2 0.3895 0.702 0.32 0.68 0.00 0.00 0.00
#> TCGA.KJ.A3U4.01 2 0.3895 0.702 0.32 0.68 0.00 0.00 0.00
#> TCGA.EO.A3KU.01 4 0.0000 0.846 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A179.01 5 0.3561 0.779 0.26 0.00 0.00 0.00 0.74
#> TCGA.AX.A1CF.01 2 0.0609 0.787 0.02 0.98 0.00 0.00 0.00
#> TCGA.PG.A915.01 3 0.4302 -0.561 0.00 0.00 0.52 0.48 0.00
#> TCGA.EY.A212.01 4 0.0000 0.846 0.00 0.00 0.00 1.00 0.00
#> TCGA.AP.A1DK.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00
#> TCGA.PG.A914.01 2 0.0000 0.787 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.EY.A3L3.01 6 0.341 0.880 0.00 0.00 0.00 0.30 0.00 0.70
#> TCGA.E6.A8L9.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A3JQ.01 4 0.000 0.806 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EO.A1Y5.01 5 0.000 0.839 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A2H5.01 5 0.000 0.839 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FI.A2D2.01 4 0.481 0.462 0.22 0.12 0.00 0.66 0.00 0.00
#> TCGA.KP.A3VZ.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.SL.A6J9.01 5 0.181 0.817 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.DI.A1NO.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2CY.01 2 0.000 0.535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KJ.A3U4.01 2 0.000 0.535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3KU.01 4 0.000 0.806 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A179.01 5 0.571 0.540 0.22 0.00 0.00 0.00 0.52 0.26
#> TCGA.AX.A1CF.01 2 0.387 -0.859 0.50 0.50 0.00 0.00 0.00 0.00
#> TCGA.PG.A915.01 6 0.561 0.882 0.12 0.00 0.02 0.28 0.00 0.58
#> TCGA.EY.A212.01 4 0.000 0.806 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AP.A1DK.01 1 0.383 0.906 0.56 0.44 0.00 0.00 0.00 0.00
#> TCGA.PG.A914.01 1 0.463 0.905 0.52 0.44 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EY.A3L3.01 6 0.4100 0.892 0.00 0.04 0.00 0.10 0.00 0.76 0.10
#> TCGA.E6.A8L9.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3JQ.01 4 0.0000 0.866 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A1Y5.01 5 0.0000 0.885 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A2H5.01 5 0.0504 0.877 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.FI.A2D2.01 4 0.4248 0.571 0.26 0.00 0.00 0.66 0.00 0.00 0.08
#> TCGA.KP.A3VZ.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.SL.A6J9.01 5 0.2278 0.785 0.00 0.04 0.00 0.00 0.88 0.08 0.00
#> TCGA.DI.A1NO.01 3 0.0504 0.984 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FI.A2CY.01 2 0.1671 0.985 0.10 0.90 0.00 0.00 0.00 0.00 0.00
#> TCGA.KJ.A3U4.01 2 0.2163 0.985 0.10 0.88 0.00 0.00 0.00 0.02 0.00
#> TCGA.EO.A3KU.01 4 0.0000 0.866 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A179.01 7 0.3525 0.000 0.00 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.AX.A1CF.01 1 0.0863 0.859 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A915.01 6 0.1671 0.892 0.00 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.EY.A212.01 4 0.0504 0.858 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.AP.A1DK.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A914.01 1 0.2708 0.772 0.78 0.00 0.00 0.00 0.00 0.00 0.22
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EY.A3L3.01 6 0.4492 0.783 0.00 0.06 0.00 0.04 0.00 0.70 0.18 0.02
#> TCGA.E6.A8L9.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3JQ.01 4 0.0000 0.784 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y5.01 5 0.0471 0.870 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.AX.A2H5.01 5 0.0000 0.870 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2D2.01 4 0.5870 0.322 0.22 0.22 0.00 0.48 0.00 0.00 0.08 0.00
#> TCGA.KP.A3VZ.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SL.A6J9.01 5 0.2569 0.748 0.00 0.16 0.00 0.00 0.82 0.02 0.00 0.00
#> TCGA.DI.A1NO.01 3 0.0471 0.983 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2CY.01 8 0.0471 1.000 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.KJ.A3U4.01 8 0.0471 1.000 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.EO.A3KU.01 4 0.0000 0.784 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A179.01 7 0.3015 0.000 0.00 0.00 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.AX.A1CF.01 1 0.0471 0.760 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.PG.A915.01 6 0.0808 0.783 0.00 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.EY.A212.01 4 0.2165 0.731 0.00 0.06 0.00 0.88 0.00 0.00 0.06 0.00
#> TCGA.AP.A1DK.01 1 0.0000 0.764 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A914.01 1 0.3329 0.494 0.52 0.48 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["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 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.990 0.996 0.3644 0.641 0.641
#> 3 3 0.703 0.935 0.955 0.7504 0.704 0.538
#> 4 4 0.750 0.699 0.767 0.1342 1.000 1.000
#> 5 5 0.737 0.652 0.808 0.0747 0.786 0.460
#> 6 6 0.720 0.585 0.659 0.0367 0.883 0.549
#> 7 7 0.740 0.739 0.838 0.0368 0.923 0.620
#> 8 8 0.780 0.770 0.867 0.0279 0.966 0.786
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.D1.A16I.01 1 0.000 0.994 1.00 0.00
#> TCGA.B5.A1MU.01 1 0.000 0.994 1.00 0.00
#> TCGA.A5.A1OH.01 1 0.000 0.994 1.00 0.00
#> TCGA.AJ.A3BF.01 1 0.000 0.994 1.00 0.00
#> TCGA.B5.A1N2.01 1 0.000 0.994 1.00 0.00
#> TCGA.AX.A1CA.01 1 0.000 0.994 1.00 0.00
#> TCGA.QS.A8F1.01 1 0.000 0.994 1.00 0.00
#> TCGA.BK.A26L.01 1 0.000 0.994 1.00 0.00
#> TCGA.KP.A3W3.01 1 0.000 0.994 1.00 0.00
#> TCGA.BK.A0CC.01 1 0.000 0.994 1.00 0.00
#> TCGA.B5.A1MS.01 1 0.000 0.994 1.00 0.00
#> TCGA.AJ.A2QM.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A1C7.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A3G4.01 1 0.529 0.864 0.88 0.12
#> TCGA.AX.A2H2.01 2 0.000 1.000 0.00 1.00
#> TCGA.EY.A1GR.01 2 0.000 1.000 0.00 1.00
#> TCGA.B5.A11I.01 1 0.000 0.994 1.00 0.00
#> TCGA.A5.A1OG.01 1 0.000 0.994 1.00 0.00
#> TCGA.FI.A2EU.01 2 0.000 1.000 0.00 1.00
#> TCGA.DI.A2QY.01 1 0.000 0.994 1.00 0.00
#> TCGA.D1.A1NX.01 1 0.000 0.994 1.00 0.00
#> TCGA.AJ.A23M.01 1 0.000 0.994 1.00 0.00
#> TCGA.KP.A3W0.01 1 0.000 0.994 1.00 0.00
#> TCGA.AP.A1E4.01 1 0.000 0.994 1.00 0.00
#> TCGA.AX.A2HF.01 1 0.000 0.994 1.00 0.00
#> TCGA.EY.A1GM.01 2 0.000 1.000 0.00 1.00
#> TCGA.FI.A2EY.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.D1.A16I.01 3 0.296 0.982 0.10 0.0 0.90
#> TCGA.B5.A1MU.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.A5.A1OH.01 1 0.619 0.135 0.58 0.0 0.42
#> TCGA.AJ.A3BF.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.B5.A1N2.01 3 0.296 0.982 0.10 0.0 0.90
#> TCGA.AX.A1CA.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.QS.A8F1.01 3 0.296 0.982 0.10 0.0 0.90
#> TCGA.BK.A26L.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.KP.A3W3.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.BK.A0CC.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.B5.A1MS.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.AJ.A2QM.01 2 0.000 0.986 0.00 1.0 0.00
#> TCGA.AX.A1C7.01 2 0.000 0.986 0.00 1.0 0.00
#> TCGA.AX.A3G4.01 3 0.000 0.866 0.00 0.0 1.00
#> TCGA.AX.A2H2.01 2 0.000 0.986 0.00 1.0 0.00
#> TCGA.EY.A1GR.01 2 0.296 0.926 0.00 0.9 0.10
#> TCGA.B5.A11I.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.A5.A1OG.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.FI.A2EU.01 2 0.000 0.986 0.00 1.0 0.00
#> TCGA.DI.A2QY.01 3 0.296 0.982 0.10 0.0 0.90
#> TCGA.D1.A1NX.01 3 0.296 0.982 0.10 0.0 0.90
#> TCGA.AJ.A23M.01 3 0.296 0.982 0.10 0.0 0.90
#> TCGA.KP.A3W0.01 3 0.296 0.982 0.10 0.0 0.90
#> TCGA.AP.A1E4.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.AX.A2HF.01 1 0.000 0.960 1.00 0.0 0.00
#> TCGA.EY.A1GM.01 2 0.000 0.986 0.00 1.0 0.00
#> TCGA.FI.A2EY.01 1 0.000 0.960 1.00 0.0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D1.A16I.01 3 0.0000 0.697 0.00 0.00 1.00 0.00
#> TCGA.B5.A1MU.01 4 0.0707 0.733 0.02 0.00 0.00 0.98
#> TCGA.A5.A1OH.01 4 0.7249 -0.131 0.26 0.00 0.20 0.54
#> TCGA.AJ.A3BF.01 4 0.4522 0.748 0.32 0.00 0.00 0.68
#> TCGA.B5.A1N2.01 3 0.7738 0.566 0.26 0.00 0.44 0.30
#> TCGA.AX.A1CA.01 4 0.4522 0.748 0.32 0.00 0.00 0.68
#> TCGA.QS.A8F1.01 3 0.0000 0.697 0.00 0.00 1.00 0.00
#> TCGA.BK.A26L.01 4 0.1637 0.712 0.06 0.00 0.00 0.94
#> TCGA.KP.A3W3.01 4 0.1637 0.715 0.06 0.00 0.00 0.94
#> TCGA.BK.A0CC.01 4 0.4522 0.748 0.32 0.00 0.00 0.68
#> TCGA.B5.A1MS.01 4 0.4522 0.748 0.32 0.00 0.00 0.68
#> TCGA.AJ.A2QM.01 2 0.4134 0.803 0.26 0.74 0.00 0.00
#> TCGA.AX.A1C7.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.AX.A3G4.01 3 0.3172 0.601 0.16 0.00 0.84 0.00
#> TCGA.AX.A2H2.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GR.01 2 0.4855 0.713 0.40 0.60 0.00 0.00
#> TCGA.B5.A11I.01 4 0.1211 0.725 0.04 0.00 0.00 0.96
#> TCGA.A5.A1OG.01 4 0.0707 0.741 0.02 0.00 0.00 0.98
#> TCGA.FI.A2EU.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.DI.A2QY.01 3 0.7805 0.561 0.28 0.00 0.42 0.30
#> TCGA.D1.A1NX.01 3 0.7738 0.566 0.26 0.00 0.44 0.30
#> TCGA.AJ.A23M.01 3 0.3610 0.681 0.20 0.00 0.80 0.00
#> TCGA.KP.A3W0.01 3 0.0707 0.693 0.02 0.00 0.98 0.00
#> TCGA.AP.A1E4.01 4 0.4522 0.748 0.32 0.00 0.00 0.68
#> TCGA.AX.A2HF.01 4 0.4522 0.748 0.32 0.00 0.00 0.68
#> TCGA.EY.A1GM.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.FI.A2EY.01 4 0.1211 0.725 0.04 0.00 0.00 0.96
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D1.A16I.01 3 0.484 0.836 0.32 0.00 0.64 0.00 0.04
#> TCGA.B5.A1MU.01 5 0.430 0.301 0.00 0.00 0.00 0.48 0.52
#> TCGA.A5.A1OH.01 5 0.410 0.539 0.20 0.00 0.00 0.04 0.76
#> TCGA.AJ.A3BF.01 4 0.000 0.891 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A1N2.01 5 0.351 0.456 0.18 0.00 0.02 0.00 0.80
#> TCGA.AX.A1CA.01 4 0.000 0.891 0.00 0.00 0.00 1.00 0.00
#> TCGA.QS.A8F1.01 3 0.507 0.838 0.30 0.00 0.64 0.00 0.06
#> TCGA.BK.A26L.01 5 0.484 0.560 0.04 0.00 0.00 0.32 0.64
#> TCGA.KP.A3W3.01 5 0.534 0.545 0.08 0.00 0.00 0.30 0.62
#> TCGA.BK.A0CC.01 4 0.000 0.891 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A1MS.01 4 0.000 0.891 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A2QM.01 2 0.000 0.676 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A1C7.01 2 0.446 0.827 0.32 0.66 0.00 0.00 0.02
#> TCGA.AX.A3G4.01 3 0.000 0.628 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A2H2.01 2 0.398 0.831 0.34 0.66 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 2 0.389 0.378 0.00 0.68 0.32 0.00 0.00
#> TCGA.B5.A11I.01 5 0.413 0.498 0.00 0.00 0.00 0.38 0.62
#> TCGA.A5.A1OG.01 4 0.426 -0.242 0.00 0.00 0.00 0.56 0.44
#> TCGA.FI.A2EU.01 2 0.398 0.831 0.34 0.66 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 5 0.233 0.556 0.08 0.00 0.02 0.00 0.90
#> TCGA.D1.A1NX.01 5 0.351 0.456 0.18 0.00 0.02 0.00 0.80
#> TCGA.AJ.A23M.01 3 0.671 0.646 0.32 0.00 0.42 0.00 0.26
#> TCGA.KP.A3W0.01 3 0.538 0.832 0.26 0.00 0.64 0.00 0.10
#> TCGA.AP.A1E4.01 4 0.000 0.891 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A2HF.01 4 0.000 0.891 0.00 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GM.01 2 0.398 0.831 0.34 0.66 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 5 0.642 0.426 0.18 0.00 0.00 0.36 0.46
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D1.A16I.01 3 0.0937 0.772 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.B5.A1MU.01 4 0.3869 -0.286 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.A5.A1OH.01 5 0.5520 0.330 0.34 0.00 0.00 0.04 0.56 0.06
#> TCGA.AJ.A3BF.01 4 0.0000 0.786 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A1N2.01 1 0.5029 0.694 0.62 0.00 0.12 0.00 0.26 0.00
#> TCGA.AX.A1CA.01 4 0.0000 0.786 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QS.A8F1.01 3 0.0547 0.784 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BK.A26L.01 5 0.5037 0.391 0.08 0.00 0.00 0.38 0.54 0.00
#> TCGA.KP.A3W3.01 5 0.4042 0.558 0.00 0.00 0.02 0.18 0.76 0.04
#> TCGA.BK.A0CC.01 4 0.0000 0.786 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A1MS.01 4 0.0000 0.786 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QM.01 6 0.3499 0.635 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.AX.A1C7.01 2 0.2048 0.861 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G4.01 3 0.6556 0.456 0.12 0.00 0.54 0.00 0.12 0.22
#> TCGA.AX.A2H2.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 6 0.1814 0.709 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.B5.A11I.01 5 0.4282 0.299 0.02 0.00 0.00 0.42 0.56 0.00
#> TCGA.A5.A1OG.01 4 0.3869 -0.286 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.FI.A2EU.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 5 0.4879 0.156 0.12 0.00 0.12 0.00 0.72 0.04
#> TCGA.D1.A1NX.01 1 0.5029 0.694 0.62 0.00 0.12 0.00 0.26 0.00
#> TCGA.AJ.A23M.01 1 0.3864 0.149 0.52 0.00 0.48 0.00 0.00 0.00
#> TCGA.KP.A3W0.01 3 0.0937 0.766 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.AP.A1E4.01 4 0.0000 0.786 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A2HF.01 4 0.0000 0.786 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GM.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 5 0.6250 0.538 0.16 0.00 0.00 0.22 0.56 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D1.A16I.01 3 0.0504 0.883 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.B5.A1MU.01 5 0.3294 0.626 0.00 0.00 0.00 0.34 0.66 0.00 0.00
#> TCGA.A5.A1OH.01 5 0.4812 0.348 0.14 0.00 0.02 0.00 0.66 0.00 0.18
#> TCGA.AJ.A3BF.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1N2.01 1 0.3388 0.818 0.76 0.00 0.04 0.00 0.20 0.00 0.00
#> TCGA.AX.A1CA.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QS.A8F1.01 3 0.0000 0.886 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A26L.01 5 0.3661 0.656 0.02 0.00 0.00 0.22 0.74 0.00 0.02
#> TCGA.KP.A3W3.01 5 0.5521 0.541 0.12 0.00 0.00 0.10 0.62 0.00 0.16
#> TCGA.BK.A0CC.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MS.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A2QM.01 6 0.2832 0.604 0.00 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.AX.A1C7.01 2 0.2313 0.883 0.06 0.88 0.00 0.00 0.00 0.00 0.06
#> TCGA.AX.A3G4.01 7 0.4842 0.000 0.00 0.00 0.16 0.00 0.00 0.24 0.60
#> TCGA.AX.A2H2.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 6 0.0000 0.527 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A11I.01 5 0.3517 0.665 0.02 0.00 0.00 0.28 0.70 0.00 0.00
#> TCGA.A5.A1OG.01 5 0.3358 0.602 0.00 0.00 0.00 0.36 0.64 0.00 0.00
#> TCGA.FI.A2EU.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 5 0.5086 0.407 0.20 0.00 0.02 0.00 0.62 0.00 0.16
#> TCGA.D1.A1NX.01 1 0.3388 0.818 0.76 0.00 0.04 0.00 0.20 0.00 0.00
#> TCGA.AJ.A23M.01 1 0.3047 0.589 0.72 0.00 0.28 0.00 0.00 0.00 0.00
#> TCGA.KP.A3W0.01 3 0.2376 0.784 0.12 0.00 0.86 0.00 0.02 0.00 0.00
#> TCGA.AP.A1E4.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GM.01 2 0.0504 0.952 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FI.A2EY.01 5 0.4840 0.466 0.06 0.00 0.00 0.08 0.68 0.00 0.18
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D1.A16I.01 3 0.0808 0.863 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.B5.A1MU.01 5 0.6857 0.639 0.20 0.00 0.00 0.18 0.34 0.00 0.02 0.26
#> TCGA.A5.A1OH.01 5 0.1947 0.242 0.14 0.00 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.AJ.A3BF.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1N2.01 1 0.0000 0.742 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CA.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A8F1.01 3 0.0000 0.874 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A26L.01 5 0.6532 0.618 0.26 0.00 0.00 0.10 0.40 0.00 0.02 0.22
#> TCGA.KP.A3W3.01 8 0.2862 0.835 0.10 0.00 0.00 0.00 0.08 0.00 0.00 0.82
#> TCGA.BK.A0CC.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MS.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QM.01 6 0.0000 0.967 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A1C7.01 2 0.3036 0.782 0.00 0.78 0.00 0.00 0.04 0.00 0.00 0.18
#> TCGA.AX.A3G4.01 7 0.0808 0.000 0.00 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.AX.A2H2.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GR.01 6 0.0808 0.967 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.B5.A11I.01 5 0.6836 0.640 0.22 0.00 0.00 0.16 0.34 0.00 0.02 0.26
#> TCGA.A5.A1OG.01 5 0.6908 0.600 0.18 0.00 0.00 0.24 0.32 0.00 0.02 0.24
#> TCGA.FI.A2EU.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.01 8 0.3299 0.847 0.18 0.00 0.00 0.00 0.06 0.00 0.00 0.76
#> TCGA.D1.A1NX.01 1 0.0000 0.742 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A23M.01 1 0.4482 0.435 0.60 0.00 0.26 0.00 0.14 0.00 0.00 0.00
#> TCGA.KP.A3W0.01 3 0.2648 0.771 0.08 0.00 0.84 0.00 0.00 0.00 0.00 0.08
#> TCGA.AP.A1E4.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HF.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GM.01 2 0.0471 0.923 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.FI.A2EY.01 5 0.5269 0.455 0.12 0.00 0.00 0.08 0.64 0.00 0.02 0.14
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node035-leaf , Node036-leaf , Node041 , Node042 , Node043 , Node051 , Node052 .
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 189 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.972 0.988 0.4986 0.504 0.504
#> 3 3 0.963 0.936 0.973 0.3407 0.712 0.487
#> 4 4 0.989 0.957 0.982 0.1252 0.838 0.565
#> 5 5 0.822 0.756 0.875 0.0569 0.921 0.701
#> 6 6 0.790 0.688 0.832 0.0404 0.939 0.725
#> 7 7 0.818 0.720 0.835 0.0240 0.945 0.711
#> 8 8 0.811 0.620 0.792 0.0199 0.952 0.711
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.AP.A1DO.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A2H7.01 2 0.000 0.979 0.00 1.00
#> TCGA.EC.A24G.01 2 0.881 0.599 0.30 0.70
#> TCGA.BG.A2AD.01 2 0.722 0.762 0.20 0.80
#> TCGA.AX.A3FW.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A16R.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A11L.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A11Z.01 1 0.000 0.998 1.00 0.00
#> TCGA.A5.A2K7.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A3FC.01 2 0.000 0.979 0.00 1.00
#> TCGA.EO.A3KX.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A1CJ.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A5W2.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A17T.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A1GQ.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A103.01 2 0.000 0.979 0.00 1.00
#> TCGA.EO.A22R.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A16Q.01 2 0.000 0.979 0.00 1.00
#> TCGA.AP.A05O.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3BI.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A11W.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A17M.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GE.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A0MK.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A161.01 2 0.000 0.979 0.00 1.00
#> TCGA.PG.A916.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A1H0.01 2 0.958 0.422 0.38 0.62
#> TCGA.BK.A13C.01 2 0.881 0.598 0.30 0.70
#> TCGA.EO.A3AU.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GI.01 1 0.000 0.998 1.00 0.00
#> TCGA.FI.A2D4.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A0ZO.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A215.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A1CK.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11S.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A1GL.01 2 0.000 0.979 0.00 1.00
#> TCGA.AP.A1DM.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A186.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A8CW.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A1NZ.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A17U.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A06D.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A3EL.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A2OM.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A175.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A2QL.01 1 0.000 0.998 1.00 0.00
#> TCGA.AP.A1DH.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A0VZ.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A22Y.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A17A.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A3B0.01 2 0.000 0.979 0.00 1.00
#> TCGA.BS.A0WQ.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A3G9.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A1O0.01 2 0.000 0.979 0.00 1.00
#> TCGA.AP.A0LS.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GW.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A167.01 1 0.000 0.998 1.00 0.00
#> TCGA.DF.A2KU.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A0ZU.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A11F.01 2 0.000 0.979 0.00 1.00
#> TCGA.SJ.A6ZJ.01 2 0.000 0.979 0.00 1.00
#> TCGA.EO.A3AY.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A220.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A0VW.01 2 0.584 0.839 0.14 0.86
#> TCGA.FI.A2F4.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3BK.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A1MX.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A0ZN.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A3DA.01 1 0.141 0.978 0.98 0.02
#> TCGA.QS.A744.01 2 0.000 0.979 0.00 1.00
#> TCGA.BS.A0VI.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A168.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A17F.01 2 0.000 0.979 0.00 1.00
#> TCGA.AP.A1E1.01 1 0.000 0.998 1.00 0.00
#> TCGA.EC.A1NJ.01 1 0.529 0.858 0.88 0.12
#> TCGA.EY.A549.01 2 0.000 0.979 0.00 1.00
#> TCGA.BK.A6W3.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A11J.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A176.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A17R.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A22S.01 1 0.000 0.998 1.00 0.00
#> TCGA.PG.A917.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A1NY.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A0W2.01 2 0.000 0.979 0.00 1.00
#> TCGA.BS.A0U5.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A15W.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A174.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A2HD.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A3GB.01 1 0.000 0.998 1.00 0.00
#> TCGA.A5.A2K5.01 2 0.242 0.944 0.04 0.96
#> TCGA.D1.A160.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A3EW.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A0MA.01 2 0.000 0.979 0.00 1.00
#> TCGA.BK.A4ZD.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A17L.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A3G8.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A11Q.01 1 0.000 0.998 1.00 0.00
#> TCGA.E6.A2P9.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A22X.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A1GU.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GH.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A0JU.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A1Y7.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A8CV.01 2 0.000 0.979 0.00 1.00
#> TCGA.BK.A56F.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A3OL.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A102.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A165.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A2HH.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A17S.01 2 0.000 0.979 0.00 1.00
#> TCGA.E6.A1LX.01 2 0.000 0.979 0.00 1.00
#> TCGA.BS.A0V4.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A1O7.01 1 0.000 0.998 1.00 0.00
#> TCGA.AP.A1E0.01 1 0.000 0.998 1.00 0.00
#> TCGA.DF.A2KS.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A2L7.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A548.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A222.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A1CI.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A16V.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A3FS.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A1GF.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A18B.01 1 0.000 0.998 1.00 0.00
#> TCGA.DI.A1BY.01 2 0.000 0.979 0.00 1.00
#> TCGA.SL.A6JA.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A547.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A11G.01 2 0.000 0.979 0.00 1.00
#> TCGA.A5.A1OK.01 2 0.141 0.962 0.02 0.98
#> TCGA.EY.A2OO.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A1MZ.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A0IS.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3I9.01 2 0.000 0.979 0.00 1.00
#> TCGA.5S.A9Q8.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A0JT.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A2QO.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A2HC.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A0MH.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A5DW.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A0J0.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A3NC.01 1 0.000 0.998 1.00 0.00
#> TCGA.AP.A1DV.01 2 0.881 0.599 0.30 0.70
#> TCGA.B5.A11P.01 2 0.000 0.979 0.00 1.00
#> TCGA.A5.A0VO.01 2 0.000 0.979 0.00 1.00
#> TCGA.EO.A22U.01 1 0.000 0.998 1.00 0.00
#> TCGA.QS.A5YQ.01 2 0.000 0.979 0.00 1.00
#> TCGA.E6.A1M0.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A17H.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A1C9.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A0JX.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11V.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A1MW.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A3FX.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A2OP.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3BG.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A2G5.01 2 0.141 0.962 0.02 0.98
#> TCGA.D1.A1O5.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A0ZQ.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GK.01 1 0.000 0.998 1.00 0.00
#> TCGA.AP.A1DR.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A0ZR.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A0VT.01 2 0.000 0.979 0.00 1.00
#> TCGA.B5.A3FH.01 2 0.327 0.925 0.06 0.94
#> TCGA.AP.A1DP.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A2HJ.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A1CE.01 2 0.722 0.762 0.20 0.80
#> TCGA.EY.A1GX.01 1 0.000 0.998 1.00 0.00
#> TCGA.QF.A5YT.01 2 0.000 0.979 0.00 1.00
#> TCGA.EY.A72D.01 2 0.000 0.979 0.00 1.00
#> TCGA.AX.A1C4.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GT.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1G8.01 2 0.000 0.979 0.00 1.00
#> TCGA.AJ.A5DV.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11E.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A17Q.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A15Z.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A17D.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A177.01 1 0.000 0.998 1.00 0.00
#> TCGA.BK.A13B.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GD.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A0W1.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3EK.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11R.01 1 0.000 0.998 1.00 0.00
#> TCGA.A5.A7WJ.01 1 0.000 0.998 1.00 0.00
#> TCGA.DF.A2L0.01 2 0.000 0.979 0.00 1.00
#> TCGA.BG.A187.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A16N.01 2 0.000 0.979 0.00 1.00
#> TCGA.D1.A163.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A16Y.01 2 0.795 0.702 0.24 0.76
#> TCGA.AX.A2HA.01 1 0.000 0.998 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AP.A1DO.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AX.A2H7.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EC.A24G.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BG.A2AD.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AX.A3FW.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A16R.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.B5.A11L.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.B5.A11Z.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.A5.A2K7.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EO.A3KX.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AX.A1CJ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EY.A5W2.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A17T.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A1GQ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EO.A22R.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AP.A05O.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AJ.A3BI.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.B5.A11W.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A17M.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BG.A0MK.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A161.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.PG.A916.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A1H0.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BK.A13C.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EO.A3AU.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EY.A1GI.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.FI.A2D4.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A0ZO.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EY.A215.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AX.A1CK.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.B5.A11S.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A1GL.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AP.A1DM.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.BG.A186.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AJ.A8CW.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A1NZ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A17U.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AX.A06D.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A3EL.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EY.A2OM.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A175.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A2QL.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AP.A1DH.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BG.A0VZ.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EO.A22Y.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A17A.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EO.A3B0.01 3 0.6302 0.167 0.00 0.48 0.52
#> TCGA.BS.A0WQ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AX.A3G9.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A1O0.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AP.A0LS.01 1 0.5948 0.464 0.64 0.00 0.36
#> TCGA.EY.A1GW.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A167.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DF.A2KU.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A0ZU.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EO.A3AY.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BG.A220.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BG.A0VW.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.FI.A2F4.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AJ.A3BK.01 3 0.6126 0.398 0.00 0.40 0.60
#> TCGA.B5.A1MX.01 1 0.5835 0.508 0.66 0.00 0.34
#> TCGA.D1.A0ZN.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A3DA.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.QS.A744.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BS.A0VI.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A168.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A17F.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AP.A1E1.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EC.A1NJ.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A549.01 3 0.6126 0.398 0.00 0.40 0.60
#> TCGA.BK.A6W3.01 3 0.1529 0.910 0.00 0.04 0.96
#> TCGA.B5.A11J.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A176.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A17R.01 1 0.4002 0.808 0.84 0.00 0.16
#> TCGA.EO.A22S.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.PG.A917.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A1NY.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BG.A0W2.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BS.A0U5.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A15W.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A174.01 1 0.5397 0.624 0.72 0.00 0.28
#> TCGA.AX.A2HD.01 3 0.5397 0.627 0.00 0.28 0.72
#> TCGA.AX.A3GB.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.A5.A2K5.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A160.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.BG.A3EW.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.BG.A0MA.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BK.A4ZD.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A17L.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AX.A3G8.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.B5.A11Q.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EO.A22X.01 3 0.6126 0.398 0.00 0.40 0.60
#> TCGA.EY.A1GU.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EY.A1GH.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.B5.A0JU.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EO.A1Y7.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A8CV.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BK.A56F.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A3OL.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A102.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A165.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AX.A2HH.01 3 0.6126 0.398 0.00 0.40 0.60
#> TCGA.D1.A17S.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E6.A1LX.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BS.A0V4.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A1O7.01 3 0.4796 0.681 0.22 0.00 0.78
#> TCGA.AP.A1E0.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DF.A2KS.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BG.A2L7.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A548.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BG.A222.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AX.A1CI.01 1 0.0892 0.962 0.98 0.00 0.02
#> TCGA.D1.A16V.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AX.A3FS.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EY.A1GF.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.BG.A18B.01 1 0.0892 0.963 0.98 0.00 0.02
#> TCGA.DI.A1BY.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.SL.A6JA.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A547.01 3 0.4555 0.742 0.00 0.20 0.80
#> TCGA.B5.A11G.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.A5.A1OK.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A2OO.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.B5.A1MZ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AX.A0IS.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AJ.A3I9.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.5S.A9Q8.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A2QO.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AX.A2HC.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A5DW.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AX.A0J0.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A3NC.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AP.A1DV.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.B5.A11P.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.A5.A0VO.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EO.A22U.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E6.A1M0.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A17H.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AX.A1C9.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.B5.A0JX.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.B5.A11V.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.B5.A1MW.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AX.A3FX.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EY.A2OP.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AJ.A3BG.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A2G5.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A1O5.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A0ZQ.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A1GK.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AP.A1DR.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A0ZR.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.BG.A0VT.01 3 0.6126 0.398 0.00 0.40 0.60
#> TCGA.B5.A3FH.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AP.A1DP.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AX.A2HJ.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AX.A1CE.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.EY.A1GX.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.QF.A5YT.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EY.A72D.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AX.A1C4.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EY.A1GT.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EY.A1G8.01 3 0.6045 0.442 0.00 0.38 0.62
#> TCGA.AJ.A5DV.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.B5.A11E.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A15Z.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A17D.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.BK.A13B.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EY.A1GD.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BG.A0W1.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.AJ.A3EK.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.B5.A11R.01 3 0.5397 0.574 0.28 0.00 0.72
#> TCGA.A5.A7WJ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DF.A2L0.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BG.A187.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.D1.A16N.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D1.A163.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.D1.A16Y.01 3 0.0000 0.943 0.00 0.00 1.00
#> TCGA.AX.A2HA.01 1 0.0000 0.980 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.AP.A1DO.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H7.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EC.A24G.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.BG.A2AD.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AX.A3FW.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.D1.A16R.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.B5.A11L.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A11Z.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KX.01 3 0.2011 0.886 0.08 0.00 0.92 0.00
#> TCGA.AX.A1CJ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EY.A5W2.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A17T.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EY.A1GQ.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EO.A22R.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AP.A05O.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3BI.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.B5.A11W.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.D1.A17M.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A0MK.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A161.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.PG.A916.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EY.A1H0.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.BK.A13C.01 3 0.0707 0.942 0.00 0.00 0.98 0.02
#> TCGA.EO.A3AU.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.FI.A2D4.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZO.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.EY.A215.01 1 0.2921 0.838 0.86 0.00 0.14 0.00
#> TCGA.AX.A1CK.01 3 0.0707 0.942 0.02 0.00 0.98 0.00
#> TCGA.B5.A11S.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EY.A1GL.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AP.A1DM.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.BG.A186.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AJ.A8CW.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A17U.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AX.A06D.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3EL.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EY.A2OM.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A175.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QL.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AP.A1DH.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.BG.A0VZ.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.EO.A22Y.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A17A.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EO.A3B0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BS.A0WQ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A3G9.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A1O0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AP.A0LS.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GW.01 4 0.4790 0.353 0.00 0.00 0.38 0.62
#> TCGA.D1.A167.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.DF.A2KU.01 3 0.5512 0.537 0.00 0.04 0.66 0.30
#> TCGA.D1.A0ZU.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EO.A3AY.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.BG.A220.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A0VW.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.FI.A2F4.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A1MX.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A0ZN.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A3DA.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.QS.A744.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BS.A0VI.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A168.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A17F.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AP.A1E1.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 3 0.1211 0.925 0.00 0.00 0.96 0.04
#> TCGA.EY.A549.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.BK.A6W3.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A11J.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A176.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 3 0.4713 0.421 0.36 0.00 0.64 0.00
#> TCGA.EO.A22S.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.PG.A917.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.D1.A1NY.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.BG.A0W2.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BS.A0U5.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A15W.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.D1.A174.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AX.A2HD.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AX.A3GB.01 1 0.4907 0.293 0.58 0.00 0.42 0.00
#> TCGA.A5.A2K5.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A160.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.BG.A3EW.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BK.A4ZD.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A17L.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AX.A3G8.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A11Q.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EO.A22X.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EY.A1GU.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A0JU.01 3 0.3801 0.702 0.22 0.00 0.78 0.00
#> TCGA.EO.A1Y7.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A8CV.01 3 0.4277 0.618 0.00 0.00 0.72 0.28
#> TCGA.BK.A56F.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3OL.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A102.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A165.01 4 0.0707 0.966 0.00 0.02 0.00 0.98
#> TCGA.AX.A2HH.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.D1.A17S.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E6.A1LX.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.BS.A0V4.01 3 0.0707 0.942 0.02 0.00 0.98 0.00
#> TCGA.D1.A1O7.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AP.A1E0.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A2L7.01 3 0.4522 0.542 0.00 0.00 0.68 0.32
#> TCGA.EY.A548.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A222.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CI.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A16V.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AX.A3FS.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.DI.A1BY.01 4 0.2921 0.832 0.00 0.14 0.00 0.86
#> TCGA.SL.A6JA.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EY.A547.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A11G.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.A5.A1OK.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.EY.A2OO.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MZ.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AX.A0IS.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3I9.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.5S.A9Q8.01 1 0.3610 0.758 0.80 0.00 0.20 0.00
#> TCGA.B5.A0JT.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QO.01 1 0.3172 0.813 0.84 0.00 0.16 0.00
#> TCGA.AX.A2HC.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A5DW.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NC.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AP.A1DV.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.B5.A11P.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.A5.A0VO.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.EO.A22U.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E6.A1M0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A17H.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A1C9.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A0JX.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.B5.A11V.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.B5.A1MW.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FX.01 2 0.0707 0.979 0.00 0.98 0.00 0.02
#> TCGA.EY.A2OP.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A2G5.01 3 0.3801 0.716 0.00 0.00 0.78 0.22
#> TCGA.D1.A1O5.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GK.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.AP.A1DR.01 1 0.2011 0.905 0.92 0.00 0.08 0.00
#> TCGA.D1.A0ZR.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.BG.A0VT.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.B5.A3FH.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AP.A1DP.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HJ.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AX.A1CE.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GX.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.QF.A5YT.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EY.A72D.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A1C4.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EY.A1G8.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AJ.A5DV.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.B5.A11E.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A17Q.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A15Z.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A17D.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.BK.A13B.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GD.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A0W1.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.B5.A11R.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.A5.A7WJ.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.DF.A2L0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A187.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A16N.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A163.01 3 0.0000 0.957 0.00 0.00 1.00 0.00
#> TCGA.D1.A16Y.01 4 0.0000 0.985 0.00 0.00 0.00 1.00
#> TCGA.AX.A2HA.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AP.A1DO.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H7.01 4 0.2331 0.9052 0.00 0.02 0.00 0.90 0.08
#> TCGA.EC.A24G.01 5 0.3684 0.4193 0.00 0.00 0.28 0.00 0.72
#> TCGA.BG.A2AD.01 5 0.3684 0.4193 0.00 0.00 0.28 0.00 0.72
#> TCGA.AX.A3FW.01 4 0.1043 0.9162 0.00 0.00 0.00 0.96 0.04
#> TCGA.D1.A16R.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11L.01 4 0.2732 0.8663 0.00 0.00 0.00 0.84 0.16
#> TCGA.B5.A11Z.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 5 0.4302 -0.1721 0.00 0.48 0.00 0.00 0.52
#> TCGA.EO.A3KX.01 3 0.0000 0.6831 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CJ.01 2 0.2020 0.8822 0.00 0.90 0.00 0.00 0.10
#> TCGA.EY.A5W2.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17T.01 4 0.1732 0.9101 0.00 0.00 0.00 0.92 0.08
#> TCGA.EY.A1GQ.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.3424 0.7553 0.00 0.76 0.00 0.00 0.24
#> TCGA.EO.A22R.01 1 0.3895 0.6511 0.68 0.00 0.32 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A05O.01 3 0.3561 0.6551 0.00 0.00 0.74 0.00 0.26
#> TCGA.AJ.A3BI.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A11W.01 4 0.1410 0.9170 0.00 0.00 0.00 0.94 0.06
#> TCGA.D1.A17M.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0MK.01 5 0.2280 0.5732 0.00 0.00 0.12 0.00 0.88
#> TCGA.D1.A161.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.PG.A916.01 4 0.2516 0.8831 0.00 0.00 0.00 0.86 0.14
#> TCGA.EY.A1H0.01 5 0.3684 0.4193 0.00 0.00 0.28 0.00 0.72
#> TCGA.BK.A13C.01 5 0.6592 0.1202 0.00 0.00 0.30 0.24 0.46
#> TCGA.EO.A3AU.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 3 0.5273 0.4950 0.00 0.00 0.68 0.16 0.16
#> TCGA.FI.A2D4.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZO.01 3 0.2280 0.7206 0.00 0.00 0.88 0.00 0.12
#> TCGA.EY.A215.01 3 0.3796 0.4881 0.30 0.00 0.70 0.00 0.00
#> TCGA.AX.A1CK.01 3 0.1410 0.7092 0.00 0.00 0.94 0.00 0.06
#> TCGA.B5.A11S.01 4 0.1732 0.9101 0.00 0.00 0.00 0.92 0.08
#> TCGA.EY.A1GL.01 5 0.2732 0.5601 0.00 0.00 0.16 0.00 0.84
#> TCGA.AP.A1DM.01 1 0.4262 0.4330 0.56 0.00 0.44 0.00 0.00
#> TCGA.BG.A186.01 4 0.0000 0.9173 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A8CW.01 1 0.2732 0.8005 0.84 0.00 0.16 0.00 0.00
#> TCGA.D1.A1NZ.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17U.01 3 0.4262 0.4205 0.00 0.00 0.56 0.00 0.44
#> TCGA.AX.A06D.01 2 0.2732 0.8457 0.00 0.84 0.00 0.00 0.16
#> TCGA.AJ.A3EL.01 5 0.4262 -0.0485 0.00 0.44 0.00 0.00 0.56
#> TCGA.EY.A2OM.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A175.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A2QL.01 3 0.4262 0.4205 0.00 0.00 0.56 0.00 0.44
#> TCGA.AP.A1DH.01 3 0.4456 0.5683 0.00 0.00 0.66 0.02 0.32
#> TCGA.BG.A0VZ.01 3 0.4287 0.3771 0.00 0.00 0.54 0.00 0.46
#> TCGA.EO.A22Y.01 5 0.2929 0.5473 0.00 0.00 0.18 0.00 0.82
#> TCGA.D1.A17A.01 1 0.0609 0.9162 0.98 0.00 0.02 0.00 0.00
#> TCGA.EO.A3B0.01 5 0.2732 0.5048 0.00 0.16 0.00 0.00 0.84
#> TCGA.BS.A0WQ.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.AX.A3G9.01 5 0.2929 0.5489 0.00 0.00 0.18 0.00 0.82
#> TCGA.D1.A1O0.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A0LS.01 3 0.1732 0.7160 0.00 0.00 0.92 0.00 0.08
#> TCGA.EY.A1GW.01 5 0.2012 0.5531 0.00 0.00 0.02 0.06 0.92
#> TCGA.D1.A167.01 3 0.2020 0.7191 0.00 0.00 0.90 0.00 0.10
#> TCGA.DF.A2KU.01 5 0.0000 0.5736 0.00 0.00 0.00 0.00 1.00
#> TCGA.D1.A0ZU.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11F.01 5 0.4287 -0.1108 0.00 0.46 0.00 0.00 0.54
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3AY.01 4 0.0609 0.9177 0.00 0.00 0.00 0.98 0.02
#> TCGA.BG.A220.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.BG.A0VW.01 4 0.1648 0.9049 0.00 0.00 0.04 0.94 0.02
#> TCGA.FI.A2F4.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 4 0.2873 0.8875 0.00 0.02 0.00 0.86 0.12
#> TCGA.B5.A1MX.01 3 0.2280 0.7206 0.00 0.00 0.88 0.00 0.12
#> TCGA.D1.A0ZN.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DA.01 4 0.2280 0.8422 0.00 0.00 0.12 0.88 0.00
#> TCGA.QS.A744.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.BS.A0VI.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A168.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A17F.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A1E1.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 3 0.6778 0.0669 0.00 0.00 0.38 0.28 0.34
#> TCGA.EY.A549.01 4 0.0000 0.9173 0.00 0.00 0.00 1.00 0.00
#> TCGA.BK.A6W3.01 5 0.4287 -0.2195 0.00 0.00 0.00 0.46 0.54
#> TCGA.B5.A11J.01 3 0.3895 0.5985 0.00 0.00 0.68 0.00 0.32
#> TCGA.D1.A176.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 3 0.2012 0.6368 0.02 0.00 0.92 0.06 0.00
#> TCGA.EO.A22S.01 1 0.3895 0.6511 0.68 0.00 0.32 0.00 0.00
#> TCGA.PG.A917.01 4 0.1216 0.9137 0.00 0.00 0.02 0.96 0.02
#> TCGA.D1.A1NY.01 3 0.4262 0.4205 0.00 0.00 0.56 0.00 0.44
#> TCGA.BG.A0W2.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.BS.A0U5.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A15W.01 4 0.2020 0.9045 0.00 0.00 0.00 0.90 0.10
#> TCGA.D1.A174.01 3 0.2280 0.7206 0.00 0.00 0.88 0.00 0.12
#> TCGA.AX.A2HD.01 4 0.3796 0.6963 0.00 0.00 0.00 0.70 0.30
#> TCGA.AX.A3GB.01 3 0.1732 0.6613 0.08 0.00 0.92 0.00 0.00
#> TCGA.A5.A2K5.01 5 0.3109 0.5326 0.00 0.00 0.20 0.00 0.80
#> TCGA.D1.A160.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3EW.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.BK.A4ZD.01 2 0.4262 0.3576 0.00 0.56 0.00 0.00 0.44
#> TCGA.D1.A17L.01 4 0.0000 0.9173 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A3G8.01 4 0.0000 0.9173 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A11Q.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22X.01 4 0.1410 0.9117 0.00 0.00 0.00 0.94 0.06
#> TCGA.EY.A1GU.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 4 0.0609 0.9177 0.00 0.00 0.00 0.98 0.02
#> TCGA.B5.A0JU.01 3 0.2797 0.7009 0.06 0.00 0.88 0.00 0.06
#> TCGA.EO.A1Y7.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A8CV.01 5 0.0609 0.5772 0.00 0.00 0.02 0.00 0.98
#> TCGA.BK.A56F.01 4 0.2012 0.9070 0.00 0.02 0.00 0.92 0.06
#> TCGA.AJ.A3OL.01 1 0.2929 0.8075 0.82 0.00 0.18 0.00 0.00
#> TCGA.D1.A102.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A165.01 4 0.3110 0.8750 0.00 0.06 0.00 0.86 0.08
#> TCGA.AX.A2HH.01 4 0.1410 0.9117 0.00 0.00 0.00 0.94 0.06
#> TCGA.D1.A17S.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.E6.A1LX.01 4 0.0000 0.9173 0.00 0.00 0.00 1.00 0.00
#> TCGA.BS.A0V4.01 3 0.2280 0.7206 0.00 0.00 0.88 0.00 0.12
#> TCGA.D1.A1O7.01 3 0.2020 0.7200 0.00 0.00 0.90 0.00 0.10
#> TCGA.AP.A1E0.01 1 0.1410 0.8902 0.94 0.00 0.06 0.00 0.00
#> TCGA.DF.A2KS.01 2 0.2732 0.8366 0.00 0.84 0.00 0.00 0.16
#> TCGA.BG.A2L7.01 5 0.0609 0.5772 0.00 0.00 0.02 0.00 0.98
#> TCGA.EY.A548.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.BG.A222.01 1 0.1410 0.8908 0.94 0.00 0.06 0.00 0.00
#> TCGA.AX.A1CI.01 1 0.5425 0.5510 0.60 0.00 0.32 0.08 0.00
#> TCGA.D1.A16V.01 3 0.4075 0.6367 0.00 0.00 0.78 0.06 0.16
#> TCGA.AX.A3FS.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.EY.A1GF.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 3 0.2280 0.7206 0.00 0.00 0.88 0.00 0.12
#> TCGA.DI.A1BY.01 4 0.5425 0.4909 0.00 0.32 0.00 0.60 0.08
#> TCGA.SL.A6JA.01 4 0.1410 0.8917 0.00 0.00 0.06 0.94 0.00
#> TCGA.EY.A547.01 4 0.3106 0.8744 0.00 0.02 0.00 0.84 0.14
#> TCGA.B5.A11G.01 5 0.2516 0.5671 0.00 0.00 0.14 0.00 0.86
#> TCGA.A5.A1OK.01 4 0.1043 0.9022 0.00 0.00 0.04 0.96 0.00
#> TCGA.EY.A2OO.01 1 0.5156 0.5783 0.62 0.00 0.32 0.06 0.00
#> TCGA.B5.A1MZ.01 4 0.2012 0.9070 0.00 0.02 0.00 0.92 0.06
#> TCGA.AX.A0IS.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3I9.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 3 0.3690 0.5991 0.20 0.00 0.78 0.00 0.02
#> TCGA.B5.A0JT.01 2 0.1410 0.9084 0.00 0.94 0.00 0.00 0.06
#> TCGA.AJ.A2QO.01 3 0.3796 0.4881 0.30 0.00 0.70 0.00 0.00
#> TCGA.AX.A2HC.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.1410 0.9084 0.00 0.94 0.00 0.00 0.06
#> TCGA.AJ.A5DW.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3NC.01 4 0.3561 0.6615 0.00 0.00 0.26 0.74 0.00
#> TCGA.AP.A1DV.01 5 0.3684 0.4193 0.00 0.00 0.28 0.00 0.72
#> TCGA.B5.A11P.01 4 0.1043 0.9162 0.00 0.00 0.00 0.96 0.04
#> TCGA.A5.A0VO.01 5 0.3109 0.5326 0.00 0.00 0.20 0.00 0.80
#> TCGA.EO.A22U.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.1043 0.9237 0.00 0.96 0.00 0.00 0.04
#> TCGA.E6.A1M0.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17H.01 2 0.3424 0.7553 0.00 0.76 0.00 0.00 0.24
#> TCGA.AX.A1C9.01 4 0.0000 0.9173 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A0JX.01 3 0.3424 0.6626 0.00 0.00 0.76 0.00 0.24
#> TCGA.B5.A11V.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A1MW.01 2 0.1410 0.9241 0.00 0.94 0.00 0.00 0.06
#> TCGA.AX.A3FX.01 2 0.3946 0.7744 0.00 0.80 0.00 0.08 0.12
#> TCGA.EY.A2OP.01 1 0.2516 0.8304 0.86 0.00 0.14 0.00 0.00
#> TCGA.AJ.A3BG.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G5.01 5 0.6386 0.2232 0.00 0.00 0.18 0.34 0.48
#> TCGA.D1.A1O5.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 3 0.4287 0.3771 0.00 0.00 0.54 0.00 0.46
#> TCGA.EY.A1GK.01 3 0.4437 0.5892 0.00 0.00 0.76 0.10 0.14
#> TCGA.AP.A1DR.01 3 0.3684 0.5187 0.28 0.00 0.72 0.00 0.00
#> TCGA.D1.A0ZR.01 4 0.0000 0.9173 0.00 0.00 0.00 1.00 0.00
#> TCGA.BG.A0VT.01 4 0.1043 0.9173 0.00 0.00 0.00 0.96 0.04
#> TCGA.B5.A3FH.01 4 0.1410 0.8913 0.00 0.00 0.06 0.94 0.00
#> TCGA.AP.A1DP.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HJ.01 4 0.2012 0.9051 0.00 0.00 0.02 0.92 0.06
#> TCGA.AX.A1CE.01 5 0.3684 0.4193 0.00 0.00 0.28 0.00 0.72
#> TCGA.EY.A1GX.01 3 0.4262 0.4205 0.00 0.00 0.56 0.00 0.44
#> TCGA.QF.A5YT.01 5 0.4307 -0.2322 0.00 0.50 0.00 0.00 0.50
#> TCGA.EY.A72D.01 2 0.2020 0.8944 0.00 0.90 0.00 0.00 0.10
#> TCGA.AX.A1C4.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1G8.01 4 0.1410 0.9117 0.00 0.00 0.00 0.94 0.06
#> TCGA.AJ.A5DV.01 3 0.3561 0.6551 0.00 0.00 0.74 0.00 0.26
#> TCGA.B5.A11E.01 3 0.2280 0.7206 0.00 0.00 0.88 0.00 0.12
#> TCGA.D1.A17Q.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A15Z.01 2 0.0609 0.9448 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A17D.01 1 0.3796 0.6266 0.70 0.00 0.30 0.00 0.00
#> TCGA.D1.A177.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A13B.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GD.01 2 0.3424 0.7553 0.00 0.76 0.00 0.00 0.24
#> TCGA.BG.A0W1.01 1 0.4182 0.5145 0.60 0.00 0.40 0.00 0.00
#> TCGA.AJ.A3EK.01 3 0.4182 0.2249 0.40 0.00 0.60 0.00 0.00
#> TCGA.B5.A11R.01 3 0.1410 0.6467 0.00 0.00 0.94 0.06 0.00
#> TCGA.A5.A7WJ.01 1 0.0000 0.9279 1.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2L0.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A187.01 3 0.2280 0.7206 0.00 0.00 0.88 0.00 0.12
#> TCGA.D1.A16N.01 2 0.0000 0.9454 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A163.01 3 0.4060 0.5481 0.00 0.00 0.64 0.00 0.36
#> TCGA.D1.A16Y.01 4 0.1410 0.8917 0.00 0.00 0.06 0.94 0.00
#> TCGA.AX.A2HA.01 1 0.0000 0.9279 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.AP.A1DO.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H7.01 4 0.3258 0.70720 0.00 0.02 0.00 0.84 0.04 0.10
#> TCGA.EC.A24G.01 5 0.3787 0.58936 0.00 0.00 0.12 0.00 0.78 0.10
#> TCGA.BG.A2AD.01 5 0.2956 0.62134 0.00 0.00 0.12 0.00 0.84 0.04
#> TCGA.AX.A3FW.01 4 0.2790 0.72464 0.00 0.00 0.00 0.84 0.02 0.14
#> TCGA.D1.A16R.01 2 0.0547 0.88939 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.B5.A11L.01 4 0.4377 0.63160 0.00 0.00 0.00 0.72 0.12 0.16
#> TCGA.B5.A11Z.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 5 0.6620 0.25716 0.00 0.28 0.00 0.06 0.48 0.18
#> TCGA.EO.A3KX.01 3 0.3198 0.52074 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.AX.A1CJ.01 2 0.5855 0.56060 0.00 0.62 0.00 0.14 0.06 0.18
#> TCGA.EY.A5W2.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17T.01 4 0.3321 0.70163 0.00 0.00 0.00 0.82 0.08 0.10
#> TCGA.EY.A1GQ.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.5390 0.58579 0.00 0.64 0.00 0.02 0.16 0.18
#> TCGA.EO.A22R.01 6 0.5354 0.56167 0.26 0.00 0.16 0.00 0.00 0.58
#> TCGA.D1.A16Q.01 2 0.0000 0.88936 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A05O.01 3 0.4723 0.50622 0.00 0.00 0.68 0.00 0.14 0.18
#> TCGA.AJ.A3BI.01 2 0.0937 0.88697 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.B5.A11W.01 4 0.3321 0.73649 0.00 0.00 0.00 0.82 0.08 0.10
#> TCGA.D1.A17M.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.88936 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MK.01 5 0.0547 0.62916 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.D1.A161.01 2 0.1092 0.87630 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.PG.A916.01 4 0.3928 0.67540 0.00 0.00 0.00 0.76 0.08 0.16
#> TCGA.EY.A1H0.01 5 0.3163 0.61836 0.00 0.00 0.14 0.00 0.82 0.04
#> TCGA.BK.A13C.01 6 0.5840 0.50028 0.00 0.00 0.02 0.16 0.26 0.56
#> TCGA.EO.A3AU.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 6 0.5256 0.65018 0.00 0.00 0.18 0.06 0.08 0.68
#> TCGA.FI.A2D4.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZO.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A215.01 3 0.0937 0.77679 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.AX.A1CK.01 3 0.0547 0.78889 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A11S.01 4 0.3045 0.70691 0.00 0.00 0.00 0.84 0.06 0.10
#> TCGA.EY.A1GL.01 5 0.1814 0.64608 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.AP.A1DM.01 6 0.5490 0.54383 0.26 0.00 0.18 0.00 0.00 0.56
#> TCGA.BG.A186.01 4 0.1556 0.74201 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.AJ.A8CW.01 1 0.3706 0.39537 0.62 0.00 0.38 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17U.01 5 0.4646 0.15573 0.00 0.00 0.46 0.00 0.50 0.04
#> TCGA.AX.A06D.01 2 0.5925 0.56274 0.00 0.62 0.00 0.12 0.08 0.18
#> TCGA.AJ.A3EL.01 5 0.5392 0.48559 0.00 0.12 0.00 0.04 0.66 0.18
#> TCGA.EY.A2OM.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A175.01 2 0.0000 0.88936 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QL.01 5 0.4646 0.15573 0.00 0.00 0.46 0.00 0.50 0.04
#> TCGA.AP.A1DH.01 6 0.5509 0.41677 0.00 0.00 0.30 0.00 0.16 0.54
#> TCGA.BG.A0VZ.01 5 0.4632 0.19899 0.00 0.00 0.44 0.00 0.52 0.04
#> TCGA.EO.A22Y.01 5 0.1865 0.63046 0.00 0.00 0.04 0.00 0.92 0.04
#> TCGA.D1.A17A.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3B0.01 5 0.4403 0.52427 0.00 0.04 0.00 0.04 0.74 0.18
#> TCGA.BS.A0WQ.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.AX.A3G9.01 5 0.1814 0.64608 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.D1.A1O0.01 2 0.0547 0.88939 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AP.A0LS.01 3 0.1556 0.75377 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.EY.A1GW.01 5 0.1556 0.60737 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.D1.A167.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DF.A2KU.01 5 0.2981 0.56550 0.00 0.00 0.00 0.02 0.82 0.16
#> TCGA.D1.A0ZU.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.B5.A11F.01 5 0.6294 0.30904 0.00 0.26 0.00 0.04 0.52 0.18
#> TCGA.SJ.A6ZJ.01 2 0.0937 0.87656 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EO.A3AY.01 4 0.3592 0.63061 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.BG.A220.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BG.A0VW.01 4 0.4337 0.09447 0.00 0.00 0.00 0.50 0.02 0.48
#> TCGA.FI.A2F4.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 4 0.4607 0.64373 0.00 0.02 0.00 0.72 0.08 0.18
#> TCGA.B5.A1MX.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZN.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DA.01 6 0.3756 0.17740 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.QS.A744.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BS.A0VI.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A168.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A17F.01 2 0.0000 0.88936 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1E1.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 6 0.5652 0.56777 0.00 0.00 0.04 0.12 0.22 0.62
#> TCGA.EY.A549.01 4 0.0937 0.74969 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BK.A6W3.01 5 0.6251 0.13785 0.00 0.02 0.00 0.28 0.48 0.22
#> TCGA.B5.A11J.01 3 0.5354 0.37143 0.00 0.00 0.58 0.00 0.26 0.16
#> TCGA.D1.A176.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 6 0.3819 0.59515 0.02 0.00 0.28 0.00 0.00 0.70
#> TCGA.EO.A22S.01 6 0.5354 0.56167 0.26 0.00 0.16 0.00 0.00 0.58
#> TCGA.PG.A917.01 4 0.3578 0.43718 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.D1.A1NY.01 5 0.4646 0.15573 0.00 0.00 0.46 0.00 0.50 0.04
#> TCGA.BG.A0W2.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BS.A0U5.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A15W.01 4 0.3073 0.71249 0.00 0.00 0.00 0.84 0.08 0.08
#> TCGA.D1.A174.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HD.01 4 0.5977 0.49444 0.00 0.04 0.00 0.58 0.16 0.22
#> TCGA.AX.A3GB.01 3 0.1267 0.76128 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.A5.A2K5.01 5 0.1814 0.64608 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.D1.A160.01 1 0.0547 0.93255 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BG.A3EW.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BK.A4ZD.01 5 0.6527 0.06573 0.00 0.36 0.00 0.04 0.42 0.18
#> TCGA.D1.A17L.01 4 0.1814 0.72994 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.AX.A3G8.01 4 0.1814 0.73621 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.B5.A11Q.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22X.01 4 0.0547 0.75170 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EY.A1GU.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 4 0.2956 0.72684 0.00 0.00 0.00 0.84 0.04 0.12
#> TCGA.B5.A0JU.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A1Y7.01 2 0.0000 0.88936 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A8CV.01 5 0.2048 0.59372 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.BK.A56F.01 4 0.1092 0.74826 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.AJ.A3OL.01 1 0.3076 0.65834 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.D1.A102.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A165.01 4 0.4733 0.64204 0.00 0.08 0.00 0.74 0.06 0.12
#> TCGA.AX.A2HH.01 4 0.0547 0.75170 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A17S.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.E6.A1LX.01 4 0.2048 0.72642 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.BS.A0V4.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A1O7.01 3 0.2260 0.70660 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.AP.A1E0.01 1 0.2941 0.69488 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 2 0.4328 0.70000 0.00 0.72 0.00 0.00 0.10 0.18
#> TCGA.BG.A2L7.01 5 0.2260 0.58691 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.EY.A548.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BG.A222.01 1 0.2793 0.72004 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.AX.A1CI.01 6 0.5637 0.65093 0.14 0.00 0.10 0.10 0.00 0.66
#> TCGA.D1.A16V.01 6 0.4380 0.62281 0.00 0.00 0.22 0.00 0.08 0.70
#> TCGA.AX.A3FS.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EY.A1GF.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DI.A1BY.01 4 0.5855 0.52159 0.00 0.18 0.00 0.62 0.06 0.14
#> TCGA.SL.A6JA.01 4 0.3797 0.31164 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.EY.A547.01 4 0.4962 0.63361 0.00 0.04 0.00 0.70 0.08 0.18
#> TCGA.B5.A11G.01 5 0.1814 0.64608 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.A5.A1OK.01 4 0.3706 0.40650 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.EY.A2OO.01 6 0.4890 0.62753 0.18 0.00 0.16 0.00 0.00 0.66
#> TCGA.B5.A1MZ.01 4 0.1092 0.74826 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.AX.A0IS.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3I9.01 2 0.0547 0.88506 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.5S.A9Q8.01 3 0.0547 0.78941 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.5157 0.65394 0.00 0.70 0.00 0.10 0.06 0.14
#> TCGA.AJ.A2QO.01 3 0.0937 0.77679 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.4360 0.59160 0.00 0.68 0.00 0.26 0.00 0.06
#> TCGA.AJ.A5DW.01 2 0.0000 0.88936 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0547 0.88939 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AJ.A3NC.01 6 0.4265 0.43895 0.00 0.00 0.04 0.30 0.00 0.66
#> TCGA.AP.A1DV.01 5 0.2790 0.62733 0.00 0.00 0.14 0.00 0.84 0.02
#> TCGA.B5.A11P.01 4 0.1807 0.74758 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.A5.A0VO.01 5 0.1814 0.64608 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.EO.A22U.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.2350 0.82386 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.E6.A1M0.01 2 0.0547 0.88506 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D1.A17H.01 2 0.5572 0.58943 0.00 0.64 0.00 0.04 0.14 0.18
#> TCGA.AX.A1C9.01 4 0.1814 0.73621 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.B5.A0JX.01 3 0.5202 0.37056 0.00 0.00 0.60 0.00 0.14 0.26
#> TCGA.B5.A11V.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.B5.A1MW.01 2 0.2094 0.85740 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.AX.A3FX.01 2 0.7005 0.11469 0.00 0.40 0.00 0.32 0.08 0.20
#> TCGA.EY.A2OP.01 1 0.3864 0.01213 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.AJ.A3BG.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G5.01 6 0.5490 0.47444 0.00 0.00 0.00 0.18 0.26 0.56
#> TCGA.D1.A1O5.01 2 0.0000 0.88936 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 5 0.4646 0.15573 0.00 0.00 0.46 0.00 0.50 0.04
#> TCGA.EY.A1GK.01 6 0.4380 0.62232 0.00 0.00 0.22 0.00 0.08 0.70
#> TCGA.AP.A1DR.01 3 0.0937 0.77679 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.D1.A0ZR.01 4 0.1814 0.72994 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.BG.A0VT.01 4 0.0547 0.75170 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.B5.A3FH.01 4 0.3851 0.22296 0.00 0.00 0.00 0.54 0.00 0.46
#> TCGA.AP.A1DP.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HJ.01 4 0.4328 0.25412 0.00 0.00 0.00 0.52 0.02 0.46
#> TCGA.AX.A1CE.01 5 0.3163 0.61836 0.00 0.00 0.14 0.00 0.82 0.04
#> TCGA.EY.A1GX.01 5 0.4646 0.15573 0.00 0.00 0.46 0.00 0.50 0.04
#> TCGA.QF.A5YT.01 5 0.6365 0.26453 0.00 0.28 0.00 0.04 0.50 0.18
#> TCGA.EY.A72D.01 2 0.2094 0.85740 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.AX.A1C4.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1G8.01 4 0.0547 0.75170 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.AJ.A5DV.01 3 0.4863 0.48461 0.00 0.00 0.66 0.00 0.14 0.20
#> TCGA.B5.A11E.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.0547 0.88506 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D1.A15Z.01 2 0.1267 0.88642 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A17D.01 3 0.3864 0.00731 0.48 0.00 0.52 0.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A13B.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GD.01 2 0.5390 0.58662 0.00 0.64 0.00 0.02 0.16 0.18
#> TCGA.BG.A0W1.01 3 0.5921 -0.00273 0.30 0.00 0.46 0.00 0.00 0.24
#> TCGA.AJ.A3EK.01 3 0.1814 0.70926 0.10 0.00 0.90 0.00 0.00 0.00
#> TCGA.B5.A11R.01 6 0.3499 0.54201 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.A5.A7WJ.01 1 0.0000 0.95129 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2L0.01 2 0.0547 0.88939 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BG.A187.01 3 0.0000 0.79710 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A16N.01 2 0.0547 0.88506 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D1.A163.01 3 0.5636 0.26332 0.00 0.00 0.52 0.00 0.30 0.18
#> TCGA.D1.A16Y.01 4 0.3756 0.35860 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.AX.A2HA.01 1 0.0000 0.95129 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.AP.A1DO.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H7.01 4 0.3911 0.6058 0.00 0.00 0.00 0.70 0.00 0.06 0.24
#> TCGA.EC.A24G.01 5 0.0863 0.8092 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.BG.A2AD.01 5 0.0504 0.8249 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.AX.A3FW.01 4 0.2912 0.7224 0.00 0.00 0.00 0.82 0.00 0.04 0.14
#> TCGA.D1.A16R.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.B5.A11L.01 4 0.4701 0.2378 0.00 0.00 0.00 0.50 0.02 0.04 0.44
#> TCGA.B5.A11Z.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 7 0.4698 0.7037 0.00 0.24 0.00 0.00 0.14 0.00 0.62
#> TCGA.EO.A3KX.01 3 0.3755 0.4895 0.00 0.00 0.64 0.00 0.00 0.34 0.02
#> TCGA.AX.A1CJ.01 7 0.6301 0.4330 0.00 0.36 0.00 0.20 0.00 0.06 0.38
#> TCGA.EY.A5W2.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17T.01 4 0.3637 0.6201 0.00 0.00 0.00 0.72 0.00 0.04 0.24
#> TCGA.EY.A1GQ.01 1 0.0504 0.9527 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D1.A103.01 7 0.4070 0.6219 0.00 0.34 0.00 0.00 0.04 0.00 0.62
#> TCGA.EO.A22R.01 6 0.4092 0.6341 0.16 0.00 0.02 0.00 0.00 0.74 0.08
#> TCGA.D1.A16Q.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AP.A05O.01 6 0.5115 0.3021 0.00 0.00 0.14 0.00 0.38 0.48 0.00
#> TCGA.AJ.A3BI.01 2 0.0504 0.9066 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B5.A11W.01 4 0.4177 0.6881 0.00 0.00 0.00 0.70 0.00 0.18 0.12
#> TCGA.D1.A17M.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BG.A0MK.01 5 0.0504 0.8274 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A161.01 2 0.1664 0.8548 0.00 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.PG.A916.01 4 0.4328 0.5816 0.00 0.00 0.00 0.60 0.00 0.06 0.34
#> TCGA.EY.A1H0.01 5 0.0504 0.8249 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BK.A13C.01 6 0.5190 0.4977 0.00 0.00 0.00 0.00 0.30 0.52 0.18
#> TCGA.EO.A3AU.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 6 0.2745 0.6662 0.00 0.00 0.00 0.00 0.16 0.82 0.02
#> TCGA.FI.A2D4.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZO.01 3 0.0504 0.8596 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EY.A215.01 3 0.1006 0.8571 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.AX.A1CK.01 3 0.0504 0.8551 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.B5.A11S.01 4 0.3637 0.6201 0.00 0.00 0.00 0.72 0.00 0.04 0.24
#> TCGA.EY.A1GL.01 5 0.0504 0.8274 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.AP.A1DM.01 6 0.4242 0.6165 0.18 0.00 0.02 0.00 0.00 0.72 0.08
#> TCGA.BG.A186.01 4 0.1718 0.7422 0.00 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.AJ.A8CW.01 3 0.2259 0.7309 0.16 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17U.01 5 0.2081 0.7682 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.AX.A06D.01 7 0.4718 0.6181 0.00 0.32 0.00 0.06 0.00 0.02 0.60
#> TCGA.AJ.A3EL.01 7 0.4742 0.6509 0.00 0.16 0.00 0.00 0.22 0.00 0.62
#> TCGA.EY.A2OM.01 2 0.1718 0.8802 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.D1.A175.01 2 0.0000 0.9120 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QL.01 5 0.2081 0.7682 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.AP.A1DH.01 6 0.4070 0.4828 0.00 0.00 0.04 0.00 0.34 0.62 0.00
#> TCGA.BG.A0VZ.01 5 0.1886 0.7810 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.EO.A22Y.01 5 0.0000 0.8290 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A17A.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3B0.01 7 0.3413 0.3860 0.00 0.00 0.00 0.00 0.38 0.00 0.62
#> TCGA.BS.A0WQ.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.AX.A3G9.01 5 0.0504 0.8274 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A1O0.01 2 0.0000 0.9120 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A0LS.01 3 0.3661 0.6368 0.00 0.00 0.74 0.00 0.02 0.22 0.02
#> TCGA.EY.A1GW.01 5 0.3546 0.1873 0.00 0.00 0.00 0.00 0.54 0.00 0.46
#> TCGA.D1.A167.01 3 0.1006 0.8579 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.DF.A2KU.01 7 0.3459 0.3527 0.00 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.D1.A0ZU.01 2 0.0000 0.9120 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11F.01 7 0.4742 0.7045 0.00 0.22 0.00 0.00 0.16 0.00 0.62
#> TCGA.SJ.A6ZJ.01 2 0.1664 0.8548 0.00 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.EO.A3AY.01 4 0.3517 0.5907 0.00 0.00 0.00 0.70 0.00 0.28 0.02
#> TCGA.BG.A220.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.BG.A0VW.01 6 0.3841 0.2874 0.00 0.00 0.00 0.28 0.00 0.68 0.04
#> TCGA.FI.A2F4.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 4 0.3911 0.6058 0.00 0.00 0.00 0.70 0.00 0.06 0.24
#> TCGA.B5.A1MX.01 3 0.0504 0.8596 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D1.A0ZN.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DA.01 6 0.4001 0.5519 0.00 0.00 0.02 0.18 0.00 0.74 0.06
#> TCGA.QS.A744.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.BS.A0VI.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A168.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.D1.A17F.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AP.A1E1.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 6 0.4939 0.5235 0.00 0.00 0.00 0.00 0.30 0.56 0.14
#> TCGA.EY.A549.01 4 0.0504 0.7471 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BK.A6W3.01 7 0.4348 0.4572 0.00 0.00 0.00 0.18 0.14 0.00 0.68
#> TCGA.B5.A11J.01 5 0.4820 0.0320 0.00 0.00 0.10 0.00 0.52 0.38 0.00
#> TCGA.D1.A176.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 6 0.3965 0.6396 0.00 0.00 0.10 0.00 0.02 0.76 0.12
#> TCGA.EO.A22S.01 6 0.4092 0.6341 0.16 0.00 0.02 0.00 0.00 0.74 0.08
#> TCGA.PG.A917.01 4 0.4889 0.5585 0.00 0.00 0.02 0.64 0.00 0.22 0.12
#> TCGA.D1.A1NY.01 5 0.2081 0.7682 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.BG.A0W2.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.BS.A0U5.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.D1.A15W.01 4 0.3519 0.6390 0.00 0.00 0.00 0.74 0.00 0.04 0.22
#> TCGA.D1.A174.01 3 0.0504 0.8596 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.AX.A2HD.01 7 0.3943 -0.0176 0.00 0.00 0.00 0.42 0.02 0.00 0.56
#> TCGA.AX.A3GB.01 3 0.0863 0.8447 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.A5.A2K5.01 5 0.0504 0.8274 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A160.01 1 0.2278 0.8539 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.BG.A3EW.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.BK.A4ZD.01 7 0.4630 0.6936 0.00 0.26 0.00 0.00 0.12 0.00 0.62
#> TCGA.D1.A17L.01 4 0.2313 0.7491 0.00 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.AX.A3G8.01 4 0.3061 0.7147 0.00 0.00 0.02 0.84 0.00 0.06 0.08
#> TCGA.B5.A11Q.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22X.01 4 0.0000 0.7461 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 4 0.3449 0.7302 0.00 0.00 0.00 0.78 0.00 0.14 0.08
#> TCGA.B5.A0JU.01 3 0.1006 0.8579 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.EO.A1Y7.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AJ.A8CV.01 5 0.3221 0.3850 0.00 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.BK.A56F.01 4 0.1664 0.7334 0.00 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.AJ.A3OL.01 1 0.4638 0.2182 0.54 0.00 0.00 0.00 0.00 0.38 0.08
#> TCGA.D1.A102.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.D1.A165.01 4 0.4856 0.5402 0.00 0.06 0.00 0.66 0.00 0.06 0.22
#> TCGA.AX.A2HH.01 4 0.2509 0.7285 0.00 0.00 0.02 0.88 0.00 0.04 0.06
#> TCGA.D1.A17S.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.E6.A1LX.01 4 0.1928 0.7364 0.00 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.BS.A0V4.01 3 0.0504 0.8596 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D1.A1O7.01 3 0.4070 0.3798 0.00 0.00 0.62 0.00 0.04 0.34 0.00
#> TCGA.AP.A1E0.01 3 0.3546 0.1882 0.46 0.00 0.54 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 7 0.3546 0.4024 0.00 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.BG.A2L7.01 7 0.3994 0.1613 0.00 0.00 0.00 0.00 0.48 0.02 0.50
#> TCGA.EY.A548.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.BG.A222.01 1 0.4248 0.5210 0.66 0.00 0.00 0.00 0.00 0.26 0.08
#> TCGA.AX.A1CI.01 6 0.4016 0.6396 0.04 0.00 0.00 0.06 0.00 0.76 0.14
#> TCGA.D1.A16V.01 6 0.3449 0.6710 0.00 0.00 0.00 0.00 0.14 0.78 0.08
#> TCGA.AX.A3FS.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.EY.A1GF.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 3 0.1006 0.8579 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.DI.A1BY.01 4 0.4856 0.5402 0.00 0.06 0.00 0.66 0.00 0.06 0.22
#> TCGA.SL.A6JA.01 4 0.5673 0.2294 0.00 0.00 0.02 0.48 0.00 0.32 0.18
#> TCGA.EY.A547.01 4 0.4547 0.5644 0.00 0.00 0.00 0.58 0.00 0.08 0.34
#> TCGA.B5.A11G.01 5 0.0504 0.8274 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.A5.A1OK.01 4 0.4191 0.4650 0.00 0.00 0.00 0.64 0.00 0.30 0.06
#> TCGA.EY.A2OO.01 6 0.3744 0.6517 0.12 0.00 0.02 0.00 0.00 0.78 0.08
#> TCGA.B5.A1MZ.01 4 0.1363 0.7350 0.00 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.AX.A0IS.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3I9.01 2 0.1006 0.9015 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.5S.A9Q8.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.4939 0.2790 0.00 0.64 0.00 0.14 0.00 0.02 0.20
#> TCGA.AJ.A2QO.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.4264 0.4803 0.00 0.70 0.00 0.22 0.00 0.02 0.06
#> TCGA.AJ.A5DW.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AX.A0J0.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AJ.A3NC.01 6 0.2803 0.6280 0.00 0.00 0.00 0.10 0.00 0.84 0.06
#> TCGA.AP.A1DV.01 5 0.0000 0.8290 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11P.01 4 0.3199 0.7247 0.00 0.00 0.00 0.80 0.00 0.06 0.14
#> TCGA.A5.A0VO.01 5 0.0504 0.8274 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EO.A22U.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.1928 0.8386 0.00 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.E6.A1M0.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D1.A17H.01 7 0.4127 0.6049 0.00 0.36 0.00 0.00 0.04 0.00 0.60
#> TCGA.AX.A1C9.01 4 0.3061 0.7147 0.00 0.00 0.02 0.84 0.00 0.06 0.08
#> TCGA.B5.A0JX.01 6 0.4597 0.4088 0.00 0.00 0.08 0.00 0.36 0.56 0.00
#> TCGA.B5.A11V.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.B5.A1MW.01 2 0.3221 0.3454 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.AX.A3FX.01 7 0.6237 0.3218 0.00 0.26 0.00 0.34 0.00 0.04 0.36
#> TCGA.EY.A2OP.01 6 0.4669 0.2059 0.40 0.00 0.00 0.00 0.00 0.52 0.08
#> TCGA.AJ.A3BG.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G5.01 6 0.5567 0.5100 0.00 0.00 0.00 0.02 0.28 0.52 0.18
#> TCGA.D1.A1O5.01 2 0.0504 0.9097 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D1.A0ZQ.01 5 0.2081 0.7682 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.EY.A1GK.01 6 0.1886 0.6797 0.00 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.AP.A1DR.01 3 0.1006 0.8571 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.D1.A0ZR.01 4 0.2163 0.7426 0.00 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.BG.A0VT.01 4 0.0504 0.7471 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.B5.A3FH.01 4 0.5134 0.1545 0.00 0.00 0.00 0.46 0.00 0.40 0.14
#> TCGA.AP.A1DP.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HJ.01 4 0.6187 0.2869 0.00 0.00 0.00 0.48 0.08 0.28 0.16
#> TCGA.AX.A1CE.01 5 0.0000 0.8290 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GX.01 5 0.2081 0.7682 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.QF.A5YT.01 7 0.4698 0.7037 0.00 0.24 0.00 0.00 0.14 0.00 0.62
#> TCGA.EY.A72D.01 2 0.3815 0.2053 0.00 0.62 0.00 0.00 0.00 0.02 0.36
#> TCGA.AX.A1C4.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1G8.01 4 0.0504 0.7471 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.AJ.A5DV.01 6 0.5115 0.3021 0.00 0.00 0.14 0.00 0.38 0.48 0.00
#> TCGA.B5.A11E.01 3 0.1006 0.8579 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.D1.A17Q.01 2 0.1006 0.9015 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.D1.A15Z.01 2 0.0863 0.9082 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.D1.A17D.01 3 0.2422 0.7112 0.18 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A13B.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GD.01 7 0.3943 0.4944 0.00 0.42 0.00 0.00 0.02 0.00 0.56
#> TCGA.BG.A0W1.01 3 0.5453 0.1540 0.22 0.00 0.44 0.00 0.00 0.34 0.00
#> TCGA.AJ.A3EK.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.B5.A11R.01 6 0.3541 0.6568 0.00 0.00 0.10 0.00 0.02 0.80 0.08
#> TCGA.A5.A7WJ.01 1 0.0000 0.9703 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2L0.01 2 0.0000 0.9120 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A187.01 3 0.0504 0.8596 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D1.A16N.01 2 0.0504 0.9066 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D1.A163.01 5 0.4820 0.0320 0.00 0.00 0.10 0.00 0.52 0.38 0.00
#> TCGA.D1.A16Y.01 4 0.5085 0.4660 0.00 0.00 0.02 0.60 0.00 0.26 0.12
#> TCGA.AX.A2HA.01 1 0.0000 0.9703 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.AP.A1DO.01 1 0.0471 0.9246 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AX.A2H7.01 8 0.4717 0.1276 0.00 0.02 0.00 0.36 0.00 0.00 0.08 0.54
#> TCGA.EC.A24G.01 5 0.3763 0.6689 0.00 0.00 0.02 0.00 0.78 0.02 0.08 0.10
#> TCGA.BG.A2AD.01 5 0.0471 0.7644 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.AX.A3FW.01 8 0.5322 0.0626 0.00 0.00 0.02 0.38 0.00 0.02 0.10 0.48
#> TCGA.D1.A16R.01 2 0.0808 0.8694 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.B5.A11L.01 7 0.4929 0.0275 0.00 0.00 0.00 0.24 0.00 0.00 0.52 0.24
#> TCGA.B5.A11Z.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.A5.A2K7.01 1 0.0471 0.9246 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B5.A3FC.01 7 0.4061 0.7061 0.00 0.12 0.00 0.00 0.14 0.00 0.72 0.02
#> TCGA.EO.A3KX.01 3 0.4284 0.3402 0.00 0.00 0.58 0.00 0.00 0.36 0.02 0.04
#> TCGA.AX.A1CJ.01 7 0.5703 0.2526 0.00 0.20 0.00 0.04 0.00 0.00 0.38 0.38
#> TCGA.EY.A5W2.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.D1.A17T.01 4 0.4914 -0.1527 0.00 0.00 0.00 0.42 0.00 0.00 0.16 0.42
#> TCGA.EY.A1GQ.01 1 0.3198 0.6245 0.72 0.00 0.00 0.00 0.00 0.26 0.00 0.02
#> TCGA.D1.A103.01 7 0.3843 0.6904 0.00 0.24 0.00 0.00 0.04 0.00 0.70 0.02
#> TCGA.EO.A22R.01 6 0.1091 0.6899 0.06 0.00 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.2025 0.8521 0.00 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.AP.A05O.01 5 0.6936 0.1621 0.00 0.00 0.16 0.00 0.40 0.26 0.08 0.10
#> TCGA.AJ.A3BI.01 2 0.0808 0.8652 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.B5.A11W.01 8 0.5342 -0.0370 0.00 0.00 0.00 0.40 0.00 0.04 0.12 0.44
#> TCGA.D1.A17M.01 1 0.0471 0.9246 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EY.A1GE.01 2 0.2025 0.8521 0.00 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.BG.A0MK.01 5 0.0471 0.7536 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.D1.A161.01 2 0.2025 0.8521 0.00 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.PG.A916.01 8 0.4669 0.2882 0.00 0.00 0.00 0.20 0.00 0.00 0.22 0.58
#> TCGA.EY.A1H0.01 5 0.1275 0.7512 0.00 0.00 0.00 0.00 0.94 0.02 0.04 0.00
#> TCGA.BK.A13C.01 8 0.7378 -0.0428 0.00 0.00 0.04 0.06 0.14 0.20 0.14 0.42
#> TCGA.EO.A3AU.01 1 0.0941 0.9195 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.EY.A1GI.01 6 0.7266 0.3664 0.00 0.00 0.04 0.14 0.12 0.46 0.08 0.16
#> TCGA.FI.A2D4.01 1 0.0941 0.9195 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.D1.A0ZO.01 3 0.0808 0.8892 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.EY.A215.01 3 0.1275 0.8782 0.04 0.00 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.AX.A1CK.01 3 0.0941 0.8859 0.00 0.00 0.96 0.00 0.02 0.02 0.00 0.00
#> TCGA.B5.A11S.01 8 0.4658 0.0712 0.00 0.00 0.00 0.38 0.00 0.00 0.12 0.50
#> TCGA.EY.A1GL.01 5 0.0000 0.7654 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A1DM.01 6 0.1557 0.6862 0.06 0.00 0.00 0.00 0.00 0.92 0.00 0.02
#> TCGA.BG.A186.01 4 0.2406 0.5028 0.00 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.AJ.A8CW.01 3 0.2534 0.6925 0.22 0.00 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 1 0.0941 0.9195 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.D1.A17U.01 5 0.1765 0.7435 0.00 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.AX.A06D.01 7 0.4211 0.6578 0.00 0.22 0.00 0.02 0.00 0.00 0.68 0.08
#> TCGA.AJ.A3EL.01 7 0.3774 0.6767 0.00 0.08 0.00 0.00 0.22 0.00 0.70 0.00
#> TCGA.EY.A2OM.01 2 0.2265 0.8154 0.00 0.88 0.00 0.00 0.00 0.02 0.08 0.02
#> TCGA.D1.A175.01 2 0.1607 0.8630 0.00 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.AJ.A2QL.01 5 0.1765 0.7435 0.00 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.AP.A1DH.01 6 0.7474 0.1045 0.00 0.00 0.04 0.08 0.30 0.34 0.08 0.16
#> TCGA.BG.A0VZ.01 5 0.1765 0.7435 0.00 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.EO.A22Y.01 5 0.0471 0.7513 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A17A.01 1 0.1557 0.8912 0.92 0.00 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.EO.A3B0.01 7 0.2938 0.5763 0.00 0.00 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.BS.A0WQ.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.AX.A3G9.01 5 0.0000 0.7654 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A1O0.01 2 0.0000 0.8690 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A0LS.01 3 0.3941 0.6525 0.00 0.00 0.76 0.00 0.02 0.14 0.04 0.04
#> TCGA.EY.A1GW.01 5 0.5301 -0.0566 0.00 0.00 0.02 0.00 0.42 0.00 0.40 0.16
#> TCGA.D1.A167.01 3 0.1275 0.8880 0.00 0.00 0.94 0.00 0.04 0.02 0.00 0.00
#> TCGA.DF.A2KU.01 7 0.3675 0.5685 0.00 0.00 0.00 0.00 0.30 0.00 0.66 0.04
#> TCGA.D1.A0ZU.01 2 0.0000 0.8690 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11F.01 7 0.4646 0.6968 0.00 0.12 0.00 0.00 0.18 0.00 0.66 0.04
#> TCGA.SJ.A6ZJ.01 2 0.2350 0.8367 0.00 0.86 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.EO.A3AY.01 4 0.5420 0.1915 0.00 0.00 0.00 0.54 0.00 0.14 0.06 0.26
#> TCGA.BG.A220.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.BG.A0VW.01 4 0.6353 -0.0429 0.00 0.00 0.00 0.36 0.00 0.24 0.12 0.28
#> TCGA.FI.A2F4.01 1 0.1408 0.9277 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.AJ.A3BK.01 8 0.4904 0.2137 0.00 0.00 0.00 0.32 0.00 0.00 0.18 0.50
#> TCGA.B5.A1MX.01 3 0.0808 0.8892 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.D1.A0ZN.01 1 0.0471 0.9246 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D1.A3DA.01 4 0.6243 -0.1864 0.00 0.00 0.02 0.38 0.00 0.38 0.10 0.12
#> TCGA.QS.A744.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.BS.A0VI.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.D1.A168.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.D1.A17F.01 2 0.2025 0.8521 0.00 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.AP.A1E1.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EC.A1NJ.01 8 0.7549 -0.1751 0.00 0.00 0.02 0.08 0.14 0.28 0.16 0.32
#> TCGA.EY.A549.01 4 0.2650 0.4773 0.00 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.BK.A6W3.01 7 0.3523 0.5612 0.00 0.00 0.00 0.02 0.10 0.00 0.78 0.10
#> TCGA.B5.A11J.01 5 0.6199 0.3967 0.00 0.00 0.10 0.00 0.54 0.20 0.08 0.08
#> TCGA.D1.A176.01 1 0.0000 0.9297 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 6 0.1091 0.6648 0.00 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.EO.A22S.01 6 0.1091 0.6899 0.06 0.00 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.PG.A917.01 4 0.3404 0.3584 0.00 0.00 0.00 0.72 0.00 0.04 0.00 0.24
#> TCGA.D1.A1NY.01 5 0.1947 0.7313 0.00 0.00 0.14 0.00 0.86 0.00 0.00 0.00
#> TCGA.BG.A0W2.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.BS.A0U5.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.D1.A15W.01 8 0.4813 0.0362 0.00 0.00 0.00 0.42 0.00 0.00 0.14 0.44
#> TCGA.D1.A174.01 3 0.0808 0.8892 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.AX.A2HD.01 7 0.3975 0.2830 0.00 0.00 0.00 0.08 0.00 0.00 0.66 0.26
#> TCGA.AX.A3GB.01 3 0.0808 0.8759 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.A5.A2K5.01 5 0.0000 0.7654 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A160.01 1 0.3658 0.3404 0.58 0.00 0.00 0.00 0.00 0.40 0.00 0.02
#> TCGA.BG.A3EW.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.BG.A0MA.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.BK.A4ZD.01 7 0.3729 0.7077 0.00 0.18 0.00 0.00 0.10 0.00 0.72 0.00
#> TCGA.D1.A17L.01 4 0.3728 0.4478 0.00 0.00 0.00 0.68 0.00 0.02 0.02 0.28
#> TCGA.AX.A3G8.01 4 0.0471 0.5247 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.B5.A11Q.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.E6.A2P9.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EO.A22X.01 4 0.2856 0.4892 0.00 0.00 0.00 0.78 0.00 0.00 0.02 0.20
#> TCGA.EY.A1GU.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EY.A1GH.01 4 0.4995 0.1040 0.00 0.00 0.00 0.52 0.00 0.04 0.08 0.36
#> TCGA.B5.A0JU.01 3 0.1275 0.8880 0.00 0.00 0.94 0.00 0.04 0.02 0.00 0.00
#> TCGA.EO.A1Y7.01 2 0.1804 0.8594 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.AJ.A8CV.01 5 0.3690 -0.0390 0.00 0.00 0.00 0.00 0.56 0.00 0.42 0.02
#> TCGA.BK.A56F.01 4 0.3142 0.3280 0.00 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.AJ.A3OL.01 6 0.2534 0.5814 0.22 0.00 0.00 0.00 0.00 0.78 0.00 0.00
#> TCGA.D1.A102.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.D1.A165.01 8 0.5949 0.1899 0.00 0.10 0.00 0.28 0.00 0.00 0.16 0.46
#> TCGA.AX.A2HH.01 4 0.1804 0.5079 0.00 0.00 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.D1.A17S.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.E6.A1LX.01 4 0.1557 0.5274 0.00 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.BS.A0V4.01 3 0.0808 0.8892 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.D1.A1O7.01 3 0.5081 0.4440 0.00 0.00 0.64 0.00 0.02 0.20 0.08 0.06
#> TCGA.AP.A1E0.01 1 0.4077 0.1864 0.56 0.00 0.40 0.00 0.00 0.02 0.00 0.02
#> TCGA.DF.A2KS.01 7 0.2938 0.6342 0.00 0.30 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.BG.A2L7.01 7 0.3943 0.4076 0.00 0.00 0.00 0.00 0.40 0.00 0.56 0.04
#> TCGA.EY.A548.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.BG.A222.01 6 0.2938 0.4504 0.30 0.00 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.AX.A1CI.01 6 0.1275 0.6832 0.04 0.00 0.00 0.02 0.00 0.94 0.00 0.00
#> TCGA.D1.A16V.01 6 0.6382 0.4038 0.00 0.00 0.04 0.06 0.02 0.50 0.12 0.26
#> TCGA.AX.A3FS.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.EY.A1GF.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.BG.A18B.01 3 0.0808 0.8892 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.DI.A1BY.01 8 0.5839 0.1993 0.00 0.10 0.00 0.28 0.00 0.00 0.14 0.48
#> TCGA.SL.A6JA.01 4 0.2856 0.3782 0.00 0.00 0.00 0.78 0.00 0.20 0.00 0.02
#> TCGA.EY.A547.01 8 0.4770 0.2964 0.00 0.00 0.02 0.18 0.00 0.00 0.18 0.62
#> TCGA.B5.A11G.01 5 0.0000 0.7654 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A5.A1OK.01 4 0.4646 0.3457 0.00 0.00 0.00 0.66 0.00 0.12 0.04 0.18
#> TCGA.EY.A2OO.01 6 0.0808 0.6876 0.04 0.00 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.B5.A1MZ.01 4 0.3193 0.2937 0.00 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.AX.A0IS.01 1 0.1408 0.9277 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.AJ.A3I9.01 2 0.2350 0.8412 0.00 0.86 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.5S.A9Q8.01 3 0.1408 0.8872 0.02 0.00 0.94 0.00 0.02 0.02 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.5450 0.2437 0.00 0.52 0.00 0.04 0.00 0.00 0.20 0.24
#> TCGA.AJ.A2QO.01 3 0.1275 0.8782 0.04 0.00 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.AX.A2HC.01 1 0.0000 0.9297 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.5058 0.2746 0.00 0.50 0.00 0.06 0.00 0.00 0.06 0.38
#> TCGA.AJ.A5DW.01 2 0.1804 0.8594 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.AX.A0J0.01 2 0.1341 0.8636 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.AJ.A3NC.01 6 0.5804 0.4575 0.00 0.00 0.02 0.18 0.00 0.56 0.08 0.16
#> TCGA.AP.A1DV.01 5 0.0000 0.7654 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11P.01 8 0.5080 0.0339 0.00 0.00 0.02 0.40 0.00 0.00 0.12 0.46
#> TCGA.A5.A0VO.01 5 0.0000 0.7654 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A22U.01 1 0.0000 0.9297 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.2623 0.8226 0.00 0.84 0.00 0.00 0.00 0.00 0.06 0.10
#> TCGA.E6.A1M0.01 2 0.2132 0.8525 0.00 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.D1.A17H.01 7 0.3843 0.6845 0.00 0.24 0.00 0.00 0.02 0.00 0.70 0.04
#> TCGA.AX.A1C9.01 4 0.0000 0.5272 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A0JX.01 5 0.7486 -0.0476 0.00 0.00 0.14 0.02 0.32 0.30 0.08 0.14
#> TCGA.B5.A11V.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.B5.A1MW.01 2 0.3690 0.0995 0.00 0.56 0.00 0.00 0.00 0.00 0.42 0.02
#> TCGA.AX.A3FX.01 8 0.5701 0.0748 0.00 0.08 0.00 0.12 0.00 0.00 0.36 0.44
#> TCGA.EY.A2OP.01 6 0.2267 0.6118 0.18 0.00 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.AJ.A3BG.01 1 0.1408 0.9277 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.D1.A2G5.01 8 0.6698 0.0521 0.00 0.00 0.02 0.06 0.08 0.20 0.14 0.50
#> TCGA.D1.A1O5.01 2 0.2025 0.8521 0.00 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.D1.A0ZQ.01 5 0.3048 0.7242 0.00 0.00 0.08 0.00 0.84 0.02 0.04 0.02
#> TCGA.EY.A1GK.01 6 0.6247 0.4746 0.00 0.00 0.04 0.10 0.04 0.58 0.08 0.16
#> TCGA.AP.A1DR.01 3 0.1275 0.8782 0.04 0.00 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.D1.A0ZR.01 4 0.3808 0.4435 0.00 0.00 0.00 0.66 0.00 0.02 0.02 0.30
#> TCGA.BG.A0VT.01 4 0.2650 0.4773 0.00 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.B5.A3FH.01 8 0.5862 -0.0788 0.00 0.00 0.00 0.38 0.00 0.12 0.10 0.40
#> TCGA.AP.A1DP.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.AX.A2HJ.01 8 0.6556 0.1477 0.00 0.00 0.02 0.20 0.00 0.18 0.16 0.44
#> TCGA.AX.A1CE.01 5 0.0000 0.7654 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GX.01 5 0.3021 0.7037 0.00 0.00 0.16 0.00 0.80 0.02 0.02 0.00
#> TCGA.QF.A5YT.01 7 0.4672 0.7034 0.00 0.14 0.00 0.00 0.16 0.00 0.66 0.04
#> TCGA.EY.A72D.01 7 0.3318 0.2161 0.00 0.46 0.00 0.00 0.00 0.00 0.54 0.00
#> TCGA.AX.A1C4.01 1 0.0000 0.9297 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GT.01 1 0.1408 0.9277 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.EY.A1G8.01 4 0.2981 0.4821 0.00 0.00 0.00 0.76 0.00 0.00 0.02 0.22
#> TCGA.AJ.A5DV.01 5 0.7088 0.0786 0.00 0.00 0.16 0.00 0.36 0.28 0.08 0.12
#> TCGA.B5.A11E.01 3 0.0808 0.8892 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.2132 0.8525 0.00 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.D1.A15Z.01 2 0.1408 0.8606 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.D1.A17D.01 3 0.3601 0.6987 0.16 0.00 0.76 0.00 0.00 0.06 0.00 0.02
#> TCGA.D1.A177.01 1 0.0941 0.9195 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.BK.A13B.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EY.A1GD.01 7 0.2938 0.6342 0.00 0.30 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.BG.A0W1.01 6 0.4570 0.3772 0.06 0.00 0.28 0.00 0.00 0.62 0.00 0.04
#> TCGA.AJ.A3EK.01 3 0.1275 0.8782 0.04 0.00 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.B5.A11R.01 6 0.3758 0.6068 0.00 0.00 0.04 0.00 0.00 0.76 0.06 0.14
#> TCGA.A5.A7WJ.01 1 0.0941 0.9317 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.DF.A2L0.01 2 0.0000 0.8690 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A187.01 3 0.0808 0.8892 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.D1.A16N.01 2 0.2132 0.8525 0.00 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.D1.A163.01 5 0.6199 0.3967 0.00 0.00 0.10 0.00 0.54 0.20 0.08 0.08
#> TCGA.D1.A16Y.01 4 0.2020 0.4851 0.00 0.00 0.00 0.90 0.00 0.06 0.02 0.02
#> TCGA.AX.A2HA.01 1 0.0941 0.9195 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["021"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 50 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.996 0.998 0.5096 0.491 0.491
#> 3 3 0.652 0.822 0.873 0.2962 0.776 0.574
#> 4 4 0.673 0.675 0.828 0.1259 0.897 0.701
#> 5 5 0.706 0.474 0.698 0.0735 0.820 0.413
#> 6 6 0.740 0.592 0.747 0.0420 0.867 0.453
#> 7 7 0.843 0.751 0.864 0.0361 0.914 0.553
#> 8 8 0.823 0.700 0.775 0.0146 0.957 0.702
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.AP.A1DO.01 2 0.000 1.000 0.0 1.0
#> TCGA.B5.A11Z.01 1 0.000 0.996 1.0 0.0
#> TCGA.A5.A2K7.01 2 0.000 1.000 0.0 1.0
#> TCGA.EY.A5W2.01 2 0.000 1.000 0.0 1.0
#> TCGA.EY.A1GQ.01 1 0.000 0.996 1.0 0.0
#> TCGA.EO.A22R.01 2 0.000 1.000 0.0 1.0
#> TCGA.D1.A17M.01 2 0.000 1.000 0.0 1.0
#> TCGA.EO.A3AU.01 2 0.000 1.000 0.0 1.0
#> TCGA.FI.A2D4.01 2 0.000 1.000 0.0 1.0
#> TCGA.EY.A215.01 1 0.000 0.996 1.0 0.0
#> TCGA.AP.A1DM.01 1 0.000 0.996 1.0 0.0
#> TCGA.AJ.A8CW.01 1 0.000 0.996 1.0 0.0
#> TCGA.D1.A1NZ.01 1 0.000 0.996 1.0 0.0
#> TCGA.D1.A17A.01 1 0.000 0.996 1.0 0.0
#> TCGA.FI.A2F4.01 1 0.000 0.996 1.0 0.0
#> TCGA.D1.A0ZN.01 1 0.000 0.996 1.0 0.0
#> TCGA.BS.A0VI.01 2 0.000 1.000 0.0 1.0
#> TCGA.AP.A1E1.01 1 0.000 0.996 1.0 0.0
#> TCGA.D1.A176.01 1 0.000 0.996 1.0 0.0
#> TCGA.EO.A22S.01 2 0.000 1.000 0.0 1.0
#> TCGA.AX.A3GB.01 1 0.000 0.996 1.0 0.0
#> TCGA.D1.A160.01 1 0.000 0.996 1.0 0.0
#> TCGA.BG.A3EW.01 2 0.000 1.000 0.0 1.0
#> TCGA.B5.A11Q.01 1 0.000 0.996 1.0 0.0
#> TCGA.E6.A2P9.01 1 0.000 0.996 1.0 0.0
#> TCGA.EY.A1GU.01 1 0.000 0.996 1.0 0.0
#> TCGA.AJ.A3OL.01 2 0.000 1.000 0.0 1.0
#> TCGA.AP.A1E0.01 2 0.000 1.000 0.0 1.0
#> TCGA.BG.A222.01 2 0.000 1.000 0.0 1.0
#> TCGA.AX.A1CI.01 1 0.000 0.996 1.0 0.0
#> TCGA.EY.A1GF.01 1 0.000 0.996 1.0 0.0
#> TCGA.EY.A2OO.01 2 0.000 1.000 0.0 1.0
#> TCGA.AX.A0IS.01 1 0.000 0.996 1.0 0.0
#> TCGA.5S.A9Q8.01 1 0.000 0.996 1.0 0.0
#> TCGA.AJ.A2QO.01 2 0.000 1.000 0.0 1.0
#> TCGA.AX.A2HC.01 2 0.000 1.000 0.0 1.0
#> TCGA.EO.A22U.01 2 0.000 1.000 0.0 1.0
#> TCGA.EY.A2OP.01 2 0.000 1.000 0.0 1.0
#> TCGA.AJ.A3BG.01 2 0.000 1.000 0.0 1.0
#> TCGA.AP.A1DR.01 2 0.000 1.000 0.0 1.0
#> TCGA.AP.A1DP.01 1 0.000 0.996 1.0 0.0
#> TCGA.AX.A1C4.01 2 0.000 1.000 0.0 1.0
#> TCGA.EY.A1GT.01 2 0.000 1.000 0.0 1.0
#> TCGA.D1.A17D.01 1 0.469 0.889 0.9 0.1
#> TCGA.D1.A177.01 2 0.000 1.000 0.0 1.0
#> TCGA.BK.A13B.01 1 0.000 0.996 1.0 0.0
#> TCGA.BG.A0W1.01 1 0.000 0.996 1.0 0.0
#> TCGA.AJ.A3EK.01 2 0.000 1.000 0.0 1.0
#> TCGA.A5.A7WJ.01 2 0.000 1.000 0.0 1.0
#> TCGA.AX.A2HA.01 2 0.000 1.000 0.0 1.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AP.A1DO.01 3 0.3340 0.676 0.00 0.12 0.88
#> TCGA.B5.A11Z.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.0000 0.884 0.00 1.00 0.00
#> TCGA.EY.A5W2.01 2 0.4796 0.791 0.00 0.78 0.22
#> TCGA.EY.A1GQ.01 3 0.5835 0.731 0.34 0.00 0.66
#> TCGA.EO.A22R.01 2 0.0000 0.884 0.00 1.00 0.00
#> TCGA.D1.A17M.01 3 0.2066 0.699 0.00 0.06 0.94
#> TCGA.EO.A3AU.01 2 0.0000 0.884 0.00 1.00 0.00
#> TCGA.FI.A2D4.01 2 0.0892 0.883 0.00 0.98 0.02
#> TCGA.EY.A215.01 3 0.2959 0.740 0.10 0.00 0.90
#> TCGA.AP.A1DM.01 3 0.3340 0.740 0.12 0.00 0.88
#> TCGA.AJ.A8CW.01 3 0.5835 0.731 0.34 0.00 0.66
#> TCGA.D1.A1NZ.01 3 0.5835 0.731 0.34 0.00 0.66
#> TCGA.D1.A17A.01 3 0.5835 0.731 0.34 0.00 0.66
#> TCGA.FI.A2F4.01 3 0.5397 0.732 0.28 0.00 0.72
#> TCGA.D1.A0ZN.01 1 0.2537 0.909 0.92 0.00 0.08
#> TCGA.BS.A0VI.01 3 0.0000 0.700 0.00 0.00 1.00
#> TCGA.AP.A1E1.01 3 0.5835 0.731 0.34 0.00 0.66
#> TCGA.D1.A176.01 1 0.2537 0.909 0.92 0.00 0.08
#> TCGA.EO.A22S.01 2 0.0892 0.883 0.00 0.98 0.02
#> TCGA.AX.A3GB.01 1 0.0892 0.949 0.98 0.00 0.02
#> TCGA.D1.A160.01 3 0.5835 0.731 0.34 0.00 0.66
#> TCGA.BG.A3EW.01 2 0.3340 0.855 0.00 0.88 0.12
#> TCGA.B5.A11Q.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.EY.A1GU.01 3 0.5835 0.731 0.34 0.00 0.66
#> TCGA.AJ.A3OL.01 3 0.5216 0.442 0.00 0.26 0.74
#> TCGA.AP.A1E0.01 2 0.0000 0.884 0.00 1.00 0.00
#> TCGA.BG.A222.01 2 0.3340 0.855 0.00 0.88 0.12
#> TCGA.AX.A1CI.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.3340 0.855 0.00 0.88 0.12
#> TCGA.AX.A0IS.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.5S.A9Q8.01 1 0.3340 0.853 0.88 0.00 0.12
#> TCGA.AJ.A2QO.01 2 0.6045 0.565 0.00 0.62 0.38
#> TCGA.AX.A2HC.01 2 0.0000 0.884 0.00 1.00 0.00
#> TCGA.EO.A22U.01 2 0.4291 0.848 0.00 0.82 0.18
#> TCGA.EY.A2OP.01 2 0.2066 0.875 0.00 0.94 0.06
#> TCGA.AJ.A3BG.01 2 0.1529 0.880 0.00 0.96 0.04
#> TCGA.AP.A1DR.01 2 0.4796 0.791 0.00 0.78 0.22
#> TCGA.AP.A1DP.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.AX.A1C4.01 2 0.0000 0.884 0.00 1.00 0.00
#> TCGA.EY.A1GT.01 2 0.3340 0.855 0.00 0.88 0.12
#> TCGA.D1.A17D.01 3 0.2066 0.731 0.06 0.00 0.94
#> TCGA.D1.A177.01 2 0.4796 0.791 0.00 0.78 0.22
#> TCGA.BK.A13B.01 1 0.2537 0.909 0.92 0.00 0.08
#> TCGA.BG.A0W1.01 1 0.0000 0.957 1.00 0.00 0.00
#> TCGA.AJ.A3EK.01 2 0.4796 0.791 0.00 0.78 0.22
#> TCGA.A5.A7WJ.01 2 0.4796 0.791 0.00 0.78 0.22
#> TCGA.AX.A2HA.01 2 0.5560 0.719 0.00 0.70 0.30
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AP.A1DO.01 4 0.462 0.2372 0.00 0.00 0.34 0.66
#> TCGA.B5.A11Z.01 1 0.000 0.8231 1.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.462 0.5547 0.00 0.66 0.00 0.34
#> TCGA.EY.A5W2.01 4 0.292 0.8008 0.00 0.14 0.00 0.86
#> TCGA.EY.A1GQ.01 3 0.164 0.8584 0.06 0.00 0.94 0.00
#> TCGA.EO.A22R.01 2 0.452 0.5775 0.00 0.68 0.00 0.32
#> TCGA.D1.A17M.01 3 0.428 0.6370 0.00 0.00 0.72 0.28
#> TCGA.EO.A3AU.01 2 0.462 0.5547 0.00 0.66 0.00 0.34
#> TCGA.FI.A2D4.01 2 0.361 0.6667 0.00 0.80 0.00 0.20
#> TCGA.EY.A215.01 3 0.234 0.8396 0.00 0.00 0.90 0.10
#> TCGA.AP.A1DM.01 3 0.234 0.8396 0.00 0.00 0.90 0.10
#> TCGA.AJ.A8CW.01 3 0.449 0.7768 0.06 0.00 0.80 0.14
#> TCGA.D1.A1NZ.01 3 0.164 0.8584 0.06 0.00 0.94 0.00
#> TCGA.D1.A17A.01 3 0.164 0.8584 0.06 0.00 0.94 0.00
#> TCGA.FI.A2F4.01 3 0.000 0.8492 0.00 0.00 1.00 0.00
#> TCGA.D1.A0ZN.01 1 0.637 0.6438 0.62 0.00 0.28 0.10
#> TCGA.BS.A0VI.01 3 0.164 0.8116 0.00 0.06 0.94 0.00
#> TCGA.AP.A1E1.01 3 0.449 0.7768 0.06 0.00 0.80 0.14
#> TCGA.D1.A176.01 1 0.637 0.6438 0.62 0.00 0.28 0.10
#> TCGA.EO.A22S.01 2 0.361 0.6667 0.00 0.80 0.00 0.20
#> TCGA.AX.A3GB.01 1 0.625 0.6615 0.64 0.00 0.26 0.10
#> TCGA.D1.A160.01 3 0.164 0.8584 0.06 0.00 0.94 0.00
#> TCGA.BG.A3EW.01 2 0.164 0.6572 0.00 0.94 0.06 0.00
#> TCGA.B5.A11Q.01 1 0.000 0.8231 1.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.000 0.8231 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 3 0.234 0.8498 0.06 0.00 0.92 0.02
#> TCGA.AJ.A3OL.01 3 0.500 0.0370 0.00 0.50 0.50 0.00
#> TCGA.AP.A1E0.01 4 0.499 -0.1614 0.00 0.48 0.00 0.52
#> TCGA.BG.A222.01 2 0.121 0.6670 0.00 0.96 0.04 0.00
#> TCGA.AX.A1CI.01 1 0.000 0.8231 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.000 0.8231 1.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.000 0.6788 0.00 1.00 0.00 0.00
#> TCGA.AX.A0IS.01 1 0.000 0.8231 1.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 1 0.702 0.5214 0.54 0.00 0.32 0.14
#> TCGA.AJ.A2QO.01 4 0.271 0.7495 0.00 0.08 0.02 0.90
#> TCGA.AX.A2HC.01 2 0.462 0.5547 0.00 0.66 0.00 0.34
#> TCGA.EO.A22U.01 2 0.607 0.3721 0.00 0.60 0.06 0.34
#> TCGA.EY.A2OP.01 2 0.000 0.6788 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3BG.01 2 0.234 0.6867 0.00 0.90 0.00 0.10
#> TCGA.AP.A1DR.01 4 0.292 0.8008 0.00 0.14 0.00 0.86
#> TCGA.AP.A1DP.01 1 0.234 0.7991 0.90 0.00 0.00 0.10
#> TCGA.AX.A1C4.01 2 0.462 0.5547 0.00 0.66 0.00 0.34
#> TCGA.EY.A1GT.01 2 0.164 0.6572 0.00 0.94 0.06 0.00
#> TCGA.D1.A17D.01 3 0.000 0.8492 0.00 0.00 1.00 0.00
#> TCGA.D1.A177.01 4 0.292 0.8008 0.00 0.14 0.00 0.86
#> TCGA.BK.A13B.01 1 0.637 0.6438 0.62 0.00 0.28 0.10
#> TCGA.BG.A0W1.01 1 0.000 0.8231 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 4 0.292 0.8008 0.00 0.14 0.00 0.86
#> TCGA.A5.A7WJ.01 4 0.292 0.8008 0.00 0.14 0.00 0.86
#> TCGA.AX.A2HA.01 2 0.495 0.0414 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.AP.A1DO.01 5 0.5131 -0.0102 0.00 0.00 0.04 0.42 0.54
#> TCGA.B5.A11Z.01 1 0.0000 0.8703 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 4 0.4262 0.0145 0.00 0.44 0.00 0.56 0.00
#> TCGA.EY.A5W2.01 4 0.3690 0.4968 0.00 0.02 0.00 0.78 0.20
#> TCGA.EY.A1GQ.01 3 0.1732 0.7015 0.00 0.00 0.92 0.00 0.08
#> TCGA.EO.A22R.01 4 0.4262 0.0145 0.00 0.44 0.00 0.56 0.00
#> TCGA.D1.A17M.01 5 0.6275 0.1866 0.00 0.00 0.18 0.30 0.52
#> TCGA.EO.A3AU.01 4 0.4262 0.0145 0.00 0.44 0.00 0.56 0.00
#> TCGA.FI.A2D4.01 2 0.4287 0.2106 0.00 0.54 0.00 0.46 0.00
#> TCGA.EY.A215.01 5 0.4990 0.3158 0.00 0.00 0.36 0.04 0.60
#> TCGA.AP.A1DM.01 5 0.4990 0.3158 0.00 0.00 0.36 0.04 0.60
#> TCGA.AJ.A8CW.01 5 0.3983 0.4953 0.00 0.00 0.34 0.00 0.66
#> TCGA.D1.A1NZ.01 3 0.1410 0.7233 0.00 0.00 0.94 0.00 0.06
#> TCGA.D1.A17A.01 3 0.1410 0.7233 0.00 0.00 0.94 0.00 0.06
#> TCGA.FI.A2F4.01 3 0.0000 0.7360 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A0ZN.01 5 0.6532 0.4371 0.24 0.00 0.28 0.00 0.48
#> TCGA.BS.A0VI.01 3 0.4818 0.5555 0.00 0.18 0.72 0.00 0.10
#> TCGA.AP.A1E1.01 5 0.3983 0.4953 0.00 0.00 0.34 0.00 0.66
#> TCGA.D1.A176.01 5 0.6723 0.3540 0.30 0.00 0.28 0.00 0.42
#> TCGA.EO.A22S.01 2 0.4287 0.2106 0.00 0.54 0.00 0.46 0.00
#> TCGA.AX.A3GB.01 1 0.6757 -0.2937 0.40 0.00 0.28 0.00 0.32
#> TCGA.D1.A160.01 3 0.1410 0.7307 0.00 0.00 0.94 0.00 0.06
#> TCGA.BG.A3EW.01 2 0.0609 0.6564 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A11Q.01 1 0.0000 0.8703 1.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 0.8703 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 3 0.2020 0.6856 0.00 0.00 0.90 0.00 0.10
#> TCGA.AJ.A3OL.01 3 0.5534 0.4653 0.00 0.36 0.58 0.02 0.04
#> TCGA.AP.A1E0.01 4 0.4456 0.1585 0.00 0.32 0.00 0.66 0.02
#> TCGA.BG.A222.01 2 0.0000 0.6636 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CI.01 1 0.0000 0.8703 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.0000 0.8703 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.0000 0.6636 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A0IS.01 1 0.0000 0.8703 1.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 5 0.4748 0.5125 0.04 0.00 0.30 0.00 0.66
#> TCGA.AJ.A2QO.01 4 0.4182 0.1917 0.00 0.00 0.00 0.60 0.40
#> TCGA.AX.A2HC.01 4 0.4182 0.0814 0.00 0.40 0.00 0.60 0.00
#> TCGA.EO.A22U.01 2 0.6145 0.2606 0.00 0.56 0.06 0.34 0.04
#> TCGA.EY.A2OP.01 2 0.2732 0.6030 0.00 0.84 0.00 0.16 0.00
#> TCGA.AJ.A3BG.01 2 0.4126 0.3799 0.00 0.62 0.00 0.38 0.00
#> TCGA.AP.A1DR.01 4 0.2732 0.5087 0.00 0.00 0.00 0.84 0.16
#> TCGA.AP.A1DP.01 1 0.3561 0.5927 0.74 0.00 0.00 0.00 0.26
#> TCGA.AX.A1C4.01 4 0.4262 0.0145 0.00 0.44 0.00 0.56 0.00
#> TCGA.EY.A1GT.01 2 0.0609 0.6564 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A17D.01 3 0.0000 0.7360 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A177.01 4 0.3319 0.5156 0.00 0.02 0.00 0.82 0.16
#> TCGA.BK.A13B.01 5 0.6723 0.3540 0.30 0.00 0.28 0.00 0.42
#> TCGA.BG.A0W1.01 1 0.0000 0.8703 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 4 0.3319 0.5156 0.00 0.02 0.00 0.82 0.16
#> TCGA.A5.A7WJ.01 4 0.3319 0.5156 0.00 0.02 0.00 0.82 0.16
#> TCGA.AX.A2HA.01 3 0.5534 0.4653 0.00 0.36 0.58 0.02 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AP.A1DO.01 4 0.4337 -0.1134 0.00 0.00 0.00 0.50 0.02 0.48
#> TCGA.B5.A11Z.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.3647 0.5509 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.EY.A5W2.01 4 0.0000 0.6990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GQ.01 3 0.6023 0.2641 0.00 0.00 0.42 0.00 0.32 0.26
#> TCGA.EO.A22R.01 2 0.3647 0.5509 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.D1.A17M.01 6 0.4754 0.4908 0.00 0.00 0.02 0.24 0.06 0.68
#> TCGA.EO.A3AU.01 2 0.3647 0.5509 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.4002 0.5569 0.00 0.66 0.00 0.32 0.00 0.02
#> TCGA.EY.A215.01 6 0.3819 0.6195 0.00 0.00 0.02 0.00 0.28 0.70
#> TCGA.AP.A1DM.01 6 0.3916 0.6185 0.00 0.00 0.02 0.00 0.30 0.68
#> TCGA.AJ.A8CW.01 5 0.0937 0.8172 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.D1.A1NZ.01 3 0.5027 0.6157 0.00 0.00 0.64 0.00 0.20 0.16
#> TCGA.D1.A17A.01 3 0.5027 0.6157 0.00 0.00 0.64 0.00 0.20 0.16
#> TCGA.FI.A2F4.01 3 0.1814 0.6218 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.D1.A0ZN.01 5 0.0547 0.8261 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BS.A0VI.01 6 0.4787 -0.2486 0.00 0.02 0.44 0.00 0.02 0.52
#> TCGA.AP.A1E1.01 5 0.0937 0.8172 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.D1.A176.01 5 0.1556 0.8297 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.EO.A22S.01 2 0.3578 0.5587 0.00 0.66 0.00 0.34 0.00 0.00
#> TCGA.AX.A3GB.01 5 0.2941 0.7242 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.D1.A160.01 3 0.5083 0.4432 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.BG.A3EW.01 2 0.4863 0.4311 0.00 0.66 0.14 0.00 0.00 0.20
#> TCGA.B5.A11Q.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 3 0.4078 0.5323 0.00 0.00 0.64 0.00 0.34 0.02
#> TCGA.AJ.A3OL.01 3 0.1092 0.5603 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.AP.A1E0.01 4 0.4892 -0.2623 0.00 0.44 0.00 0.50 0.00 0.06
#> TCGA.BG.A222.01 2 0.4244 0.4723 0.00 0.72 0.08 0.00 0.00 0.20
#> TCGA.AX.A1CI.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.4244 0.4723 0.00 0.72 0.08 0.00 0.00 0.20
#> TCGA.AX.A0IS.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 5 0.0937 0.8172 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.AJ.A2QO.01 4 0.3460 0.4608 0.00 0.00 0.00 0.76 0.02 0.22
#> TCGA.AX.A2HC.01 2 0.3851 0.3621 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.EO.A22U.01 4 0.7026 0.0797 0.00 0.16 0.36 0.38 0.00 0.10
#> TCGA.EY.A2OP.01 2 0.2048 0.5127 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.AJ.A3BG.01 2 0.3523 0.5520 0.00 0.78 0.00 0.18 0.00 0.04
#> TCGA.AP.A1DR.01 4 0.0547 0.6939 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.AP.A1DP.01 5 0.3756 0.4134 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.AX.A1C4.01 2 0.3647 0.5509 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.EY.A1GT.01 2 0.4863 0.4311 0.00 0.66 0.14 0.00 0.00 0.20
#> TCGA.D1.A17D.01 3 0.2728 0.6346 0.00 0.00 0.86 0.00 0.04 0.10
#> TCGA.D1.A177.01 4 0.0000 0.6990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BK.A13B.01 5 0.1556 0.8297 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.BG.A0W1.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 4 0.0000 0.6990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A7WJ.01 4 0.0000 0.6990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A2HA.01 3 0.1480 0.5461 0.00 0.02 0.94 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AP.A1DO.01 4 0.3815 0.49539 0.00 0.00 0.02 0.62 0.00 0.36 0.00
#> TCGA.B5.A11Z.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.1860 0.92416 0.00 0.92 0.02 0.02 0.00 0.04 0.00
#> TCGA.EY.A5W2.01 4 0.0504 0.93061 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 6 0.4597 0.43887 0.00 0.00 0.36 0.00 0.08 0.56 0.00
#> TCGA.EO.A22R.01 2 0.0504 0.93499 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D1.A17M.01 6 0.1886 0.61937 0.00 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.EO.A3AU.01 2 0.0504 0.93499 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.0504 0.92845 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EY.A215.01 6 0.2654 0.67109 0.00 0.00 0.02 0.00 0.10 0.86 0.02
#> TCGA.AP.A1DM.01 6 0.2163 0.67578 0.00 0.00 0.02 0.00 0.10 0.88 0.00
#> TCGA.AJ.A8CW.01 5 0.1006 0.81169 0.00 0.02 0.02 0.00 0.96 0.00 0.00
#> TCGA.D1.A1NZ.01 3 0.5589 0.00878 0.00 0.00 0.40 0.00 0.32 0.28 0.00
#> TCGA.D1.A17A.01 3 0.5589 0.00878 0.00 0.00 0.40 0.00 0.32 0.28 0.00
#> TCGA.FI.A2F4.01 3 0.1928 0.50789 0.00 0.00 0.90 0.00 0.02 0.08 0.00
#> TCGA.D1.A0ZN.01 5 0.1363 0.80908 0.00 0.00 0.00 0.02 0.94 0.00 0.04
#> TCGA.BS.A0VI.01 6 0.3052 0.63662 0.00 0.00 0.20 0.00 0.00 0.78 0.02
#> TCGA.AP.A1E1.01 5 0.1006 0.81169 0.00 0.02 0.02 0.00 0.96 0.00 0.00
#> TCGA.D1.A176.01 5 0.1006 0.81361 0.02 0.00 0.02 0.00 0.96 0.00 0.00
#> TCGA.EO.A22S.01 2 0.0504 0.92845 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AX.A3GB.01 5 0.1928 0.78485 0.08 0.00 0.02 0.00 0.90 0.00 0.00
#> TCGA.D1.A160.01 6 0.4381 0.46639 0.00 0.00 0.36 0.00 0.06 0.58 0.00
#> TCGA.BG.A3EW.01 7 0.1928 0.88488 0.00 0.08 0.02 0.00 0.00 0.00 0.90
#> TCGA.B5.A11Q.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 5 0.4214 0.09416 0.00 0.00 0.40 0.00 0.56 0.04 0.00
#> TCGA.AJ.A3OL.01 3 0.2422 0.54582 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.AP.A1E0.01 2 0.2376 0.84906 0.00 0.86 0.00 0.12 0.00 0.02 0.00
#> TCGA.BG.A222.01 7 0.2722 0.89211 0.00 0.12 0.00 0.00 0.00 0.04 0.84
#> TCGA.AX.A1CI.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 7 0.2376 0.89614 0.00 0.12 0.00 0.00 0.00 0.02 0.86
#> TCGA.AX.A0IS.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 5 0.1860 0.80811 0.00 0.02 0.00 0.02 0.92 0.00 0.04
#> TCGA.AJ.A2QO.01 4 0.1006 0.90669 0.00 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.AX.A2HC.01 2 0.2509 0.89776 0.00 0.88 0.02 0.06 0.00 0.04 0.00
#> TCGA.EO.A22U.01 3 0.6065 0.30546 0.00 0.18 0.58 0.08 0.00 0.02 0.14
#> TCGA.EY.A2OP.01 7 0.3139 0.70685 0.00 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.AJ.A3BG.01 2 0.1928 0.85716 0.00 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.AP.A1DR.01 4 0.0504 0.93061 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.AP.A1DP.01 5 0.4577 0.36762 0.36 0.00 0.00 0.02 0.58 0.00 0.04
#> TCGA.AX.A1C4.01 2 0.1505 0.92902 0.00 0.94 0.02 0.02 0.00 0.02 0.00
#> TCGA.EY.A1GT.01 7 0.1928 0.88488 0.00 0.08 0.02 0.00 0.00 0.00 0.90
#> TCGA.D1.A17D.01 3 0.1363 0.52721 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.D1.A177.01 4 0.0504 0.93061 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BK.A13B.01 5 0.1860 0.80922 0.02 0.00 0.00 0.02 0.92 0.00 0.04
#> TCGA.BG.A0W1.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 4 0.0504 0.93061 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.A5.A7WJ.01 4 0.0504 0.93061 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.AX.A2HA.01 3 0.2422 0.54582 0.00 0.00 0.82 0.00 0.00 0.00 0.18
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AP.A1DO.01 6 0.333 0.00903 0.00 0.00 0.00 0.50 0.00 0.50 0.00 0.00
#> TCGA.B5.A11Z.01 1 0.000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 2 0.176 0.83663 0.00 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.EY.A5W2.01 4 0.156 0.96503 0.00 0.06 0.00 0.92 0.00 0.02 0.00 0.00
#> TCGA.EY.A1GQ.01 8 0.128 0.45386 0.00 0.00 0.00 0.00 0.04 0.02 0.00 0.94
#> TCGA.EO.A22R.01 2 0.000 0.86366 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17M.01 6 0.437 0.68116 0.00 0.00 0.00 0.08 0.00 0.52 0.00 0.40
#> TCGA.EO.A3AU.01 2 0.000 0.86366 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D4.01 2 0.000 0.86366 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A215.01 6 0.437 0.69221 0.00 0.00 0.00 0.00 0.08 0.52 0.00 0.40
#> TCGA.AP.A1DM.01 6 0.437 0.69221 0.00 0.00 0.00 0.00 0.08 0.52 0.00 0.40
#> TCGA.AJ.A8CW.01 5 0.540 0.70075 0.00 0.00 0.14 0.04 0.64 0.08 0.10 0.00
#> TCGA.D1.A1NZ.01 8 0.448 0.45933 0.00 0.00 0.12 0.00 0.30 0.00 0.00 0.58
#> TCGA.D1.A17A.01 8 0.448 0.45933 0.00 0.00 0.12 0.00 0.30 0.00 0.00 0.58
#> TCGA.FI.A2F4.01 8 0.414 -0.33101 0.00 0.00 0.46 0.00 0.02 0.00 0.02 0.50
#> TCGA.D1.A0ZN.01 5 0.156 0.75236 0.02 0.00 0.00 0.00 0.92 0.06 0.00 0.00
#> TCGA.BS.A0VI.01 8 0.253 -0.11110 0.00 0.00 0.00 0.00 0.00 0.22 0.00 0.78
#> TCGA.AP.A1E1.01 5 0.510 0.69823 0.00 0.00 0.14 0.02 0.66 0.08 0.10 0.00
#> TCGA.D1.A176.01 5 0.308 0.74207 0.02 0.00 0.06 0.00 0.84 0.02 0.06 0.00
#> TCGA.EO.A22S.01 2 0.000 0.86366 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3GB.01 5 0.286 0.67198 0.20 0.00 0.00 0.00 0.78 0.00 0.00 0.02
#> TCGA.D1.A160.01 8 0.128 0.45386 0.00 0.00 0.00 0.00 0.04 0.02 0.00 0.94
#> TCGA.BG.A3EW.01 7 0.384 0.85495 0.00 0.10 0.04 0.00 0.00 0.10 0.76 0.00
#> TCGA.B5.A11Q.01 1 0.000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GU.01 8 0.463 0.39374 0.00 0.00 0.12 0.00 0.36 0.00 0.00 0.52
#> TCGA.AJ.A3OL.01 3 0.343 0.62773 0.00 0.00 0.74 0.00 0.00 0.00 0.06 0.20
#> TCGA.AP.A1E0.01 2 0.486 0.65823 0.00 0.66 0.10 0.10 0.00 0.14 0.00 0.00
#> TCGA.BG.A222.01 7 0.326 0.82888 0.00 0.10 0.02 0.00 0.00 0.02 0.82 0.04
#> TCGA.AX.A1CI.01 1 0.000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 7 0.222 0.84765 0.00 0.12 0.02 0.00 0.00 0.00 0.86 0.00
#> TCGA.AX.A0IS.01 1 0.000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 5 0.461 0.73542 0.02 0.00 0.06 0.04 0.74 0.10 0.04 0.00
#> TCGA.AJ.A2QO.01 4 0.109 0.89512 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.AX.A2HC.01 2 0.326 0.76796 0.00 0.78 0.00 0.10 0.00 0.12 0.00 0.00
#> TCGA.EO.A22U.01 3 0.483 0.42693 0.00 0.12 0.70 0.06 0.00 0.08 0.04 0.00
#> TCGA.EY.A2OP.01 7 0.413 0.72594 0.00 0.30 0.00 0.00 0.00 0.08 0.62 0.00
#> TCGA.AJ.A3BG.01 2 0.343 0.56786 0.00 0.74 0.02 0.00 0.00 0.02 0.22 0.00
#> TCGA.AP.A1DR.01 4 0.109 0.96333 0.00 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DP.01 5 0.375 0.46397 0.32 0.00 0.00 0.00 0.64 0.04 0.00 0.00
#> TCGA.AX.A1C4.01 2 0.134 0.84953 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.EY.A1GT.01 7 0.384 0.85495 0.00 0.10 0.04 0.00 0.00 0.10 0.76 0.00
#> TCGA.D1.A17D.01 3 0.401 -0.01026 0.00 0.00 0.48 0.00 0.04 0.00 0.00 0.48
#> TCGA.D1.A177.01 4 0.189 0.96269 0.00 0.06 0.00 0.90 0.00 0.04 0.00 0.00
#> TCGA.BK.A13B.01 5 0.174 0.74101 0.02 0.00 0.00 0.00 0.92 0.04 0.00 0.02
#> TCGA.BG.A0W1.01 1 0.000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 4 0.156 0.96127 0.00 0.06 0.00 0.92 0.00 0.02 0.00 0.00
#> TCGA.A5.A7WJ.01 4 0.156 0.96503 0.00 0.06 0.00 0.92 0.00 0.02 0.00 0.00
#> TCGA.AX.A2HA.01 3 0.343 0.62773 0.00 0.00 0.74 0.00 0.00 0.00 0.06 0.20
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: Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02121-leaf , Node02122-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node02341-leaf , Node02342-leaf , Node04111-leaf , Node04112-leaf , Node04311-leaf , Node04312-leaf , Node04313-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0211"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 24 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.4896 0.511 0.511
#> 3 3 1.000 1.000 1.000 0.3253 0.841 0.688
#> 4 4 0.771 0.725 0.807 0.1273 0.899 0.711
#> 5 5 0.779 0.803 0.837 0.0886 0.935 0.739
#> 6 6 0.810 0.780 0.864 0.0513 0.957 0.765
#> 7 7 0.926 0.701 0.859 0.0375 0.971 0.810
#> 8 8 0.913 0.660 0.831 0.0210 0.953 0.675
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 3 7
There is also optional best \(k\) = 2 3 7 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.B5.A11Z.01 1 0 1 1 0
#> TCGA.EY.A1GQ.01 2 0 1 0 1
#> TCGA.EY.A215.01 2 0 1 0 1
#> TCGA.AP.A1DM.01 2 0 1 0 1
#> TCGA.AJ.A8CW.01 2 0 1 0 1
#> TCGA.D1.A1NZ.01 2 0 1 0 1
#> TCGA.D1.A17A.01 2 0 1 0 1
#> TCGA.FI.A2F4.01 1 0 1 1 0
#> TCGA.D1.A0ZN.01 2 0 1 0 1
#> TCGA.AP.A1E1.01 2 0 1 0 1
#> TCGA.D1.A176.01 2 0 1 0 1
#> TCGA.AX.A3GB.01 2 0 1 0 1
#> TCGA.D1.A160.01 1 0 1 1 0
#> TCGA.B5.A11Q.01 1 0 1 1 0
#> TCGA.E6.A2P9.01 1 0 1 1 0
#> TCGA.EY.A1GU.01 2 0 1 0 1
#> TCGA.AX.A1CI.01 1 0 1 1 0
#> TCGA.EY.A1GF.01 1 0 1 1 0
#> TCGA.AX.A0IS.01 1 0 1 1 0
#> TCGA.5S.A9Q8.01 2 0 1 0 1
#> TCGA.AP.A1DP.01 2 0 1 0 1
#> TCGA.D1.A17D.01 2 0 1 0 1
#> TCGA.BK.A13B.01 2 0 1 0 1
#> TCGA.BG.A0W1.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B5.A11Z.01 1 0 1 1 0 0
#> TCGA.EY.A1GQ.01 2 0 1 0 1 0
#> TCGA.EY.A215.01 3 0 1 0 0 1
#> TCGA.AP.A1DM.01 2 0 1 0 1 0
#> TCGA.AJ.A8CW.01 3 0 1 0 0 1
#> TCGA.D1.A1NZ.01 2 0 1 0 1 0
#> TCGA.D1.A17A.01 2 0 1 0 1 0
#> TCGA.FI.A2F4.01 1 0 1 1 0 0
#> TCGA.D1.A0ZN.01 2 0 1 0 1 0
#> TCGA.AP.A1E1.01 3 0 1 0 0 1
#> TCGA.D1.A176.01 2 0 1 0 1 0
#> TCGA.AX.A3GB.01 2 0 1 0 1 0
#> TCGA.D1.A160.01 1 0 1 1 0 0
#> TCGA.B5.A11Q.01 1 0 1 1 0 0
#> TCGA.E6.A2P9.01 1 0 1 1 0 0
#> TCGA.EY.A1GU.01 2 0 1 0 1 0
#> TCGA.AX.A1CI.01 1 0 1 1 0 0
#> TCGA.EY.A1GF.01 1 0 1 1 0 0
#> TCGA.AX.A0IS.01 1 0 1 1 0 0
#> TCGA.5S.A9Q8.01 3 0 1 0 0 1
#> TCGA.AP.A1DP.01 2 0 1 0 1 0
#> TCGA.D1.A17D.01 2 0 1 0 1 0
#> TCGA.BK.A13B.01 2 0 1 0 1 0
#> TCGA.BG.A0W1.01 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.B5.A11Z.01 1 0.000 0.8420 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.428 0.2999 0.00 0.72 0.00 0.28
#> TCGA.EY.A215.01 3 0.121 0.9746 0.00 0.00 0.96 0.04
#> TCGA.AP.A1DM.01 2 0.428 0.2999 0.00 0.72 0.00 0.28
#> TCGA.AJ.A8CW.01 3 0.000 0.9916 0.00 0.00 1.00 0.00
#> TCGA.D1.A1NZ.01 2 0.441 0.0315 0.00 0.70 0.00 0.30
#> TCGA.D1.A17A.01 4 0.498 1.0000 0.00 0.46 0.00 0.54
#> TCGA.FI.A2F4.01 1 0.491 0.7244 0.58 0.00 0.00 0.42
#> TCGA.D1.A0ZN.01 2 0.428 0.2999 0.00 0.72 0.00 0.28
#> TCGA.AP.A1E1.01 3 0.000 0.9916 0.00 0.00 1.00 0.00
#> TCGA.D1.A176.01 4 0.498 1.0000 0.00 0.46 0.00 0.54
#> TCGA.AX.A3GB.01 4 0.498 1.0000 0.00 0.46 0.00 0.54
#> TCGA.D1.A160.01 1 0.491 0.7244 0.58 0.00 0.00 0.42
#> TCGA.B5.A11Q.01 1 0.000 0.8420 1.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 1 0.491 0.7244 0.58 0.00 0.00 0.42
#> TCGA.EY.A1GU.01 2 0.317 0.3104 0.00 0.84 0.00 0.16
#> TCGA.AX.A1CI.01 1 0.000 0.8420 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.340 0.8077 0.82 0.00 0.00 0.18
#> TCGA.AX.A0IS.01 1 0.000 0.8420 1.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 3 0.000 0.9916 0.00 0.00 1.00 0.00
#> TCGA.AP.A1DP.01 2 0.000 0.5067 0.00 1.00 0.00 0.00
#> TCGA.D1.A17D.01 4 0.498 1.0000 0.00 0.46 0.00 0.54
#> TCGA.BK.A13B.01 2 0.000 0.5067 0.00 1.00 0.00 0.00
#> TCGA.BG.A0W1.01 1 0.000 0.8420 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.B5.A11Z.01 1 0.000 0.910 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.513 0.575 0.00 0.68 0.00 0.22 0.10
#> TCGA.EY.A215.01 3 0.208 0.941 0.00 0.00 0.92 0.04 0.04
#> TCGA.AP.A1DM.01 2 0.513 0.575 0.00 0.68 0.00 0.22 0.10
#> TCGA.AJ.A8CW.01 3 0.000 0.981 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A1NZ.01 2 0.538 0.438 0.00 0.64 0.00 0.26 0.10
#> TCGA.D1.A17A.01 4 0.228 1.000 0.00 0.12 0.00 0.88 0.00
#> TCGA.FI.A2F4.01 5 0.530 0.928 0.36 0.00 0.00 0.06 0.58
#> TCGA.D1.A0ZN.01 2 0.513 0.575 0.00 0.68 0.00 0.22 0.10
#> TCGA.AP.A1E1.01 3 0.000 0.981 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A176.01 4 0.228 1.000 0.00 0.12 0.00 0.88 0.00
#> TCGA.AX.A3GB.01 4 0.228 1.000 0.00 0.12 0.00 0.88 0.00
#> TCGA.D1.A160.01 5 0.406 0.964 0.36 0.00 0.00 0.00 0.64
#> TCGA.B5.A11Q.01 1 0.000 0.910 1.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 5 0.406 0.964 0.36 0.00 0.00 0.00 0.64
#> TCGA.EY.A1GU.01 2 0.603 0.366 0.00 0.58 0.00 0.20 0.22
#> TCGA.AX.A1CI.01 1 0.000 0.910 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.413 0.276 0.72 0.00 0.00 0.02 0.26
#> TCGA.AX.A0IS.01 1 0.000 0.910 1.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 3 0.000 0.981 0.00 0.00 1.00 0.00 0.00
#> TCGA.AP.A1DP.01 2 0.000 0.617 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17D.01 4 0.228 1.000 0.00 0.12 0.00 0.88 0.00
#> TCGA.BK.A13B.01 2 0.311 0.561 0.00 0.80 0.00 0.00 0.20
#> TCGA.BG.A0W1.01 1 0.000 0.910 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.B5.A11Z.01 1 0.000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.383 0.6951 0.00 0.76 0.00 0.18 0.06 0.00
#> TCGA.EY.A215.01 3 0.301 0.8794 0.00 0.04 0.86 0.00 0.08 0.02
#> TCGA.AP.A1DM.01 2 0.263 0.7247 0.00 0.82 0.00 0.18 0.00 0.00
#> TCGA.AJ.A8CW.01 3 0.000 0.9616 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 6 0.659 0.1292 0.00 0.34 0.00 0.12 0.08 0.46
#> TCGA.D1.A17A.01 4 0.000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FI.A2F4.01 5 0.457 0.9001 0.26 0.04 0.00 0.00 0.68 0.02
#> TCGA.D1.A0ZN.01 2 0.409 0.7084 0.00 0.74 0.00 0.18 0.08 0.00
#> TCGA.AP.A1E1.01 3 0.000 0.9616 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A176.01 4 0.000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A3GB.01 4 0.000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A160.01 5 0.331 0.8935 0.28 0.00 0.00 0.00 0.72 0.00
#> TCGA.B5.A11Q.01 1 0.000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 5 0.279 0.8815 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.EY.A1GU.01 6 0.209 0.6203 0.00 0.02 0.00 0.08 0.00 0.90
#> TCGA.AX.A1CI.01 1 0.000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.486 0.2943 0.66 0.02 0.00 0.00 0.26 0.06
#> TCGA.AX.A0IS.01 1 0.000 0.9103 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 3 0.000 0.9616 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A1DP.01 2 0.568 -0.0262 0.00 0.56 0.00 0.02 0.12 0.30
#> TCGA.D1.A17D.01 4 0.000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BK.A13B.01 6 0.387 0.5795 0.00 0.16 0.00 0.02 0.04 0.78
#> TCGA.BG.A0W1.01 1 0.000 0.9103 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.B5.A11Z.01 1 0.0000 0.8779 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 2 0.1928 0.5748 0.00 0.90 0.00 0.08 0.02 0.00 0.00
#> TCGA.EY.A215.01 3 0.3307 0.7631 0.00 0.02 0.74 0.00 0.00 0.00 0.24
#> TCGA.AP.A1DM.01 2 0.1433 0.5731 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.AJ.A8CW.01 3 0.0000 0.9167 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 2 0.5606 0.0601 0.00 0.48 0.00 0.06 0.08 0.38 0.00
#> TCGA.D1.A17A.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2F4.01 5 0.2213 0.9074 0.04 0.04 0.00 0.00 0.90 0.00 0.02
#> TCGA.D1.A0ZN.01 2 0.4487 0.1227 0.00 0.60 0.00 0.08 0.00 0.00 0.32
#> TCGA.AP.A1E1.01 3 0.0000 0.9167 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A176.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3GB.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A160.01 5 0.1671 0.8843 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.B5.A11Q.01 1 0.0000 0.8779 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 5 0.0504 0.9107 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.EY.A1GU.01 6 0.0863 0.5845 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.AX.A1CI.01 1 0.0000 0.8779 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 1 0.6021 -0.1621 0.40 0.00 0.00 0.00 0.38 0.04 0.18
#> TCGA.AX.A0IS.01 1 0.0000 0.8779 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 3 0.1006 0.9087 0.00 0.02 0.96 0.00 0.02 0.00 0.00
#> TCGA.AP.A1DP.01 7 0.5083 0.0000 0.00 0.24 0.00 0.00 0.00 0.20 0.56
#> TCGA.D1.A17D.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BK.A13B.01 6 0.3637 0.4844 0.00 0.04 0.00 0.00 0.00 0.72 0.24
#> TCGA.BG.A0W1.01 1 0.0000 0.8779 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.B5.A11Z.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GQ.01 6 0.3714 -0.547 0.00 0.44 0.00 0.02 0.00 0.54 0.00 0.00
#> TCGA.EY.A215.01 3 0.3934 0.710 0.00 0.00 0.70 0.00 0.00 0.00 0.16 0.14
#> TCGA.AP.A1DM.01 2 0.3570 0.392 0.00 0.62 0.00 0.02 0.00 0.36 0.00 0.00
#> TCGA.AJ.A8CW.01 3 0.0000 0.902 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NZ.01 6 0.0000 0.225 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A17A.01 4 0.0471 0.989 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FI.A2F4.01 5 0.2404 0.780 0.00 0.00 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.D1.A0ZN.01 2 0.4174 0.503 0.00 0.62 0.00 0.02 0.00 0.04 0.32 0.00
#> TCGA.AP.A1E1.01 3 0.0000 0.902 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A176.01 4 0.0000 0.989 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3GB.01 4 0.0471 0.989 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D1.A160.01 5 0.0000 0.875 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11Q.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A2P9.01 5 0.0471 0.873 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EY.A1GU.01 6 0.5030 -0.213 0.00 0.34 0.00 0.00 0.00 0.46 0.00 0.20
#> TCGA.AX.A1CI.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GF.01 8 0.5221 0.000 0.26 0.00 0.00 0.00 0.36 0.00 0.00 0.38
#> TCGA.AX.A0IS.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5S.A9Q8.01 3 0.0808 0.893 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.AP.A1DP.01 7 0.2725 0.327 0.00 0.04 0.00 0.00 0.00 0.14 0.82 0.00
#> TCGA.D1.A17D.01 4 0.0000 0.989 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A13B.01 7 0.5978 0.319 0.00 0.36 0.00 0.00 0.00 0.12 0.40 0.12
#> TCGA.BG.A0W1.01 1 0.0471 0.976 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02121-leaf , Node02122-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node02341-leaf , Node02342-leaf , Node04111-leaf , Node04112-leaf , Node04311-leaf , Node04312-leaf , Node04313-leaf , Node05111-leaf , Node05112-leaf , Node05113-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 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 0.972 0.985 0.4968 0.508 0.508
#> 3 3 0.938 0.921 0.964 0.3692 0.646 0.404
#> 4 4 0.938 0.859 0.939 0.0988 0.902 0.706
#> 5 5 0.768 0.662 0.861 0.0516 0.957 0.831
#> 6 6 0.736 0.561 0.816 0.0356 0.929 0.713
#> 7 7 0.793 0.689 0.845 0.0381 0.929 0.662
#> 8 8 0.753 0.587 0.814 0.0204 0.997 0.979
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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.AP.A1DO.01 1 0.000 1.000 1.00 0.00
#> TCGA.A5.A2K7.01 2 0.402 0.918 0.08 0.92
#> TCGA.EY.A5W2.01 1 0.000 1.000 1.00 0.00
#> TCGA.EO.A22R.01 2 0.000 0.975 0.00 1.00
#> TCGA.D1.A17M.01 1 0.000 1.000 1.00 0.00
#> TCGA.EO.A3AU.01 2 0.402 0.918 0.08 0.92
#> TCGA.FI.A2D4.01 2 0.000 0.975 0.00 1.00
#> TCGA.BS.A0VI.01 2 0.000 0.975 0.00 1.00
#> TCGA.EO.A22S.01 2 0.000 0.975 0.00 1.00
#> TCGA.BG.A3EW.01 2 0.000 0.975 0.00 1.00
#> TCGA.AJ.A3OL.01 2 0.000 0.975 0.00 1.00
#> TCGA.AP.A1E0.01 2 0.722 0.774 0.20 0.80
#> TCGA.BG.A222.01 2 0.000 0.975 0.00 1.00
#> TCGA.EY.A2OO.01 2 0.000 0.975 0.00 1.00
#> TCGA.AJ.A2QO.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A2HC.01 1 0.000 1.000 1.00 0.00
#> TCGA.EO.A22U.01 2 0.000 0.975 0.00 1.00
#> TCGA.EY.A2OP.01 2 0.000 0.975 0.00 1.00
#> TCGA.AJ.A3BG.01 2 0.141 0.963 0.02 0.98
#> TCGA.AP.A1DR.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A1C4.01 1 0.000 1.000 1.00 0.00
#> TCGA.EY.A1GT.01 2 0.000 0.975 0.00 1.00
#> TCGA.D1.A177.01 1 0.000 1.000 1.00 0.00
#> TCGA.AJ.A3EK.01 1 0.000 1.000 1.00 0.00
#> TCGA.A5.A7WJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A2HA.01 2 0.000 0.975 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AP.A1DO.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.A5.A2K7.01 3 0.000 0.902 0.00 0.00 1.00
#> TCGA.EY.A5W2.01 3 0.000 0.902 0.00 0.00 1.00
#> TCGA.EO.A22R.01 3 0.334 0.822 0.00 0.12 0.88
#> TCGA.D1.A17M.01 3 0.000 0.902 0.00 0.00 1.00
#> TCGA.EO.A3AU.01 3 0.000 0.902 0.00 0.00 1.00
#> TCGA.FI.A2D4.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BS.A0VI.01 3 0.153 0.886 0.00 0.04 0.96
#> TCGA.EO.A22S.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BG.A3EW.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A3OL.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.AP.A1E0.01 3 0.000 0.902 0.00 0.00 1.00
#> TCGA.BG.A222.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.EY.A2OO.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A2QO.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.AX.A2HC.01 1 0.153 0.956 0.96 0.00 0.04
#> TCGA.EO.A22U.01 3 0.207 0.874 0.00 0.06 0.94
#> TCGA.EY.A2OP.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.AJ.A3BG.01 3 0.000 0.902 0.00 0.00 1.00
#> TCGA.AP.A1DR.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.AX.A1C4.01 3 0.583 0.524 0.34 0.00 0.66
#> TCGA.EY.A1GT.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.D1.A177.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.AJ.A3EK.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.A5.A7WJ.01 3 0.583 0.522 0.34 0.00 0.66
#> TCGA.AX.A2HA.01 2 0.000 1.000 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AP.A1DO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 3 0.2345 0.835 0.00 0.00 0.90 0.10
#> TCGA.EY.A5W2.01 3 0.0000 0.889 0.00 0.00 1.00 0.00
#> TCGA.EO.A22R.01 4 0.7877 0.133 0.00 0.36 0.28 0.36
#> TCGA.D1.A17M.01 3 0.2011 0.851 0.00 0.00 0.92 0.08
#> TCGA.EO.A3AU.01 3 0.0000 0.889 0.00 0.00 1.00 0.00
#> TCGA.FI.A2D4.01 2 0.1637 0.945 0.00 0.94 0.00 0.06
#> TCGA.BS.A0VI.01 3 0.0707 0.879 0.00 0.02 0.98 0.00
#> TCGA.EO.A22S.01 2 0.1211 0.962 0.00 0.96 0.00 0.04
#> TCGA.BG.A3EW.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.AP.A1E0.01 4 0.0000 0.724 0.00 0.00 0.00 1.00
#> TCGA.BG.A222.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 4 0.3172 0.600 0.16 0.00 0.00 0.84
#> TCGA.EO.A22U.01 4 0.0000 0.724 0.00 0.00 0.00 1.00
#> TCGA.EY.A2OP.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3BG.01 3 0.0000 0.889 0.00 0.00 1.00 0.00
#> TCGA.AP.A1DR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AX.A1C4.01 3 0.4907 0.291 0.42 0.00 0.58 0.00
#> TCGA.EY.A1GT.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A5.A7WJ.01 3 0.0707 0.882 0.02 0.00 0.98 0.00
#> TCGA.AX.A2HA.01 2 0.1211 0.962 0.00 0.96 0.00 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AP.A1DO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 3 0.6865 0.431 0.00 0.04 0.54 0.26 0.16
#> TCGA.EY.A5W2.01 3 0.0000 0.841 0.00 0.00 1.00 0.00 0.00
#> TCGA.EO.A22R.01 4 0.5546 0.411 0.00 0.20 0.10 0.68 0.02
#> TCGA.D1.A17M.01 3 0.2012 0.827 0.00 0.00 0.92 0.06 0.02
#> TCGA.EO.A3AU.01 3 0.0609 0.842 0.00 0.00 0.98 0.00 0.02
#> TCGA.FI.A2D4.01 4 0.4262 -0.117 0.00 0.44 0.00 0.56 0.00
#> TCGA.BS.A0VI.01 3 0.3034 0.803 0.00 0.06 0.88 0.04 0.02
#> TCGA.EO.A22S.01 2 0.4182 0.300 0.00 0.60 0.00 0.40 0.00
#> TCGA.BG.A3EW.01 2 0.0000 0.841 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.0609 0.829 0.00 0.98 0.00 0.02 0.00
#> TCGA.AP.A1E0.01 4 0.4302 0.102 0.00 0.00 0.00 0.52 0.48
#> TCGA.BG.A222.01 2 0.0000 0.841 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.0000 0.841 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A2QO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 5 0.2732 0.000 0.16 0.00 0.00 0.00 0.84
#> TCGA.EO.A22U.01 4 0.4613 0.260 0.00 0.00 0.02 0.62 0.36
#> TCGA.EY.A2OP.01 2 0.0000 0.841 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 3 0.1043 0.840 0.00 0.00 0.96 0.04 0.00
#> TCGA.AP.A1DR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C4.01 3 0.5685 0.583 0.20 0.00 0.68 0.08 0.04
#> TCGA.EY.A1GT.01 2 0.0000 0.841 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3EK.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A7WJ.01 3 0.2438 0.810 0.04 0.00 0.90 0.06 0.00
#> TCGA.AX.A2HA.01 2 0.4227 0.247 0.00 0.58 0.00 0.42 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AP.A1DO.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K7.01 6 0.6796 0.157 0.00 0.00 0.28 0.12 0.12 0.48
#> TCGA.EY.A5W2.01 3 0.0547 0.609 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EO.A22R.01 4 0.7432 0.268 0.00 0.18 0.12 0.46 0.02 0.22
#> TCGA.D1.A17M.01 3 0.6086 -0.112 0.00 0.00 0.48 0.16 0.02 0.34
#> TCGA.EO.A3AU.01 3 0.4812 0.330 0.00 0.00 0.68 0.04 0.04 0.24
#> TCGA.FI.A2D4.01 2 0.5922 0.299 0.00 0.44 0.00 0.22 0.00 0.34
#> TCGA.BS.A0VI.01 3 0.4125 0.527 0.00 0.08 0.80 0.02 0.02 0.08
#> TCGA.EO.A22S.01 2 0.5481 0.438 0.00 0.52 0.00 0.14 0.00 0.34
#> TCGA.BG.A3EW.01 2 0.0000 0.779 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.0937 0.765 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AP.A1E0.01 4 0.2350 0.328 0.00 0.00 0.00 0.88 0.10 0.02
#> TCGA.BG.A222.01 2 0.0000 0.779 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.0000 0.779 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QO.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.01 5 0.3592 0.000 0.02 0.00 0.00 0.24 0.74 0.00
#> TCGA.EO.A22U.01 4 0.0547 0.430 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.EY.A2OP.01 2 0.0000 0.779 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 3 0.0547 0.612 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.AP.A1DR.01 1 0.1092 0.967 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.AX.A1C4.01 6 0.8041 0.278 0.16 0.00 0.24 0.04 0.18 0.38
#> TCGA.EY.A1GT.01 2 0.0000 0.779 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0547 0.980 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AJ.A3EK.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A7WJ.01 3 0.3567 0.456 0.10 0.00 0.80 0.00 0.00 0.10
#> TCGA.AX.A2HA.01 2 0.5618 0.413 0.00 0.50 0.00 0.16 0.00 0.34
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AP.A1DO.01 1 0.0863 0.945 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.A5.A2K7.01 6 0.3386 0.135 0.00 0.00 0.18 0.02 0.02 0.78 0.00
#> TCGA.EY.A5W2.01 3 0.1860 0.635 0.00 0.00 0.92 0.00 0.02 0.04 0.02
#> TCGA.EO.A22R.01 7 0.5624 0.351 0.00 0.02 0.10 0.22 0.02 0.02 0.62
#> TCGA.D1.A17M.01 3 0.5700 0.313 0.02 0.00 0.58 0.08 0.02 0.28 0.02
#> TCGA.EO.A3AU.01 3 0.4635 0.508 0.00 0.00 0.70 0.10 0.00 0.16 0.04
#> TCGA.FI.A2D4.01 7 0.3086 0.790 0.00 0.16 0.00 0.04 0.00 0.00 0.80
#> TCGA.BS.A0VI.01 3 0.5436 0.489 0.00 0.08 0.70 0.06 0.02 0.10 0.04
#> TCGA.EO.A22S.01 7 0.2259 0.804 0.00 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.BG.A3EW.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.0863 0.951 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.AP.A1E0.01 4 0.3055 0.586 0.00 0.00 0.02 0.82 0.14 0.00 0.02
#> TCGA.BG.A222.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OO.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QO.01 1 0.0504 0.951 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AX.A2HC.01 5 0.2081 0.000 0.00 0.00 0.00 0.14 0.86 0.00 0.00
#> TCGA.EO.A22U.01 4 0.4001 0.640 0.00 0.00 0.06 0.74 0.00 0.02 0.18
#> TCGA.EY.A2OP.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 3 0.1006 0.648 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.AP.A1DR.01 1 0.1166 0.930 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.AX.A1C4.01 6 0.8297 0.025 0.12 0.00 0.30 0.08 0.08 0.32 0.10
#> TCGA.EY.A1GT.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.1006 0.946 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.AJ.A3EK.01 1 0.1006 0.949 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.A5.A7WJ.01 3 0.4118 0.558 0.06 0.00 0.80 0.04 0.06 0.02 0.02
#> TCGA.AX.A2HA.01 7 0.2422 0.795 0.00 0.18 0.00 0.00 0.00 0.00 0.82
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AP.A1DO.01 1 0.2132 0.8519 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.A5.A2K7.01 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A5W2.01 3 0.1741 0.5241 0.00 0.00 0.92 0.00 0.02 0.02 0.00 0.04
#> TCGA.EO.A22R.01 7 0.7471 -0.2034 0.00 0.00 0.20 0.24 0.06 0.02 0.34 0.14
#> TCGA.D1.A17M.01 3 0.6443 0.1669 0.06 0.00 0.46 0.02 0.06 0.32 0.00 0.08
#> TCGA.EO.A3AU.01 3 0.5284 0.4073 0.00 0.00 0.58 0.02 0.02 0.22 0.00 0.16
#> TCGA.FI.A2D4.01 7 0.2719 0.6999 0.00 0.18 0.00 0.00 0.00 0.00 0.80 0.02
#> TCGA.BS.A0VI.01 3 0.4896 0.4585 0.00 0.12 0.68 0.00 0.02 0.12 0.00 0.06
#> TCGA.EO.A22S.01 7 0.2406 0.6897 0.00 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.BG.A3EW.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3OL.01 2 0.1765 0.8342 0.00 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.AP.A1E0.01 4 0.1275 0.5600 0.00 0.00 0.00 0.94 0.04 0.02 0.00 0.00
#> TCGA.BG.A222.01 2 0.0471 0.9518 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EY.A2OO.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QO.01 1 0.0471 0.9013 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AX.A2HC.01 5 0.2719 0.0000 0.02 0.00 0.00 0.18 0.80 0.00 0.00 0.00
#> TCGA.EO.A22U.01 4 0.4720 0.6130 0.00 0.00 0.12 0.70 0.00 0.06 0.10 0.02
#> TCGA.EY.A2OP.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BG.01 3 0.3586 0.5081 0.00 0.00 0.78 0.00 0.00 0.06 0.04 0.12
#> TCGA.AP.A1DR.01 1 0.2350 0.8436 0.86 0.00 0.00 0.00 0.04 0.00 0.00 0.10
#> TCGA.AX.A1C4.01 8 0.5916 0.0000 0.12 0.00 0.08 0.02 0.06 0.10 0.00 0.62
#> TCGA.EY.A1GT.01 2 0.0000 0.9656 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A177.01 1 0.0941 0.8966 0.96 0.00 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.AJ.A3EK.01 1 0.0941 0.9016 0.96 0.00 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.A5.A7WJ.01 3 0.5774 0.0981 0.02 0.00 0.50 0.00 0.08 0.02 0.04 0.34
#> TCGA.AX.A2HA.01 7 0.2114 0.7002 0.00 0.16 0.00 0.00 0.00 0.00 0.84 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 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 51 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.978 0.989 0.3326 0.678 0.678
#> 3 3 0.988 0.953 0.980 0.4451 0.848 0.777
#> 4 4 0.886 0.933 0.963 0.2155 0.890 0.796
#> 5 5 0.757 0.735 0.873 0.0737 0.990 0.976
#> 6 6 0.809 0.702 0.858 0.0340 0.940 0.858
#> 7 7 0.675 0.651 0.830 0.0389 0.964 0.905
#> 8 8 0.679 0.574 0.815 0.0291 0.985 0.958
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.D1.A16R.01 2 0.000 0.987 0.00 1.00
#> TCGA.B5.A3FC.01 2 0.000 0.987 0.00 1.00
#> TCGA.AX.A1CJ.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A103.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A16Q.01 2 0.000 0.987 0.00 1.00
#> TCGA.AJ.A3BI.01 2 0.242 0.956 0.04 0.96
#> TCGA.EY.A1GE.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A161.01 2 0.000 0.987 0.00 1.00
#> TCGA.AX.A06D.01 1 0.000 0.995 1.00 0.00
#> TCGA.AJ.A3EL.01 2 0.760 0.731 0.22 0.78
#> TCGA.EY.A2OM.01 1 0.000 0.995 1.00 0.00
#> TCGA.D1.A175.01 2 0.000 0.987 0.00 1.00
#> TCGA.EO.A3B0.01 1 0.242 0.957 0.96 0.04
#> TCGA.BS.A0WQ.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A1O0.01 2 0.242 0.956 0.04 0.96
#> TCGA.D1.A0ZU.01 2 0.000 0.987 0.00 1.00
#> TCGA.B5.A11F.01 2 0.000 0.987 0.00 1.00
#> TCGA.SJ.A6ZJ.01 2 0.000 0.987 0.00 1.00
#> TCGA.BG.A220.01 1 0.000 0.995 1.00 0.00
#> TCGA.QS.A744.01 1 0.000 0.995 1.00 0.00
#> TCGA.D1.A168.01 1 0.000 0.995 1.00 0.00
#> TCGA.D1.A17F.01 2 0.000 0.987 0.00 1.00
#> TCGA.BG.A0W2.01 2 0.000 0.987 0.00 1.00
#> TCGA.BS.A0U5.01 2 0.000 0.987 0.00 1.00
#> TCGA.BG.A0MA.01 2 0.000 0.987 0.00 1.00
#> TCGA.BK.A4ZD.01 2 0.529 0.864 0.12 0.88
#> TCGA.EO.A1Y7.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A102.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A17S.01 2 0.000 0.987 0.00 1.00
#> TCGA.DF.A2KS.01 1 0.000 0.995 1.00 0.00
#> TCGA.EY.A548.01 2 0.242 0.956 0.04 0.96
#> TCGA.AX.A3FS.01 1 0.000 0.995 1.00 0.00
#> TCGA.AJ.A3I9.01 2 0.000 0.987 0.00 1.00
#> TCGA.B5.A0JT.01 2 0.000 0.987 0.00 1.00
#> TCGA.BG.A0MH.01 2 0.000 0.987 0.00 1.00
#> TCGA.AJ.A5DW.01 2 0.000 0.987 0.00 1.00
#> TCGA.AX.A0J0.01 2 0.000 0.987 0.00 1.00
#> TCGA.QS.A5YQ.01 2 0.000 0.987 0.00 1.00
#> TCGA.E6.A1M0.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A17H.01 2 0.000 0.987 0.00 1.00
#> TCGA.B5.A11V.01 2 0.000 0.987 0.00 1.00
#> TCGA.B5.A1MW.01 1 0.000 0.995 1.00 0.00
#> TCGA.AX.A3FX.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A1O5.01 2 0.000 0.987 0.00 1.00
#> TCGA.QF.A5YT.01 2 0.000 0.987 0.00 1.00
#> TCGA.EY.A72D.01 1 0.000 0.995 1.00 0.00
#> TCGA.D1.A17Q.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A15Z.01 2 0.000 0.987 0.00 1.00
#> TCGA.EY.A1GD.01 2 0.000 0.987 0.00 1.00
#> TCGA.DF.A2L0.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A16N.01 2 0.242 0.956 0.04 0.96
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D1.A16R.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.B5.A3FC.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AX.A1CJ.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A103.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A16Q.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AJ.A3BI.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.EY.A1GE.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A161.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AX.A06D.01 1 0.000 0.959 1.00 0.00 0.00
#> TCGA.AJ.A3EL.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.EY.A2OM.01 1 0.334 0.850 0.88 0.00 0.12
#> TCGA.D1.A175.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.EO.A3B0.01 1 0.334 0.786 0.88 0.12 0.00
#> TCGA.BS.A0WQ.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A1O0.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D1.A0ZU.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.B5.A11F.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.BG.A220.01 1 0.000 0.959 1.00 0.00 0.00
#> TCGA.QS.A744.01 1 0.000 0.959 1.00 0.00 0.00
#> TCGA.D1.A168.01 1 0.000 0.959 1.00 0.00 0.00
#> TCGA.D1.A17F.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.BG.A0W2.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.BS.A0U5.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.BG.A0MA.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.BK.A4ZD.01 2 0.207 0.920 0.06 0.94 0.00
#> TCGA.EO.A1Y7.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A102.01 2 0.207 0.922 0.00 0.94 0.06
#> TCGA.D1.A17S.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DF.A2KS.01 1 0.000 0.959 1.00 0.00 0.00
#> TCGA.EY.A548.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.AX.A3FS.01 1 0.000 0.959 1.00 0.00 0.00
#> TCGA.AJ.A3I9.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.B5.A0JT.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.BG.A0MH.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AJ.A5DW.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AX.A0J0.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.QS.A5YQ.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.E6.A1M0.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A17H.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.B5.A11V.01 2 0.583 0.507 0.00 0.66 0.34
#> TCGA.B5.A1MW.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.AX.A3FX.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A1O5.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.QF.A5YT.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.EY.A72D.01 1 0.000 0.959 1.00 0.00 0.00
#> TCGA.D1.A17Q.01 2 0.556 0.588 0.00 0.70 0.30
#> TCGA.D1.A15Z.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.EY.A1GD.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DF.A2L0.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.D1.A16N.01 3 0.000 1.000 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.D1.A16R.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.3972 0.823 0.00 0.84 0.08 0.08
#> TCGA.AX.A1CJ.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3BI.01 3 0.0000 0.984 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.AX.A06D.01 1 0.0000 0.974 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EL.01 3 0.0000 0.984 0.00 0.00 1.00 0.00
#> TCGA.EY.A2OM.01 1 0.2830 0.913 0.90 0.00 0.06 0.04
#> TCGA.D1.A175.01 2 0.4227 0.797 0.00 0.82 0.12 0.06
#> TCGA.EO.A3B0.01 4 0.2335 0.879 0.06 0.02 0.00 0.92
#> TCGA.BS.A0WQ.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A1O0.01 3 0.0000 0.984 0.00 0.00 1.00 0.00
#> TCGA.D1.A0ZU.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.B5.A11F.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.BG.A220.01 1 0.1211 0.960 0.96 0.00 0.00 0.04
#> TCGA.QS.A744.01 1 0.0707 0.969 0.98 0.00 0.00 0.02
#> TCGA.D1.A168.01 1 0.0000 0.974 1.00 0.00 0.00 0.00
#> TCGA.D1.A17F.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.BG.A0W2.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.BS.A0U5.01 2 0.0707 0.945 0.00 0.98 0.00 0.02
#> TCGA.BG.A0MA.01 2 0.2647 0.848 0.00 0.88 0.00 0.12
#> TCGA.BK.A4ZD.01 4 0.2411 0.904 0.04 0.04 0.00 0.92
#> TCGA.EO.A1Y7.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A102.01 2 0.3198 0.861 0.00 0.88 0.08 0.04
#> TCGA.D1.A17S.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.DF.A2KS.01 1 0.0707 0.967 0.98 0.00 0.00 0.02
#> TCGA.EY.A548.01 3 0.1637 0.945 0.00 0.00 0.94 0.06
#> TCGA.AX.A3FS.01 1 0.0000 0.974 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3I9.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.B5.A0JT.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.AJ.A5DW.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.E6.A1M0.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A17H.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.B5.A11V.01 2 0.4553 0.744 0.00 0.78 0.18 0.04
#> TCGA.B5.A1MW.01 3 0.0707 0.968 0.02 0.00 0.98 0.00
#> TCGA.AX.A3FX.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A1O5.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.QF.A5YT.01 4 0.2011 0.921 0.00 0.08 0.00 0.92
#> TCGA.EY.A72D.01 1 0.0707 0.967 0.98 0.00 0.00 0.02
#> TCGA.D1.A17Q.01 2 0.5512 0.554 0.00 0.66 0.30 0.04
#> TCGA.D1.A15Z.01 4 0.2647 0.838 0.00 0.12 0.00 0.88
#> TCGA.EY.A1GD.01 4 0.2011 0.921 0.00 0.08 0.00 0.92
#> TCGA.DF.A2L0.01 2 0.0000 0.961 0.00 1.00 0.00 0.00
#> TCGA.D1.A16N.01 3 0.0000 0.984 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.D1.A16R.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.5326 0.717 0.00 0.74 0.08 0.08 0.10
#> TCGA.AX.A1CJ.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.1043 0.895 0.00 0.96 0.00 0.00 0.04
#> TCGA.D1.A16Q.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3BI.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A06D.01 1 0.3424 0.648 0.76 0.00 0.00 0.00 0.24
#> TCGA.AJ.A3EL.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A2OM.01 5 0.5178 -0.610 0.48 0.00 0.04 0.00 0.48
#> TCGA.D1.A175.01 2 0.6072 0.638 0.00 0.68 0.10 0.10 0.12
#> TCGA.EO.A3B0.01 4 0.2873 0.733 0.12 0.00 0.00 0.86 0.02
#> TCGA.BS.A0WQ.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A1O0.01 3 0.0609 0.947 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A0ZU.01 2 0.0609 0.900 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A11F.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A220.01 1 0.4262 0.359 0.56 0.00 0.00 0.00 0.44
#> TCGA.QS.A744.01 1 0.3895 0.571 0.68 0.00 0.00 0.00 0.32
#> TCGA.D1.A168.01 1 0.0000 0.732 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17F.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0W2.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.BS.A0U5.01 2 0.2012 0.865 0.00 0.92 0.00 0.06 0.02
#> TCGA.BG.A0MA.01 2 0.3319 0.774 0.00 0.82 0.00 0.16 0.02
#> TCGA.BK.A4ZD.01 4 0.2331 0.751 0.08 0.00 0.00 0.90 0.02
#> TCGA.EO.A1Y7.01 2 0.1216 0.894 0.00 0.96 0.02 0.00 0.02
#> TCGA.D1.A102.01 2 0.6968 0.386 0.00 0.54 0.10 0.08 0.28
#> TCGA.D1.A17S.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 1 0.2249 0.700 0.92 0.00 0.02 0.04 0.02
#> TCGA.EY.A548.01 5 0.5131 -0.367 0.00 0.00 0.42 0.04 0.54
#> TCGA.AX.A3FS.01 1 0.1043 0.734 0.96 0.00 0.00 0.00 0.04
#> TCGA.AJ.A3I9.01 2 0.0609 0.901 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A0JT.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.0609 0.898 0.00 0.98 0.00 0.02 0.00
#> TCGA.AJ.A5DW.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.E6.A1M0.01 2 0.2012 0.872 0.00 0.92 0.06 0.00 0.02
#> TCGA.D1.A17H.01 2 0.1216 0.894 0.00 0.96 0.02 0.00 0.02
#> TCGA.B5.A11V.01 2 0.7889 -0.115 0.00 0.36 0.22 0.08 0.34
#> TCGA.B5.A1MW.01 3 0.2438 0.833 0.06 0.00 0.90 0.00 0.04
#> TCGA.AX.A3FX.01 2 0.2331 0.858 0.00 0.90 0.08 0.00 0.02
#> TCGA.D1.A1O5.01 2 0.0000 0.907 0.00 1.00 0.00 0.00 0.00
#> TCGA.QF.A5YT.01 4 0.1732 0.773 0.00 0.08 0.00 0.92 0.00
#> TCGA.EY.A72D.01 1 0.2249 0.700 0.92 0.00 0.02 0.04 0.02
#> TCGA.D1.A17Q.01 2 0.6776 0.238 0.00 0.48 0.34 0.02 0.16
#> TCGA.D1.A15Z.01 4 0.5394 0.412 0.00 0.06 0.00 0.54 0.40
#> TCGA.EY.A1GD.01 4 0.2020 0.755 0.00 0.10 0.00 0.90 0.00
#> TCGA.DF.A2L0.01 2 0.2331 0.858 0.00 0.90 0.08 0.00 0.02
#> TCGA.D1.A16N.01 3 0.0609 0.947 0.00 0.00 0.98 0.00 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D1.A16R.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.6448 0.299 0.00 0.60 0.08 0.14 0.02 0.16
#> TCGA.AX.A1CJ.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.1556 0.866 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.D1.A16Q.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BI.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06D.01 1 0.3688 0.538 0.80 0.00 0.00 0.02 0.14 0.04
#> TCGA.AJ.A3EL.01 3 0.0937 0.927 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EY.A2OM.01 5 0.5459 0.690 0.32 0.00 0.06 0.00 0.58 0.04
#> TCGA.D1.A175.01 2 0.5932 0.315 0.00 0.60 0.06 0.12 0.00 0.22
#> TCGA.EO.A3B0.01 4 0.2629 0.820 0.02 0.00 0.00 0.88 0.08 0.02
#> TCGA.BS.A0WQ.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O0.01 3 0.1092 0.920 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.D1.A0ZU.01 2 0.0547 0.896 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.B5.A11F.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A220.01 5 0.4310 0.629 0.44 0.00 0.00 0.00 0.54 0.02
#> TCGA.QS.A744.01 1 0.3647 -0.186 0.64 0.00 0.00 0.00 0.36 0.00
#> TCGA.D1.A168.01 1 0.1480 0.673 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.D1.A17F.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0W2.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0U5.01 2 0.2260 0.765 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.BG.A0MA.01 2 0.3829 0.629 0.00 0.76 0.00 0.18 0.00 0.06
#> TCGA.BK.A4ZD.01 4 0.1556 0.834 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.EO.A1Y7.01 2 0.1267 0.880 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A102.01 6 0.4646 0.146 0.00 0.46 0.04 0.00 0.00 0.50
#> TCGA.D1.A17S.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 1 0.3045 0.635 0.86 0.00 0.00 0.06 0.06 0.02
#> TCGA.EY.A548.01 6 0.6016 -0.267 0.00 0.00 0.24 0.00 0.38 0.38
#> TCGA.AX.A3FS.01 1 0.2629 0.664 0.88 0.00 0.00 0.02 0.08 0.02
#> TCGA.AJ.A3I9.01 2 0.1267 0.880 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.B5.A0JT.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.0937 0.888 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AJ.A5DW.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1M0.01 2 0.1267 0.880 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A17H.01 2 0.1267 0.880 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.B5.A11V.01 6 0.4993 0.355 0.00 0.36 0.08 0.00 0.00 0.56
#> TCGA.B5.A1MW.01 3 0.3572 0.827 0.06 0.00 0.82 0.00 0.10 0.02
#> TCGA.AX.A3FX.01 2 0.1807 0.867 0.00 0.92 0.02 0.00 0.00 0.06
#> TCGA.D1.A1O5.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QF.A5YT.01 4 0.2403 0.825 0.00 0.04 0.00 0.90 0.02 0.04
#> TCGA.EY.A72D.01 1 0.3324 0.630 0.84 0.00 0.02 0.06 0.08 0.00
#> TCGA.D1.A17Q.01 2 0.6682 -0.369 0.00 0.38 0.22 0.04 0.00 0.36
#> TCGA.D1.A15Z.01 6 0.5452 -0.494 0.00 0.00 0.00 0.44 0.12 0.44
#> TCGA.EY.A1GD.01 4 0.3045 0.781 0.00 0.06 0.00 0.86 0.02 0.06
#> TCGA.DF.A2L0.01 2 0.1807 0.867 0.00 0.92 0.02 0.00 0.00 0.06
#> TCGA.D1.A16N.01 3 0.0547 0.931 0.00 0.00 0.98 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.D1.A16R.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.6079 0.36981 0.04 0.62 0.08 0.06 0.00 0.18 0.02
#> TCGA.AX.A1CJ.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.0504 0.87369 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16Q.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BI.01 3 0.0504 0.73279 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06D.01 5 0.5474 -0.04840 0.22 0.00 0.00 0.00 0.42 0.00 0.36
#> TCGA.AJ.A3EL.01 3 0.1718 0.72199 0.04 0.00 0.92 0.00 0.00 0.00 0.04
#> TCGA.EY.A2OM.01 5 0.3689 0.50605 0.06 0.00 0.04 0.00 0.82 0.04 0.04
#> TCGA.D1.A175.01 2 0.8001 -0.16392 0.08 0.42 0.16 0.14 0.00 0.16 0.04
#> TCGA.EO.A3B0.01 4 0.2803 0.71068 0.06 0.00 0.00 0.84 0.00 0.00 0.10
#> TCGA.BS.A0WQ.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O0.01 3 0.1006 0.72144 0.02 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.D1.A0ZU.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11F.01 2 0.1006 0.86491 0.02 0.96 0.00 0.02 0.00 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A220.01 5 0.1664 0.58932 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.QS.A744.01 5 0.3388 0.53370 0.04 0.00 0.00 0.00 0.76 0.00 0.20
#> TCGA.D1.A168.01 7 0.3911 0.52184 0.06 0.00 0.00 0.00 0.24 0.00 0.70
#> TCGA.D1.A17F.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0W2.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0U5.01 2 0.3887 0.71093 0.08 0.80 0.00 0.06 0.02 0.04 0.00
#> TCGA.BG.A0MA.01 2 0.5626 0.40844 0.06 0.66 0.00 0.16 0.02 0.08 0.02
#> TCGA.BK.A4ZD.01 4 0.0504 0.76747 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EO.A1Y7.01 2 0.3488 0.78554 0.02 0.84 0.06 0.02 0.00 0.02 0.04
#> TCGA.D1.A102.01 6 0.4175 0.39153 0.00 0.38 0.04 0.00 0.00 0.58 0.00
#> TCGA.D1.A17S.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 7 0.3541 0.61378 0.02 0.00 0.00 0.08 0.10 0.00 0.80
#> TCGA.EY.A548.01 6 0.6788 -0.00287 0.16 0.00 0.20 0.00 0.14 0.48 0.02
#> TCGA.AX.A3FS.01 7 0.4783 0.29573 0.10 0.00 0.00 0.00 0.36 0.00 0.54
#> TCGA.AJ.A3I9.01 2 0.3542 0.78920 0.04 0.84 0.04 0.02 0.00 0.02 0.04
#> TCGA.B5.A0JT.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.0504 0.87298 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AJ.A5DW.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.0504 0.87369 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1M0.01 2 0.3628 0.76346 0.02 0.82 0.10 0.02 0.00 0.02 0.02
#> TCGA.D1.A17H.01 2 0.3399 0.78467 0.02 0.84 0.08 0.02 0.00 0.02 0.02
#> TCGA.B5.A11V.01 6 0.4248 0.44234 0.00 0.26 0.08 0.00 0.00 0.66 0.00
#> TCGA.B5.A1MW.01 3 0.4055 0.60479 0.18 0.00 0.74 0.00 0.04 0.00 0.04
#> TCGA.AX.A3FX.01 2 0.4171 0.72229 0.02 0.78 0.12 0.02 0.00 0.02 0.04
#> TCGA.D1.A1O5.01 2 0.0000 0.88131 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QF.A5YT.01 4 0.4751 0.73172 0.08 0.08 0.00 0.74 0.00 0.06 0.04
#> TCGA.EY.A72D.01 7 0.3940 0.57243 0.08 0.00 0.00 0.06 0.08 0.00 0.78
#> TCGA.D1.A17Q.01 3 0.6770 -0.26783 0.02 0.32 0.36 0.02 0.00 0.26 0.02
#> TCGA.D1.A15Z.01 6 0.6950 0.12848 0.38 0.10 0.00 0.10 0.02 0.38 0.02
#> TCGA.EY.A1GD.01 4 0.3922 0.76338 0.06 0.06 0.00 0.80 0.00 0.06 0.02
#> TCGA.DF.A2L0.01 2 0.4927 0.56674 0.02 0.68 0.22 0.02 0.00 0.02 0.04
#> TCGA.D1.A16N.01 3 0.0000 0.73510 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.D1.A16R.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FC.01 2 0.6864 -0.363 0.02 0.44 0.12 0.04 0.00 0.26 0.00 0.12
#> TCGA.AX.A1CJ.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A103.01 2 0.2224 0.754 0.00 0.86 0.00 0.00 0.00 0.12 0.00 0.02
#> TCGA.D1.A16Q.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3BI.01 3 0.0471 0.882 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EY.A1GE.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A161.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06D.01 5 0.4754 0.335 0.00 0.00 0.00 0.02 0.62 0.04 0.28 0.04
#> TCGA.AJ.A3EL.01 3 0.0000 0.875 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2OM.01 5 0.5170 0.366 0.06 0.00 0.04 0.00 0.70 0.04 0.10 0.06
#> TCGA.D1.A175.01 2 0.7529 -0.517 0.02 0.34 0.12 0.12 0.00 0.32 0.02 0.06
#> TCGA.EO.A3B0.01 4 0.1091 0.517 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.BS.A0WQ.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O0.01 3 0.1887 0.838 0.06 0.00 0.90 0.00 0.00 0.04 0.00 0.00
#> TCGA.D1.A0ZU.01 2 0.1947 0.750 0.00 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.B5.A11F.01 2 0.1341 0.787 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.SJ.A6ZJ.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A220.01 5 0.0941 0.539 0.00 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.QS.A744.01 5 0.2674 0.539 0.00 0.00 0.00 0.00 0.86 0.04 0.06 0.04
#> TCGA.D1.A168.01 7 0.4800 0.364 0.00 0.00 0.00 0.00 0.36 0.06 0.54 0.04
#> TCGA.D1.A17F.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0W2.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0U5.01 2 0.3675 0.597 0.02 0.76 0.00 0.00 0.00 0.08 0.00 0.14
#> TCGA.BG.A0MA.01 2 0.6320 -0.308 0.04 0.50 0.00 0.08 0.00 0.28 0.02 0.08
#> TCGA.BK.A4ZD.01 4 0.0941 0.546 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.EO.A1Y7.01 2 0.3036 0.688 0.00 0.78 0.00 0.00 0.00 0.18 0.00 0.04
#> TCGA.D1.A102.01 6 0.5171 0.639 0.06 0.34 0.04 0.00 0.00 0.54 0.00 0.02
#> TCGA.D1.A17S.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KS.01 7 0.3404 0.541 0.00 0.00 0.00 0.04 0.24 0.00 0.72 0.00
#> TCGA.EY.A548.01 1 0.1557 0.000 0.92 0.00 0.06 0.00 0.00 0.02 0.00 0.00
#> TCGA.AX.A3FS.01 5 0.4004 -0.187 0.00 0.00 0.00 0.04 0.50 0.00 0.46 0.00
#> TCGA.AJ.A3I9.01 2 0.2725 0.731 0.00 0.82 0.00 0.00 0.00 0.14 0.00 0.04
#> TCGA.B5.A0JT.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MH.01 2 0.1947 0.760 0.00 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.AJ.A5DW.01 2 0.0471 0.806 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AX.A0J0.01 2 0.1341 0.791 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.QS.A5YQ.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1M0.01 2 0.3021 0.713 0.00 0.80 0.02 0.00 0.00 0.16 0.00 0.02
#> TCGA.D1.A17H.01 2 0.2719 0.713 0.00 0.80 0.00 0.00 0.00 0.18 0.00 0.02
#> TCGA.B5.A11V.01 6 0.5762 0.454 0.18 0.24 0.04 0.00 0.00 0.52 0.00 0.02
#> TCGA.B5.A1MW.01 3 0.4896 0.592 0.00 0.00 0.68 0.02 0.00 0.06 0.12 0.12
#> TCGA.AX.A3FX.01 2 0.3483 0.670 0.00 0.76 0.02 0.00 0.00 0.18 0.00 0.04
#> TCGA.D1.A1O5.01 2 0.0000 0.812 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QF.A5YT.01 4 0.5758 0.437 0.00 0.04 0.00 0.56 0.00 0.20 0.04 0.16
#> TCGA.EY.A72D.01 7 0.5314 0.475 0.02 0.00 0.00 0.06 0.14 0.10 0.66 0.02
#> TCGA.D1.A17Q.01 6 0.5566 0.528 0.00 0.30 0.16 0.02 0.00 0.50 0.00 0.02
#> TCGA.D1.A15Z.01 8 0.5456 0.000 0.10 0.02 0.00 0.14 0.00 0.12 0.00 0.62
#> TCGA.EY.A1GD.01 4 0.5254 0.448 0.00 0.08 0.00 0.60 0.00 0.18 0.00 0.14
#> TCGA.DF.A2L0.01 2 0.4472 0.535 0.00 0.68 0.10 0.00 0.00 0.18 0.00 0.04
#> TCGA.D1.A16N.01 3 0.0471 0.882 0.00 0.00 0.98 0.00 0.00 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["023"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 48 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.987 0.994 0.4967 0.504 0.504
#> 3 3 0.696 0.804 0.890 0.3186 0.692 0.469
#> 4 4 0.845 0.962 0.970 0.1437 0.789 0.478
#> 5 5 0.813 0.772 0.845 0.0569 0.947 0.788
#> 6 6 0.775 0.701 0.798 0.0425 0.986 0.932
#> 7 7 0.769 0.533 0.781 0.0240 0.971 0.857
#> 8 8 0.783 0.618 0.760 0.0174 0.976 0.870
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.EC.A24G.01 1 0.000 0.993 1.00 0.00
#> TCGA.BG.A2AD.01 2 0.000 0.994 0.00 1.00
#> TCGA.EO.A3KX.01 2 0.000 0.994 0.00 1.00
#> TCGA.AP.A05O.01 2 0.000 0.994 0.00 1.00
#> TCGA.BG.A0MK.01 2 0.000 0.994 0.00 1.00
#> TCGA.EY.A1H0.01 2 0.000 0.994 0.00 1.00
#> TCGA.BK.A13C.01 2 0.000 0.994 0.00 1.00
#> TCGA.EY.A1GI.01 1 0.327 0.938 0.94 0.06
#> TCGA.D1.A0ZO.01 1 0.000 0.993 1.00 0.00
#> TCGA.AX.A1CK.01 2 0.000 0.994 0.00 1.00
#> TCGA.EY.A1GL.01 1 0.402 0.916 0.92 0.08
#> TCGA.D1.A17U.01 1 0.000 0.993 1.00 0.00
#> TCGA.AJ.A2QL.01 2 0.000 0.994 0.00 1.00
#> TCGA.AP.A1DH.01 1 0.000 0.993 1.00 0.00
#> TCGA.BG.A0VZ.01 2 0.000 0.994 0.00 1.00
#> TCGA.EO.A22Y.01 2 0.000 0.994 0.00 1.00
#> TCGA.AX.A3G9.01 1 0.000 0.993 1.00 0.00
#> TCGA.AP.A0LS.01 2 0.000 0.994 0.00 1.00
#> TCGA.D1.A167.01 2 0.000 0.994 0.00 1.00
#> TCGA.DF.A2KU.01 1 0.000 0.993 1.00 0.00
#> TCGA.B5.A1MX.01 1 0.000 0.993 1.00 0.00
#> TCGA.EC.A1NJ.01 2 0.000 0.994 0.00 1.00
#> TCGA.B5.A11J.01 2 0.000 0.994 0.00 1.00
#> TCGA.D1.A17R.01 2 0.000 0.994 0.00 1.00
#> TCGA.D1.A1NY.01 1 0.000 0.993 1.00 0.00
#> TCGA.D1.A174.01 1 0.000 0.993 1.00 0.00
#> TCGA.A5.A2K5.01 1 0.000 0.993 1.00 0.00
#> TCGA.B5.A0JU.01 1 0.000 0.993 1.00 0.00
#> TCGA.AJ.A8CV.01 1 0.000 0.993 1.00 0.00
#> TCGA.BS.A0V4.01 1 0.000 0.993 1.00 0.00
#> TCGA.D1.A1O7.01 2 0.000 0.994 0.00 1.00
#> TCGA.BG.A2L7.01 2 0.000 0.994 0.00 1.00
#> TCGA.D1.A16V.01 2 0.000 0.994 0.00 1.00
#> TCGA.BG.A18B.01 1 0.000 0.993 1.00 0.00
#> TCGA.B5.A11G.01 2 0.000 0.994 0.00 1.00
#> TCGA.AP.A1DV.01 1 0.000 0.993 1.00 0.00
#> TCGA.A5.A0VO.01 2 0.000 0.994 0.00 1.00
#> TCGA.B5.A0JX.01 2 0.000 0.994 0.00 1.00
#> TCGA.D1.A2G5.01 2 0.000 0.994 0.00 1.00
#> TCGA.D1.A0ZQ.01 1 0.000 0.993 1.00 0.00
#> TCGA.EY.A1GK.01 2 0.000 0.994 0.00 1.00
#> TCGA.AX.A1CE.01 1 0.000 0.993 1.00 0.00
#> TCGA.EY.A1GX.01 2 0.000 0.994 0.00 1.00
#> TCGA.AJ.A5DV.01 2 0.000 0.994 0.00 1.00
#> TCGA.B5.A11E.01 2 0.584 0.837 0.14 0.86
#> TCGA.B5.A11R.01 2 0.000 0.994 0.00 1.00
#> TCGA.BG.A187.01 2 0.141 0.975 0.02 0.98
#> TCGA.D1.A163.01 1 0.000 0.993 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EC.A24G.01 1 0.571 0.726 0.68 0.00 0.32
#> TCGA.BG.A2AD.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.EO.A3KX.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.AP.A05O.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.BG.A0MK.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.EY.A1H0.01 3 0.595 0.941 0.00 0.36 0.64
#> TCGA.BK.A13C.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.EY.A1GI.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.D1.A0ZO.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.AX.A1CK.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.EY.A1GL.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.D1.A17U.01 1 0.571 0.726 0.68 0.00 0.32
#> TCGA.AJ.A2QL.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.AP.A1DH.01 1 0.571 0.726 0.68 0.00 0.32
#> TCGA.BG.A0VZ.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.EO.A22Y.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.AX.A3G9.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.AP.A0LS.01 3 0.619 0.857 0.00 0.42 0.58
#> TCGA.D1.A167.01 2 0.334 0.464 0.00 0.88 0.12
#> TCGA.DF.A2KU.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.B5.A1MX.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.EC.A1NJ.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.B5.A11J.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.D1.A17R.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.D1.A1NY.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.D1.A174.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.A5.A2K5.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.B5.A0JU.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.AJ.A8CV.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.BS.A0V4.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.D1.A1O7.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.BG.A2L7.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.D1.A16V.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.BG.A18B.01 1 0.571 0.726 0.68 0.00 0.32
#> TCGA.B5.A11G.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.AP.A1DV.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.A5.A0VO.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.B5.A0JX.01 2 0.480 0.176 0.00 0.78 0.22
#> TCGA.D1.A2G5.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.D1.A0ZQ.01 1 0.000 0.879 1.00 0.00 0.00
#> TCGA.EY.A1GK.01 2 0.000 0.671 0.00 1.00 0.00
#> TCGA.AX.A1CE.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.EY.A1GX.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.AJ.A5DV.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.B5.A11E.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.B5.A11R.01 3 0.571 0.982 0.00 0.32 0.68
#> TCGA.BG.A187.01 2 0.571 0.793 0.00 0.68 0.32
#> TCGA.D1.A163.01 1 0.571 0.726 0.68 0.00 0.32
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EC.A24G.01 4 0.234 0.918 0.1 0.00 0.00 0.90
#> TCGA.BG.A2AD.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.EO.A3KX.01 2 0.201 0.952 0.0 0.92 0.00 0.08
#> TCGA.AP.A05O.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.BG.A0MK.01 2 0.234 0.948 0.0 0.90 0.00 0.10
#> TCGA.EY.A1H0.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.BK.A13C.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.EY.A1GI.01 4 0.000 0.944 0.0 0.00 0.00 1.00
#> TCGA.D1.A0ZO.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.AX.A1CK.01 2 0.234 0.948 0.0 0.90 0.00 0.10
#> TCGA.EY.A1GL.01 4 0.000 0.944 0.0 0.00 0.00 1.00
#> TCGA.D1.A17U.01 4 0.234 0.918 0.1 0.00 0.00 0.90
#> TCGA.AJ.A2QL.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.AP.A1DH.01 4 0.234 0.918 0.1 0.00 0.00 0.90
#> TCGA.BG.A0VZ.01 2 0.201 0.952 0.0 0.92 0.00 0.08
#> TCGA.EO.A22Y.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.AX.A3G9.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.AP.A0LS.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.D1.A167.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.DF.A2KU.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.B5.A1MX.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 3 0.201 0.922 0.0 0.08 0.92 0.00
#> TCGA.B5.A11J.01 2 0.234 0.948 0.0 0.90 0.00 0.10
#> TCGA.D1.A17R.01 2 0.234 0.948 0.0 0.90 0.00 0.10
#> TCGA.D1.A1NY.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.D1.A174.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.A5.A2K5.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.B5.A0JU.01 4 0.000 0.944 0.0 0.00 0.00 1.00
#> TCGA.AJ.A8CV.01 4 0.000 0.944 0.0 0.00 0.00 1.00
#> TCGA.BS.A0V4.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.D1.A1O7.01 2 0.234 0.948 0.0 0.90 0.00 0.10
#> TCGA.BG.A2L7.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.D1.A16V.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.BG.A18B.01 4 0.234 0.918 0.1 0.00 0.00 0.90
#> TCGA.B5.A11G.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.AP.A1DV.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.A5.A0VO.01 2 0.201 0.952 0.0 0.92 0.00 0.08
#> TCGA.B5.A0JX.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.D1.A2G5.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.D1.A0ZQ.01 1 0.000 1.000 1.0 0.00 0.00 0.00
#> TCGA.EY.A1GK.01 2 0.000 0.948 0.0 1.00 0.00 0.00
#> TCGA.AX.A1CE.01 4 0.000 0.944 0.0 0.00 0.00 1.00
#> TCGA.EY.A1GX.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.AJ.A5DV.01 2 0.234 0.948 0.0 0.90 0.00 0.10
#> TCGA.B5.A11E.01 4 0.000 0.944 0.0 0.00 0.00 1.00
#> TCGA.B5.A11R.01 3 0.000 0.991 0.0 0.00 1.00 0.00
#> TCGA.BG.A187.01 4 0.000 0.944 0.0 0.00 0.00 1.00
#> TCGA.D1.A163.01 4 0.234 0.918 0.1 0.00 0.00 0.90
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EC.A24G.01 4 0.0609 0.851 0.00 0.02 0.00 0.98 0.00
#> TCGA.BG.A2AD.01 2 0.4287 0.465 0.00 0.54 0.00 0.00 0.46
#> TCGA.EO.A3KX.01 2 0.4262 0.748 0.00 0.56 0.00 0.00 0.44
#> TCGA.AP.A05O.01 2 0.4287 0.723 0.00 0.54 0.00 0.00 0.46
#> TCGA.BG.A0MK.01 5 0.2020 0.472 0.00 0.10 0.00 0.00 0.90
#> TCGA.EY.A1H0.01 5 0.2929 0.415 0.00 0.18 0.00 0.00 0.82
#> TCGA.BK.A13C.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GI.01 4 0.4676 0.841 0.00 0.12 0.00 0.74 0.14
#> TCGA.D1.A0ZO.01 1 0.4075 0.852 0.78 0.06 0.00 0.16 0.00
#> TCGA.AX.A1CK.01 2 0.3895 0.740 0.00 0.68 0.00 0.00 0.32
#> TCGA.EY.A1GL.01 4 0.5258 0.814 0.00 0.14 0.00 0.68 0.18
#> TCGA.D1.A17U.01 4 0.2012 0.827 0.00 0.06 0.00 0.92 0.02
#> TCGA.AJ.A2QL.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00
#> TCGA.AP.A1DH.01 4 0.1410 0.829 0.00 0.06 0.00 0.94 0.00
#> TCGA.BG.A0VZ.01 2 0.4227 0.754 0.00 0.58 0.00 0.00 0.42
#> TCGA.EO.A22Y.01 3 0.1043 0.967 0.00 0.00 0.96 0.00 0.04
#> TCGA.AX.A3G9.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A0LS.01 2 0.4262 0.696 0.00 0.56 0.00 0.00 0.44
#> TCGA.D1.A167.01 2 0.4302 0.429 0.00 0.52 0.00 0.00 0.48
#> TCGA.DF.A2KU.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MX.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00
#> TCGA.EC.A1NJ.01 3 0.2012 0.933 0.00 0.02 0.92 0.00 0.06
#> TCGA.B5.A11J.01 2 0.3983 0.765 0.00 0.66 0.00 0.00 0.34
#> TCGA.D1.A17R.01 2 0.3983 0.765 0.00 0.66 0.00 0.00 0.34
#> TCGA.D1.A1NY.01 1 0.4075 0.852 0.78 0.06 0.00 0.16 0.00
#> TCGA.D1.A174.01 1 0.0609 0.904 0.98 0.02 0.00 0.00 0.00
#> TCGA.A5.A2K5.01 1 0.4075 0.852 0.78 0.06 0.00 0.16 0.00
#> TCGA.B5.A0JU.01 4 0.4075 0.858 0.00 0.06 0.00 0.78 0.16
#> TCGA.AJ.A8CV.01 4 0.3291 0.862 0.00 0.04 0.00 0.84 0.12
#> TCGA.BS.A0V4.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O7.01 2 0.3983 0.765 0.00 0.66 0.00 0.00 0.34
#> TCGA.BG.A2L7.01 3 0.1043 0.967 0.00 0.00 0.96 0.00 0.04
#> TCGA.D1.A16V.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00
#> TCGA.BG.A18B.01 4 0.1043 0.849 0.00 0.04 0.00 0.96 0.00
#> TCGA.B5.A11G.01 5 0.2929 0.436 0.00 0.18 0.00 0.00 0.82
#> TCGA.AP.A1DV.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A0VO.01 5 0.1043 0.507 0.00 0.04 0.00 0.00 0.96
#> TCGA.B5.A0JX.01 5 0.4307 -0.750 0.00 0.50 0.00 0.00 0.50
#> TCGA.D1.A2G5.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 1 0.4075 0.852 0.78 0.06 0.00 0.16 0.00
#> TCGA.EY.A1GK.01 2 0.4287 0.723 0.00 0.54 0.00 0.00 0.46
#> TCGA.AX.A1CE.01 4 0.4458 0.842 0.00 0.12 0.00 0.76 0.12
#> TCGA.EY.A1GX.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A5DV.01 2 0.4227 0.754 0.00 0.58 0.00 0.00 0.42
#> TCGA.B5.A11E.01 4 0.5083 0.813 0.00 0.16 0.00 0.70 0.14
#> TCGA.B5.A11R.01 3 0.0000 0.982 0.00 0.00 1.00 0.00 0.00
#> TCGA.BG.A187.01 4 0.4872 0.832 0.00 0.12 0.00 0.72 0.16
#> TCGA.D1.A163.01 4 0.2012 0.827 0.00 0.06 0.00 0.92 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EC.A24G.01 4 0.2941 0.725 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.BG.A2AD.01 2 0.5012 -0.030 0.10 0.60 0.00 0.00 0.30 0.00
#> TCGA.EO.A3KX.01 2 0.1480 0.648 0.04 0.94 0.00 0.02 0.00 0.00
#> TCGA.AP.A05O.01 2 0.0547 0.652 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BG.A0MK.01 5 0.7078 0.600 0.14 0.28 0.00 0.14 0.44 0.00
#> TCGA.EY.A1H0.01 5 0.3578 0.599 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.BK.A13C.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 4 0.4179 0.660 0.16 0.02 0.00 0.76 0.06 0.00
#> TCGA.D1.A0ZO.01 6 0.3578 0.744 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.AX.A1CK.01 2 0.4926 0.560 0.12 0.64 0.00 0.00 0.24 0.00
#> TCGA.EY.A1GL.01 4 0.4172 0.622 0.28 0.00 0.00 0.68 0.04 0.00
#> TCGA.D1.A17U.01 4 0.3578 0.701 0.34 0.00 0.00 0.66 0.00 0.00
#> TCGA.AJ.A2QL.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A1DH.01 4 0.3409 0.708 0.30 0.00 0.00 0.70 0.00 0.00
#> TCGA.BG.A0VZ.01 2 0.3103 0.643 0.04 0.86 0.00 0.04 0.06 0.00
#> TCGA.EO.A22Y.01 3 0.2790 0.861 0.02 0.00 0.84 0.00 0.14 0.00
#> TCGA.AX.A3G9.01 6 0.0000 0.843 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AP.A0LS.01 2 0.3711 0.543 0.02 0.72 0.00 0.00 0.26 0.00
#> TCGA.D1.A167.01 2 0.5265 -0.146 0.10 0.50 0.00 0.00 0.40 0.00
#> TCGA.DF.A2KU.01 6 0.0000 0.843 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B5.A1MX.01 6 0.0000 0.843 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EC.A1NJ.01 3 0.3873 0.799 0.02 0.04 0.78 0.00 0.16 0.00
#> TCGA.B5.A11J.01 2 0.3460 0.653 0.02 0.76 0.00 0.00 0.22 0.00
#> TCGA.D1.A17R.01 2 0.3460 0.653 0.02 0.76 0.00 0.00 0.22 0.00
#> TCGA.D1.A1NY.01 6 0.3578 0.744 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.D1.A174.01 6 0.0000 0.843 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A5.A2K5.01 6 0.3578 0.744 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.B5.A0JU.01 4 0.2981 0.708 0.16 0.00 0.00 0.82 0.02 0.00
#> TCGA.AJ.A8CV.01 4 0.1556 0.733 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.BS.A0V4.01 6 0.0000 0.843 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D1.A1O7.01 2 0.2941 0.661 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.BG.A2L7.01 3 0.2790 0.861 0.02 0.00 0.84 0.00 0.14 0.00
#> TCGA.D1.A16V.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 4 0.3499 0.692 0.32 0.00 0.00 0.68 0.00 0.00
#> TCGA.B5.A11G.01 5 0.4609 0.650 0.04 0.42 0.00 0.00 0.54 0.00
#> TCGA.AP.A1DV.01 6 0.0000 0.843 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A5.A0VO.01 5 0.6727 0.696 0.14 0.34 0.00 0.08 0.44 0.00
#> TCGA.B5.A0JX.01 2 0.2094 0.611 0.02 0.90 0.00 0.00 0.08 0.00
#> TCGA.D1.A2G5.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 6 0.3578 0.744 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.EY.A1GK.01 2 0.0547 0.652 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.AX.A1CE.01 4 0.3821 0.669 0.22 0.00 0.00 0.74 0.04 0.00
#> TCGA.EY.A1GX.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A5DV.01 2 0.2725 0.654 0.02 0.88 0.00 0.04 0.06 0.00
#> TCGA.B5.A11E.01 4 0.3950 0.630 0.24 0.00 0.00 0.72 0.04 0.00
#> TCGA.B5.A11R.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A187.01 4 0.4607 0.630 0.18 0.02 0.00 0.72 0.08 0.00
#> TCGA.D1.A163.01 4 0.3578 0.701 0.34 0.00 0.00 0.66 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.EC.A24G.01 4 0.0504 0.3806 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.BG.A2AD.01 7 0.3496 0.5316 0.00 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.EO.A3KX.01 2 0.1928 0.6276 0.08 0.90 0.00 0.00 0.00 0.00 0.02
#> TCGA.AP.A05O.01 2 0.0504 0.6622 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BG.A0MK.01 5 0.6839 0.6695 0.16 0.30 0.00 0.00 0.36 0.00 0.18
#> TCGA.EY.A1H0.01 5 0.6777 0.2437 0.00 0.16 0.32 0.00 0.36 0.00 0.16
#> TCGA.BK.A13C.01 3 0.3358 0.8421 0.00 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.EY.A1GI.01 4 0.4317 -0.3913 0.38 0.02 0.00 0.58 0.02 0.00 0.00
#> TCGA.D1.A0ZO.01 6 0.5668 0.7458 0.10 0.00 0.00 0.12 0.12 0.64 0.02
#> TCGA.AX.A1CK.01 2 0.5775 0.4564 0.12 0.56 0.00 0.00 0.08 0.00 0.24
#> TCGA.EY.A1GL.01 1 0.3459 0.0000 0.60 0.00 0.00 0.40 0.00 0.00 0.00
#> TCGA.D1.A17U.01 4 0.3530 0.4297 0.20 0.00 0.00 0.76 0.02 0.00 0.02
#> TCGA.AJ.A2QL.01 3 0.3358 0.8421 0.00 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.AP.A1DH.01 4 0.3530 0.4297 0.20 0.00 0.00 0.76 0.02 0.00 0.02
#> TCGA.BG.A0VZ.01 2 0.1433 0.6357 0.08 0.92 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22Y.01 3 0.0504 0.6272 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G9.01 6 0.0000 0.8299 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AP.A0LS.01 2 0.5040 0.1841 0.00 0.54 0.36 0.00 0.02 0.00 0.08
#> TCGA.D1.A167.01 7 0.5182 0.5382 0.00 0.24 0.22 0.00 0.00 0.00 0.54
#> TCGA.DF.A2KU.01 6 0.0000 0.8299 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A1MX.01 6 0.0000 0.8299 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EC.A1NJ.01 3 0.0504 0.6272 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.B5.A11J.01 2 0.3965 0.6468 0.10 0.76 0.00 0.00 0.02 0.00 0.12
#> TCGA.D1.A17R.01 2 0.4308 0.6239 0.10 0.72 0.00 0.00 0.02 0.00 0.16
#> TCGA.D1.A1NY.01 6 0.5804 0.7476 0.10 0.00 0.00 0.10 0.12 0.64 0.04
#> TCGA.D1.A174.01 6 0.1718 0.8214 0.04 0.00 0.00 0.00 0.04 0.92 0.00
#> TCGA.A5.A2K5.01 6 0.5668 0.7458 0.10 0.00 0.00 0.12 0.12 0.64 0.02
#> TCGA.B5.A0JU.01 4 0.3867 -0.1446 0.38 0.00 0.00 0.60 0.02 0.00 0.00
#> TCGA.AJ.A8CV.01 4 0.2163 0.2775 0.10 0.00 0.00 0.88 0.02 0.00 0.00
#> TCGA.BS.A0V4.01 6 0.0000 0.8299 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A1O7.01 2 0.3765 0.6500 0.10 0.78 0.00 0.00 0.02 0.00 0.10
#> TCGA.BG.A2L7.01 3 0.0504 0.6272 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.D1.A16V.01 3 0.3358 0.8421 0.00 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.BG.A18B.01 4 0.2569 0.2988 0.02 0.00 0.00 0.84 0.14 0.00 0.00
#> TCGA.B5.A11G.01 5 0.6599 0.6411 0.02 0.34 0.04 0.00 0.36 0.00 0.24
#> TCGA.AP.A1DV.01 6 0.0000 0.8299 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A5.A0VO.01 5 0.6726 0.6907 0.12 0.32 0.00 0.00 0.36 0.00 0.20
#> TCGA.B5.A0JX.01 2 0.3186 0.4573 0.00 0.76 0.22 0.00 0.00 0.00 0.02
#> TCGA.D1.A2G5.01 3 0.3358 0.8421 0.00 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.D1.A0ZQ.01 6 0.5804 0.7476 0.10 0.00 0.00 0.10 0.12 0.64 0.04
#> TCGA.EY.A1GK.01 2 0.0504 0.6622 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AX.A1CE.01 4 0.4266 -0.0971 0.44 0.00 0.00 0.52 0.00 0.00 0.04
#> TCGA.EY.A1GX.01 3 0.3755 0.8357 0.02 0.00 0.64 0.00 0.34 0.00 0.00
#> TCGA.AJ.A5DV.01 2 0.1006 0.6743 0.02 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.B5.A11E.01 4 0.4995 -0.1392 0.46 0.04 0.00 0.46 0.00 0.00 0.04
#> TCGA.B5.A11R.01 3 0.3358 0.8421 0.00 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.BG.A187.01 4 0.4317 -0.3913 0.38 0.02 0.00 0.58 0.02 0.00 0.00
#> TCGA.D1.A163.01 4 0.3530 0.4297 0.20 0.00 0.00 0.76 0.02 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EC.A24G.01 4 0.4069 0.447 0.18 0.00 0.00 0.68 0.00 0.00 0.00 0.14
#> TCGA.BG.A2AD.01 7 0.3589 0.820 0.00 0.16 0.00 0.00 0.10 0.00 0.74 0.00
#> TCGA.EO.A3KX.01 2 0.3808 0.649 0.02 0.66 0.00 0.02 0.30 0.00 0.00 0.00
#> TCGA.AP.A05O.01 2 0.2114 0.760 0.00 0.84 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.BG.A0MK.01 5 0.1741 0.742 0.02 0.04 0.00 0.02 0.92 0.00 0.00 0.00
#> TCGA.EY.A1H0.01 5 0.4758 0.404 0.00 0.02 0.00 0.00 0.60 0.00 0.12 0.26
#> TCGA.BK.A13C.01 3 0.0471 0.833 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 4 0.1741 0.249 0.00 0.02 0.00 0.92 0.00 0.00 0.04 0.02
#> TCGA.D1.A0ZO.01 6 0.4407 0.604 0.04 0.00 0.00 0.02 0.00 0.48 0.00 0.46
#> TCGA.AX.A1CK.01 2 0.5057 0.324 0.16 0.62 0.00 0.00 0.00 0.00 0.06 0.16
#> TCGA.EY.A1GL.01 4 0.5201 -0.354 0.28 0.00 0.00 0.58 0.08 0.00 0.04 0.02
#> TCGA.D1.A17U.01 4 0.6001 0.409 0.30 0.00 0.00 0.38 0.00 0.00 0.06 0.26
#> TCGA.AJ.A2QL.01 3 0.0000 0.838 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A1DH.01 4 0.5958 0.421 0.30 0.00 0.00 0.40 0.00 0.00 0.06 0.24
#> TCGA.BG.A0VZ.01 2 0.3808 0.653 0.02 0.66 0.00 0.02 0.30 0.00 0.00 0.00
#> TCGA.EO.A22Y.01 3 0.4350 0.648 0.00 0.00 0.62 0.00 0.02 0.00 0.06 0.30
#> TCGA.AX.A3G9.01 6 0.0000 0.747 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AP.A0LS.01 2 0.4642 0.395 0.00 0.60 0.00 0.00 0.04 0.00 0.06 0.30
#> TCGA.D1.A167.01 7 0.3663 0.820 0.00 0.10 0.00 0.00 0.06 0.00 0.78 0.06
#> TCGA.DF.A2KU.01 6 0.0000 0.747 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A1MX.01 6 0.0000 0.747 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EC.A1NJ.01 3 0.4350 0.648 0.00 0.00 0.62 0.00 0.02 0.00 0.06 0.30
#> TCGA.B5.A11J.01 2 0.0000 0.739 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17R.01 2 0.0471 0.737 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NY.01 6 0.4533 0.628 0.02 0.00 0.00 0.02 0.00 0.50 0.02 0.44
#> TCGA.D1.A174.01 6 0.1765 0.731 0.00 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.A5.A2K5.01 6 0.4137 0.626 0.02 0.00 0.00 0.02 0.00 0.50 0.00 0.46
#> TCGA.B5.A0JU.01 4 0.4779 0.367 0.28 0.00 0.00 0.60 0.00 0.00 0.08 0.04
#> TCGA.AJ.A8CV.01 4 0.2407 0.368 0.08 0.00 0.00 0.86 0.00 0.00 0.00 0.06
#> TCGA.BS.A0V4.01 6 0.0000 0.747 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A1O7.01 2 0.0000 0.739 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A2L7.01 3 0.4350 0.648 0.00 0.00 0.62 0.00 0.02 0.00 0.06 0.30
#> TCGA.D1.A16V.01 3 0.0000 0.838 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 4 0.3970 0.423 0.08 0.00 0.00 0.72 0.00 0.00 0.02 0.18
#> TCGA.B5.A11G.01 5 0.2020 0.722 0.00 0.02 0.00 0.00 0.90 0.00 0.06 0.02
#> TCGA.AP.A1DV.01 6 0.0000 0.747 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A0VO.01 5 0.1275 0.751 0.02 0.04 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.B5.A0JX.01 2 0.3503 0.689 0.00 0.78 0.00 0.00 0.08 0.00 0.02 0.12
#> TCGA.D1.A2G5.01 3 0.0000 0.838 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A0ZQ.01 6 0.4533 0.628 0.02 0.00 0.00 0.02 0.00 0.50 0.02 0.44
#> TCGA.EY.A1GK.01 2 0.2114 0.760 0.00 0.84 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.AX.A1CE.01 1 0.3570 0.672 0.62 0.00 0.00 0.36 0.00 0.00 0.00 0.02
#> TCGA.EY.A1GX.01 3 0.0941 0.826 0.02 0.00 0.96 0.00 0.00 0.00 0.02 0.00
#> TCGA.AJ.A5DV.01 2 0.2114 0.760 0.00 0.84 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.B5.A11E.01 1 0.4333 0.716 0.62 0.00 0.00 0.26 0.12 0.00 0.00 0.00
#> TCGA.B5.A11R.01 3 0.0000 0.838 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A187.01 4 0.3048 0.162 0.00 0.02 0.00 0.84 0.08 0.00 0.04 0.02
#> TCGA.D1.A163.01 4 0.5958 0.421 0.30 0.00 0.00 0.40 0.00 0.00 0.06 0.24
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: Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02121-leaf , Node02122-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node02341-leaf , Node02342-leaf , Node04111-leaf , Node04112-leaf , Node04311-leaf , Node04312-leaf , Node04313-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0232"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 17 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.990 0.995 0.4823 0.515 0.515
#> 3 3 1.000 1.000 1.000 0.1291 0.941 0.886
#> 4 4 0.926 0.876 0.961 0.2027 0.868 0.710
#> 5 5 0.897 0.831 0.945 0.0465 0.978 0.932
#> 6 6 0.809 0.720 0.921 0.0570 0.993 0.976
#> 7 7 0.713 0.575 0.853 0.0879 0.985 0.950
#> 8 8 0.794 0.578 0.894 0.0440 0.941 0.789
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.BG.A2AD.01 1 0.000 1.000 1.00 0.00
#> TCGA.EO.A3KX.01 1 0.000 1.000 1.00 0.00
#> TCGA.AP.A05O.01 1 0.000 1.000 1.00 0.00
#> TCGA.BG.A0MK.01 2 0.000 0.984 0.00 1.00
#> TCGA.EY.A1H0.01 2 0.000 0.984 0.00 1.00
#> TCGA.AX.A1CK.01 2 0.000 0.984 0.00 1.00
#> TCGA.BG.A0VZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.AP.A0LS.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A167.01 1 0.000 1.000 1.00 0.00
#> TCGA.B5.A11J.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A17R.01 2 0.402 0.913 0.08 0.92
#> TCGA.D1.A1O7.01 1 0.000 1.000 1.00 0.00
#> TCGA.B5.A11G.01 2 0.000 0.984 0.00 1.00
#> TCGA.A5.A0VO.01 2 0.000 0.984 0.00 1.00
#> TCGA.B5.A0JX.01 1 0.000 1.000 1.00 0.00
#> TCGA.EY.A1GK.01 1 0.000 1.000 1.00 0.00
#> TCGA.AJ.A5DV.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.BG.A2AD.01 1 0 1 1 0 0
#> TCGA.EO.A3KX.01 1 0 1 1 0 0
#> TCGA.AP.A05O.01 1 0 1 1 0 0
#> TCGA.BG.A0MK.01 2 0 1 0 1 0
#> TCGA.EY.A1H0.01 2 0 1 0 1 0
#> TCGA.AX.A1CK.01 3 0 1 0 0 1
#> TCGA.BG.A0VZ.01 1 0 1 1 0 0
#> TCGA.AP.A0LS.01 1 0 1 1 0 0
#> TCGA.D1.A167.01 1 0 1 1 0 0
#> TCGA.B5.A11J.01 1 0 1 1 0 0
#> TCGA.D1.A17R.01 3 0 1 0 0 1
#> TCGA.D1.A1O7.01 1 0 1 1 0 0
#> TCGA.B5.A11G.01 2 0 1 0 1 0
#> TCGA.A5.A0VO.01 2 0 1 0 1 0
#> TCGA.B5.A0JX.01 1 0 1 1 0 0
#> TCGA.EY.A1GK.01 1 0 1 1 0 0
#> TCGA.AJ.A5DV.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.BG.A2AD.01 4 0.0000 1.0000 0.00 0 0.00 1.00
#> TCGA.EO.A3KX.01 1 0.1637 0.9397 0.94 0 0.00 0.06
#> TCGA.AP.A05O.01 1 0.1637 0.9379 0.94 0 0.00 0.06
#> TCGA.BG.A0MK.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.EY.A1H0.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.AX.A1CK.01 3 0.0000 0.1467 0.00 0 1.00 0.00
#> TCGA.BG.A0VZ.01 1 0.0000 0.9708 1.00 0 0.00 0.00
#> TCGA.AP.A0LS.01 1 0.0000 0.9708 1.00 0 0.00 0.00
#> TCGA.D1.A167.01 4 0.0000 1.0000 0.00 0 0.00 1.00
#> TCGA.B5.A11J.01 1 0.0000 0.9708 1.00 0 0.00 0.00
#> TCGA.D1.A17R.01 3 0.4994 0.0955 0.48 0 0.52 0.00
#> TCGA.D1.A1O7.01 1 0.0000 0.9708 1.00 0 0.00 0.00
#> TCGA.B5.A11G.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.A5.A0VO.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.B5.A0JX.01 1 0.1211 0.9547 0.96 0 0.00 0.04
#> TCGA.EY.A1GK.01 1 0.0000 0.9708 1.00 0 0.00 0.00
#> TCGA.AJ.A5DV.01 1 0.0707 0.9656 0.98 0 0.00 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BG.A2AD.01 4 0.0000 1.000 0.00 0.00 0.0 1.00 0.00
#> TCGA.EO.A3KX.01 1 0.0000 0.991 1.00 0.00 0.0 0.00 0.00
#> TCGA.AP.A05O.01 1 0.0609 0.978 0.98 0.00 0.0 0.02 0.00
#> TCGA.BG.A0MK.01 2 0.0000 0.809 0.00 1.00 0.0 0.00 0.00
#> TCGA.EY.A1H0.01 2 0.3561 0.643 0.00 0.74 0.0 0.00 0.26
#> TCGA.AX.A1CK.01 3 0.0000 0.466 0.00 0.00 1.0 0.00 0.00
#> TCGA.BG.A0VZ.01 1 0.0609 0.977 0.98 0.00 0.0 0.00 0.02
#> TCGA.AP.A0LS.01 1 0.0000 0.991 1.00 0.00 0.0 0.00 0.00
#> TCGA.D1.A167.01 4 0.0000 1.000 0.00 0.00 0.0 1.00 0.00
#> TCGA.B5.A11J.01 1 0.0000 0.991 1.00 0.00 0.0 0.00 0.00
#> TCGA.D1.A17R.01 3 0.4527 0.516 0.26 0.00 0.7 0.00 0.04
#> TCGA.D1.A1O7.01 1 0.0000 0.991 1.00 0.00 0.0 0.00 0.00
#> TCGA.B5.A11G.01 5 0.3895 0.000 0.00 0.32 0.0 0.00 0.68
#> TCGA.A5.A0VO.01 2 0.0000 0.809 0.00 1.00 0.0 0.00 0.00
#> TCGA.B5.A0JX.01 1 0.0609 0.978 0.98 0.00 0.0 0.02 0.00
#> TCGA.EY.A1GK.01 1 0.0000 0.991 1.00 0.00 0.0 0.00 0.00
#> TCGA.AJ.A5DV.01 1 0.0000 0.991 1.00 0.00 0.0 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BG.A2AD.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KX.01 1 0.2190 0.888 0.90 0.00 0.00 0.06 0.00 0.04
#> TCGA.AP.A05O.01 1 0.1480 0.914 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.BG.A0MK.01 2 0.3076 0.796 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.EY.A1H0.01 2 0.1556 0.609 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.AX.A1CK.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0VZ.01 1 0.2941 0.725 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.AP.A0LS.01 1 0.0547 0.923 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D1.A167.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11J.01 1 0.1267 0.899 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.D1.A17R.01 6 0.4004 0.000 0.12 0.00 0.12 0.00 0.00 0.76
#> TCGA.D1.A1O7.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11G.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A5.A0VO.01 2 0.3076 0.796 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.B5.A0JX.01 1 0.1480 0.914 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.EY.A1GK.01 1 0.0547 0.923 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AJ.A5DV.01 1 0.0000 0.926 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.BG.A2AD.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3KX.01 1 0.3000 0.7484 0.86 0.00 0.02 0.06 0.00 0.02 0.04
#> TCGA.AP.A05O.01 1 0.2159 0.7607 0.90 0.00 0.02 0.00 0.02 0.00 0.06
#> TCGA.BG.A0MK.01 2 0.0863 0.8937 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EY.A1H0.01 7 0.3139 0.0000 0.00 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.AX.A1CK.01 3 0.1671 0.0000 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.BG.A0VZ.01 1 0.6391 0.0152 0.40 0.02 0.08 0.00 0.40 0.10 0.00
#> TCGA.AP.A0LS.01 1 0.3404 0.7520 0.82 0.00 0.00 0.00 0.08 0.06 0.04
#> TCGA.D1.A167.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11J.01 1 0.4937 0.6469 0.68 0.00 0.00 0.00 0.12 0.14 0.06
#> TCGA.D1.A17R.01 6 0.0504 0.0000 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.D1.A1O7.01 1 0.1006 0.7799 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.B5.A11G.01 5 0.5190 0.0000 0.00 0.30 0.00 0.00 0.52 0.00 0.18
#> TCGA.A5.A0VO.01 2 0.1006 0.8950 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.B5.A0JX.01 1 0.2159 0.7607 0.90 0.00 0.02 0.00 0.02 0.00 0.06
#> TCGA.EY.A1GK.01 1 0.3656 0.7419 0.80 0.00 0.00 0.00 0.08 0.08 0.04
#> TCGA.AJ.A5DV.01 1 0.1505 0.7726 0.94 0.00 0.02 0.00 0.02 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BG.A2AD.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3KX.01 1 0.3903 0.719 0.78 0.00 0.00 0.08 0.02 0.00 0.06 0.06
#> TCGA.AP.A05O.01 1 0.1741 0.797 0.92 0.00 0.00 0.02 0.00 0.00 0.02 0.04
#> TCGA.BG.A0MK.01 2 0.1804 0.880 0.00 0.90 0.00 0.00 0.02 0.00 0.08 0.00
#> TCGA.EY.A1H0.01 7 0.2267 0.000 0.00 0.18 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.AX.A1CK.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VZ.01 8 0.1275 0.000 0.04 0.00 0.00 0.00 0.00 0.02 0.00 0.94
#> TCGA.AP.A0LS.01 1 0.4405 0.744 0.72 0.00 0.00 0.00 0.04 0.04 0.16 0.04
#> TCGA.D1.A167.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11J.01 1 0.5599 0.635 0.62 0.00 0.00 0.00 0.04 0.12 0.12 0.10
#> TCGA.D1.A17R.01 6 0.0808 0.000 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.D1.A1O7.01 1 0.0941 0.814 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.B5.A11G.01 5 0.1091 0.000 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.A5.A0VO.01 2 0.0000 0.884 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A0JX.01 1 0.2071 0.788 0.90 0.00 0.00 0.04 0.00 0.00 0.02 0.04
#> TCGA.EY.A1GK.01 1 0.3847 0.757 0.78 0.00 0.00 0.00 0.02 0.06 0.10 0.04
#> TCGA.AJ.A5DV.01 1 0.0808 0.813 0.96 0.00 0.00 0.00 0.00 0.00 0.04 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: Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02121-leaf , Node02122-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node02341-leaf , Node02342-leaf , Node04111-leaf , Node04112-leaf , Node04311-leaf , Node04312-leaf , Node04313-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0234"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 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 0.3037 0.697 0.697
#> 3 3 0.561 0.709 0.818 0.8622 0.636 0.478
#> 4 4 0.864 0.870 0.947 0.2245 0.803 0.519
#> 5 5 0.758 0.756 0.863 0.1599 0.879 0.579
#> 6 6 0.818 0.668 0.840 0.0573 1.000 1.000
#> 7 7 0.909 0.646 0.888 0.0517 0.924 0.545
#> 8 8 0.894 0.573 0.893 0.0369 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
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.EC.A24G.01 1 0 1 1 0
#> TCGA.EY.A1GI.01 1 0 1 1 0
#> TCGA.EY.A1GL.01 1 0 1 1 0
#> TCGA.D1.A17U.01 1 0 1 1 0
#> TCGA.AP.A1DH.01 1 0 1 1 0
#> TCGA.B5.A0JU.01 1 0 1 1 0
#> TCGA.AJ.A8CV.01 1 0 1 1 0
#> TCGA.BG.A18B.01 1 0 1 1 0
#> TCGA.AX.A1CE.01 2 0 1 0 1
#> TCGA.B5.A11E.01 2 0 1 0 1
#> TCGA.BG.A187.01 1 0 1 1 0
#> TCGA.D1.A163.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EC.A24G.01 1 0.5835 0.877 0.66 0.00 0.34
#> TCGA.EY.A1GI.01 3 0.6302 -0.560 0.48 0.00 0.52
#> TCGA.EY.A1GL.01 1 0.0892 0.458 0.98 0.00 0.02
#> TCGA.D1.A17U.01 1 0.5835 0.877 0.66 0.00 0.34
#> TCGA.AP.A1DH.01 1 0.5835 0.877 0.66 0.00 0.34
#> TCGA.B5.A0JU.01 3 0.0000 0.749 0.00 0.00 1.00
#> TCGA.AJ.A8CV.01 1 0.5835 0.877 0.66 0.00 0.34
#> TCGA.BG.A18B.01 3 0.0000 0.749 0.00 0.00 1.00
#> TCGA.AX.A1CE.01 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.B5.A11E.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.BG.A187.01 3 0.0000 0.749 0.00 0.00 1.00
#> TCGA.D1.A163.01 1 0.5835 0.877 0.66 0.00 0.34
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EC.A24G.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 1 0.201 0.890 0.92 0.00 0.08 0.00
#> TCGA.EY.A1GL.01 4 0.234 0.000 0.10 0.00 0.00 0.90
#> TCGA.D1.A17U.01 1 0.121 0.951 0.96 0.00 0.00 0.04
#> TCGA.AP.A1DH.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.B5.A0JU.01 3 0.201 1.000 0.08 0.00 0.92 0.00
#> TCGA.AJ.A8CV.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 3 0.201 1.000 0.08 0.00 0.92 0.00
#> TCGA.AX.A1CE.01 2 0.361 0.881 0.00 0.86 0.08 0.06
#> TCGA.B5.A11E.01 2 0.000 0.881 0.00 1.00 0.00 0.00
#> TCGA.BG.A187.01 3 0.201 1.000 0.08 0.00 0.92 0.00
#> TCGA.D1.A163.01 1 0.121 0.951 0.96 0.00 0.00 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EC.A24G.01 1 0.0000 0.788 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 1 0.5130 0.462 0.68 0.00 0.22 0.00 0.10
#> TCGA.EY.A1GL.01 4 0.0609 0.000 0.02 0.00 0.00 0.98 0.00
#> TCGA.D1.A17U.01 5 0.4287 1.000 0.46 0.00 0.00 0.00 0.54
#> TCGA.AP.A1DH.01 1 0.0000 0.788 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A0JU.01 3 0.3274 0.755 0.00 0.00 0.78 0.00 0.22
#> TCGA.AJ.A8CV.01 1 0.0000 0.788 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A18B.01 3 0.0000 0.885 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A1CE.01 2 0.3106 0.862 0.00 0.84 0.00 0.02 0.14
#> TCGA.B5.A11E.01 2 0.0000 0.862 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A187.01 3 0.0000 0.885 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A163.01 5 0.4287 1.000 0.46 0.00 0.00 0.00 0.54
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EC.A24G.01 1 0.000 0.786 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EY.A1GI.01 1 0.510 0.349 0.50 0.00 0.08 0 0.00 0.42
#> TCGA.EY.A1GL.01 4 0.000 0.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.D1.A17U.01 5 0.331 1.000 0.28 0.00 0.00 0 0.72 0.00
#> TCGA.AP.A1DH.01 1 0.000 0.786 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.B5.A0JU.01 3 0.588 0.424 0.00 0.00 0.48 0 0.26 0.26
#> TCGA.AJ.A8CV.01 1 0.000 0.786 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.BG.A18B.01 3 0.000 0.749 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.AX.A1CE.01 2 0.400 0.692 0.00 0.66 0.00 0 0.02 0.32
#> TCGA.B5.A11E.01 2 0.000 0.692 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.BG.A187.01 3 0.000 0.749 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.D1.A163.01 5 0.331 1.000 0.28 0.00 0.00 0 0.72 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EC.A24G.01 1 0.0000 0.952 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.EY.A1GI.01 6 0.2945 0.000 0.26 0.00 0.00 0 0.00 0.74 0.00
#> TCGA.EY.A1GL.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D1.A17U.01 5 0.2313 0.950 0.06 0.00 0.00 0 0.88 0.00 0.06
#> TCGA.AP.A1DH.01 1 0.1433 0.901 0.92 0.00 0.00 0 0.00 0.00 0.08
#> TCGA.B5.A0JU.01 7 0.3221 0.000 0.00 0.00 0.32 0 0.00 0.00 0.68
#> TCGA.AJ.A8CV.01 1 0.0000 0.952 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.BG.A18B.01 3 0.0863 0.951 0.00 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.AX.A1CE.01 2 0.0000 0.570 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B5.A11E.01 2 0.5498 0.570 0.00 0.54 0.00 0 0.02 0.26 0.18
#> TCGA.BG.A187.01 3 0.0000 0.951 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.D1.A163.01 5 0.1166 0.950 0.06 0.00 0.00 0 0.94 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.EC.A24G.01 1 0.000 0.880 1.00 0.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.EY.A1GI.01 6 0.000 0.000 0.00 0.00 0.00 0 0.00 1 0.00 0.00
#> TCGA.EY.A1GL.01 4 0.000 0.000 0.00 0.00 0.00 1 0.00 0 0.00 0.00
#> TCGA.D1.A17U.01 5 0.301 0.712 0.00 0.32 0.00 0 0.68 0 0.00 0.00
#> TCGA.AP.A1DH.01 1 0.343 0.744 0.74 0.20 0.00 0 0.00 0 0.06 0.00
#> TCGA.B5.A0JU.01 7 0.195 0.000 0.00 0.00 0.14 0 0.00 0 0.86 0.00
#> TCGA.AJ.A8CV.01 1 0.000 0.880 1.00 0.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.BG.A18B.01 3 0.000 0.860 0.00 0.00 1.00 0 0.00 0 0.00 0.00
#> TCGA.AX.A1CE.01 8 0.425 0.611 0.00 0.34 0.00 0 0.00 0 0.08 0.58
#> TCGA.B5.A11E.01 8 0.000 0.611 0.00 0.00 0.00 0 0.00 0 0.00 1.00
#> TCGA.BG.A187.01 3 0.195 0.860 0.00 0.14 0.86 0 0.00 0 0.00 0.00
#> TCGA.D1.A163.01 5 0.000 0.712 0.00 0.00 0.00 0 1.00 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["024"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 40 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.975 0.990 0.4178 0.591 0.591
#> 3 3 1.000 0.947 0.982 0.5525 0.731 0.555
#> 4 4 1.000 1.000 1.000 0.1803 0.818 0.525
#> 5 5 0.933 0.942 0.955 0.0426 0.973 0.885
#> 6 6 0.856 0.843 0.886 0.0339 1.000 1.000
#> 7 7 0.799 0.676 0.795 0.0334 0.962 0.815
#> 8 8 0.811 0.599 0.788 0.0163 0.936 0.660
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AX.A2H7.01 2 0.000 0.986 0.00 1.00
#> TCGA.AX.A3FW.01 2 0.000 0.986 0.00 1.00
#> TCGA.B5.A11L.01 2 0.958 0.387 0.38 0.62
#> TCGA.D1.A17T.01 2 0.000 0.986 0.00 1.00
#> TCGA.B5.A11W.01 2 0.000 0.986 0.00 1.00
#> TCGA.PG.A916.01 2 0.000 0.986 0.00 1.00
#> TCGA.B5.A11S.01 2 0.000 0.986 0.00 1.00
#> TCGA.BG.A186.01 2 0.000 0.986 0.00 1.00
#> TCGA.EY.A1GW.01 2 0.000 0.986 0.00 1.00
#> TCGA.EO.A3AY.01 1 0.000 1.000 1.00 0.00
#> TCGA.BG.A0VW.01 2 0.000 0.986 0.00 1.00
#> TCGA.AJ.A3BK.01 2 0.000 0.986 0.00 1.00
#> TCGA.D1.A3DA.01 1 0.000 1.000 1.00 0.00
#> TCGA.EY.A549.01 2 0.000 0.986 0.00 1.00
#> TCGA.BK.A6W3.01 2 0.000 0.986 0.00 1.00
#> TCGA.PG.A917.01 2 0.000 0.986 0.00 1.00
#> TCGA.D1.A15W.01 2 0.000 0.986 0.00 1.00
#> TCGA.AX.A2HD.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A17L.01 2 0.000 0.986 0.00 1.00
#> TCGA.AX.A3G8.01 1 0.000 1.000 1.00 0.00
#> TCGA.EO.A22X.01 1 0.000 1.000 1.00 0.00
#> TCGA.EY.A1GH.01 2 0.000 0.986 0.00 1.00
#> TCGA.BK.A56F.01 2 0.000 0.986 0.00 1.00
#> TCGA.D1.A165.01 2 0.000 0.986 0.00 1.00
#> TCGA.AX.A2HH.01 1 0.000 1.000 1.00 0.00
#> TCGA.E6.A1LX.01 1 0.000 1.000 1.00 0.00
#> TCGA.DI.A1BY.01 2 0.000 0.986 0.00 1.00
#> TCGA.SL.A6JA.01 1 0.000 1.000 1.00 0.00
#> TCGA.EY.A547.01 2 0.000 0.986 0.00 1.00
#> TCGA.A5.A1OK.01 2 0.000 0.986 0.00 1.00
#> TCGA.B5.A1MZ.01 2 0.000 0.986 0.00 1.00
#> TCGA.AJ.A3NC.01 2 0.000 0.986 0.00 1.00
#> TCGA.B5.A11P.01 2 0.000 0.986 0.00 1.00
#> TCGA.AX.A1C9.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A0ZR.01 2 0.000 0.986 0.00 1.00
#> TCGA.BG.A0VT.01 2 0.000 0.986 0.00 1.00
#> TCGA.B5.A3FH.01 2 0.000 0.986 0.00 1.00
#> TCGA.AX.A2HJ.01 2 0.000 0.986 0.00 1.00
#> TCGA.EY.A1G8.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A16Y.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.AX.A2H7.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.AX.A3FW.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.B5.A11L.01 1 0.630 0.0757 0.52 0.48 0.00
#> TCGA.D1.A17T.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.B5.A11W.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.PG.A916.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.B5.A11S.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.BG.A186.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.EY.A1GW.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.EO.A3AY.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.BG.A0VW.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.AJ.A3BK.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.D1.A3DA.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.EY.A549.01 2 0.522 0.6459 0.00 0.74 0.26
#> TCGA.BK.A6W3.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.PG.A917.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.D1.A15W.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.AX.A2HD.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.D1.A17L.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.AX.A3G8.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.EO.A22X.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.EY.A1GH.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.BK.A56F.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.D1.A165.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.AX.A2HH.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.E6.A1LX.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.DI.A1BY.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.SL.A6JA.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.EY.A547.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.A5.A1OK.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.B5.A1MZ.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.AJ.A3NC.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.B5.A11P.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.AX.A1C9.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.D1.A0ZR.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.BG.A0VT.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.B5.A3FH.01 2 0.000 0.9852 0.00 1.00 0.00
#> TCGA.AX.A2HJ.01 3 0.000 1.0000 0.00 0.00 1.00
#> TCGA.EY.A1G8.01 1 0.000 0.9467 1.00 0.00 0.00
#> TCGA.D1.A16Y.01 1 0.000 0.9467 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.AX.A2H7.01 3 0 1 0 0 1 0
#> TCGA.AX.A3FW.01 3 0 1 0 0 1 0
#> TCGA.B5.A11L.01 4 0 1 0 0 0 1
#> TCGA.D1.A17T.01 4 0 1 0 0 0 1
#> TCGA.B5.A11W.01 4 0 1 0 0 0 1
#> TCGA.PG.A916.01 4 0 1 0 0 0 1
#> TCGA.B5.A11S.01 2 0 1 0 1 0 0
#> TCGA.BG.A186.01 2 0 1 0 1 0 0
#> TCGA.EY.A1GW.01 3 0 1 0 0 1 0
#> TCGA.EO.A3AY.01 4 0 1 0 0 0 1
#> TCGA.BG.A0VW.01 4 0 1 0 0 0 1
#> TCGA.AJ.A3BK.01 3 0 1 0 0 1 0
#> TCGA.D1.A3DA.01 1 0 1 1 0 0 0
#> TCGA.EY.A549.01 2 0 1 0 1 0 0
#> TCGA.BK.A6W3.01 4 0 1 0 0 0 1
#> TCGA.PG.A917.01 3 0 1 0 0 1 0
#> TCGA.D1.A15W.01 4 0 1 0 0 0 1
#> TCGA.AX.A2HD.01 1 0 1 1 0 0 0
#> TCGA.D1.A17L.01 2 0 1 0 1 0 0
#> TCGA.AX.A3G8.01 1 0 1 1 0 0 0
#> TCGA.EO.A22X.01 1 0 1 1 0 0 0
#> TCGA.EY.A1GH.01 4 0 1 0 0 0 1
#> TCGA.BK.A56F.01 4 0 1 0 0 0 1
#> TCGA.D1.A165.01 2 0 1 0 1 0 0
#> TCGA.AX.A2HH.01 1 0 1 1 0 0 0
#> TCGA.E6.A1LX.01 1 0 1 1 0 0 0
#> TCGA.DI.A1BY.01 4 0 1 0 0 0 1
#> TCGA.SL.A6JA.01 1 0 1 1 0 0 0
#> TCGA.EY.A547.01 3 0 1 0 0 1 0
#> TCGA.A5.A1OK.01 2 0 1 0 1 0 0
#> TCGA.B5.A1MZ.01 2 0 1 0 1 0 0
#> TCGA.AJ.A3NC.01 2 0 1 0 1 0 0
#> TCGA.B5.A11P.01 3 0 1 0 0 1 0
#> TCGA.AX.A1C9.01 1 0 1 1 0 0 0
#> TCGA.D1.A0ZR.01 2 0 1 0 1 0 0
#> TCGA.BG.A0VT.01 2 0 1 0 1 0 0
#> TCGA.B5.A3FH.01 2 0 1 0 1 0 0
#> TCGA.AX.A2HJ.01 3 0 1 0 0 1 0
#> TCGA.EY.A1G8.01 1 0 1 1 0 0 0
#> TCGA.D1.A16Y.01 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.AX.A2H7.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FW.01 3 0.0609 0.989 0.00 0.00 0.98 0.00 0.02
#> TCGA.B5.A11L.01 4 0.1732 0.921 0.00 0.00 0.00 0.92 0.08
#> TCGA.D1.A17T.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A11W.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00
#> TCGA.PG.A916.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A186.01 2 0.1410 0.925 0.00 0.94 0.00 0.00 0.06
#> TCGA.EY.A1GW.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00
#> TCGA.EO.A3AY.01 4 0.3110 0.876 0.06 0.00 0.00 0.86 0.08
#> TCGA.BG.A0VW.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3BK.01 3 0.0609 0.989 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A3DA.01 1 0.0609 0.980 0.98 0.00 0.00 0.00 0.02
#> TCGA.EY.A549.01 2 0.1732 0.920 0.00 0.92 0.00 0.00 0.08
#> TCGA.BK.A6W3.01 4 0.2732 0.849 0.00 0.00 0.00 0.84 0.16
#> TCGA.PG.A917.01 3 0.0609 0.989 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A15W.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A2HD.01 1 0.1043 0.936 0.96 0.00 0.00 0.00 0.04
#> TCGA.D1.A17L.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3G8.01 1 0.0609 0.980 0.98 0.00 0.00 0.00 0.02
#> TCGA.EO.A22X.01 1 0.0609 0.980 0.98 0.00 0.00 0.00 0.02
#> TCGA.EY.A1GH.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00
#> TCGA.BK.A56F.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A165.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HH.01 1 0.0609 0.980 0.98 0.00 0.00 0.00 0.02
#> TCGA.E6.A1LX.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A1BY.01 4 0.1216 0.938 0.00 0.00 0.02 0.96 0.02
#> TCGA.SL.A6JA.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A547.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A1OK.01 2 0.2280 0.903 0.00 0.88 0.00 0.00 0.12
#> TCGA.B5.A1MZ.01 2 0.3109 0.838 0.00 0.80 0.00 0.00 0.20
#> TCGA.AJ.A3NC.01 2 0.3561 0.750 0.00 0.74 0.00 0.00 0.26
#> TCGA.B5.A11P.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A1C9.01 5 0.2020 0.929 0.10 0.00 0.00 0.00 0.90
#> TCGA.D1.A0ZR.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0VT.01 2 0.1732 0.921 0.00 0.92 0.00 0.00 0.08
#> TCGA.B5.A3FH.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HJ.01 3 0.0609 0.989 0.00 0.00 0.98 0.00 0.02
#> TCGA.EY.A1G8.01 5 0.3109 0.884 0.20 0.00 0.00 0.00 0.80
#> TCGA.D1.A16Y.01 5 0.2280 0.938 0.12 0.00 0.00 0.00 0.88
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AX.A2H7.01 3 0.1814 0.895 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AX.A3FW.01 3 0.0547 0.944 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A11L.01 4 0.2260 0.835 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.D1.A17T.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11W.01 4 0.1267 0.880 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.PG.A916.01 4 0.2190 0.848 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.B5.A11S.01 2 0.0000 0.834 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A186.01 2 0.3309 0.806 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.EY.A1GW.01 3 0.0000 0.945 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A3AY.01 4 0.5087 0.447 0.04 0.00 0.00 0.52 0.02 0.42
#> TCGA.BG.A0VW.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3BK.01 3 0.0937 0.940 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.D1.A3DA.01 1 0.0547 0.854 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EY.A549.01 2 0.3797 0.732 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.BK.A6W3.01 4 0.4680 0.676 0.00 0.00 0.00 0.68 0.12 0.20
#> TCGA.PG.A917.01 3 0.3076 0.798 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.D1.A15W.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A2HD.01 1 0.3409 0.766 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.D1.A17L.01 2 0.0547 0.835 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AX.A3G8.01 1 0.0547 0.854 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EO.A22X.01 1 0.0547 0.854 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EY.A1GH.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BK.A56F.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A165.01 2 0.0937 0.819 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.AX.A2HH.01 1 0.0547 0.854 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E6.A1LX.01 1 0.3198 0.793 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.DI.A1BY.01 4 0.1267 0.871 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.SL.A6JA.01 1 0.3076 0.802 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.EY.A547.01 3 0.0000 0.945 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A5.A1OK.01 2 0.4067 0.798 0.00 0.70 0.00 0.00 0.04 0.26
#> TCGA.B5.A1MZ.01 2 0.3928 0.803 0.00 0.76 0.00 0.00 0.08 0.16
#> TCGA.AJ.A3NC.01 2 0.4094 0.730 0.00 0.74 0.00 0.00 0.18 0.08
#> TCGA.B5.A11P.01 3 0.0000 0.945 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A1C9.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A0ZR.01 2 0.0547 0.835 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BG.A0VT.01 2 0.3076 0.820 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.B5.A3FH.01 2 0.2454 0.804 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.AX.A2HJ.01 3 0.0937 0.940 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EY.A1G8.01 5 0.2048 0.870 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.D1.A16Y.01 5 0.0547 0.933 0.02 0.00 0.00 0.00 0.98 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AX.A2H7.01 3 0.5852 0.584 0.00 0.16 0.58 0.00 0.14 0.00 0.12
#> TCGA.AX.A3FW.01 3 0.2163 0.794 0.00 0.00 0.88 0.00 0.10 0.02 0.00
#> TCGA.B5.A11L.01 4 0.3388 0.700 0.00 0.00 0.00 0.76 0.20 0.00 0.04
#> TCGA.D1.A17T.01 4 0.0504 0.808 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.B5.A11W.01 4 0.0863 0.805 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.PG.A916.01 4 0.5347 0.581 0.00 0.22 0.02 0.62 0.12 0.02 0.00
#> TCGA.B5.A11S.01 2 0.2832 0.685 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.BG.A186.01 2 0.4705 -0.222 0.00 0.48 0.00 0.00 0.08 0.00 0.44
#> TCGA.EY.A1GW.01 3 0.0000 0.811 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AY.01 4 0.4701 0.440 0.02 0.00 0.00 0.50 0.44 0.00 0.04
#> TCGA.BG.A0VW.01 4 0.0000 0.809 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 3 0.3055 0.780 0.00 0.00 0.82 0.00 0.14 0.02 0.02
#> TCGA.D1.A3DA.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A549.01 7 0.5282 0.105 0.00 0.34 0.00 0.00 0.18 0.00 0.48
#> TCGA.BK.A6W3.01 4 0.4939 0.615 0.00 0.00 0.00 0.64 0.20 0.02 0.14
#> TCGA.PG.A917.01 3 0.6707 0.431 0.00 0.12 0.38 0.00 0.30 0.00 0.20
#> TCGA.D1.A15W.01 4 0.0863 0.805 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.AX.A2HD.01 1 0.3294 0.742 0.66 0.00 0.00 0.00 0.34 0.00 0.00
#> TCGA.D1.A17L.01 2 0.2832 0.685 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.AX.A3G8.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22X.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 4 0.0000 0.809 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BK.A56F.01 4 0.1664 0.794 0.00 0.06 0.00 0.92 0.02 0.00 0.00
#> TCGA.D1.A165.01 2 0.2708 0.675 0.00 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.AX.A2HH.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1LX.01 1 0.2945 0.802 0.74 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.DI.A1BY.01 4 0.5686 0.579 0.00 0.06 0.12 0.62 0.18 0.02 0.00
#> TCGA.SL.A6JA.01 1 0.2572 0.829 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.EY.A547.01 3 0.0000 0.811 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A1OK.01 7 0.3617 0.569 0.00 0.16 0.00 0.00 0.00 0.08 0.76
#> TCGA.B5.A1MZ.01 7 0.4963 0.543 0.00 0.18 0.00 0.02 0.00 0.16 0.64
#> TCGA.AJ.A3NC.01 7 0.5164 0.383 0.00 0.26 0.00 0.00 0.00 0.20 0.54
#> TCGA.B5.A11P.01 3 0.1363 0.805 0.00 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.AX.A1C9.01 6 0.0863 0.884 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.D1.A0ZR.01 2 0.2945 0.662 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.BG.A0VT.01 7 0.3417 0.456 0.00 0.26 0.00 0.00 0.00 0.02 0.72
#> TCGA.B5.A3FH.01 2 0.1363 0.422 0.00 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.AX.A2HJ.01 3 0.2278 0.807 0.00 0.00 0.88 0.00 0.08 0.00 0.04
#> TCGA.EY.A1G8.01 6 0.2376 0.842 0.12 0.00 0.00 0.00 0.02 0.86 0.00
#> TCGA.D1.A16Y.01 6 0.0863 0.902 0.04 0.00 0.00 0.00 0.00 0.96 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.AX.A2H7.01 8 0.4213 0.6532 0.00 0.00 0.18 0.00 0.00 0.00 0.16 0.66
#> TCGA.AX.A3FW.01 8 0.1947 0.8157 0.00 0.00 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.B5.A11L.01 4 0.3272 0.2637 0.00 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.D1.A17T.01 4 0.0471 0.8018 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.B5.A11W.01 4 0.1563 0.7667 0.00 0.00 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.PG.A916.01 4 0.3873 0.5743 0.00 0.06 0.20 0.72 0.02 0.00 0.00 0.00
#> TCGA.B5.A11S.01 2 0.0000 0.6335 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A186.01 7 0.3193 0.5792 0.00 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.EY.A1GW.01 8 0.0000 0.8212 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EO.A3AY.01 5 0.2938 0.1571 0.00 0.00 0.00 0.30 0.70 0.00 0.00 0.00
#> TCGA.BG.A0VW.01 4 0.1341 0.7748 0.00 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.AJ.A3BK.01 8 0.2267 0.8085 0.00 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.D1.A3DA.01 1 0.0000 0.8236 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A549.01 7 0.2114 0.5744 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.BK.A6W3.01 5 0.6615 0.0957 0.00 0.00 0.16 0.26 0.44 0.08 0.06 0.00
#> TCGA.PG.A917.01 8 0.5211 0.4570 0.00 0.00 0.26 0.00 0.00 0.00 0.34 0.40
#> TCGA.D1.A15W.01 4 0.0000 0.8010 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HD.01 5 0.4803 -0.4514 0.44 0.00 0.08 0.00 0.46 0.00 0.02 0.00
#> TCGA.D1.A17L.01 2 0.0000 0.6335 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G8.01 1 0.0000 0.8236 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22X.01 1 0.0000 0.8236 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GH.01 4 0.0471 0.8018 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BK.A56F.01 4 0.0000 0.8010 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A165.01 2 0.1091 0.6037 0.00 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HH.01 1 0.0000 0.8236 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E6.A1LX.01 1 0.4487 0.5127 0.62 0.00 0.08 0.00 0.28 0.00 0.02 0.00
#> TCGA.DI.A1BY.01 4 0.4190 0.4699 0.00 0.00 0.20 0.66 0.00 0.00 0.00 0.14
#> TCGA.SL.A6JA.01 1 0.4314 0.5701 0.66 0.00 0.08 0.00 0.24 0.00 0.02 0.00
#> TCGA.EY.A547.01 8 0.0000 0.8212 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A5.A1OK.01 7 0.5599 0.6041 0.00 0.30 0.12 0.00 0.00 0.08 0.50 0.00
#> TCGA.B5.A1MZ.01 2 0.7246 -0.1849 0.00 0.42 0.12 0.04 0.04 0.18 0.20 0.00
#> TCGA.AJ.A3NC.01 2 0.6115 0.0715 0.00 0.48 0.10 0.00 0.02 0.28 0.12 0.00
#> TCGA.B5.A11P.01 8 0.0808 0.8155 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.AX.A1C9.01 6 0.0471 0.8773 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.D1.A0ZR.01 2 0.0471 0.6210 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BG.A0VT.01 7 0.4955 0.6208 0.00 0.34 0.08 0.00 0.00 0.04 0.54 0.00
#> TCGA.B5.A3FH.01 2 0.3991 0.4077 0.00 0.70 0.22 0.02 0.00 0.00 0.06 0.00
#> TCGA.AX.A2HJ.01 8 0.2114 0.8182 0.00 0.00 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.EY.A1G8.01 6 0.3850 0.7861 0.00 0.00 0.12 0.00 0.06 0.76 0.06 0.00
#> TCGA.D1.A16Y.01 6 0.0471 0.8785 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node035-leaf , Node036-leaf , Node041 , Node042 , Node043 , Node051 , Node052 .
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 52 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.964 0.987 0.43594 0.566 0.566
#> 3 3 1.000 0.986 0.988 0.54343 0.735 0.542
#> 4 4 0.729 0.800 0.858 0.09751 0.905 0.719
#> 5 5 0.918 0.953 0.961 0.09051 0.842 0.479
#> 6 6 1.000 0.999 1.000 0.04531 0.939 0.703
#> 7 7 0.995 0.945 0.985 0.00654 0.996 0.976
#> 8 8 0.929 0.833 0.903 0.02084 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 5
There is also optional best \(k\) = 2 3 5 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AX.A2H5.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YU.11 1 0.000 0.988 1.0 0.0
#> TCGA.BK.A6W4.01 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A2H8.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A2HC.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YV.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YF.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YM.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YQ.11 1 0.000 0.988 1.0 0.0
#> TCGA.BG.A3EW.11 1 0.000 0.988 1.0 0.0
#> TCGA.FI.A2CX.01 2 0.000 0.979 0.0 1.0
#> TCGA.FL.A1YL.11 1 0.000 0.988 1.0 0.0
#> TCGA.BG.A2L7.11 2 0.000 0.979 0.0 1.0
#> TCGA.AX.A1CI.11 2 0.000 0.979 0.0 1.0
#> TCGA.AX.A05Y.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A1CJ.11 2 0.000 0.979 0.0 1.0
#> TCGA.FL.A1YH.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A3WE.11 1 0.000 0.988 1.0 0.0
#> TCGA.EY.A1GV.01 2 0.000 0.979 0.0 1.0
#> TCGA.BG.A2AE.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YI.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A1CK.11 2 0.000 0.979 0.0 1.0
#> TCGA.DI.A2QU.11 1 0.000 0.988 1.0 0.0
#> TCGA.AJ.A3NE.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YN.11 1 0.000 0.988 1.0 0.0
#> TCGA.EO.A22S.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A2HA.11 2 0.000 0.979 0.0 1.0
#> TCGA.AJ.A3NH.11 2 0.000 0.979 0.0 1.0
#> TCGA.BG.A2AD.11 1 0.000 0.988 1.0 0.0
#> TCGA.DI.A1NO.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A2HD.11 2 0.000 0.979 0.0 1.0
#> TCGA.AX.A2H7.11 1 0.000 0.988 1.0 0.0
#> TCGA.BG.A3PP.11 1 0.000 0.988 1.0 0.0
#> TCGA.BG.A0MA.11 1 0.971 0.305 0.6 0.4
#> TCGA.BK.A4ZD.11 1 0.000 0.988 1.0 0.0
#> TCGA.FL.A1YT.11 1 0.000 0.988 1.0 0.0
#> TCGA.DI.A1NN.11 2 0.881 0.560 0.3 0.7
#> TCGA.FL.A1YG.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A2H4.11 1 0.000 0.988 1.0 0.0
#> TCGA.EO.A22T.11 1 0.000 0.988 1.0 0.0
#> TCGA.EO.A22R.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A1CC.01 2 0.000 0.979 0.0 1.0
#> TCGA.AX.A0IZ.11 1 0.000 0.988 1.0 0.0
#> TCGA.BK.A13C.11 1 0.000 0.988 1.0 0.0
#> TCGA.AJ.A3NF.01 2 0.000 0.979 0.0 1.0
#> TCGA.AX.A0J0.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A1CF.11 2 0.000 0.979 0.0 1.0
#> TCGA.AJ.A3NC.11 1 0.000 0.988 1.0 0.0
#> TCGA.DI.A2QY.11 2 0.000 0.979 0.0 1.0
#> TCGA.AJ.A2QL.11 2 0.000 0.979 0.0 1.0
#> TCGA.E6.A1M0.11 1 0.000 0.988 1.0 0.0
#> TCGA.AX.A3G3.01 2 0.000 0.979 0.0 1.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AX.A2H5.11 1 0.2066 0.960 0.94 0 0.06
#> TCGA.FL.A1YU.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.BK.A6W4.01 1 0.0000 0.968 1.00 0 0.00
#> TCGA.AX.A2H8.11 1 0.0892 0.968 0.98 0 0.02
#> TCGA.AX.A2HC.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FL.A1YV.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.FL.A1YF.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FL.A1YM.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FL.A1YQ.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.BG.A3EW.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FI.A2CX.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.FL.A1YL.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.BG.A2L7.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AX.A1CI.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AX.A05Y.11 1 0.2066 0.960 0.94 0 0.06
#> TCGA.AX.A1CJ.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.FL.A1YH.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FL.A3WE.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.EY.A1GV.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.BG.A2AE.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FL.A1YI.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.AX.A1CK.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DI.A2QU.11 1 0.2537 0.947 0.92 0 0.08
#> TCGA.AJ.A3NE.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FL.A1YN.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.EO.A22S.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.AX.A2HA.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AJ.A3NH.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.BG.A2AD.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.DI.A1NO.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.AX.A2HD.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AX.A2H7.11 1 0.2066 0.960 0.94 0 0.06
#> TCGA.BG.A3PP.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.BG.A0MA.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.BK.A4ZD.11 1 0.1529 0.965 0.96 0 0.04
#> TCGA.FL.A1YT.11 1 0.2537 0.947 0.92 0 0.08
#> TCGA.DI.A1NN.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.FL.A1YG.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.AX.A2H4.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.EO.A22T.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.EO.A22R.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.AX.A1CC.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AX.A0IZ.11 1 0.2066 0.960 0.94 0 0.06
#> TCGA.BK.A13C.11 3 0.0000 1.000 0.00 0 1.00
#> TCGA.AJ.A3NF.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AX.A0J0.11 1 0.2537 0.947 0.92 0 0.08
#> TCGA.AX.A1CF.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AJ.A3NC.11 1 0.2066 0.960 0.94 0 0.06
#> TCGA.DI.A2QY.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AJ.A2QL.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.E6.A1M0.11 1 0.0000 0.968 1.00 0 0.00
#> TCGA.AX.A3G3.01 2 0.0000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AX.A2H5.11 1 0.692 0.536 0.58 0.00 0.16 0.26
#> TCGA.FL.A1YU.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BK.A6W4.01 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H8.11 1 0.433 0.699 0.80 0.00 0.04 0.16
#> TCGA.AX.A2HC.11 4 0.452 0.839 0.00 0.00 0.32 0.68
#> TCGA.FL.A1YV.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.FL.A1YF.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FL.A1YM.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FL.A1YQ.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BG.A3EW.11 4 0.452 0.839 0.00 0.00 0.32 0.68
#> TCGA.FI.A2CX.01 2 0.000 0.848 0.00 1.00 0.00 0.00
#> TCGA.FL.A1YL.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.BG.A2L7.11 2 0.452 0.818 0.00 0.68 0.00 0.32
#> TCGA.AX.A1CI.11 2 0.452 0.818 0.00 0.68 0.00 0.32
#> TCGA.AX.A05Y.11 1 0.692 0.536 0.58 0.00 0.16 0.26
#> TCGA.AX.A1CJ.11 2 0.000 0.848 0.00 1.00 0.00 0.00
#> TCGA.FL.A1YH.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FL.A3WE.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GV.01 2 0.000 0.848 0.00 1.00 0.00 0.00
#> TCGA.BG.A2AE.11 4 0.452 0.839 0.00 0.00 0.32 0.68
#> TCGA.FL.A1YI.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A1CK.11 2 0.000 0.848 0.00 1.00 0.00 0.00
#> TCGA.DI.A2QU.11 1 0.778 0.104 0.42 0.00 0.32 0.26
#> TCGA.AJ.A3NE.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FL.A1YN.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.EO.A22S.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HA.11 2 0.452 0.818 0.00 0.68 0.00 0.32
#> TCGA.AJ.A3NH.11 2 0.452 0.818 0.00 0.68 0.00 0.32
#> TCGA.BG.A2AD.11 4 0.452 0.839 0.00 0.00 0.32 0.68
#> TCGA.DI.A1NO.11 4 0.452 0.839 0.00 0.00 0.32 0.68
#> TCGA.AX.A2HD.11 2 0.452 0.818 0.00 0.68 0.00 0.32
#> TCGA.AX.A2H7.11 1 0.692 0.536 0.58 0.00 0.16 0.26
#> TCGA.BG.A3PP.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.11 4 0.000 0.589 0.00 0.00 0.00 1.00
#> TCGA.BK.A4ZD.11 1 0.632 0.606 0.66 0.00 0.16 0.18
#> TCGA.FL.A1YT.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DI.A1NN.11 4 0.000 0.589 0.00 0.00 0.00 1.00
#> TCGA.FL.A1YG.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.EO.A22T.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.EO.A22R.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CC.01 2 0.452 0.818 0.00 0.68 0.00 0.32
#> TCGA.AX.A0IZ.11 1 0.692 0.536 0.58 0.00 0.16 0.26
#> TCGA.BK.A13C.11 4 0.452 0.839 0.00 0.00 0.32 0.68
#> TCGA.AJ.A3NF.01 2 0.452 0.818 0.00 0.68 0.00 0.32
#> TCGA.AX.A0J0.11 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AX.A1CF.11 2 0.000 0.848 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NC.11 1 0.692 0.536 0.58 0.00 0.16 0.26
#> TCGA.DI.A2QY.11 2 0.000 0.848 0.00 1.00 0.00 0.00
#> TCGA.AJ.A2QL.11 2 0.000 0.848 0.00 1.00 0.00 0.00
#> TCGA.E6.A1M0.11 1 0.000 0.780 1.00 0.00 0.00 0.00
#> TCGA.AX.A3G3.01 2 0.000 0.848 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.AX.A2H5.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.FL.A1YU.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BK.A6W4.01 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.AX.A2H8.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.AX.A2HC.11 4 0.228 0.891 0.00 0.00 0 0.88 0.12
#> TCGA.FL.A1YV.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.FL.A1YF.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FL.A1YM.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FL.A1YQ.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BG.A3EW.11 4 0.228 0.891 0.00 0.00 0 0.88 0.12
#> TCGA.FI.A2CX.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.FL.A1YL.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.BG.A2L7.11 5 0.228 0.953 0.00 0.12 0 0.00 0.88
#> TCGA.AX.A1CI.11 5 0.228 0.953 0.00 0.12 0 0.00 0.88
#> TCGA.AX.A05Y.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.AX.A1CJ.11 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.FL.A1YH.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FL.A3WE.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EY.A1GV.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.BG.A2AE.11 4 0.228 0.891 0.00 0.00 0 0.88 0.12
#> TCGA.FL.A1YI.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A1CK.11 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.DI.A2QU.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.AJ.A3NE.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FL.A1YN.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EO.A22S.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.AX.A2HA.11 5 0.228 0.953 0.00 0.12 0 0.00 0.88
#> TCGA.AJ.A3NH.11 5 0.228 0.953 0.00 0.12 0 0.00 0.88
#> TCGA.BG.A2AD.11 4 0.228 0.891 0.00 0.00 0 0.88 0.12
#> TCGA.DI.A1NO.11 4 0.000 0.938 0.00 0.00 0 1.00 0.00
#> TCGA.AX.A2HD.11 5 0.228 0.953 0.00 0.12 0 0.00 0.88
#> TCGA.AX.A2H7.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.BG.A3PP.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.BG.A0MA.11 5 0.104 0.841 0.00 0.00 0 0.04 0.96
#> TCGA.BK.A4ZD.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.FL.A1YT.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DI.A1NN.11 5 0.104 0.841 0.00 0.00 0 0.04 0.96
#> TCGA.FL.A1YG.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.AX.A2H4.11 1 0.389 0.528 0.68 0.00 0 0.32 0.00
#> TCGA.EO.A22T.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.EO.A22R.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.AX.A1CC.01 5 0.228 0.953 0.00 0.12 0 0.00 0.88
#> TCGA.AX.A0IZ.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.BK.A13C.11 4 0.000 0.938 0.00 0.00 0 1.00 0.00
#> TCGA.AJ.A3NF.01 5 0.228 0.953 0.00 0.12 0 0.00 0.88
#> TCGA.AX.A0J0.11 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A1CF.11 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.AJ.A3NC.11 4 0.104 0.948 0.04 0.00 0 0.96 0.00
#> TCGA.DI.A2QY.11 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.AJ.A2QL.11 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.E6.A1M0.11 1 0.000 0.961 1.00 0.00 0 0.00 0.00
#> TCGA.AX.A3G3.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AX.A2H5.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.FL.A1YU.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.BK.A6W4.01 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.AX.A2H8.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.AX.A2HC.11 6 0.0000 1.000 0 0 0.00 0.00 0 1
#> TCGA.FL.A1YV.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.FL.A1YF.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.FL.A1YM.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.FL.A1YQ.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.BG.A3EW.11 6 0.0000 1.000 0 0 0.00 0.00 0 1
#> TCGA.FI.A2CX.01 2 0.0000 1.000 0 1 0.00 0.00 0 0
#> TCGA.FL.A1YL.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.BG.A2L7.11 5 0.0000 1.000 0 0 0.00 0.00 1 0
#> TCGA.AX.A1CI.11 5 0.0000 1.000 0 0 0.00 0.00 1 0
#> TCGA.AX.A05Y.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.AX.A1CJ.11 2 0.0000 1.000 0 1 0.00 0.00 0 0
#> TCGA.FL.A1YH.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.FL.A3WE.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.EY.A1GV.01 2 0.0000 1.000 0 1 0.00 0.00 0 0
#> TCGA.BG.A2AE.11 6 0.0000 1.000 0 0 0.00 0.00 0 1
#> TCGA.FL.A1YI.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.AX.A1CK.11 2 0.0000 1.000 0 1 0.00 0.00 0 0
#> TCGA.DI.A2QU.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.AJ.A3NE.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.FL.A1YN.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.EO.A22S.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.AX.A2HA.11 5 0.0000 1.000 0 0 0.00 0.00 1 0
#> TCGA.AJ.A3NH.11 5 0.0000 1.000 0 0 0.00 0.00 1 0
#> TCGA.BG.A2AD.11 6 0.0000 1.000 0 0 0.00 0.00 0 1
#> TCGA.DI.A1NO.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.AX.A2HD.11 5 0.0000 1.000 0 0 0.00 0.00 1 0
#> TCGA.AX.A2H7.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.BG.A3PP.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.BG.A0MA.11 6 0.0000 1.000 0 0 0.00 0.00 0 1
#> TCGA.BK.A4ZD.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.FL.A1YT.11 3 0.0000 0.998 0 0 1.00 0.00 0 0
#> TCGA.DI.A1NN.11 6 0.0000 1.000 0 0 0.00 0.00 0 1
#> TCGA.FL.A1YG.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.AX.A2H4.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.EO.A22T.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.EO.A22R.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.AX.A1CC.01 5 0.0000 1.000 0 0 0.00 0.00 1 0
#> TCGA.AX.A0IZ.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.BK.A13C.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.AJ.A3NF.01 5 0.0000 1.000 0 0 0.00 0.00 1 0
#> TCGA.AX.A0J0.11 3 0.0547 0.977 0 0 0.98 0.02 0 0
#> TCGA.AX.A1CF.11 2 0.0000 1.000 0 1 0.00 0.00 0 0
#> TCGA.AJ.A3NC.11 4 0.0000 1.000 0 0 0.00 1.00 0 0
#> TCGA.DI.A2QY.11 2 0.0000 1.000 0 1 0.00 0.00 0 0
#> TCGA.AJ.A2QL.11 2 0.0000 1.000 0 1 0.00 0.00 0 0
#> TCGA.E6.A1M0.11 1 0.0000 1.000 1 0 0.00 0.00 0 0
#> TCGA.AX.A3G3.01 2 0.0000 1.000 0 1 0.00 0.00 0 0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AX.A2H5.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.FL.A1YU.11 3 0.0000 0.981 0.00 0 1.00 0.00 0 0.00 0.00
#> TCGA.BK.A6W4.01 1 0.0504 0.987 0.98 0 0.00 0.00 0 0.00 0.02
#> TCGA.AX.A2H8.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.AX.A2HC.11 6 0.0000 0.869 0.00 0 0.00 0.00 0 1.00 0.00
#> TCGA.FL.A1YV.11 1 0.0504 0.987 0.98 0 0.00 0.00 0 0.00 0.02
#> TCGA.FL.A1YF.11 3 0.0000 0.981 0.00 0 1.00 0.00 0 0.00 0.00
#> TCGA.FL.A1YM.11 3 0.0000 0.981 0.00 0 1.00 0.00 0 0.00 0.00
#> TCGA.FL.A1YQ.11 3 0.0504 0.977 0.00 0 0.98 0.00 0 0.00 0.02
#> TCGA.BG.A3EW.11 6 0.0000 0.869 0.00 0 0.00 0.00 0 1.00 0.00
#> TCGA.FI.A2CX.01 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
#> TCGA.FL.A1YL.11 1 0.0504 0.987 0.98 0 0.00 0.00 0 0.00 0.02
#> TCGA.BG.A2L7.11 5 0.0000 1.000 0.00 0 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A1CI.11 5 0.0000 1.000 0.00 0 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A05Y.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.AX.A1CJ.11 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
#> TCGA.FL.A1YH.11 3 0.0504 0.977 0.00 0 0.98 0.00 0 0.00 0.02
#> TCGA.FL.A3WE.11 3 0.0000 0.981 0.00 0 1.00 0.00 0 0.00 0.00
#> TCGA.EY.A1GV.01 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
#> TCGA.BG.A2AE.11 6 0.0000 0.869 0.00 0 0.00 0.00 0 1.00 0.00
#> TCGA.FL.A1YI.11 3 0.0000 0.981 0.00 0 1.00 0.00 0 0.00 0.00
#> TCGA.AX.A1CK.11 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
#> TCGA.DI.A2QU.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.AJ.A3NE.11 3 0.0000 0.981 0.00 0 1.00 0.00 0 0.00 0.00
#> TCGA.FL.A1YN.11 3 0.0504 0.977 0.00 0 0.98 0.00 0 0.00 0.02
#> TCGA.EO.A22S.11 1 0.0000 0.990 1.00 0 0.00 0.00 0 0.00 0.00
#> TCGA.AX.A2HA.11 5 0.0000 1.000 0.00 0 0.00 0.00 1 0.00 0.00
#> TCGA.AJ.A3NH.11 5 0.0000 1.000 0.00 0 0.00 0.00 1 0.00 0.00
#> TCGA.BG.A2AD.11 6 0.0000 0.869 0.00 0 0.00 0.00 0 1.00 0.00
#> TCGA.DI.A1NO.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.AX.A2HD.11 5 0.0000 1.000 0.00 0 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A2H7.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.BG.A3PP.11 1 0.0000 0.990 1.00 0 0.00 0.00 0 0.00 0.00
#> TCGA.BG.A0MA.11 6 0.3546 0.080 0.00 0 0.00 0.00 0 0.54 0.46
#> TCGA.BK.A4ZD.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.FL.A1YT.11 3 0.0863 0.964 0.00 0 0.96 0.00 0 0.00 0.04
#> TCGA.DI.A1NN.11 7 0.0863 0.000 0.00 0 0.00 0.00 0 0.04 0.96
#> TCGA.FL.A1YG.11 1 0.0504 0.987 0.98 0 0.00 0.00 0 0.00 0.02
#> TCGA.AX.A2H4.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.EO.A22T.11 1 0.0000 0.990 1.00 0 0.00 0.00 0 0.00 0.00
#> TCGA.EO.A22R.11 1 0.0000 0.990 1.00 0 0.00 0.00 0 0.00 0.00
#> TCGA.AX.A1CC.01 5 0.0000 1.000 0.00 0 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A0IZ.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.BK.A13C.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.AJ.A3NF.01 5 0.0000 1.000 0.00 0 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A0J0.11 3 0.2016 0.897 0.00 0 0.90 0.06 0 0.00 0.04
#> TCGA.AX.A1CF.11 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
#> TCGA.AJ.A3NC.11 4 0.0000 1.000 0.00 0 0.00 1.00 0 0.00 0.00
#> TCGA.DI.A2QY.11 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
#> TCGA.AJ.A2QL.11 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
#> TCGA.E6.A1M0.11 1 0.0000 0.990 1.00 0 0.00 0.00 0 0.00 0.00
#> TCGA.AX.A3G3.01 2 0.0000 1.000 0.00 1 0.00 0.00 0 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AX.A2H5.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YU.11 3 0.0000 0.793 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A6W4.01 1 0.0000 0.677 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H8.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HC.11 6 0.1563 0.818 0.00 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.FL.A1YV.11 1 0.0000 0.677 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YF.11 3 0.0000 0.793 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YM.11 3 0.0000 0.793 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YQ.11 3 0.3675 0.716 0.00 0.30 0.66 0.00 0.00 0.00 0.04 0.00
#> TCGA.BG.A3EW.11 6 0.0000 0.874 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FI.A2CX.01 8 0.1765 0.932 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
#> TCGA.FL.A1YL.11 1 0.0000 0.677 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A2L7.11 5 0.0000 0.994 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CI.11 5 0.0000 0.994 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A05Y.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CJ.11 8 0.1765 0.932 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
#> TCGA.FL.A1YH.11 3 0.3675 0.716 0.00 0.30 0.66 0.00 0.00 0.00 0.04 0.00
#> TCGA.FL.A3WE.11 3 0.0000 0.793 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GV.01 8 0.1765 0.932 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
#> TCGA.BG.A2AE.11 6 0.0000 0.874 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FL.A1YI.11 3 0.0000 0.793 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CK.11 8 0.0000 0.932 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DI.A2QU.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NE.11 3 0.0000 0.793 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YN.11 3 0.3504 0.731 0.00 0.26 0.70 0.00 0.00 0.00 0.04 0.00
#> TCGA.EO.A22S.11 1 0.3299 0.753 0.56 0.44 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HA.11 5 0.0000 0.994 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3NH.11 5 0.0000 0.994 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A2AD.11 6 0.0000 0.874 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DI.A1NO.11 4 0.1091 0.934 0.00 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HD.11 5 0.0000 0.994 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H7.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A3PP.11 1 0.3299 0.753 0.56 0.44 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0MA.11 6 0.3746 0.441 0.00 0.04 0.00 0.00 0.00 0.64 0.32 0.00
#> TCGA.BK.A4ZD.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FL.A1YT.11 3 0.5433 0.581 0.16 0.30 0.50 0.00 0.00 0.00 0.04 0.00
#> TCGA.DI.A1NN.11 7 0.0808 0.000 0.00 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.FL.A1YG.11 1 0.0000 0.677 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.11 4 0.1765 0.853 0.12 0.00 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.EO.A22T.11 1 0.3299 0.753 0.56 0.44 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22R.11 1 0.3299 0.753 0.56 0.44 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CC.01 5 0.0471 0.984 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.AX.A0IZ.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A13C.11 4 0.1341 0.918 0.00 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NF.01 5 0.0471 0.984 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.AX.A0J0.11 3 0.5837 0.560 0.16 0.30 0.48 0.02 0.00 0.00 0.04 0.00
#> TCGA.AX.A1CF.11 8 0.0000 0.932 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3NC.11 4 0.0000 0.972 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QY.11 8 0.0000 0.932 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A2QL.11 8 0.0000 0.932 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.E6.A1M0.11 1 0.3299 0.753 0.56 0.44 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3G3.01 8 0.1765 0.932 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node035-leaf , Node036-leaf , Node041 , Node042 , Node043 , Node051 , Node052 .
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 99 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 0.4425 0.558 0.558
#> 3 3 1.000 0.960 0.980 0.5028 0.707 0.505
#> 4 4 0.819 0.896 0.932 0.0965 0.857 0.620
#> 5 5 0.770 0.697 0.853 0.0772 0.939 0.784
#> 6 6 0.811 0.628 0.791 0.0483 0.847 0.451
#> 7 7 0.790 0.699 0.761 0.0123 0.922 0.609
#> 8 8 0.795 0.835 0.858 0.0225 0.986 0.911
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.D1.A0ZV.01 1 0 1 1 0
#> TCGA.A5.A3LO.01 1 0 1 1 0
#> TCGA.AP.A0LM.01 1 0 1 1 0
#> TCGA.D1.A101.01 1 0 1 1 0
#> TCGA.A5.A1OF.01 2 0 1 0 1
#> TCGA.FI.A2D0.01 1 0 1 1 0
#> TCGA.BG.A18A.01 1 0 1 1 0
#> TCGA.PG.A6IB.01 2 0 1 0 1
#> TCGA.BG.A221.01 2 0 1 0 1
#> TCGA.EO.A22T.01 2 0 1 0 1
#> TCGA.D1.A17N.01 1 0 1 1 0
#> TCGA.D1.A1NS.01 1 0 1 1 0
#> TCGA.D1.A16O.01 1 0 1 1 0
#> TCGA.AX.A1C5.01 1 0 1 1 0
#> TCGA.BS.A0V7.01 1 0 1 1 0
#> TCGA.AX.A0IZ.01 1 0 1 1 0
#> TCGA.B5.A11H.01 1 0 1 1 0
#> TCGA.FI.A2D6.01 2 0 1 0 1
#> TCGA.AX.A3FT.01 2 0 1 0 1
#> TCGA.B5.A1MR.01 2 0 1 0 1
#> TCGA.D1.A15X.01 2 0 1 0 1
#> TCGA.QF.A5YS.01 1 0 1 1 0
#> TCGA.BK.A0CA.01 1 0 1 1 0
#> TCGA.D1.A16F.01 1 0 1 1 0
#> TCGA.EY.A3QX.01 1 0 1 1 0
#> TCGA.EY.A1GS.01 2 0 1 0 1
#> TCGA.D1.A16X.01 1 0 1 1 0
#> TCGA.B5.A1MV.01 1 0 1 1 0
#> TCGA.A5.A0G1.01 2 0 1 0 1
#> TCGA.B5.A3FA.01 1 0 1 1 0
#> TCGA.AJ.A3OJ.01 2 0 1 0 1
#> TCGA.AJ.A8CT.01 1 0 1 1 0
#> TCGA.BG.A2AE.01 2 0 1 0 1
#> TCGA.D1.A2G6.01 1 0 1 1 0
#> TCGA.B5.A11N.01 1 0 1 1 0
#> TCGA.BS.A0UA.01 1 0 1 1 0
#> TCGA.BS.A0V6.01 1 0 1 1 0
#> TCGA.AJ.A3NE.01 1 0 1 1 0
#> TCGA.D1.A17B.01 1 0 1 1 0
#> TCGA.A5.AB3J.01 1 0 1 1 0
#> TCGA.DF.A2KN.01 2 0 1 0 1
#> TCGA.B5.A5OC.01 2 0 1 0 1
#> TCGA.BK.A139.02 1 0 1 1 0
#> TCGA.BK.A139.01 1 0 1 1 0
#> TCGA.D1.A16G.01 2 0 1 0 1
#> TCGA.AJ.A3BH.01 2 0 1 0 1
#> TCGA.AX.A06L.01 1 0 1 1 0
#> TCGA.AX.A06H.01 1 0 1 1 0
#> TCGA.A5.A0GQ.01 1 0 1 1 0
#> TCGA.B5.A11X.01 1 0 1 1 0
#> TCGA.D1.A16E.01 1 0 1 1 0
#> TCGA.BG.A0VV.01 1 0 1 1 0
#> TCGA.EY.A1G7.01 2 0 1 0 1
#> TCGA.DF.A2KY.01 2 0 1 0 1
#> TCGA.AX.A2H4.01 2 0 1 0 1
#> TCGA.DF.A2KZ.01 1 0 1 1 0
#> TCGA.AP.A1E3.01 1 0 1 1 0
#> TCGA.D1.A0ZS.01 2 0 1 0 1
#> TCGA.EC.A1QX.01 2 0 1 0 1
#> TCGA.4E.A92E.01 1 0 1 1 0
#> TCGA.BS.A0UL.01 1 0 1 1 0
#> TCGA.B5.A11O.01 1 0 1 1 0
#> TCGA.AJ.A3NG.01 1 0 1 1 0
#> TCGA.AX.A2HG.01 2 0 1 0 1
#> TCGA.D1.A16J.01 2 0 1 0 1
#> TCGA.QS.A5YR.01 1 0 1 1 0
#> TCGA.EO.A3L0.01 1 0 1 1 0
#> TCGA.DI.A1BU.01 2 0 1 0 1
#> TCGA.BS.A0T9.01 1 0 1 1 0
#> TCGA.B5.A3F9.01 1 0 1 1 0
#> TCGA.DF.A2KR.01 1 0 1 1 0
#> TCGA.SJ.A6ZI.01 2 0 1 0 1
#> TCGA.DF.A2KV.01 1 0 1 1 0
#> TCGA.A5.A2K3.01 2 0 1 0 1
#> TCGA.BG.A0VX.01 1 0 1 1 0
#> TCGA.A5.A0GG.01 1 0 1 1 0
#> TCGA.A5.A1OJ.01 1 0 1 1 0
#> TCGA.B5.A121.01 1 0 1 1 0
#> TCGA.B5.A11M.01 1 0 1 1 0
#> TCGA.B5.A3S1.01 1 0 1 1 0
#> TCGA.AJ.A3OK.01 1 0 1 1 0
#> TCGA.B5.A11Y.01 1 0 1 1 0
#> TCGA.EO.A3AS.01 1 0 1 1 0
#> TCGA.D1.A2G0.01 2 0 1 0 1
#> TCGA.D1.A17C.01 1 0 1 1 0
#> TCGA.EO.A3AV.01 2 0 1 0 1
#> TCGA.D1.A16D.01 1 0 1 1 0
#> TCGA.EO.A3AZ.01 2 0 1 0 1
#> TCGA.D1.A169.01 1 0 1 1 0
#> TCGA.AJ.A6NU.01 1 0 1 1 0
#> TCGA.D1.A16B.01 1 0 1 1 0
#> TCGA.AP.A059.01 2 0 1 0 1
#> TCGA.AJ.A2QK.01 1 0 1 1 0
#> TCGA.D1.A1O8.01 1 0 1 1 0
#> TCGA.D1.A162.01 1 0 1 1 0
#> TCGA.FI.A2D5.01 1 0 1 1 0
#> TCGA.E6.A2P8.01 2 0 1 0 1
#> TCGA.AX.A2IN.01 2 0 1 0 1
#> TCGA.AJ.A23O.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D1.A0ZV.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.A5.A3LO.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.AP.A0LM.01 3 0.2066 0.930 0.06 0.00 0.94
#> TCGA.D1.A101.01 3 0.2066 0.930 0.06 0.00 0.94
#> TCGA.A5.A1OF.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.FI.A2D0.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.BG.A18A.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.PG.A6IB.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.BG.A221.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EO.A22T.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.D1.A17N.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.D1.A1NS.01 3 0.2959 0.891 0.10 0.00 0.90
#> TCGA.D1.A16O.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.AX.A1C5.01 3 0.2066 0.930 0.06 0.00 0.94
#> TCGA.BS.A0V7.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.AX.A0IZ.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.B5.A11H.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.FI.A2D6.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.AX.A3FT.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.B5.A1MR.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.D1.A15X.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.QF.A5YS.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.BK.A0CA.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.D1.A16F.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.EY.A3QX.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.EY.A1GS.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.D1.A16X.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.B5.A1MV.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.A5.A0G1.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.B5.A3FA.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.AJ.A3OJ.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.AJ.A8CT.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.BG.A2AE.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.D1.A2G6.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.B5.A11N.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.BS.A0UA.01 3 0.2066 0.930 0.06 0.00 0.94
#> TCGA.BS.A0V6.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.AJ.A3NE.01 3 0.2066 0.930 0.06 0.00 0.94
#> TCGA.D1.A17B.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.A5.AB3J.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.DF.A2KN.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.B5.A5OC.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.BK.A139.02 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.BK.A139.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.D1.A16G.01 2 0.4291 0.820 0.00 0.82 0.18
#> TCGA.AJ.A3BH.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.AX.A06L.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.AX.A06H.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.A5.A0GQ.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.B5.A11X.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.D1.A16E.01 3 0.6192 0.294 0.42 0.00 0.58
#> TCGA.BG.A0VV.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.EY.A1G7.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.DF.A2KY.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.AX.A2H4.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.DF.A2KZ.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.AP.A1E3.01 1 0.5706 0.505 0.68 0.00 0.32
#> TCGA.D1.A0ZS.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.EC.A1QX.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.4E.A92E.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.BS.A0UL.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.B5.A11O.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.AJ.A3NG.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.AX.A2HG.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.D1.A16J.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.QS.A5YR.01 3 0.2066 0.930 0.06 0.00 0.94
#> TCGA.EO.A3L0.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.DI.A1BU.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.BS.A0T9.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.B5.A3F9.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.DF.A2KR.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.SJ.A6ZI.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.DF.A2KV.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.A5.A2K3.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.BG.A0VX.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.A5.A0GG.01 1 0.0892 0.968 0.98 0.00 0.02
#> TCGA.A5.A1OJ.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.B5.A121.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.B5.A11M.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.B5.A3S1.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.AJ.A3OK.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.B5.A11Y.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.EO.A3AS.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.D1.A2G0.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.D1.A17C.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.EO.A3AV.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.D1.A16D.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.EO.A3AZ.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.D1.A169.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.D1.A16B.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.AP.A059.01 2 0.2066 0.955 0.00 0.94 0.06
#> TCGA.AJ.A2QK.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.D1.A1O8.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.D1.A162.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.FI.A2D5.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.E6.A2P8.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.AX.A2IN.01 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.AJ.A23O.01 3 0.0000 0.973 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.D1.A0ZV.01 1 0.3975 0.727 0.76 0.00 0.24 0.00
#> TCGA.A5.A3LO.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.AP.A0LM.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.D1.A101.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.A5.A1OF.01 4 0.4277 0.714 0.00 0.28 0.00 0.72
#> TCGA.FI.A2D0.01 3 0.3975 0.795 0.00 0.00 0.76 0.24
#> TCGA.BG.A18A.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.PG.A6IB.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A221.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EO.A22T.01 4 0.1637 0.859 0.00 0.06 0.00 0.94
#> TCGA.D1.A17N.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.D1.A16O.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.AX.A1C5.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.BS.A0V7.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.AX.A0IZ.01 3 0.3801 0.810 0.00 0.00 0.78 0.22
#> TCGA.B5.A11H.01 1 0.3400 0.803 0.82 0.00 0.18 0.00
#> TCGA.FI.A2D6.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FT.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.B5.A1MR.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A15X.01 4 0.2647 0.838 0.00 0.12 0.00 0.88
#> TCGA.QF.A5YS.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.BK.A0CA.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.D1.A16F.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.EY.A3QX.01 3 0.3975 0.795 0.00 0.00 0.76 0.24
#> TCGA.EY.A1GS.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A16X.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MV.01 1 0.2921 0.847 0.86 0.00 0.14 0.00
#> TCGA.A5.A0G1.01 4 0.4277 0.714 0.00 0.28 0.00 0.72
#> TCGA.B5.A3FA.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
#> TCGA.AJ.A3OJ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A8CT.01 1 0.2011 0.903 0.92 0.00 0.08 0.00
#> TCGA.BG.A2AE.01 4 0.1637 0.849 0.00 0.00 0.06 0.94
#> TCGA.D1.A2G6.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
#> TCGA.B5.A11N.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
#> TCGA.BS.A0UA.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.BS.A0V6.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3NE.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.D1.A17B.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.A5.AB3J.01 3 0.2011 0.832 0.08 0.00 0.92 0.00
#> TCGA.DF.A2KN.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.B5.A5OC.01 4 0.3975 0.755 0.00 0.24 0.00 0.76
#> TCGA.BK.A139.02 3 0.4134 0.791 0.00 0.00 0.74 0.26
#> TCGA.BK.A139.01 3 0.3801 0.810 0.00 0.00 0.78 0.22
#> TCGA.D1.A16G.01 4 0.1637 0.859 0.00 0.06 0.00 0.94
#> TCGA.AJ.A3BH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A06L.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.AX.A06H.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
#> TCGA.A5.A0GQ.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.B5.A11X.01 3 0.3172 0.838 0.00 0.00 0.84 0.16
#> TCGA.D1.A16E.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.BG.A0VV.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.EY.A1G7.01 4 0.1637 0.849 0.00 0.00 0.06 0.94
#> TCGA.DF.A2KY.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A2H4.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DF.A2KZ.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.AP.A1E3.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.D1.A0ZS.01 4 0.1637 0.849 0.00 0.00 0.06 0.94
#> TCGA.EC.A1QX.01 4 0.1637 0.849 0.00 0.00 0.06 0.94
#> TCGA.4E.A92E.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.BS.A0UL.01 3 0.1211 0.873 0.00 0.00 0.96 0.04
#> TCGA.B5.A11O.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3NG.01 1 0.0707 0.954 0.98 0.00 0.00 0.02
#> TCGA.AX.A2HG.01 4 0.4277 0.714 0.00 0.28 0.00 0.72
#> TCGA.D1.A16J.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.QS.A5YR.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.EO.A3L0.01 3 0.3610 0.832 0.00 0.00 0.80 0.20
#> TCGA.DI.A1BU.01 4 0.1637 0.859 0.00 0.06 0.00 0.94
#> TCGA.BS.A0T9.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.B5.A3F9.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.DF.A2KR.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
#> TCGA.SJ.A6ZI.01 4 0.0707 0.847 0.00 0.02 0.00 0.98
#> TCGA.DF.A2KV.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.A5.A2K3.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BG.A0VX.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.A5.A0GG.01 3 0.1637 0.847 0.06 0.00 0.94 0.00
#> TCGA.A5.A1OJ.01 3 0.2345 0.814 0.10 0.00 0.90 0.00
#> TCGA.B5.A121.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.B5.A11M.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.B5.A3S1.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3OK.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.B5.A11Y.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.EO.A3AS.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
#> TCGA.D1.A2G0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A17C.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.EO.A3AV.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A16D.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.EO.A3AZ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A169.01 1 0.2921 0.847 0.86 0.00 0.14 0.00
#> TCGA.AJ.A6NU.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
#> TCGA.D1.A16B.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.AP.A059.01 4 0.4277 0.714 0.00 0.28 0.00 0.72
#> TCGA.AJ.A2QK.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.D1.A1O8.01 3 0.0000 0.885 0.00 0.00 1.00 0.00
#> TCGA.D1.A162.01 1 0.0000 0.968 1.00 0.00 0.00 0.00
#> TCGA.FI.A2D5.01 3 0.2345 0.814 0.10 0.00 0.90 0.00
#> TCGA.E6.A2P8.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.1637 0.849 0.00 0.00 0.06 0.94
#> TCGA.AJ.A23O.01 3 0.4134 0.801 0.00 0.00 0.74 0.26
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D1.A0ZV.01 3 0.4262 0.288 0.44 0.00 0.56 0.00 0.00
#> TCGA.A5.A3LO.01 3 0.3561 0.258 0.00 0.00 0.74 0.00 0.26
#> TCGA.AP.A0LM.01 3 0.0000 0.640 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A101.01 3 0.0000 0.640 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A1OF.01 4 0.1410 0.900 0.00 0.06 0.00 0.94 0.00
#> TCGA.FI.A2D0.01 5 0.4263 0.769 0.00 0.00 0.18 0.06 0.76
#> TCGA.BG.A18A.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A6IB.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A221.01 2 0.3390 0.877 0.00 0.84 0.00 0.10 0.06
#> TCGA.EO.A22T.01 4 0.0000 0.911 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A17N.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.D1.A1NS.01 3 0.2280 0.628 0.12 0.00 0.88 0.00 0.00
#> TCGA.D1.A16O.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.AX.A1C5.01 3 0.2873 0.624 0.12 0.00 0.86 0.00 0.02
#> TCGA.BS.A0V7.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.AX.A0IZ.01 3 0.4227 -0.113 0.00 0.00 0.58 0.00 0.42
#> TCGA.B5.A11H.01 1 0.3895 0.408 0.68 0.00 0.32 0.00 0.00
#> TCGA.FI.A2D6.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A1MR.01 2 0.1043 0.958 0.00 0.96 0.00 0.00 0.04
#> TCGA.D1.A15X.01 4 0.0609 0.911 0.00 0.02 0.00 0.98 0.00
#> TCGA.QF.A5YS.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.BK.A0CA.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16F.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A3QX.01 5 0.5979 0.479 0.00 0.00 0.36 0.12 0.52
#> TCGA.EY.A1GS.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A16X.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MV.01 1 0.2516 0.729 0.86 0.00 0.14 0.00 0.00
#> TCGA.A5.A0G1.01 4 0.1410 0.900 0.00 0.06 0.00 0.94 0.00
#> TCGA.B5.A3FA.01 5 0.4854 0.762 0.00 0.00 0.26 0.06 0.68
#> TCGA.AJ.A3OJ.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A8CT.01 1 0.1410 0.815 0.94 0.00 0.06 0.00 0.00
#> TCGA.BG.A2AE.01 4 0.2929 0.817 0.00 0.00 0.00 0.82 0.18
#> TCGA.D1.A2G6.01 3 0.5457 -0.487 0.00 0.00 0.48 0.06 0.46
#> TCGA.B5.A11N.01 3 0.5457 -0.487 0.00 0.00 0.48 0.06 0.46
#> TCGA.BS.A0UA.01 3 0.0000 0.640 0.00 0.00 1.00 0.00 0.00
#> TCGA.BS.A0V6.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NE.01 3 0.0000 0.640 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A17B.01 3 0.1410 0.597 0.00 0.00 0.94 0.00 0.06
#> TCGA.A5.AB3J.01 3 0.3513 0.604 0.18 0.00 0.80 0.00 0.02
#> TCGA.DF.A2KN.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A5OC.01 4 0.2012 0.893 0.00 0.06 0.00 0.92 0.02
#> TCGA.BK.A139.02 5 0.4263 0.769 0.00 0.00 0.18 0.06 0.76
#> TCGA.BK.A139.01 5 0.4263 0.769 0.00 0.00 0.18 0.06 0.76
#> TCGA.D1.A16G.01 4 0.0000 0.911 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3BH.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.AX.A06H.01 3 0.5457 -0.487 0.00 0.00 0.48 0.06 0.46
#> TCGA.A5.A0GQ.01 3 0.0000 0.640 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11X.01 3 0.3946 0.467 0.00 0.00 0.80 0.08 0.12
#> TCGA.D1.A16E.01 3 0.2929 0.608 0.18 0.00 0.82 0.00 0.00
#> TCGA.BG.A0VV.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.EY.A1G7.01 4 0.3796 0.681 0.00 0.00 0.00 0.70 0.30
#> TCGA.DF.A2KY.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.01 2 0.3390 0.877 0.00 0.84 0.00 0.10 0.06
#> TCGA.DF.A2KZ.01 3 0.3796 0.148 0.00 0.00 0.70 0.00 0.30
#> TCGA.AP.A1E3.01 3 0.2929 0.608 0.18 0.00 0.82 0.00 0.00
#> TCGA.D1.A0ZS.01 4 0.2020 0.876 0.00 0.00 0.00 0.90 0.10
#> TCGA.EC.A1QX.01 4 0.2020 0.876 0.00 0.00 0.00 0.90 0.10
#> TCGA.4E.A92E.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.BS.A0UL.01 3 0.4227 -0.251 0.00 0.00 0.58 0.00 0.42
#> TCGA.B5.A11O.01 3 0.0000 0.640 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NG.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.AX.A2HG.01 4 0.1410 0.900 0.00 0.06 0.00 0.94 0.00
#> TCGA.D1.A16J.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.QS.A5YR.01 3 0.2280 0.628 0.12 0.00 0.88 0.00 0.00
#> TCGA.EO.A3L0.01 3 0.5457 -0.487 0.00 0.00 0.48 0.06 0.46
#> TCGA.DI.A1BU.01 4 0.0000 0.911 0.00 0.00 0.00 1.00 0.00
#> TCGA.BS.A0T9.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.B5.A3F9.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.DF.A2KR.01 5 0.5068 0.734 0.00 0.00 0.30 0.06 0.64
#> TCGA.SJ.A6ZI.01 4 0.0609 0.908 0.00 0.00 0.00 0.98 0.02
#> TCGA.DF.A2KV.01 3 0.0609 0.633 0.00 0.00 0.98 0.00 0.02
#> TCGA.A5.A2K3.01 2 0.1043 0.958 0.00 0.96 0.00 0.00 0.04
#> TCGA.BG.A0VX.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.A5.A0GG.01 3 0.2929 0.608 0.18 0.00 0.82 0.00 0.00
#> TCGA.A5.A1OJ.01 3 0.2929 0.608 0.18 0.00 0.82 0.00 0.00
#> TCGA.B5.A121.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.B5.A11M.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.B5.A3S1.01 3 0.3796 0.283 0.00 0.00 0.70 0.00 0.30
#> TCGA.AJ.A3OK.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.B5.A11Y.01 3 0.0000 0.640 0.00 0.00 1.00 0.00 0.00
#> TCGA.EO.A3AS.01 5 0.5447 0.528 0.00 0.00 0.44 0.06 0.50
#> TCGA.D1.A2G0.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17C.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AV.01 2 0.1043 0.958 0.00 0.96 0.00 0.00 0.04
#> TCGA.D1.A16D.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AZ.01 2 0.1043 0.958 0.00 0.96 0.00 0.00 0.04
#> TCGA.D1.A169.01 1 0.2732 0.703 0.84 0.00 0.16 0.00 0.00
#> TCGA.AJ.A6NU.01 5 0.5447 0.528 0.00 0.00 0.44 0.06 0.50
#> TCGA.D1.A16B.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.AP.A059.01 4 0.1410 0.900 0.00 0.06 0.00 0.94 0.00
#> TCGA.AJ.A2QK.01 1 0.0000 0.859 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O8.01 3 0.1410 0.610 0.00 0.00 0.94 0.00 0.06
#> TCGA.D1.A162.01 1 0.2929 0.897 0.82 0.00 0.00 0.00 0.18
#> TCGA.FI.A2D5.01 3 0.2929 0.608 0.18 0.00 0.82 0.00 0.00
#> TCGA.E6.A2P8.01 2 0.3390 0.877 0.00 0.84 0.00 0.10 0.06
#> TCGA.AX.A2IN.01 4 0.2020 0.876 0.00 0.00 0.00 0.90 0.10
#> TCGA.AJ.A23O.01 3 0.5457 -0.487 0.00 0.00 0.48 0.06 0.46
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D1.A0ZV.01 3 0.0547 0.435 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.A5.A3LO.01 6 0.5888 0.597 0.00 0.00 0.22 0.00 0.32 0.46
#> TCGA.AP.A0LM.01 6 0.5115 0.577 0.00 0.00 0.46 0.00 0.08 0.46
#> TCGA.D1.A101.01 3 0.5115 -0.626 0.00 0.00 0.46 0.00 0.08 0.46
#> TCGA.A5.A1OF.01 4 0.0547 0.903 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.FI.A2D0.01 6 0.3864 -0.378 0.00 0.00 0.00 0.00 0.48 0.52
#> TCGA.BG.A18A.01 3 0.4328 0.125 0.46 0.00 0.52 0.02 0.00 0.00
#> TCGA.PG.A6IB.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A221.01 2 0.2350 0.888 0.00 0.88 0.00 0.10 0.00 0.02
#> TCGA.EO.A22T.01 4 0.0547 0.906 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.D1.A17N.01 1 0.0547 0.985 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.D1.A1NS.01 3 0.3706 -0.337 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.D1.A16O.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1C5.01 3 0.3864 -0.498 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.BS.A0V7.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A0IZ.01 6 0.5259 0.613 0.00 0.00 0.16 0.00 0.24 0.60
#> TCGA.B5.A11H.01 3 0.1814 0.468 0.10 0.00 0.90 0.00 0.00 0.00
#> TCGA.FI.A2D6.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MR.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A15X.01 4 0.0547 0.906 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.QF.A5YS.01 1 0.0547 0.985 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BK.A0CA.01 3 0.4328 0.125 0.46 0.00 0.52 0.02 0.00 0.00
#> TCGA.D1.A16F.01 3 0.3851 0.152 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.EY.A3QX.01 6 0.2350 0.412 0.00 0.00 0.00 0.02 0.10 0.88
#> TCGA.EY.A1GS.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16X.01 3 0.3851 0.152 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.B5.A1MV.01 3 0.2631 0.488 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.A5.A0G1.01 4 0.0547 0.903 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.B5.A3FA.01 5 0.1807 0.868 0.00 0.00 0.02 0.00 0.92 0.06
#> TCGA.AJ.A3OJ.01 2 0.0547 0.964 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AJ.A8CT.01 3 0.2793 0.488 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.BG.A2AE.01 4 0.4348 0.726 0.00 0.00 0.00 0.64 0.04 0.32
#> TCGA.D1.A2G6.01 5 0.0547 0.904 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.B5.A11N.01 5 0.0547 0.904 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.BS.A0UA.01 3 0.5115 -0.626 0.00 0.00 0.46 0.00 0.08 0.46
#> TCGA.BS.A0V6.01 3 0.4328 0.125 0.46 0.00 0.52 0.02 0.00 0.00
#> TCGA.AJ.A3NE.01 3 0.5115 -0.626 0.00 0.00 0.46 0.00 0.08 0.46
#> TCGA.D1.A17B.01 6 0.5295 0.595 0.00 0.00 0.44 0.00 0.10 0.46
#> TCGA.A5.AB3J.01 3 0.0937 0.419 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.DF.A2KN.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A5OC.01 4 0.1092 0.896 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.BK.A139.02 5 0.3578 0.605 0.00 0.00 0.00 0.00 0.66 0.34
#> TCGA.BK.A139.01 5 0.3869 0.196 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.D1.A16G.01 4 0.0547 0.906 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.AJ.A3BH.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06H.01 5 0.0547 0.904 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.A5.A0GQ.01 3 0.5115 -0.626 0.00 0.00 0.46 0.00 0.08 0.46
#> TCGA.B5.A11X.01 6 0.5007 0.626 0.00 0.00 0.24 0.02 0.08 0.66
#> TCGA.D1.A16E.01 3 0.0000 0.424 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0VV.01 1 0.0547 0.985 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EY.A1G7.01 4 0.4609 0.620 0.00 0.00 0.00 0.54 0.04 0.42
#> TCGA.DF.A2KY.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.01 2 0.2981 0.822 0.00 0.82 0.00 0.16 0.00 0.02
#> TCGA.DF.A2KZ.01 6 0.5888 0.598 0.00 0.00 0.22 0.00 0.32 0.46
#> TCGA.AP.A1E3.01 3 0.0000 0.424 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZS.01 4 0.3821 0.802 0.00 0.00 0.00 0.74 0.04 0.22
#> TCGA.EC.A1QX.01 4 0.2350 0.870 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.4E.A92E.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0UL.01 5 0.1480 0.864 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.B5.A11O.01 6 0.5115 0.577 0.00 0.00 0.46 0.00 0.08 0.46
#> TCGA.AJ.A3NG.01 1 0.1807 0.941 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.AX.A2HG.01 4 0.1092 0.903 0.00 0.02 0.00 0.96 0.02 0.00
#> TCGA.D1.A16J.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YR.01 3 0.4534 -0.421 0.00 0.00 0.58 0.00 0.04 0.38
#> TCGA.EO.A3L0.01 5 0.0547 0.904 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.DI.A1BU.01 4 0.0547 0.906 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BS.A0T9.01 1 0.0547 0.985 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.B5.A3F9.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KR.01 5 0.1480 0.887 0.00 0.00 0.02 0.00 0.94 0.04
#> TCGA.SJ.A6ZI.01 4 0.1480 0.892 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.DF.A2KV.01 6 0.5110 0.587 0.00 0.00 0.44 0.00 0.08 0.48
#> TCGA.A5.A2K3.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VX.01 1 0.0547 0.985 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.A5.A0GG.01 3 0.0000 0.424 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A5.A1OJ.01 3 0.0000 0.424 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A121.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11M.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3S1.01 6 0.2474 0.533 0.00 0.00 0.08 0.00 0.04 0.88
#> TCGA.AJ.A3OK.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11Y.01 3 0.5115 -0.626 0.00 0.00 0.46 0.00 0.08 0.46
#> TCGA.EO.A3AS.01 5 0.1092 0.895 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.D1.A2G0.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17C.01 3 0.3851 0.152 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.EO.A3AV.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16D.01 3 0.3851 0.152 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.EO.A3AZ.01 2 0.0000 0.974 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A169.01 3 0.2631 0.488 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 5 0.0547 0.904 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.D1.A16B.01 1 0.0547 0.985 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AP.A059.01 4 0.0547 0.903 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.AJ.A2QK.01 3 0.3851 0.152 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.D1.A1O8.01 6 0.5110 0.587 0.00 0.00 0.44 0.00 0.08 0.48
#> TCGA.D1.A162.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2D5.01 3 0.0000 0.424 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E6.A2P8.01 2 0.2350 0.888 0.00 0.88 0.00 0.10 0.00 0.02
#> TCGA.AX.A2IN.01 4 0.3351 0.835 0.00 0.00 0.00 0.80 0.04 0.16
#> TCGA.AJ.A23O.01 5 0.0547 0.904 0.00 0.00 0.02 0.00 0.98 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D1.A0ZV.01 3 0.3546 0.3416 0.00 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.A5.A3LO.01 6 0.2572 0.6328 0.00 0.00 0.00 0.00 0.20 0.80 0.00
#> TCGA.AP.A0LM.01 6 0.0863 0.8541 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.D1.A101.01 6 0.0863 0.8541 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.A5.A1OF.01 4 0.1505 0.8953 0.02 0.02 0.00 0.94 0.02 0.00 0.00
#> TCGA.FI.A2D0.01 7 0.5760 0.4509 0.02 0.00 0.00 0.02 0.28 0.14 0.54
#> TCGA.BG.A18A.01 3 0.1363 0.2503 0.04 0.00 0.94 0.00 0.00 0.00 0.02
#> TCGA.PG.A6IB.01 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A221.01 2 0.3661 0.8289 0.22 0.74 0.00 0.02 0.02 0.00 0.00
#> TCGA.EO.A22T.01 4 0.0000 0.9002 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A17N.01 1 0.3994 0.9430 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.D1.A1NS.01 6 0.1886 0.7598 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.D1.A16O.01 1 0.4875 0.8814 0.46 0.00 0.44 0.00 0.00 0.00 0.10
#> TCGA.AX.A1C5.01 6 0.1433 0.8087 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.BS.A0V7.01 1 0.3994 0.9471 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.AX.A0IZ.01 6 0.4298 0.5231 0.04 0.00 0.00 0.00 0.10 0.74 0.12
#> TCGA.B5.A11H.01 3 0.3358 0.4831 0.00 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.FI.A2D6.01 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MR.01 2 0.2259 0.8864 0.16 0.84 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A15X.01 4 0.1006 0.8991 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.QF.A5YS.01 1 0.4408 0.9204 0.52 0.00 0.44 0.00 0.02 0.00 0.02
#> TCGA.BK.A0CA.01 3 0.1928 0.1436 0.08 0.00 0.90 0.00 0.00 0.00 0.02
#> TCGA.D1.A16F.01 3 0.0863 0.4415 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.EY.A3QX.01 7 0.4479 0.5865 0.00 0.00 0.00 0.06 0.02 0.26 0.66
#> TCGA.EY.A1GS.01 2 0.0504 0.9197 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D1.A16X.01 3 0.1363 0.4182 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.B5.A1MV.01 3 0.2945 0.5776 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.A5.A0G1.01 4 0.1505 0.8953 0.02 0.02 0.00 0.94 0.02 0.00 0.00
#> TCGA.B5.A3FA.01 5 0.3876 0.7589 0.04 0.00 0.00 0.02 0.78 0.02 0.14
#> TCGA.AJ.A3OJ.01 2 0.1363 0.9074 0.04 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.AJ.A8CT.01 3 0.2832 0.5873 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.BG.A2AE.01 7 0.4692 -0.0043 0.08 0.00 0.00 0.42 0.00 0.00 0.50
#> TCGA.D1.A2G6.01 5 0.1928 0.9302 0.00 0.00 0.00 0.02 0.90 0.08 0.00
#> TCGA.B5.A11N.01 5 0.1928 0.9302 0.00 0.00 0.00 0.02 0.90 0.08 0.00
#> TCGA.BS.A0UA.01 6 0.0863 0.8541 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.BS.A0V6.01 3 0.1505 0.3546 0.02 0.00 0.94 0.00 0.00 0.02 0.02
#> TCGA.AJ.A3NE.01 6 0.0504 0.8585 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.D1.A17B.01 6 0.1166 0.8146 0.00 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.A5.AB3J.01 3 0.5047 0.3430 0.00 0.00 0.52 0.00 0.14 0.34 0.00
#> TCGA.DF.A2KN.01 2 0.0504 0.9184 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.B5.A5OC.01 4 0.1433 0.8655 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.BK.A139.02 7 0.5123 0.2574 0.00 0.00 0.00 0.02 0.42 0.08 0.48
#> TCGA.BK.A139.01 7 0.5931 0.3519 0.00 0.00 0.00 0.02 0.34 0.24 0.40
#> TCGA.D1.A16G.01 4 0.0000 0.9002 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3BH.01 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 1 0.3994 0.9471 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.AX.A06H.01 5 0.1928 0.9302 0.00 0.00 0.00 0.02 0.90 0.08 0.00
#> TCGA.A5.A0GQ.01 6 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A11X.01 6 0.3734 0.5880 0.04 0.00 0.00 0.04 0.00 0.78 0.14
#> TCGA.D1.A16E.01 3 0.3558 0.3045 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.BG.A0VV.01 3 0.3994 -0.9352 0.48 0.00 0.50 0.00 0.00 0.00 0.02
#> TCGA.EY.A1G7.01 7 0.4872 0.3045 0.08 0.00 0.00 0.30 0.00 0.02 0.60
#> TCGA.DF.A2KY.01 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.01 2 0.4500 0.7681 0.22 0.68 0.00 0.08 0.02 0.00 0.00
#> TCGA.DF.A2KZ.01 6 0.3221 0.4133 0.00 0.00 0.00 0.00 0.32 0.68 0.00
#> TCGA.AP.A1E3.01 3 0.3558 0.3045 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.D1.A0ZS.01 4 0.4338 0.4713 0.08 0.00 0.00 0.64 0.00 0.00 0.28
#> TCGA.EC.A1QX.01 4 0.1363 0.8725 0.04 0.00 0.00 0.94 0.00 0.00 0.02
#> TCGA.4E.A92E.01 1 0.4692 0.8687 0.50 0.00 0.42 0.00 0.00 0.00 0.08
#> TCGA.BS.A0UL.01 5 0.2163 0.8945 0.00 0.00 0.02 0.00 0.88 0.10 0.00
#> TCGA.B5.A11O.01 6 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3NG.01 3 0.5665 -0.8034 0.40 0.00 0.42 0.00 0.02 0.00 0.16
#> TCGA.AX.A2HG.01 4 0.2652 0.8750 0.06 0.02 0.00 0.88 0.02 0.00 0.02
#> TCGA.D1.A16J.01 2 0.0504 0.9184 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.QS.A5YR.01 6 0.2081 0.7396 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.EO.A3L0.01 5 0.1928 0.9302 0.00 0.00 0.00 0.02 0.90 0.08 0.00
#> TCGA.DI.A1BU.01 4 0.0000 0.9002 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BS.A0T9.01 1 0.3994 0.9430 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.B5.A3F9.01 1 0.3558 0.9467 0.52 0.00 0.48 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KR.01 5 0.3887 0.8403 0.08 0.00 0.00 0.02 0.80 0.04 0.06
#> TCGA.SJ.A6ZI.01 4 0.1928 0.8501 0.08 0.00 0.00 0.90 0.02 0.00 0.00
#> TCGA.DF.A2KV.01 6 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A5.A2K3.01 2 0.1886 0.8990 0.12 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VX.01 1 0.3994 0.9430 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.A5.A0GG.01 3 0.3558 0.3045 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.A5.A1OJ.01 3 0.3558 0.3045 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.B5.A121.01 1 0.3994 0.9471 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.B5.A11M.01 1 0.3994 0.9471 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.B5.A3S1.01 7 0.3755 0.4781 0.00 0.00 0.00 0.00 0.02 0.34 0.64
#> TCGA.AJ.A3OK.01 1 0.4705 0.8851 0.48 0.00 0.44 0.00 0.00 0.00 0.08
#> TCGA.B5.A11Y.01 6 0.0504 0.8585 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.EO.A3AS.01 5 0.3798 0.8938 0.08 0.00 0.00 0.02 0.80 0.08 0.02
#> TCGA.D1.A2G0.01 2 0.0504 0.9197 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D1.A17C.01 3 0.0863 0.4415 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.EO.A3AV.01 2 0.2259 0.8864 0.16 0.84 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16D.01 3 0.1363 0.4182 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.EO.A3AZ.01 2 0.1886 0.8990 0.12 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A169.01 3 0.2945 0.5776 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.AJ.A6NU.01 5 0.3257 0.9113 0.04 0.00 0.00 0.02 0.84 0.08 0.02
#> TCGA.D1.A16B.01 1 0.3994 0.9430 0.50 0.00 0.48 0.00 0.00 0.00 0.02
#> TCGA.AP.A059.01 4 0.1505 0.8953 0.02 0.02 0.00 0.94 0.02 0.00 0.00
#> TCGA.AJ.A2QK.01 3 0.1363 0.4182 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.D1.A1O8.01 6 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A162.01 1 0.3985 0.9409 0.52 0.00 0.46 0.00 0.00 0.00 0.02
#> TCGA.FI.A2D5.01 3 0.3558 0.3045 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.E6.A2P8.01 2 0.3661 0.8289 0.22 0.74 0.00 0.02 0.02 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.2572 0.8182 0.08 0.00 0.00 0.86 0.00 0.00 0.06
#> TCGA.AJ.A23O.01 5 0.1928 0.9302 0.00 0.00 0.00 0.02 0.90 0.08 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D1.A0ZV.01 3 0.3426 0.773 0.02 0.00 0.74 0.00 0.00 0.22 0.02 0.00
#> TCGA.A5.A3LO.01 6 0.1557 0.881 0.00 0.00 0.02 0.00 0.06 0.92 0.00 0.00
#> TCGA.AP.A0LM.01 6 0.0000 0.927 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A101.01 6 0.0000 0.927 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A1OF.01 4 0.1804 0.879 0.00 0.02 0.00 0.90 0.00 0.00 0.08 0.00
#> TCGA.FI.A2D0.01 8 0.4521 0.715 0.00 0.00 0.02 0.00 0.08 0.06 0.12 0.72
#> TCGA.BG.A18A.01 3 0.3198 0.737 0.26 0.00 0.72 0.00 0.00 0.00 0.02 0.00
#> TCGA.PG.A6IB.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A221.01 2 0.3293 0.814 0.00 0.74 0.00 0.04 0.00 0.00 0.22 0.00
#> TCGA.EO.A22T.01 4 0.0941 0.880 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.D1.A17N.01 1 0.0471 0.915 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D1.A1NS.01 6 0.1563 0.838 0.00 0.00 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.D1.A16O.01 1 0.1765 0.887 0.88 0.00 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.AX.A1C5.01 6 0.0941 0.912 0.00 0.00 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.BS.A0V7.01 1 0.1091 0.915 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.AX.A0IZ.01 6 0.3131 0.819 0.00 0.00 0.02 0.00 0.04 0.84 0.06 0.04
#> TCGA.B5.A11H.01 3 0.3434 0.814 0.10 0.00 0.76 0.00 0.00 0.14 0.00 0.00
#> TCGA.FI.A2D6.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MR.01 2 0.2114 0.879 0.00 0.84 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.D1.A15X.01 4 0.1804 0.879 0.00 0.02 0.00 0.90 0.00 0.00 0.08 0.00
#> TCGA.QF.A5YS.01 1 0.2807 0.893 0.84 0.00 0.00 0.02 0.00 0.00 0.10 0.04
#> TCGA.BK.A0CA.01 3 0.3570 0.585 0.36 0.00 0.62 0.00 0.00 0.00 0.02 0.00
#> TCGA.D1.A16F.01 3 0.2650 0.766 0.24 0.00 0.76 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A3QX.01 8 0.2484 0.741 0.00 0.00 0.00 0.00 0.02 0.10 0.02 0.86
#> TCGA.EY.A1GS.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16X.01 3 0.2650 0.766 0.24 0.00 0.76 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MV.01 3 0.3434 0.814 0.10 0.00 0.76 0.00 0.00 0.14 0.00 0.00
#> TCGA.A5.A0G1.01 4 0.1804 0.879 0.00 0.02 0.00 0.90 0.00 0.00 0.08 0.00
#> TCGA.B5.A3FA.01 5 0.4371 0.689 0.00 0.00 0.00 0.00 0.68 0.02 0.16 0.14
#> TCGA.AJ.A3OJ.01 2 0.0808 0.914 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.AJ.A8CT.01 3 0.3450 0.814 0.12 0.00 0.76 0.00 0.00 0.12 0.00 0.00
#> TCGA.BG.A2AE.01 8 0.5439 0.185 0.00 0.00 0.02 0.36 0.02 0.00 0.12 0.48
#> TCGA.D1.A2G6.01 5 0.1741 0.889 0.00 0.00 0.02 0.00 0.92 0.04 0.02 0.00
#> TCGA.B5.A11N.01 5 0.1275 0.889 0.00 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.BS.A0UA.01 6 0.0000 0.927 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BS.A0V6.01 3 0.3198 0.737 0.26 0.00 0.72 0.00 0.00 0.00 0.02 0.00
#> TCGA.AJ.A3NE.01 6 0.0000 0.927 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A17B.01 6 0.1557 0.881 0.00 0.00 0.02 0.00 0.06 0.92 0.00 0.00
#> TCGA.A5.AB3J.01 3 0.4620 0.681 0.00 0.00 0.68 0.00 0.12 0.14 0.06 0.00
#> TCGA.DF.A2KN.01 2 0.0808 0.914 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.B5.A5OC.01 4 0.1804 0.863 0.00 0.02 0.00 0.90 0.00 0.00 0.08 0.00
#> TCGA.BK.A139.02 8 0.4492 0.677 0.00 0.00 0.02 0.00 0.18 0.04 0.06 0.70
#> TCGA.BK.A139.01 8 0.4963 0.650 0.00 0.00 0.02 0.00 0.18 0.08 0.06 0.66
#> TCGA.D1.A16G.01 4 0.0941 0.884 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.AJ.A3BH.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 1 0.2165 0.901 0.88 0.00 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.AX.A06H.01 5 0.1607 0.885 0.00 0.00 0.04 0.00 0.92 0.04 0.00 0.00
#> TCGA.A5.A0GQ.01 6 0.0471 0.926 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.B5.A11X.01 6 0.2807 0.832 0.00 0.00 0.02 0.02 0.00 0.86 0.06 0.04
#> TCGA.D1.A16E.01 3 0.3660 0.751 0.00 0.00 0.70 0.00 0.00 0.24 0.06 0.00
#> TCGA.BG.A0VV.01 1 0.1557 0.889 0.92 0.00 0.06 0.00 0.00 0.00 0.02 0.00
#> TCGA.EY.A1G7.01 8 0.4540 0.669 0.00 0.00 0.06 0.10 0.02 0.00 0.10 0.72
#> TCGA.DF.A2KY.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.01 2 0.3660 0.774 0.00 0.70 0.00 0.06 0.00 0.00 0.24 0.00
#> TCGA.DF.A2KZ.01 6 0.3337 0.730 0.00 0.00 0.04 0.00 0.16 0.78 0.02 0.00
#> TCGA.AP.A1E3.01 3 0.3660 0.751 0.00 0.00 0.70 0.00 0.00 0.24 0.06 0.00
#> TCGA.D1.A0ZS.01 4 0.4471 0.651 0.00 0.00 0.02 0.70 0.02 0.00 0.10 0.16
#> TCGA.EC.A1QX.01 4 0.2482 0.841 0.00 0.00 0.02 0.88 0.02 0.00 0.06 0.02
#> TCGA.4E.A92E.01 1 0.1947 0.870 0.86 0.00 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.BS.A0UL.01 5 0.3078 0.801 0.00 0.00 0.02 0.00 0.82 0.10 0.06 0.00
#> TCGA.B5.A11O.01 6 0.0471 0.926 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.AJ.A3NG.01 1 0.4061 0.738 0.72 0.00 0.12 0.00 0.00 0.00 0.14 0.02
#> TCGA.AX.A2HG.01 4 0.2859 0.849 0.00 0.02 0.02 0.82 0.00 0.00 0.14 0.00
#> TCGA.D1.A16J.01 2 0.0808 0.914 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.QS.A5YR.01 6 0.1557 0.863 0.00 0.00 0.06 0.00 0.00 0.92 0.02 0.00
#> TCGA.EO.A3L0.01 5 0.0808 0.890 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.DI.A1BU.01 4 0.0941 0.880 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.BS.A0T9.01 1 0.1557 0.889 0.92 0.00 0.06 0.00 0.00 0.00 0.02 0.00
#> TCGA.B5.A3F9.01 1 0.0000 0.916 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KR.01 5 0.3847 0.794 0.00 0.00 0.04 0.00 0.78 0.02 0.10 0.06
#> TCGA.SJ.A6ZI.01 4 0.2132 0.852 0.00 0.00 0.00 0.88 0.04 0.00 0.08 0.00
#> TCGA.DF.A2KV.01 6 0.0471 0.926 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.A5.A2K3.01 2 0.1563 0.900 0.00 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.BG.A0VX.01 1 0.0471 0.915 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.A5.A0GG.01 3 0.3660 0.751 0.00 0.00 0.70 0.00 0.00 0.24 0.06 0.00
#> TCGA.A5.A1OJ.01 3 0.3660 0.751 0.00 0.00 0.70 0.00 0.00 0.24 0.06 0.00
#> TCGA.B5.A121.01 1 0.2165 0.901 0.88 0.00 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.B5.A11M.01 1 0.1091 0.915 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.B5.A3S1.01 8 0.2114 0.713 0.00 0.00 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.AJ.A3OK.01 1 0.1563 0.888 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.B5.A11Y.01 6 0.0000 0.927 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EO.A3AS.01 5 0.3770 0.833 0.00 0.00 0.02 0.00 0.78 0.04 0.12 0.04
#> TCGA.D1.A2G0.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17C.01 3 0.3660 0.764 0.24 0.00 0.70 0.00 0.00 0.00 0.06 0.00
#> TCGA.EO.A3AV.01 2 0.2114 0.879 0.00 0.84 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.D1.A16D.01 3 0.2650 0.766 0.24 0.00 0.76 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AZ.01 2 0.1563 0.900 0.00 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.D1.A169.01 3 0.3434 0.814 0.10 0.00 0.76 0.00 0.00 0.14 0.00 0.00
#> TCGA.AJ.A6NU.01 5 0.1887 0.879 0.00 0.00 0.00 0.00 0.90 0.04 0.06 0.00
#> TCGA.D1.A16B.01 1 0.0471 0.915 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.AP.A059.01 4 0.1804 0.879 0.00 0.02 0.00 0.90 0.00 0.00 0.08 0.00
#> TCGA.AJ.A2QK.01 3 0.2650 0.766 0.24 0.00 0.76 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1O8.01 6 0.0471 0.926 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.D1.A162.01 1 0.2165 0.901 0.88 0.00 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.FI.A2D5.01 3 0.3660 0.751 0.00 0.00 0.70 0.00 0.00 0.24 0.06 0.00
#> TCGA.E6.A2P8.01 2 0.3293 0.814 0.00 0.74 0.00 0.04 0.00 0.00 0.22 0.00
#> TCGA.AX.A2IN.01 4 0.3454 0.794 0.00 0.00 0.02 0.80 0.02 0.00 0.12 0.04
#> TCGA.AJ.A23O.01 5 0.2071 0.884 0.00 0.00 0.04 0.00 0.90 0.04 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["041"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 34 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.995 0.998 0.3346 0.663 0.663
#> 3 3 0.823 0.885 0.949 0.7651 0.684 0.547
#> 4 4 0.611 0.608 0.808 0.1865 0.695 0.394
#> 5 5 0.881 0.839 0.926 0.0774 0.807 0.468
#> 6 6 0.780 0.781 0.844 0.0538 0.963 0.862
#> 7 7 0.776 0.672 0.794 0.0578 0.809 0.409
#> 8 8 0.796 0.704 0.826 0.0317 0.900 0.525
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.D1.A0ZV.01 1 0.000 1.000 1.00 0.00
#> TCGA.BG.A18A.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A17N.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A16O.01 1 0.000 1.000 1.00 0.00
#> TCGA.BS.A0V7.01 1 0.000 1.000 1.00 0.00
#> TCGA.B5.A11H.01 2 0.000 0.987 0.00 1.00
#> TCGA.QF.A5YS.01 1 0.000 1.000 1.00 0.00
#> TCGA.BK.A0CA.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A16F.01 2 0.402 0.913 0.08 0.92
#> TCGA.D1.A16X.01 1 0.000 1.000 1.00 0.00
#> TCGA.B5.A1MV.01 2 0.000 0.987 0.00 1.00
#> TCGA.AJ.A8CT.01 1 0.000 1.000 1.00 0.00
#> TCGA.BS.A0V6.01 1 0.000 1.000 1.00 0.00
#> TCGA.A5.AB3J.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A06L.01 1 0.000 1.000 1.00 0.00
#> TCGA.BG.A0VV.01 1 0.000 1.000 1.00 0.00
#> TCGA.AP.A1E3.01 1 0.000 1.000 1.00 0.00
#> TCGA.4E.A92E.01 1 0.000 1.000 1.00 0.00
#> TCGA.AJ.A3NG.01 2 0.000 0.987 0.00 1.00
#> TCGA.BS.A0T9.01 2 0.000 0.987 0.00 1.00
#> TCGA.B5.A3F9.01 1 0.000 1.000 1.00 0.00
#> TCGA.BG.A0VX.01 1 0.000 1.000 1.00 0.00
#> TCGA.A5.A0GG.01 1 0.000 1.000 1.00 0.00
#> TCGA.A5.A1OJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.B5.A121.01 1 0.000 1.000 1.00 0.00
#> TCGA.B5.A11M.01 1 0.000 1.000 1.00 0.00
#> TCGA.AJ.A3OK.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A17C.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A16D.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A169.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A16B.01 1 0.000 1.000 1.00 0.00
#> TCGA.AJ.A2QK.01 2 0.000 0.987 0.00 1.00
#> TCGA.D1.A162.01 1 0.000 1.000 1.00 0.00
#> TCGA.FI.A2D5.01 2 0.000 0.987 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D1.A0ZV.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.BG.A18A.01 1 0.540 0.648 0.72 0.00 0.28
#> TCGA.D1.A17N.01 1 0.480 0.725 0.78 0.00 0.22
#> TCGA.D1.A16O.01 1 0.556 0.618 0.70 0.00 0.30
#> TCGA.BS.A0V7.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.B5.A11H.01 2 0.000 0.856 0.00 1.00 0.00
#> TCGA.QF.A5YS.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BK.A0CA.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.D1.A16F.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.D1.A16X.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.B5.A1MV.01 2 0.540 0.707 0.28 0.72 0.00
#> TCGA.AJ.A8CT.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BS.A0V6.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.A5.AB3J.01 1 0.604 0.468 0.62 0.00 0.38
#> TCGA.AX.A06L.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.BG.A0VV.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.AP.A1E3.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.4E.A92E.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.AJ.A3NG.01 2 0.000 0.856 0.00 1.00 0.00
#> TCGA.BS.A0T9.01 2 0.000 0.856 0.00 1.00 0.00
#> TCGA.B5.A3F9.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.BG.A0VX.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.A5.A0GG.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.A5.A1OJ.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.B5.A121.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.B5.A11M.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.AJ.A3OK.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D1.A17C.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D1.A16D.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.D1.A169.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.D1.A16B.01 1 0.000 0.924 1.00 0.00 0.00
#> TCGA.AJ.A2QK.01 2 0.540 0.707 0.28 0.72 0.00
#> TCGA.D1.A162.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.FI.A2D5.01 2 0.000 0.856 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D1.A0ZV.01 4 0.1637 0.704 0.06 0.00 0.00 0.94
#> TCGA.BG.A18A.01 4 0.0000 0.739 0.00 0.00 0.00 1.00
#> TCGA.D1.A17N.01 4 0.0000 0.739 0.00 0.00 0.00 1.00
#> TCGA.D1.A16O.01 4 0.0000 0.739 0.00 0.00 0.00 1.00
#> TCGA.BS.A0V7.01 4 0.4134 0.512 0.00 0.00 0.26 0.74
#> TCGA.B5.A11H.01 2 0.0000 0.937 0.00 1.00 0.00 0.00
#> TCGA.QF.A5YS.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BK.A0CA.01 1 0.4948 0.606 0.56 0.00 0.00 0.44
#> TCGA.D1.A16F.01 1 0.0000 0.424 1.00 0.00 0.00 0.00
#> TCGA.D1.A16X.01 4 0.1637 0.704 0.06 0.00 0.00 0.94
#> TCGA.B5.A1MV.01 1 0.4948 -0.473 0.56 0.44 0.00 0.00
#> TCGA.AJ.A8CT.01 4 0.4948 0.129 0.00 0.00 0.44 0.56
#> TCGA.BS.A0V6.01 1 0.3801 0.632 0.78 0.00 0.00 0.22
#> TCGA.A5.AB3J.01 4 0.0707 0.732 0.00 0.00 0.02 0.98
#> TCGA.AX.A06L.01 1 0.4977 0.577 0.54 0.00 0.00 0.46
#> TCGA.BG.A0VV.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AP.A1E3.01 4 0.4713 -0.162 0.36 0.00 0.00 0.64
#> TCGA.4E.A92E.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3NG.01 2 0.0000 0.937 0.00 1.00 0.00 0.00
#> TCGA.BS.A0T9.01 2 0.3801 0.808 0.22 0.78 0.00 0.00
#> TCGA.B5.A3F9.01 1 0.3801 0.632 0.78 0.00 0.00 0.22
#> TCGA.BG.A0VX.01 1 0.4624 0.657 0.66 0.00 0.00 0.34
#> TCGA.A5.A0GG.01 1 0.4624 0.657 0.66 0.00 0.00 0.34
#> TCGA.A5.A1OJ.01 1 0.4522 0.657 0.68 0.00 0.00 0.32
#> TCGA.B5.A121.01 1 0.4994 0.539 0.52 0.00 0.00 0.48
#> TCGA.B5.A11M.01 4 0.1637 0.704 0.06 0.00 0.00 0.94
#> TCGA.AJ.A3OK.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A17C.01 4 0.4948 0.129 0.00 0.00 0.44 0.56
#> TCGA.D1.A16D.01 4 0.0707 0.732 0.02 0.00 0.00 0.98
#> TCGA.D1.A169.01 1 0.4948 0.606 0.56 0.00 0.00 0.44
#> TCGA.D1.A16B.01 1 0.4948 0.606 0.56 0.00 0.00 0.44
#> TCGA.AJ.A2QK.01 1 0.4948 -0.473 0.56 0.44 0.00 0.00
#> TCGA.D1.A162.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FI.A2D5.01 2 0.0000 0.937 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.D1.A0ZV.01 1 0.4767 0.303 0.56 0.02 0.00 0.42 0.00
#> TCGA.BG.A18A.01 4 0.1216 0.912 0.02 0.02 0.00 0.96 0.00
#> TCGA.D1.A17N.01 4 0.1216 0.912 0.02 0.02 0.00 0.96 0.00
#> TCGA.D1.A16O.01 4 0.2249 0.884 0.02 0.04 0.00 0.92 0.02
#> TCGA.BS.A0V7.01 4 0.0609 0.915 0.02 0.00 0.00 0.98 0.00
#> TCGA.B5.A11H.01 2 0.1410 0.992 0.00 0.94 0.00 0.00 0.06
#> TCGA.QF.A5YS.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BK.A0CA.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16F.01 5 0.1732 0.886 0.08 0.00 0.00 0.00 0.92
#> TCGA.D1.A16X.01 1 0.4726 0.351 0.58 0.02 0.00 0.40 0.00
#> TCGA.B5.A1MV.01 5 0.0609 0.948 0.02 0.00 0.00 0.00 0.98
#> TCGA.AJ.A8CT.01 4 0.0609 0.906 0.00 0.00 0.02 0.98 0.00
#> TCGA.BS.A0V6.01 1 0.0609 0.840 0.98 0.00 0.00 0.00 0.02
#> TCGA.A5.AB3J.01 4 0.0609 0.915 0.02 0.00 0.00 0.98 0.00
#> TCGA.AX.A06L.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.BG.A0VV.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.AP.A1E3.01 1 0.3690 0.676 0.78 0.02 0.00 0.20 0.00
#> TCGA.4E.A92E.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NG.01 2 0.2012 0.984 0.00 0.92 0.00 0.02 0.06
#> TCGA.BS.A0T9.01 5 0.1043 0.916 0.00 0.04 0.00 0.00 0.96
#> TCGA.B5.A3F9.01 1 0.0609 0.840 0.98 0.00 0.00 0.00 0.02
#> TCGA.BG.A0VX.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A0GG.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A1OJ.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A121.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11M.01 1 0.4798 0.246 0.54 0.02 0.00 0.44 0.00
#> TCGA.AJ.A3OK.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A17C.01 4 0.0609 0.906 0.00 0.00 0.02 0.98 0.00
#> TCGA.D1.A16D.01 4 0.4456 0.411 0.32 0.02 0.00 0.66 0.00
#> TCGA.D1.A169.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16B.01 1 0.0000 0.856 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A2QK.01 5 0.0609 0.948 0.02 0.00 0.00 0.00 0.98
#> TCGA.D1.A162.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.FI.A2D5.01 2 0.1410 0.992 0.00 0.94 0.00 0.00 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D1.A0ZV.01 6 0.5419 0.574 0.20 0.00 0 0.22 0.00 0.58
#> TCGA.BG.A18A.01 4 0.1556 0.880 0.08 0.00 0 0.92 0.00 0.00
#> TCGA.D1.A17N.01 4 0.1556 0.880 0.08 0.00 0 0.92 0.00 0.00
#> TCGA.D1.A16O.01 4 0.4902 0.462 0.46 0.06 0 0.48 0.00 0.00
#> TCGA.BS.A0V7.01 4 0.0000 0.903 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B5.A11H.01 2 0.1267 1.000 0.00 0.94 0 0.00 0.06 0.00
#> TCGA.QF.A5YS.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.BK.A0CA.01 6 0.2793 0.688 0.20 0.00 0 0.00 0.00 0.80
#> TCGA.D1.A16F.01 5 0.3499 0.567 0.00 0.00 0 0.00 0.68 0.32
#> TCGA.D1.A16X.01 6 0.5419 0.574 0.20 0.00 0 0.22 0.00 0.58
#> TCGA.B5.A1MV.01 5 0.0000 0.849 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.AJ.A8CT.01 4 0.0000 0.903 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BS.A0V6.01 6 0.2631 0.686 0.18 0.00 0 0.00 0.00 0.82
#> TCGA.A5.AB3J.01 4 0.0000 0.903 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.AX.A06L.01 6 0.3851 0.663 0.46 0.00 0 0.00 0.00 0.54
#> TCGA.BG.A0VV.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.AP.A1E3.01 6 0.2794 0.672 0.06 0.00 0 0.08 0.00 0.86
#> TCGA.4E.A92E.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.AJ.A3NG.01 2 0.1267 1.000 0.00 0.94 0 0.00 0.06 0.00
#> TCGA.BS.A0T9.01 5 0.0547 0.843 0.02 0.00 0 0.00 0.98 0.00
#> TCGA.B5.A3F9.01 6 0.2454 0.699 0.16 0.00 0 0.00 0.00 0.84
#> TCGA.BG.A0VX.01 6 0.2793 0.688 0.20 0.00 0 0.00 0.00 0.80
#> TCGA.A5.A0GG.01 6 0.1556 0.714 0.08 0.00 0 0.00 0.00 0.92
#> TCGA.A5.A1OJ.01 6 0.0000 0.697 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.B5.A121.01 6 0.3851 0.663 0.46 0.00 0 0.00 0.00 0.54
#> TCGA.B5.A11M.01 6 0.5419 0.574 0.20 0.00 0 0.22 0.00 0.58
#> TCGA.AJ.A3OK.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D1.A17C.01 4 0.0000 0.903 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.D1.A16D.01 6 0.5618 0.344 0.16 0.00 0 0.34 0.00 0.50
#> TCGA.D1.A169.01 6 0.2048 0.704 0.12 0.00 0 0.00 0.00 0.88
#> TCGA.D1.A16B.01 6 0.3851 0.663 0.46 0.00 0 0.00 0.00 0.54
#> TCGA.AJ.A2QK.01 5 0.0000 0.849 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.D1.A162.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.FI.A2D5.01 2 0.1267 1.000 0.00 0.94 0 0.00 0.06 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D1.A0ZV.01 4 0.7004 0.270 0.00 0.00 0.00 0.32 0.28 0.18 0.22
#> TCGA.BG.A18A.01 4 0.1671 0.652 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.D1.A17N.01 4 0.1671 0.652 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.D1.A16O.01 4 0.3943 0.419 0.00 0.00 0.00 0.56 0.42 0.00 0.02
#> TCGA.BS.A0V7.01 4 0.0000 0.647 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11H.01 2 0.0000 0.958 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QF.A5YS.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CA.01 6 0.3307 0.487 0.00 0.00 0.00 0.00 0.02 0.74 0.24
#> TCGA.D1.A16F.01 6 0.4244 0.181 0.42 0.00 0.00 0.00 0.04 0.54 0.00
#> TCGA.D1.A16X.01 4 0.7054 0.244 0.00 0.00 0.00 0.30 0.28 0.20 0.22
#> TCGA.B5.A1MV.01 1 0.0000 0.885 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A8CT.01 4 0.0863 0.631 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.BS.A0V6.01 6 0.3519 0.514 0.00 0.00 0.00 0.00 0.04 0.74 0.22
#> TCGA.A5.AB3J.01 4 0.0000 0.647 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 7 0.2081 1.000 0.00 0.00 0.00 0.00 0.00 0.14 0.86
#> TCGA.BG.A0VV.01 3 0.0504 0.988 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AP.A1E3.01 6 0.4649 0.390 0.00 0.00 0.00 0.06 0.30 0.62 0.02
#> TCGA.4E.A92E.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NG.01 2 0.2016 0.915 0.00 0.90 0.00 0.00 0.06 0.00 0.04
#> TCGA.BS.A0T9.01 1 0.4260 0.748 0.74 0.08 0.00 0.00 0.14 0.00 0.04
#> TCGA.B5.A3F9.01 6 0.1718 0.591 0.00 0.00 0.00 0.00 0.04 0.92 0.04
#> TCGA.BG.A0VX.01 6 0.4015 0.456 0.00 0.00 0.00 0.00 0.06 0.68 0.26
#> TCGA.A5.A0GG.01 6 0.4030 0.432 0.00 0.00 0.00 0.00 0.16 0.72 0.12
#> TCGA.A5.A1OJ.01 6 0.0000 0.604 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B5.A121.01 7 0.2081 1.000 0.00 0.00 0.00 0.00 0.00 0.14 0.86
#> TCGA.B5.A11M.01 4 0.6970 0.287 0.00 0.00 0.00 0.32 0.30 0.18 0.20
#> TCGA.AJ.A3OK.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17C.01 4 0.0863 0.631 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.D1.A16D.01 4 0.6211 0.384 0.00 0.00 0.00 0.42 0.34 0.06 0.18
#> TCGA.D1.A169.01 6 0.4338 0.410 0.00 0.00 0.00 0.00 0.28 0.64 0.08
#> TCGA.D1.A16B.01 7 0.2081 1.000 0.00 0.00 0.00 0.00 0.00 0.14 0.86
#> TCGA.AJ.A2QK.01 1 0.0000 0.885 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A162.01 3 0.0504 0.988 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FI.A2D5.01 2 0.0000 0.958 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.D1.A0ZV.01 5 0.4896 0.558 0.00 0.00 0.00 0.16 0.46 0.00 0.38 0.00
#> TCGA.BG.A18A.01 4 0.3083 0.392 0.00 0.00 0.00 0.66 0.34 0.00 0.00 0.00
#> TCGA.D1.A17N.01 4 0.3083 0.392 0.00 0.00 0.00 0.66 0.34 0.00 0.00 0.00
#> TCGA.D1.A16O.01 8 0.4340 0.000 0.00 0.00 0.00 0.38 0.08 0.00 0.00 0.54
#> TCGA.BS.A0V7.01 4 0.0000 0.707 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11H.01 2 0.0000 0.959 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QF.A5YS.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A0CA.01 6 0.3523 0.668 0.00 0.00 0.00 0.00 0.10 0.78 0.10 0.02
#> TCGA.D1.A16F.01 6 0.2406 0.609 0.20 0.00 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.D1.A16X.01 5 0.4896 0.558 0.00 0.00 0.00 0.16 0.46 0.00 0.38 0.00
#> TCGA.B5.A1MV.01 1 0.0000 0.925 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A8CT.01 4 0.0000 0.707 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0V6.01 6 0.0471 0.710 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.A5.AB3J.01 4 0.0000 0.707 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 7 0.0471 1.000 0.00 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.BG.A0VV.01 3 0.0471 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AP.A1E3.01 5 0.4241 0.246 0.00 0.00 0.00 0.00 0.66 0.26 0.04 0.04
#> TCGA.4E.A92E.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NG.01 2 0.1804 0.917 0.00 0.90 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.BS.A0T9.01 1 0.2914 0.845 0.84 0.04 0.00 0.00 0.08 0.00 0.00 0.04
#> TCGA.B5.A3F9.01 6 0.4098 0.613 0.00 0.00 0.00 0.00 0.10 0.74 0.06 0.10
#> TCGA.BG.A0VX.01 6 0.4993 0.608 0.00 0.00 0.00 0.00 0.14 0.64 0.08 0.14
#> TCGA.A5.A0GG.01 6 0.6099 0.273 0.00 0.00 0.00 0.00 0.28 0.44 0.14 0.14
#> TCGA.A5.A1OJ.01 6 0.2547 0.695 0.00 0.00 0.00 0.00 0.12 0.84 0.00 0.04
#> TCGA.B5.A121.01 7 0.0471 1.000 0.00 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.B5.A11M.01 5 0.4799 0.598 0.00 0.00 0.00 0.18 0.54 0.00 0.28 0.00
#> TCGA.AJ.A3OK.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17C.01 4 0.0000 0.707 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16D.01 5 0.4849 0.539 0.00 0.00 0.00 0.22 0.54 0.00 0.24 0.00
#> TCGA.D1.A169.01 5 0.5350 0.170 0.00 0.00 0.00 0.00 0.54 0.28 0.12 0.06
#> TCGA.D1.A16B.01 7 0.0471 1.000 0.00 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.AJ.A2QK.01 1 0.0000 0.925 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A162.01 3 0.0471 0.987 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FI.A2D5.01 2 0.0000 0.959 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: Node041. Child nodes: Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02121-leaf , Node02122-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node02341-leaf , Node02342-leaf , Node04111-leaf , Node04112-leaf , Node04311-leaf , Node04312-leaf , Node04313-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0411"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.939 0.978 0.3459 0.641 0.641
#> 3 3 0.561 0.865 0.892 0.7153 0.601 0.433
#> 4 4 0.900 0.928 0.926 0.1711 0.915 0.767
#> 5 5 0.900 0.852 0.936 0.0763 0.923 0.752
#> 6 6 0.760 0.553 0.822 0.0671 0.889 0.610
#> 7 7 0.727 0.521 0.696 0.0452 0.889 0.585
#> 8 8 0.750 0.483 0.724 0.0353 0.877 0.494
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 4
There is also optional best \(k\) = 2 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.D1.A0ZV.01 1 0.000 0.991 1.00 0.00
#> TCGA.BG.A18A.01 1 0.000 0.991 1.00 0.00
#> TCGA.D1.A17N.01 1 0.000 0.991 1.00 0.00
#> TCGA.D1.A16O.01 1 0.000 0.991 1.00 0.00
#> TCGA.BS.A0V7.01 1 0.000 0.991 1.00 0.00
#> TCGA.QF.A5YS.01 2 0.000 0.909 0.00 1.00
#> TCGA.BK.A0CA.01 1 0.000 0.991 1.00 0.00
#> TCGA.D1.A16X.01 1 0.000 0.991 1.00 0.00
#> TCGA.AJ.A8CT.01 2 0.000 0.909 0.00 1.00
#> TCGA.BS.A0V6.01 1 0.000 0.991 1.00 0.00
#> TCGA.A5.AB3J.01 2 0.990 0.192 0.44 0.56
#> TCGA.AX.A06L.01 1 0.000 0.991 1.00 0.00
#> TCGA.BG.A0VV.01 1 0.634 0.788 0.84 0.16
#> TCGA.AP.A1E3.01 1 0.000 0.991 1.00 0.00
#> TCGA.4E.A92E.01 2 0.000 0.909 0.00 1.00
#> TCGA.B5.A3F9.01 1 0.000 0.991 1.00 0.00
#> TCGA.BG.A0VX.01 1 0.000 0.991 1.00 0.00
#> TCGA.A5.A0GG.01 1 0.000 0.991 1.00 0.00
#> TCGA.A5.A1OJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.B5.A121.01 1 0.000 0.991 1.00 0.00
#> TCGA.B5.A11M.01 1 0.000 0.991 1.00 0.00
#> TCGA.AJ.A3OK.01 2 0.000 0.909 0.00 1.00
#> TCGA.D1.A17C.01 1 0.000 0.991 1.00 0.00
#> TCGA.D1.A16D.01 1 0.000 0.991 1.00 0.00
#> TCGA.D1.A169.01 1 0.000 0.991 1.00 0.00
#> TCGA.D1.A16B.01 1 0.000 0.991 1.00 0.00
#> TCGA.D1.A162.01 2 0.000 0.909 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D1.A0ZV.01 1 0.369 0.779 0.86 0 0.14
#> TCGA.BG.A18A.01 1 0.613 0.697 0.60 0 0.40
#> TCGA.D1.A17N.01 1 0.613 0.697 0.60 0 0.40
#> TCGA.D1.A16O.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BS.A0V7.01 1 0.613 0.697 0.60 0 0.40
#> TCGA.QF.A5YS.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BK.A0CA.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D1.A16X.01 1 0.334 0.776 0.88 0 0.12
#> TCGA.AJ.A8CT.01 1 0.000 0.688 1.00 0 0.00
#> TCGA.BS.A0V6.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.A5.AB3J.01 1 0.000 0.688 1.00 0 0.00
#> TCGA.AX.A06L.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BG.A0VV.01 1 0.000 0.688 1.00 0 0.00
#> TCGA.AP.A1E3.01 1 0.613 0.697 0.60 0 0.40
#> TCGA.4E.A92E.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B5.A3F9.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BG.A0VX.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.A5.A0GG.01 1 0.369 0.779 0.86 0 0.14
#> TCGA.A5.A1OJ.01 1 0.613 0.697 0.60 0 0.40
#> TCGA.B5.A121.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.B5.A11M.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.AJ.A3OK.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.D1.A17C.01 1 0.334 0.776 0.88 0 0.12
#> TCGA.D1.A16D.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D1.A169.01 1 0.613 0.697 0.60 0 0.40
#> TCGA.D1.A16B.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D1.A162.01 2 0.000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D1.A0ZV.01 1 0.0707 0.919 0.98 0 0.02 0.0
#> TCGA.BG.A18A.01 1 0.2011 0.947 0.92 0 0.08 0.0
#> TCGA.D1.A17N.01 1 0.2011 0.947 0.92 0 0.08 0.0
#> TCGA.D1.A16O.01 3 0.6933 0.506 0.14 0 0.56 0.3
#> TCGA.BS.A0V7.01 1 0.2011 0.947 0.92 0 0.08 0.0
#> TCGA.QF.A5YS.01 2 0.0000 1.000 0.00 1 0.00 0.0
#> TCGA.BK.A0CA.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.D1.A16X.01 1 0.0000 0.896 1.00 0 0.00 0.0
#> TCGA.AJ.A8CT.01 4 0.4406 1.000 0.30 0 0.00 0.7
#> TCGA.BS.A0V6.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.A5.AB3J.01 4 0.4406 1.000 0.30 0 0.00 0.7
#> TCGA.AX.A06L.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.BG.A0VV.01 4 0.4406 1.000 0.30 0 0.00 0.7
#> TCGA.AP.A1E3.01 1 0.2011 0.947 0.92 0 0.08 0.0
#> TCGA.4E.A92E.01 2 0.0000 1.000 0.00 1 0.00 0.0
#> TCGA.B5.A3F9.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.BG.A0VX.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.A5.A0GG.01 1 0.0707 0.919 0.98 0 0.02 0.0
#> TCGA.A5.A1OJ.01 1 0.2011 0.947 0.92 0 0.08 0.0
#> TCGA.B5.A121.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.B5.A11M.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.AJ.A3OK.01 2 0.0000 1.000 0.00 1 0.00 0.0
#> TCGA.D1.A17C.01 1 0.0000 0.896 1.00 0 0.00 0.0
#> TCGA.D1.A16D.01 3 0.3172 0.770 0.16 0 0.84 0.0
#> TCGA.D1.A169.01 1 0.2011 0.947 0.92 0 0.08 0.0
#> TCGA.D1.A16B.01 3 0.0000 0.935 0.00 0 1.00 0.0
#> TCGA.D1.A162.01 2 0.0000 1.000 0.00 1 0.00 0.0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D1.A0ZV.01 1 0.1410 0.882 0.94 0.00 0.00 0.00 0.06
#> TCGA.BG.A18A.01 1 0.0609 0.891 0.98 0.00 0.00 0.00 0.02
#> TCGA.D1.A17N.01 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16O.01 5 0.4458 0.000 0.12 0.00 0.12 0.00 0.76
#> TCGA.BS.A0V7.01 1 0.1410 0.898 0.94 0.00 0.00 0.00 0.06
#> TCGA.QF.A5YS.01 2 0.0609 0.964 0.00 0.98 0.00 0.00 0.02
#> TCGA.BK.A0CA.01 3 0.1732 0.894 0.00 0.00 0.92 0.00 0.08
#> TCGA.D1.A16X.01 1 0.1410 0.882 0.94 0.00 0.00 0.00 0.06
#> TCGA.AJ.A8CT.01 4 0.0000 0.983 0.00 0.00 0.00 1.00 0.00
#> TCGA.BS.A0V6.01 3 0.1732 0.894 0.00 0.00 0.92 0.00 0.08
#> TCGA.A5.AB3J.01 4 0.0000 0.983 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A06L.01 3 0.0000 0.908 0.00 0.00 1.00 0.00 0.00
#> TCGA.BG.A0VV.01 4 0.1043 0.967 0.00 0.00 0.00 0.96 0.04
#> TCGA.AP.A1E3.01 1 0.1410 0.898 0.94 0.00 0.00 0.00 0.06
#> TCGA.4E.A92E.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A3F9.01 3 0.3697 0.788 0.08 0.00 0.82 0.00 0.10
#> TCGA.BG.A0VX.01 3 0.0000 0.908 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A0GG.01 1 0.2020 0.881 0.90 0.00 0.00 0.00 0.10
#> TCGA.A5.A1OJ.01 1 0.1410 0.898 0.94 0.00 0.00 0.00 0.06
#> TCGA.B5.A121.01 3 0.0000 0.908 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11M.01 3 0.3521 0.804 0.04 0.00 0.82 0.00 0.14
#> TCGA.AJ.A3OK.01 2 0.1732 0.928 0.00 0.92 0.00 0.00 0.08
#> TCGA.D1.A17C.01 1 0.1410 0.898 0.94 0.00 0.00 0.00 0.06
#> TCGA.D1.A16D.01 1 0.5263 0.302 0.66 0.00 0.24 0.00 0.10
#> TCGA.D1.A169.01 1 0.0609 0.891 0.98 0.00 0.00 0.00 0.02
#> TCGA.D1.A16B.01 3 0.0000 0.908 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A162.01 2 0.0000 0.971 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.D1.A0ZV.01 6 0.3864 0.3590 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.BG.A18A.01 1 0.3198 0.1180 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.D1.A17N.01 1 0.2454 0.4090 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.D1.A16O.01 5 0.2190 0.0000 0.04 0.00 0.00 0.00 0.90 0.06
#> TCGA.BS.A0V7.01 1 0.0937 0.5410 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.QF.A5YS.01 2 0.0547 0.9315 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BK.A0CA.01 3 0.3076 0.7906 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.D1.A16X.01 6 0.3864 0.3590 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.AJ.A8CT.01 4 0.0000 0.9650 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BS.A0V6.01 3 0.3198 0.7834 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.A5.AB3J.01 4 0.0000 0.9650 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A06L.01 3 0.0000 0.7754 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0VV.01 4 0.1807 0.9285 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.AP.A1E3.01 1 0.0547 0.5462 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.4E.A92E.01 2 0.0000 0.9385 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3F9.01 3 0.5734 0.4875 0.10 0.00 0.48 0.00 0.02 0.40
#> TCGA.BG.A0VX.01 3 0.2793 0.7994 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.A5.A0GG.01 1 0.2941 0.3215 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.A5.A1OJ.01 1 0.0000 0.5494 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A121.01 3 0.0000 0.7754 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11M.01 1 0.6039 -0.2613 0.42 0.00 0.30 0.00 0.00 0.28
#> TCGA.AJ.A3OK.01 2 0.3321 0.8208 0.00 0.82 0.00 0.00 0.08 0.10
#> TCGA.D1.A17C.01 1 0.0937 0.5315 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.D1.A16D.01 6 0.5992 0.0715 0.36 0.00 0.14 0.00 0.02 0.48
#> TCGA.D1.A169.01 1 0.4199 -0.2957 0.60 0.00 0.00 0.00 0.02 0.38
#> TCGA.D1.A16B.01 3 0.0000 0.7754 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A162.01 2 0.0000 0.9385 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.D1.A0ZV.01 1 0.3496 0.416 0.58 0.00 0.42 0.00 0 0.00 0.00
#> TCGA.BG.A18A.01 1 0.2722 0.531 0.84 0.00 0.12 0.00 0 0.04 0.00
#> TCGA.D1.A17N.01 1 0.3388 0.585 0.76 0.00 0.04 0.00 0 0.20 0.00
#> TCGA.D1.A16O.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.BS.A0V7.01 1 0.3745 0.577 0.70 0.00 0.04 0.00 0 0.26 0.00
#> TCGA.QF.A5YS.01 2 0.1166 0.887 0.00 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.BK.A0CA.01 7 0.3496 0.325 0.00 0.00 0.00 0.00 0 0.42 0.58
#> TCGA.D1.A16X.01 1 0.3496 0.416 0.58 0.00 0.42 0.00 0 0.00 0.00
#> TCGA.AJ.A8CT.01 4 0.0000 0.850 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.BS.A0V6.01 7 0.3994 0.120 0.00 0.00 0.02 0.00 0 0.48 0.50
#> TCGA.A5.AB3J.01 4 0.0504 0.855 0.00 0.00 0.02 0.98 0 0.00 0.00
#> TCGA.AX.A06L.01 7 0.0000 0.598 0.00 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.BG.A0VV.01 4 0.3745 0.716 0.00 0.00 0.26 0.70 0 0.04 0.00
#> TCGA.AP.A1E3.01 1 0.4487 0.512 0.60 0.00 0.08 0.00 0 0.32 0.00
#> TCGA.4E.A92E.01 2 0.0000 0.904 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.B5.A3F9.01 6 0.5317 0.273 0.14 0.00 0.02 0.00 0 0.56 0.28
#> TCGA.BG.A0VX.01 7 0.3459 0.357 0.00 0.00 0.00 0.00 0 0.40 0.60
#> TCGA.A5.A0GG.01 1 0.5341 0.499 0.50 0.00 0.24 0.00 0 0.26 0.00
#> TCGA.A5.A1OJ.01 1 0.2945 0.580 0.74 0.00 0.00 0.00 0 0.26 0.00
#> TCGA.B5.A121.01 7 0.0000 0.598 0.00 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.B5.A11M.01 6 0.4260 0.446 0.08 0.00 0.04 0.00 0 0.74 0.14
#> TCGA.AJ.A3OK.01 2 0.4001 0.739 0.00 0.74 0.18 0.02 0 0.06 0.00
#> TCGA.D1.A17C.01 1 0.3667 0.595 0.74 0.00 0.06 0.00 0 0.20 0.00
#> TCGA.D1.A16D.01 1 0.5791 -0.246 0.44 0.00 0.10 0.00 0 0.40 0.06
#> TCGA.D1.A169.01 1 0.4146 0.438 0.68 0.00 0.24 0.00 0 0.08 0.00
#> TCGA.D1.A16B.01 7 0.0000 0.598 0.00 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.D1.A162.01 2 0.0000 0.904 0.00 1.00 0.00 0.00 0 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D1.A0ZV.01 3 0.4073 1.0000 0.24 0.00 0.66 0.0 0.00 0.00 0.00 0.10
#> TCGA.BG.A18A.01 1 0.4642 0.1670 0.60 0.00 0.06 0.0 0.00 0.04 0.00 0.30
#> TCGA.D1.A17N.01 1 0.5245 0.4062 0.58 0.00 0.08 0.0 0.00 0.24 0.00 0.10
#> TCGA.D1.A16O.01 5 0.0471 0.0000 0.00 0.00 0.00 0.0 0.98 0.00 0.00 0.02
#> TCGA.BS.A0V7.01 1 0.3975 0.4513 0.66 0.00 0.08 0.0 0.00 0.26 0.00 0.00
#> TCGA.QF.A5YS.01 2 0.2482 0.7869 0.00 0.88 0.02 0.0 0.02 0.02 0.00 0.06
#> TCGA.BK.A0CA.01 7 0.4588 0.3789 0.00 0.00 0.00 0.0 0.00 0.12 0.54 0.34
#> TCGA.D1.A16X.01 3 0.4073 1.0000 0.24 0.00 0.66 0.0 0.00 0.00 0.00 0.10
#> TCGA.AJ.A8CT.01 4 0.0000 0.8608 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BS.A0V6.01 8 0.4480 -0.0322 0.00 0.00 0.00 0.0 0.00 0.12 0.30 0.58
#> TCGA.A5.AB3J.01 4 0.0000 0.8608 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.AX.A06L.01 7 0.0471 0.6921 0.00 0.00 0.02 0.0 0.00 0.00 0.98 0.00
#> TCGA.BG.A0VV.01 4 0.3660 0.6987 0.00 0.00 0.06 0.7 0.00 0.24 0.00 0.00
#> TCGA.AP.A1E3.01 1 0.1947 0.4907 0.86 0.00 0.00 0.0 0.00 0.14 0.00 0.00
#> TCGA.4E.A92E.01 2 0.0000 0.8210 0.00 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.B5.A3F9.01 8 0.4848 -0.1410 0.02 0.00 0.00 0.0 0.00 0.34 0.10 0.54
#> TCGA.BG.A0VX.01 7 0.4538 0.4116 0.00 0.00 0.00 0.0 0.00 0.12 0.56 0.32
#> TCGA.A5.A0GG.01 1 0.4165 0.3370 0.64 0.00 0.26 0.0 0.00 0.10 0.00 0.00
#> TCGA.A5.A1OJ.01 1 0.3873 0.5214 0.72 0.00 0.06 0.0 0.00 0.20 0.00 0.02
#> TCGA.B5.A121.01 7 0.0000 0.6936 0.00 0.00 0.00 0.0 0.00 0.00 1.00 0.00
#> TCGA.B5.A11M.01 6 0.5665 0.0000 0.20 0.00 0.00 0.0 0.00 0.54 0.10 0.16
#> TCGA.AJ.A3OK.01 2 0.5314 0.4910 0.00 0.54 0.26 0.0 0.00 0.16 0.00 0.04
#> TCGA.D1.A17C.01 1 0.1741 0.4745 0.92 0.00 0.02 0.0 0.00 0.04 0.00 0.02
#> TCGA.D1.A16D.01 8 0.2407 0.3555 0.08 0.00 0.00 0.0 0.00 0.00 0.06 0.86
#> TCGA.D1.A169.01 8 0.4757 -0.1923 0.20 0.00 0.24 0.0 0.00 0.00 0.00 0.56
#> TCGA.D1.A16B.01 7 0.0471 0.6958 0.00 0.00 0.00 0.0 0.00 0.00 0.98 0.02
#> TCGA.D1.A162.01 2 0.0000 0.8210 0.00 1.00 0.00 0.0 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["042"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 27 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 0.5019 0.499 0.499
#> 3 3 1.000 0.984 0.976 0.3295 0.772 0.568
#> 4 4 0.746 0.795 0.810 0.1154 0.932 0.791
#> 5 5 0.877 0.919 0.925 0.0800 0.860 0.524
#> 6 6 0.880 0.782 0.900 0.0322 0.949 0.750
#> 7 7 0.823 0.748 0.881 0.0251 0.946 0.712
#> 8 8 0.847 0.625 0.789 0.0271 0.934 0.641
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.A5.A1OF.01 2 0 1 0 1
#> TCGA.PG.A6IB.01 2 0 1 0 1
#> TCGA.BG.A221.01 1 0 1 1 0
#> TCGA.EO.A22T.01 2 0 1 0 1
#> TCGA.FI.A2D6.01 2 0 1 0 1
#> TCGA.AX.A3FT.01 1 0 1 1 0
#> TCGA.B5.A1MR.01 1 0 1 1 0
#> TCGA.D1.A15X.01 2 0 1 0 1
#> TCGA.EY.A1GS.01 1 0 1 1 0
#> TCGA.A5.A0G1.01 2 0 1 0 1
#> TCGA.AJ.A3OJ.01 2 0 1 0 1
#> TCGA.DF.A2KN.01 2 0 1 0 1
#> TCGA.B5.A5OC.01 1 0 1 1 0
#> TCGA.D1.A16G.01 1 0 1 1 0
#> TCGA.AJ.A3BH.01 1 0 1 1 0
#> TCGA.DF.A2KY.01 2 0 1 0 1
#> TCGA.AX.A2H4.01 2 0 1 0 1
#> TCGA.AX.A2HG.01 2 0 1 0 1
#> TCGA.D1.A16J.01 1 0 1 1 0
#> TCGA.DI.A1BU.01 1 0 1 1 0
#> TCGA.SJ.A6ZI.01 2 0 1 0 1
#> TCGA.A5.A2K3.01 2 0 1 0 1
#> TCGA.D1.A2G0.01 2 0 1 0 1
#> TCGA.EO.A3AV.01 2 0 1 0 1
#> TCGA.EO.A3AZ.01 1 0 1 1 0
#> TCGA.AP.A059.01 1 0 1 1 0
#> TCGA.E6.A2P8.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A5.A1OF.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.PG.A6IB.01 3 0.207 1.000 0.00 0.06 0.94
#> TCGA.BG.A221.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.EO.A22T.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.FI.A2D6.01 3 0.207 1.000 0.00 0.06 0.94
#> TCGA.AX.A3FT.01 1 0.207 0.966 0.94 0.00 0.06
#> TCGA.B5.A1MR.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.D1.A15X.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.EY.A1GS.01 1 0.207 0.966 0.94 0.00 0.06
#> TCGA.A5.A0G1.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.AJ.A3OJ.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.DF.A2KN.01 3 0.207 1.000 0.00 0.06 0.94
#> TCGA.B5.A5OC.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.D1.A16G.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.AJ.A3BH.01 1 0.207 0.966 0.94 0.00 0.06
#> TCGA.DF.A2KY.01 3 0.207 1.000 0.00 0.06 0.94
#> TCGA.AX.A2H4.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.AX.A2HG.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.D1.A16J.01 1 0.207 0.966 0.94 0.00 0.06
#> TCGA.DI.A1BU.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.A5.A2K3.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.D1.A2G0.01 3 0.207 1.000 0.00 0.06 0.94
#> TCGA.EO.A3AV.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.EO.A3AZ.01 1 0.000 0.978 1.00 0.00 0.00
#> TCGA.AP.A059.01 2 0.207 0.925 0.06 0.94 0.00
#> TCGA.E6.A2P8.01 3 0.207 1.000 0.00 0.06 0.94
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.A5.A1OF.01 2 0.164 0.770 0.00 0.94 0.00 0.06
#> TCGA.PG.A6IB.01 3 0.000 0.743 0.00 0.00 1.00 0.00
#> TCGA.BG.A221.01 1 0.234 0.746 0.90 0.00 0.00 0.10
#> TCGA.EO.A22T.01 2 0.485 0.599 0.00 0.60 0.00 0.40
#> TCGA.FI.A2D6.01 3 0.000 0.743 0.00 0.00 1.00 0.00
#> TCGA.AX.A3FT.01 4 0.498 1.000 0.46 0.00 0.00 0.54
#> TCGA.B5.A1MR.01 1 0.000 0.934 1.00 0.00 0.00 0.00
#> TCGA.D1.A15X.01 2 0.000 0.790 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GS.01 4 0.498 1.000 0.46 0.00 0.00 0.54
#> TCGA.A5.A0G1.01 2 0.164 0.770 0.00 0.94 0.00 0.06
#> TCGA.AJ.A3OJ.01 2 0.485 0.599 0.00 0.60 0.00 0.40
#> TCGA.DF.A2KN.01 3 0.485 0.724 0.00 0.00 0.60 0.40
#> TCGA.B5.A5OC.01 1 0.000 0.934 1.00 0.00 0.00 0.00
#> TCGA.D1.A16G.01 1 0.164 0.845 0.94 0.00 0.00 0.06
#> TCGA.AJ.A3BH.01 4 0.498 1.000 0.46 0.00 0.00 0.54
#> TCGA.DF.A2KY.01 3 0.000 0.743 0.00 0.00 1.00 0.00
#> TCGA.AX.A2H4.01 2 0.000 0.790 0.00 1.00 0.00 0.00
#> TCGA.AX.A2HG.01 2 0.485 0.599 0.00 0.60 0.00 0.40
#> TCGA.D1.A16J.01 4 0.498 1.000 0.46 0.00 0.00 0.54
#> TCGA.DI.A1BU.01 1 0.000 0.934 1.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 2 0.485 0.599 0.00 0.60 0.00 0.40
#> TCGA.A5.A2K3.01 2 0.000 0.790 0.00 1.00 0.00 0.00
#> TCGA.D1.A2G0.01 3 0.485 0.724 0.00 0.00 0.60 0.40
#> TCGA.EO.A3AV.01 2 0.000 0.790 0.00 1.00 0.00 0.00
#> TCGA.EO.A3AZ.01 1 0.000 0.934 1.00 0.00 0.00 0.00
#> TCGA.AP.A059.01 2 0.394 0.695 0.10 0.84 0.00 0.06
#> TCGA.E6.A2P8.01 3 0.626 0.665 0.00 0.06 0.54 0.40
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.A5.A1OF.01 2 0.1043 0.929 0.00 0.96 0.04 0.00 0.00
#> TCGA.PG.A6IB.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.BG.A221.01 1 0.1043 0.934 0.96 0.00 0.00 0.04 0.00
#> TCGA.EO.A22T.01 3 0.1216 0.933 0.00 0.02 0.96 0.02 0.00
#> TCGA.FI.A2D6.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A3FT.01 4 0.3561 0.898 0.26 0.00 0.00 0.74 0.00
#> TCGA.B5.A1MR.01 1 0.0609 0.942 0.98 0.00 0.02 0.00 0.00
#> TCGA.D1.A15X.01 2 0.2077 0.923 0.00 0.92 0.04 0.04 0.00
#> TCGA.EY.A1GS.01 4 0.3274 0.927 0.22 0.00 0.00 0.78 0.00
#> TCGA.A5.A0G1.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3OJ.01 3 0.1216 0.931 0.00 0.02 0.96 0.02 0.00
#> TCGA.DF.A2KN.01 3 0.1410 0.916 0.00 0.00 0.94 0.00 0.06
#> TCGA.B5.A5OC.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.D1.A16G.01 1 0.2331 0.866 0.90 0.08 0.02 0.00 0.00
#> TCGA.AJ.A3BH.01 4 0.3274 0.927 0.22 0.00 0.00 0.78 0.00
#> TCGA.DF.A2KY.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A2H4.01 2 0.2077 0.923 0.00 0.92 0.04 0.04 0.00
#> TCGA.AX.A2HG.01 3 0.1648 0.929 0.00 0.02 0.94 0.04 0.00
#> TCGA.D1.A16J.01 4 0.2020 0.833 0.10 0.00 0.00 0.90 0.00
#> TCGA.DI.A1BU.01 1 0.0000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 3 0.0609 0.934 0.00 0.02 0.98 0.00 0.00
#> TCGA.A5.A2K3.01 2 0.3274 0.766 0.00 0.78 0.22 0.00 0.00
#> TCGA.D1.A2G0.01 3 0.3868 0.812 0.00 0.00 0.80 0.14 0.06
#> TCGA.EO.A3AV.01 2 0.1043 0.929 0.00 0.96 0.04 0.00 0.00
#> TCGA.EO.A3AZ.01 1 0.0609 0.951 0.98 0.00 0.00 0.02 0.00
#> TCGA.AP.A059.01 2 0.1648 0.880 0.04 0.94 0.02 0.00 0.00
#> TCGA.E6.A2P8.01 3 0.2012 0.917 0.00 0.00 0.92 0.02 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.A5.A1OF.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A6IB.01 5 0.0937 0.960 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.BG.A221.01 1 0.0547 0.905 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EO.A22T.01 3 0.0937 0.776 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.FI.A2D6.01 5 0.0000 0.980 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A3FT.01 4 0.3499 0.665 0.32 0.00 0.00 0.68 0.00 0.00
#> TCGA.B5.A1MR.01 1 0.0937 0.885 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.D1.A15X.01 2 0.1480 0.894 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.EY.A1GS.01 4 0.1814 0.880 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.A5.A0G1.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3OJ.01 3 0.2094 0.717 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.DF.A2KN.01 3 0.0937 0.753 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.B5.A5OC.01 1 0.0547 0.905 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.D1.A16G.01 1 0.4002 0.598 0.66 0.02 0.00 0.00 0.00 0.32
#> TCGA.AJ.A3BH.01 4 0.1814 0.880 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.DF.A2KY.01 5 0.0000 0.980 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A2H4.01 2 0.1480 0.894 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.AX.A2HG.01 3 0.1814 0.756 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.D1.A16J.01 4 0.0937 0.829 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.DI.A1BU.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 3 0.0000 0.770 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A5.A2K3.01 3 0.3647 0.204 0.00 0.36 0.64 0.00 0.00 0.00
#> TCGA.D1.A2G0.01 6 0.4902 0.000 0.00 0.00 0.46 0.06 0.00 0.48
#> TCGA.EO.A3AV.01 2 0.0000 0.909 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AZ.01 1 0.0547 0.905 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AP.A059.01 2 0.4002 0.599 0.02 0.66 0.00 0.00 0.00 0.32
#> TCGA.E6.A2P8.01 3 0.1556 0.759 0.00 0.00 0.92 0.00 0.00 0.08
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.A5.A1OF.01 2 0.2708 0.841 0.00 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.PG.A6IB.01 5 0.1664 0.905 0.00 0.00 0.02 0.00 0.92 0.00 0.06
#> TCGA.BG.A221.01 1 0.0000 0.863 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22T.01 3 0.0504 0.836 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FI.A2D6.01 5 0.0000 0.953 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FT.01 1 0.3459 0.175 0.60 0.00 0.00 0.40 0.00 0.00 0.00
#> TCGA.B5.A1MR.01 1 0.1928 0.767 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.D1.A15X.01 2 0.0000 0.776 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GS.01 4 0.1671 0.968 0.10 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.A5.A0G1.01 2 0.2708 0.841 0.00 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.AJ.A3OJ.01 3 0.3914 0.794 0.00 0.00 0.78 0.06 0.00 0.06 0.10
#> TCGA.DF.A2KN.01 3 0.2421 0.828 0.00 0.00 0.88 0.02 0.00 0.02 0.08
#> TCGA.B5.A5OC.01 1 0.0000 0.863 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16G.01 7 0.4070 0.315 0.34 0.00 0.00 0.00 0.00 0.04 0.62
#> TCGA.AJ.A3BH.01 4 0.1671 0.968 0.10 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.DF.A2KY.01 5 0.0000 0.953 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A2H4.01 2 0.0000 0.776 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2HG.01 3 0.1363 0.832 0.00 0.00 0.94 0.04 0.00 0.02 0.00
#> TCGA.D1.A16J.01 4 0.2769 0.934 0.08 0.00 0.00 0.86 0.00 0.02 0.04
#> TCGA.DI.A1BU.01 1 0.0000 0.863 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 3 0.3000 0.819 0.00 0.00 0.84 0.02 0.00 0.04 0.10
#> TCGA.A5.A2K3.01 3 0.4146 0.587 0.00 0.02 0.64 0.00 0.00 0.02 0.32
#> TCGA.D1.A2G0.01 6 0.1433 0.000 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.EO.A3AV.01 2 0.2832 0.824 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.EO.A3AZ.01 1 0.0000 0.863 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A059.01 7 0.2572 0.242 0.00 0.20 0.00 0.00 0.00 0.00 0.80
#> TCGA.E6.A2P8.01 3 0.1166 0.821 0.00 0.00 0.94 0.00 0.00 0.00 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.A5.A1OF.01 2 0.3333 0.708 0.00 0.50 0.00 0.00 0.00 0.00 0.50 0.00
#> TCGA.PG.A6IB.01 5 0.2856 0.725 0.00 0.00 0.00 0.02 0.78 0.00 0.00 0.20
#> TCGA.BG.A221.01 1 0.0000 0.860 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A22T.01 3 0.3142 0.603 0.00 0.00 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.FI.A2D6.01 5 0.0000 0.869 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3FT.01 4 0.3318 0.249 0.46 0.00 0.00 0.54 0.00 0.00 0.00 0.00
#> TCGA.B5.A1MR.01 1 0.1607 0.817 0.92 0.04 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.D1.A15X.01 7 0.0471 0.968 0.00 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.EY.A1GS.01 4 0.0471 0.763 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.A5.A0G1.01 2 0.3333 0.708 0.00 0.50 0.00 0.00 0.00 0.00 0.50 0.00
#> TCGA.AJ.A3OJ.01 3 0.3880 0.344 0.00 0.08 0.68 0.00 0.00 0.00 0.00 0.24
#> TCGA.DF.A2KN.01 3 0.3374 0.583 0.00 0.00 0.68 0.02 0.00 0.00 0.00 0.30
#> TCGA.B5.A5OC.01 1 0.0000 0.860 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16G.01 1 0.5445 0.171 0.42 0.36 0.00 0.00 0.00 0.02 0.00 0.20
#> TCGA.AJ.A3BH.01 4 0.0471 0.763 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KY.01 5 0.0000 0.869 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H4.01 7 0.0000 0.967 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A2HG.01 3 0.3922 0.578 0.00 0.06 0.64 0.00 0.00 0.00 0.00 0.30
#> TCGA.D1.A16J.01 4 0.2025 0.731 0.02 0.00 0.00 0.88 0.00 0.00 0.00 0.10
#> TCGA.DI.A1BU.01 1 0.0000 0.860 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SJ.A6ZI.01 3 0.0471 0.552 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A2K3.01 3 0.3333 -0.152 0.00 0.50 0.50 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G0.01 6 0.0941 0.000 0.00 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.EO.A3AV.01 2 0.3329 0.706 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.EO.A3AZ.01 1 0.0000 0.860 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A059.01 2 0.3227 0.333 0.00 0.78 0.00 0.00 0.00 0.00 0.14 0.08
#> TCGA.E6.A2P8.01 3 0.3299 0.579 0.00 0.00 0.56 0.00 0.00 0.00 0.00 0.44
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["043"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 38 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.997 0.998 0.4243 0.578 0.578
#> 3 3 0.742 0.722 0.887 0.5164 0.784 0.626
#> 4 4 0.655 0.662 0.764 0.1053 0.787 0.497
#> 5 5 0.630 0.505 0.747 0.0555 0.781 0.414
#> 6 6 0.698 0.766 0.845 0.0428 0.963 0.857
#> 7 7 0.752 0.617 0.834 0.0382 0.980 0.911
#> 8 8 0.743 0.629 0.730 0.0271 0.980 0.903
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.A5.A3LO.01 1 0.000 0.998 1.00 0.00
#> TCGA.AP.A0LM.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A101.01 1 0.000 0.998 1.00 0.00
#> TCGA.FI.A2D0.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A1NS.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A1C5.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A0IZ.01 1 0.327 0.936 0.94 0.06
#> TCGA.EY.A3QX.01 2 0.000 1.000 0.00 1.00
#> TCGA.B5.A3FA.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A2AE.01 2 0.000 1.000 0.00 1.00
#> TCGA.D1.A2G6.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11N.01 1 0.000 0.998 1.00 0.00
#> TCGA.BS.A0UA.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3NE.01 2 0.000 1.000 0.00 1.00
#> TCGA.D1.A17B.01 1 0.000 0.998 1.00 0.00
#> TCGA.BK.A139.02 2 0.000 1.000 0.00 1.00
#> TCGA.BK.A139.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A06H.01 1 0.000 0.998 1.00 0.00
#> TCGA.A5.A0GQ.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11X.01 2 0.000 1.000 0.00 1.00
#> TCGA.D1.A16E.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1G7.01 2 0.000 1.000 0.00 1.00
#> TCGA.DF.A2KZ.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A0ZS.01 2 0.000 1.000 0.00 1.00
#> TCGA.EC.A1QX.01 1 0.000 0.998 1.00 0.00
#> TCGA.BS.A0UL.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11O.01 1 0.000 0.998 1.00 0.00
#> TCGA.QS.A5YR.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A3L0.01 1 0.000 0.998 1.00 0.00
#> TCGA.DF.A2KR.01 1 0.000 0.998 1.00 0.00
#> TCGA.DF.A2KV.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A3S1.01 2 0.000 1.000 0.00 1.00
#> TCGA.B5.A11Y.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A3AS.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A6NU.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A1O8.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A2IN.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A23O.01 1 0.000 0.998 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A5.A3LO.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.AP.A0LM.01 1 0.6126 0.407 0.60 0.00 0.40
#> TCGA.D1.A101.01 3 0.6045 0.234 0.38 0.00 0.62
#> TCGA.FI.A2D0.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.D1.A1NS.01 3 0.0892 0.843 0.02 0.00 0.98
#> TCGA.AX.A1C5.01 2 0.0000 0.961 0.00 1.00 0.00
#> TCGA.AX.A0IZ.01 3 0.0000 0.831 0.00 0.00 1.00
#> TCGA.EY.A3QX.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.B5.A3FA.01 3 0.0892 0.843 0.02 0.00 0.98
#> TCGA.BG.A2AE.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.D1.A2G6.01 1 0.6244 0.321 0.56 0.00 0.44
#> TCGA.B5.A11N.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.BS.A0UA.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.AJ.A3NE.01 2 0.0000 0.961 0.00 1.00 0.00
#> TCGA.D1.A17B.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.BK.A139.02 2 0.0000 0.961 0.00 1.00 0.00
#> TCGA.BK.A139.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.AX.A06H.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.A5.A0GQ.01 1 0.6126 0.407 0.60 0.00 0.40
#> TCGA.B5.A11X.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.D1.A16E.01 3 0.0892 0.843 0.02 0.00 0.98
#> TCGA.EY.A1G7.01 2 0.0000 0.961 0.00 1.00 0.00
#> TCGA.DF.A2KZ.01 1 0.6244 0.321 0.56 0.00 0.44
#> TCGA.D1.A0ZS.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.EC.A1QX.01 3 0.0892 0.843 0.02 0.00 0.98
#> TCGA.BS.A0UL.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.B5.A11O.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.QS.A5YR.01 1 0.6126 0.407 0.60 0.00 0.40
#> TCGA.EO.A3L0.01 1 0.6309 0.123 0.50 0.00 0.50
#> TCGA.DF.A2KR.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.DF.A2KV.01 3 0.6045 0.234 0.38 0.00 0.62
#> TCGA.B5.A3S1.01 2 0.0000 0.961 0.00 1.00 0.00
#> TCGA.B5.A11Y.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.EO.A3AS.01 1 0.0000 0.781 1.00 0.00 0.00
#> TCGA.AJ.A6NU.01 1 0.6192 0.368 0.58 0.00 0.42
#> TCGA.D1.A1O8.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.AX.A2IN.01 3 0.0000 0.831 0.00 0.00 1.00
#> TCGA.AJ.A23O.01 1 0.0000 0.781 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.A5.A3LO.01 1 0.3975 0.7749 0.76 0.00 0.24 0.00
#> TCGA.AP.A0LM.01 3 0.4134 0.6386 0.26 0.00 0.74 0.00
#> TCGA.D1.A101.01 3 0.3400 0.6627 0.18 0.00 0.82 0.00
#> TCGA.FI.A2D0.01 1 0.0000 0.8038 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 3 0.4624 -0.0938 0.00 0.00 0.66 0.34
#> TCGA.AX.A1C5.01 2 0.0000 0.9402 0.00 1.00 0.00 0.00
#> TCGA.AX.A0IZ.01 3 0.5000 -0.4865 0.00 0.00 0.50 0.50
#> TCGA.EY.A3QX.01 4 0.5713 0.3996 0.00 0.34 0.04 0.62
#> TCGA.B5.A3FA.01 4 0.4406 0.6885 0.00 0.00 0.30 0.70
#> TCGA.BG.A2AE.01 2 0.1211 0.9219 0.00 0.96 0.00 0.04
#> TCGA.D1.A2G6.01 3 0.4134 0.6386 0.26 0.00 0.74 0.00
#> TCGA.B5.A11N.01 1 0.0000 0.8038 1.00 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 1 0.3975 0.7749 0.76 0.00 0.24 0.00
#> TCGA.AJ.A3NE.01 2 0.0000 0.9402 0.00 1.00 0.00 0.00
#> TCGA.D1.A17B.01 1 0.3975 0.7749 0.76 0.00 0.24 0.00
#> TCGA.BK.A139.02 2 0.0707 0.9340 0.00 0.98 0.00 0.02
#> TCGA.BK.A139.01 2 0.0707 0.9340 0.00 0.98 0.00 0.02
#> TCGA.AX.A06H.01 1 0.3975 0.7749 0.76 0.00 0.24 0.00
#> TCGA.A5.A0GQ.01 3 0.4134 0.6386 0.26 0.00 0.74 0.00
#> TCGA.B5.A11X.01 2 0.0000 0.9402 0.00 1.00 0.00 0.00
#> TCGA.D1.A16E.01 3 0.4624 -0.0938 0.00 0.00 0.66 0.34
#> TCGA.EY.A1G7.01 2 0.3801 0.7763 0.00 0.78 0.00 0.22
#> TCGA.DF.A2KZ.01 3 0.4134 0.6386 0.26 0.00 0.74 0.00
#> TCGA.D1.A0ZS.01 2 0.0000 0.9402 0.00 1.00 0.00 0.00
#> TCGA.EC.A1QX.01 3 0.4624 -0.0938 0.00 0.00 0.66 0.34
#> TCGA.BS.A0UL.01 1 0.0000 0.8038 1.00 0.00 0.00 0.00
#> TCGA.B5.A11O.01 1 0.4522 0.6513 0.68 0.00 0.32 0.00
#> TCGA.QS.A5YR.01 3 0.4134 0.6386 0.26 0.00 0.74 0.00
#> TCGA.EO.A3L0.01 3 0.4079 0.6521 0.18 0.00 0.80 0.02
#> TCGA.DF.A2KR.01 1 0.1913 0.7518 0.94 0.00 0.04 0.02
#> TCGA.DF.A2KV.01 3 0.3400 0.6627 0.18 0.00 0.82 0.00
#> TCGA.B5.A3S1.01 2 0.3801 0.7763 0.00 0.78 0.00 0.22
#> TCGA.B5.A11Y.01 1 0.3975 0.7749 0.76 0.00 0.24 0.00
#> TCGA.EO.A3AS.01 1 0.0000 0.8038 1.00 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.4284 0.6444 0.20 0.00 0.78 0.02
#> TCGA.D1.A1O8.01 2 0.0000 0.9402 0.00 1.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.4277 0.6863 0.00 0.00 0.28 0.72
#> TCGA.AJ.A23O.01 1 0.0000 0.8038 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.A5.A3LO.01 3 0.4829 0.0123 0.48 0.00 0.50 0.00 0.02
#> TCGA.AP.A0LM.01 3 0.0000 0.6324 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A101.01 3 0.1732 0.5448 0.00 0.00 0.92 0.08 0.00
#> TCGA.FI.A2D0.01 1 0.2732 0.9649 0.84 0.00 0.16 0.00 0.00
#> TCGA.D1.A1NS.01 4 0.3895 0.7446 0.00 0.00 0.32 0.68 0.00
#> TCGA.AX.A1C5.01 2 0.2280 0.5281 0.00 0.88 0.00 0.00 0.12
#> TCGA.AX.A0IZ.01 4 0.3852 0.7146 0.00 0.02 0.22 0.76 0.00
#> TCGA.EY.A3QX.01 2 0.7426 -0.1173 0.04 0.40 0.00 0.22 0.34
#> TCGA.B5.A3FA.01 4 0.5705 0.4085 0.06 0.00 0.02 0.60 0.32
#> TCGA.BG.A2AE.01 2 0.3513 0.4413 0.02 0.80 0.00 0.00 0.18
#> TCGA.D1.A2G6.01 3 0.0609 0.6281 0.00 0.00 0.98 0.00 0.02
#> TCGA.B5.A11N.01 1 0.2732 0.9649 0.84 0.00 0.16 0.00 0.00
#> TCGA.BS.A0UA.01 3 0.4829 0.0123 0.48 0.00 0.50 0.00 0.02
#> TCGA.AJ.A3NE.01 2 0.1410 0.6182 0.00 0.94 0.00 0.00 0.06
#> TCGA.D1.A17B.01 3 0.4829 0.0123 0.48 0.00 0.50 0.00 0.02
#> TCGA.BK.A139.02 2 0.2280 0.6221 0.00 0.88 0.00 0.00 0.12
#> TCGA.BK.A139.01 2 0.1410 0.6315 0.00 0.94 0.00 0.00 0.06
#> TCGA.AX.A06H.01 3 0.4829 0.0123 0.48 0.00 0.50 0.00 0.02
#> TCGA.A5.A0GQ.01 3 0.0000 0.6324 0.00 0.00 1.00 0.00 0.00
#> TCGA.B5.A11X.01 2 0.0000 0.6564 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A16E.01 4 0.3895 0.7446 0.00 0.00 0.32 0.68 0.00
#> TCGA.EY.A1G7.01 5 0.5695 0.0000 0.04 0.46 0.00 0.02 0.48
#> TCGA.DF.A2KZ.01 3 0.0609 0.6281 0.00 0.00 0.98 0.00 0.02
#> TCGA.D1.A0ZS.01 2 0.0000 0.6564 0.00 1.00 0.00 0.00 0.00
#> TCGA.EC.A1QX.01 4 0.3895 0.7446 0.00 0.00 0.32 0.68 0.00
#> TCGA.BS.A0UL.01 1 0.3319 0.9465 0.82 0.00 0.16 0.00 0.02
#> TCGA.B5.A11O.01 3 0.4360 0.3617 0.30 0.00 0.68 0.00 0.02
#> TCGA.QS.A5YR.01 3 0.0609 0.6361 0.02 0.00 0.98 0.00 0.00
#> TCGA.EO.A3L0.01 3 0.3878 0.5033 0.04 0.00 0.82 0.02 0.12
#> TCGA.DF.A2KR.01 1 0.3037 0.8494 0.86 0.00 0.10 0.00 0.04
#> TCGA.DF.A2KV.01 3 0.2331 0.5350 0.00 0.00 0.90 0.08 0.02
#> TCGA.B5.A3S1.01 2 0.4262 -0.6716 0.00 0.56 0.00 0.00 0.44
#> TCGA.B5.A11Y.01 3 0.4829 0.0123 0.48 0.00 0.50 0.00 0.02
#> TCGA.EO.A3AS.01 1 0.2732 0.9649 0.84 0.00 0.16 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.3291 0.5325 0.04 0.00 0.84 0.00 0.12
#> TCGA.D1.A1O8.01 2 0.0000 0.6564 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.4570 0.4785 0.02 0.00 0.02 0.72 0.24
#> TCGA.AJ.A23O.01 1 0.2732 0.9649 0.84 0.00 0.16 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.A5.A3LO.01 3 0.4144 0.548 0.36 0.00 0.62 0.00 0.02 0.00
#> TCGA.AP.A0LM.01 3 0.0000 0.724 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A101.01 3 0.1092 0.710 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.FI.A2D0.01 1 0.0547 0.982 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 4 0.2793 0.987 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.AX.A1C5.01 2 0.0547 0.879 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AX.A0IZ.01 4 0.3156 0.962 0.00 0.00 0.18 0.80 0.02 0.00
#> TCGA.EY.A3QX.01 5 0.4733 0.504 0.00 0.12 0.00 0.06 0.74 0.08
#> TCGA.B5.A3FA.01 6 0.2094 0.853 0.00 0.00 0.02 0.08 0.00 0.90
#> TCGA.BG.A2AE.01 5 0.3309 0.588 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.D1.A2G6.01 3 0.2190 0.700 0.00 0.00 0.90 0.00 0.06 0.04
#> TCGA.B5.A11N.01 1 0.0547 0.982 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 3 0.4144 0.548 0.36 0.00 0.62 0.00 0.02 0.00
#> TCGA.AJ.A3NE.01 2 0.0000 0.883 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17B.01 3 0.4144 0.548 0.36 0.00 0.62 0.00 0.02 0.00
#> TCGA.BK.A139.02 2 0.1814 0.824 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.BK.A139.01 2 0.2048 0.818 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.AX.A06H.01 3 0.4144 0.548 0.36 0.00 0.62 0.00 0.02 0.00
#> TCGA.A5.A0GQ.01 3 0.0000 0.724 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B5.A11X.01 2 0.0547 0.886 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D1.A16E.01 4 0.2793 0.987 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.EY.A1G7.01 5 0.6693 0.322 0.02 0.32 0.00 0.14 0.48 0.04
#> TCGA.DF.A2KZ.01 3 0.2190 0.700 0.00 0.00 0.90 0.00 0.06 0.04
#> TCGA.D1.A0ZS.01 2 0.0937 0.876 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.EC.A1QX.01 4 0.2793 0.987 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.BS.A0UL.01 1 0.1092 0.966 0.96 0.00 0.02 0.00 0.02 0.00
#> TCGA.B5.A11O.01 3 0.3315 0.672 0.20 0.00 0.78 0.00 0.02 0.00
#> TCGA.QS.A5YR.01 3 0.0547 0.722 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EO.A3L0.01 3 0.3873 0.654 0.00 0.00 0.78 0.02 0.04 0.16
#> TCGA.DF.A2KR.01 1 0.1635 0.930 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.DF.A2KV.01 3 0.2725 0.682 0.00 0.00 0.88 0.02 0.06 0.04
#> TCGA.B5.A3S1.01 2 0.4958 0.509 0.02 0.72 0.00 0.08 0.16 0.02
#> TCGA.B5.A11Y.01 3 0.4144 0.548 0.36 0.00 0.62 0.00 0.02 0.00
#> TCGA.EO.A3AS.01 1 0.0547 0.982 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.3873 0.654 0.00 0.00 0.78 0.02 0.04 0.16
#> TCGA.D1.A1O8.01 2 0.0547 0.886 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.AX.A2IN.01 6 0.3315 0.853 0.00 0.00 0.02 0.20 0.00 0.78
#> TCGA.AJ.A23O.01 1 0.0547 0.982 0.98 0.00 0.02 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.A5.A3LO.01 3 0.3606 0.56143 0.30 0.00 0.68 0.00 0.02 0.00 0.00
#> TCGA.AP.A0LM.01 3 0.0504 0.55572 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D1.A101.01 3 0.1718 0.53192 0.00 0.00 0.92 0.04 0.00 0.00 0.04
#> TCGA.FI.A2D0.01 1 0.0000 0.96381 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 4 0.1433 0.96315 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.AX.A1C5.01 2 0.0504 0.85313 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AX.A0IZ.01 4 0.1363 0.91850 0.00 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.EY.A3QX.01 5 0.6513 0.53262 0.00 0.22 0.00 0.08 0.38 0.00 0.32
#> TCGA.B5.A3FA.01 6 0.0504 0.71815 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.BG.A2AE.01 5 0.6227 0.48094 0.00 0.36 0.00 0.06 0.40 0.00 0.18
#> TCGA.D1.A2G6.01 3 0.3047 0.05382 0.00 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.B5.A11N.01 1 0.0000 0.96381 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 3 0.3606 0.56143 0.30 0.00 0.68 0.00 0.02 0.00 0.00
#> TCGA.AJ.A3NE.01 2 0.0000 0.86190 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17B.01 3 0.3606 0.56143 0.30 0.00 0.68 0.00 0.02 0.00 0.00
#> TCGA.BK.A139.02 2 0.1363 0.82731 0.00 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.BK.A139.01 2 0.1363 0.82731 0.00 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.AX.A06H.01 3 0.3606 0.56143 0.30 0.00 0.68 0.00 0.02 0.00 0.00
#> TCGA.A5.A0GQ.01 3 0.0863 0.55023 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.B5.A11X.01 2 0.0000 0.86190 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16E.01 4 0.1433 0.96315 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.EY.A1G7.01 5 0.2259 0.22234 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.DF.A2KZ.01 3 0.2745 0.41578 0.00 0.00 0.82 0.02 0.00 0.00 0.16
#> TCGA.D1.A0ZS.01 2 0.0863 0.83914 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.EC.A1QX.01 4 0.1928 0.95939 0.00 0.00 0.08 0.90 0.00 0.00 0.02
#> TCGA.BS.A0UL.01 1 0.0000 0.96381 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11O.01 3 0.2163 0.57336 0.10 0.00 0.88 0.00 0.02 0.00 0.00
#> TCGA.QS.A5YR.01 3 0.1363 0.54313 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.EO.A3L0.01 3 0.5539 -1.00000 0.00 0.00 0.38 0.00 0.00 0.24 0.38
#> TCGA.DF.A2KR.01 1 0.2422 0.79835 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.DF.A2KV.01 3 0.3086 0.37058 0.00 0.00 0.80 0.04 0.00 0.00 0.16
#> TCGA.B5.A3S1.01 2 0.3994 0.00756 0.00 0.50 0.00 0.00 0.48 0.02 0.00
#> TCGA.B5.A11Y.01 3 0.3606 0.56143 0.30 0.00 0.68 0.00 0.02 0.00 0.00
#> TCGA.EO.A3AS.01 1 0.0000 0.96381 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 7 0.5539 0.00000 0.00 0.00 0.38 0.00 0.00 0.24 0.38
#> TCGA.D1.A1O8.01 2 0.0000 0.86190 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2IN.01 6 0.4121 0.71533 0.00 0.00 0.00 0.10 0.00 0.70 0.20
#> TCGA.AJ.A23O.01 1 0.0000 0.96381 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.A5.A3LO.01 3 0.2756 0.6212 0.26 0.00 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A0LM.01 3 0.1557 0.5703 0.00 0.00 0.92 0.02 0.00 0.00 0.06 0.00
#> TCGA.D1.A101.01 3 0.3154 0.5346 0.00 0.00 0.78 0.16 0.00 0.00 0.00 0.06
#> TCGA.FI.A2D0.01 1 0.0000 0.9007 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 8 0.0808 0.9776 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.AX.A1C5.01 2 0.0941 0.7507 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.AX.A0IZ.01 8 0.0000 0.9318 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EY.A3QX.01 5 0.5943 0.4829 0.00 0.14 0.02 0.24 0.54 0.02 0.04 0.00
#> TCGA.B5.A3FA.01 6 0.4077 0.5403 0.00 0.00 0.00 0.02 0.00 0.56 0.40 0.02
#> TCGA.BG.A2AE.01 5 0.4833 0.3958 0.00 0.28 0.02 0.12 0.58 0.00 0.00 0.00
#> TCGA.D1.A2G6.01 3 0.4804 -0.2364 0.00 0.00 0.46 0.14 0.00 0.00 0.40 0.00
#> TCGA.B5.A11N.01 1 0.0000 0.9007 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 3 0.2756 0.6212 0.26 0.00 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NE.01 2 0.0000 0.7643 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A17B.01 3 0.2756 0.6212 0.26 0.00 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.BK.A139.02 2 0.2719 0.6442 0.00 0.80 0.02 0.00 0.18 0.00 0.00 0.00
#> TCGA.BK.A139.01 2 0.3426 0.6382 0.00 0.74 0.02 0.00 0.22 0.00 0.00 0.02
#> TCGA.AX.A06H.01 3 0.2756 0.6212 0.26 0.00 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.A5.A0GQ.01 3 0.2818 0.5572 0.00 0.00 0.82 0.12 0.00 0.00 0.00 0.06
#> TCGA.B5.A11X.01 2 0.1887 0.7654 0.00 0.90 0.00 0.00 0.06 0.00 0.00 0.04
#> TCGA.D1.A16E.01 8 0.0808 0.9776 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.EY.A1G7.01 5 0.5591 0.1283 0.00 0.12 0.02 0.16 0.60 0.00 0.10 0.00
#> TCGA.DF.A2KZ.01 3 0.5420 0.1006 0.00 0.00 0.54 0.14 0.00 0.00 0.26 0.06
#> TCGA.D1.A0ZS.01 2 0.2348 0.7585 0.00 0.88 0.00 0.00 0.06 0.00 0.02 0.04
#> TCGA.EC.A1QX.01 8 0.0808 0.9776 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.BS.A0UL.01 1 0.0471 0.8842 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11O.01 3 0.1765 0.6183 0.12 0.00 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.QS.A5YR.01 3 0.2994 0.5457 0.00 0.00 0.80 0.14 0.00 0.00 0.00 0.06
#> TCGA.EO.A3L0.01 7 0.2534 1.0000 0.00 0.00 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.DF.A2KR.01 1 0.4383 0.3559 0.52 0.00 0.00 0.42 0.00 0.02 0.04 0.00
#> TCGA.DF.A2KV.01 3 0.5541 0.0726 0.00 0.00 0.52 0.16 0.00 0.00 0.26 0.06
#> TCGA.B5.A3S1.01 2 0.4516 0.0947 0.00 0.52 0.00 0.02 0.42 0.02 0.02 0.00
#> TCGA.B5.A11Y.01 3 0.2756 0.6212 0.26 0.00 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A3AS.01 1 0.0000 0.9007 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 7 0.2534 1.0000 0.00 0.00 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.D1.A1O8.01 2 0.1557 0.7700 0.00 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.AX.A2IN.01 6 0.1091 0.5818 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.AJ.A23O.01 1 0.0000 0.9007 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: Node043. Child nodes: Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02121-leaf , Node02122-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node02341-leaf , Node02342-leaf , Node04111-leaf , Node04112-leaf , Node04311-leaf , Node04312-leaf , Node04313-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0431"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.653 0.796 0.913 0.4876 0.481 0.481
#> 3 3 1.000 1.000 1.000 0.3445 0.772 0.568
#> 4 4 0.833 0.876 0.933 0.1370 0.900 0.718
#> 5 5 0.750 0.686 0.790 0.0673 0.892 0.604
#> 6 6 0.737 0.590 0.804 0.0311 0.886 0.500
#> 7 7 0.743 0.580 0.822 0.0199 0.966 0.810
#> 8 8 0.757 0.559 0.801 0.0307 0.906 0.535
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.A5.A3LO.01 2 0.925 0.619 0.34 0.66
#> TCGA.AP.A0LM.01 2 0.000 0.828 0.00 1.00
#> TCGA.D1.A101.01 1 0.000 0.951 1.00 0.00
#> TCGA.FI.A2D0.01 2 0.000 0.828 0.00 1.00
#> TCGA.D1.A1NS.01 1 0.000 0.951 1.00 0.00
#> TCGA.AX.A0IZ.01 1 0.000 0.951 1.00 0.00
#> TCGA.B5.A3FA.01 2 0.000 0.828 0.00 1.00
#> TCGA.D1.A2G6.01 1 0.000 0.951 1.00 0.00
#> TCGA.B5.A11N.01 2 0.584 0.798 0.14 0.86
#> TCGA.BS.A0UA.01 1 0.000 0.951 1.00 0.00
#> TCGA.D1.A17B.01 1 0.000 0.951 1.00 0.00
#> TCGA.AX.A06H.01 1 0.000 0.951 1.00 0.00
#> TCGA.A5.A0GQ.01 1 0.000 0.951 1.00 0.00
#> TCGA.D1.A16E.01 1 0.000 0.951 1.00 0.00
#> TCGA.DF.A2KZ.01 1 0.000 0.951 1.00 0.00
#> TCGA.EC.A1QX.01 1 0.000 0.951 1.00 0.00
#> TCGA.BS.A0UL.01 2 0.584 0.798 0.14 0.86
#> TCGA.B5.A11O.01 1 0.000 0.951 1.00 0.00
#> TCGA.QS.A5YR.01 1 0.000 0.951 1.00 0.00
#> TCGA.EO.A3L0.01 2 0.925 0.619 0.34 0.66
#> TCGA.DF.A2KR.01 2 0.000 0.828 0.00 1.00
#> TCGA.DF.A2KV.01 2 0.327 0.822 0.06 0.94
#> TCGA.B5.A11Y.01 2 0.925 0.619 0.34 0.66
#> TCGA.EO.A3AS.01 2 0.000 0.828 0.00 1.00
#> TCGA.AJ.A6NU.01 2 0.000 0.828 0.00 1.00
#> TCGA.AX.A2IN.01 1 1.000 -0.339 0.50 0.50
#> TCGA.AJ.A23O.01 2 1.000 0.229 0.50 0.50
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A5.A3LO.01 2 0 1 0 1 0
#> TCGA.AP.A0LM.01 2 0 1 0 1 0
#> TCGA.D1.A101.01 1 0 1 1 0 0
#> TCGA.FI.A2D0.01 3 0 1 0 0 1
#> TCGA.D1.A1NS.01 1 0 1 1 0 0
#> TCGA.AX.A0IZ.01 1 0 1 1 0 0
#> TCGA.B5.A3FA.01 3 0 1 0 0 1
#> TCGA.D1.A2G6.01 2 0 1 0 1 0
#> TCGA.B5.A11N.01 2 0 1 0 1 0
#> TCGA.BS.A0UA.01 1 0 1 1 0 0
#> TCGA.D1.A17B.01 1 0 1 1 0 0
#> TCGA.AX.A06H.01 1 0 1 1 0 0
#> TCGA.A5.A0GQ.01 1 0 1 1 0 0
#> TCGA.D1.A16E.01 1 0 1 1 0 0
#> TCGA.DF.A2KZ.01 1 0 1 1 0 0
#> TCGA.EC.A1QX.01 1 0 1 1 0 0
#> TCGA.BS.A0UL.01 2 0 1 0 1 0
#> TCGA.B5.A11O.01 1 0 1 1 0 0
#> TCGA.QS.A5YR.01 1 0 1 1 0 0
#> TCGA.EO.A3L0.01 2 0 1 0 1 0
#> TCGA.DF.A2KR.01 3 0 1 0 0 1
#> TCGA.DF.A2KV.01 2 0 1 0 1 0
#> TCGA.B5.A11Y.01 2 0 1 0 1 0
#> TCGA.EO.A3AS.01 3 0 1 0 0 1
#> TCGA.AJ.A6NU.01 3 0 1 0 0 1
#> TCGA.AX.A2IN.01 2 0 1 0 1 0
#> TCGA.AJ.A23O.01 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.A5.A3LO.01 2 0.0000 0.910 0.00 1.00 0 0.00
#> TCGA.AP.A0LM.01 2 0.0707 0.898 0.00 0.98 0 0.02
#> TCGA.D1.A101.01 1 0.3400 0.863 0.82 0.00 0 0.18
#> TCGA.FI.A2D0.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D1.A1NS.01 1 0.0000 0.896 1.00 0.00 0 0.00
#> TCGA.AX.A0IZ.01 1 0.4134 0.787 0.74 0.00 0 0.26
#> TCGA.B5.A3FA.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D1.A2G6.01 4 0.0707 0.877 0.00 0.02 0 0.98
#> TCGA.B5.A11N.01 2 0.0000 0.910 0.00 1.00 0 0.00
#> TCGA.BS.A0UA.01 1 0.0000 0.896 1.00 0.00 0 0.00
#> TCGA.D1.A17B.01 1 0.0000 0.896 1.00 0.00 0 0.00
#> TCGA.AX.A06H.01 1 0.0000 0.896 1.00 0.00 0 0.00
#> TCGA.A5.A0GQ.01 1 0.0000 0.896 1.00 0.00 0 0.00
#> TCGA.D1.A16E.01 1 0.3400 0.863 0.82 0.00 0 0.18
#> TCGA.DF.A2KZ.01 1 0.3610 0.849 0.80 0.00 0 0.20
#> TCGA.EC.A1QX.01 4 0.1637 0.836 0.06 0.00 0 0.94
#> TCGA.BS.A0UL.01 2 0.0000 0.910 0.00 1.00 0 0.00
#> TCGA.B5.A11O.01 1 0.0000 0.896 1.00 0.00 0 0.00
#> TCGA.QS.A5YR.01 1 0.3400 0.863 0.82 0.00 0 0.18
#> TCGA.EO.A3L0.01 2 0.4907 0.206 0.00 0.58 0 0.42
#> TCGA.DF.A2KR.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.DF.A2KV.01 2 0.0707 0.905 0.00 0.98 0 0.02
#> TCGA.B5.A11Y.01 2 0.0707 0.905 0.00 0.98 0 0.02
#> TCGA.EO.A3AS.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.AJ.A6NU.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.AX.A2IN.01 4 0.2345 0.873 0.00 0.10 0 0.90
#> TCGA.AJ.A23O.01 4 0.2921 0.831 0.00 0.14 0 0.86
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.A5.A3LO.01 2 0.0000 0.865 0.00 1.00 0 0.00 0.00
#> TCGA.AP.A0LM.01 2 0.5130 0.611 0.00 0.68 0 0.10 0.22
#> TCGA.D1.A101.01 1 0.2929 0.478 0.82 0.00 0 0.00 0.18
#> TCGA.FI.A2D0.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.D1.A1NS.01 5 0.4060 0.955 0.36 0.00 0 0.00 0.64
#> TCGA.AX.A0IZ.01 1 0.2012 0.618 0.92 0.00 0 0.06 0.02
#> TCGA.B5.A3FA.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.4637 0.669 0.16 0.10 0 0.74 0.00
#> TCGA.B5.A11N.01 2 0.0000 0.865 0.00 1.00 0 0.00 0.00
#> TCGA.BS.A0UA.01 1 0.4287 -0.501 0.54 0.00 0 0.00 0.46
#> TCGA.D1.A17B.01 5 0.3983 0.985 0.34 0.00 0 0.00 0.66
#> TCGA.AX.A06H.01 1 0.4060 -0.123 0.64 0.00 0 0.00 0.36
#> TCGA.A5.A0GQ.01 5 0.3983 0.985 0.34 0.00 0 0.00 0.66
#> TCGA.D1.A16E.01 1 0.0000 0.658 1.00 0.00 0 0.00 0.00
#> TCGA.DF.A2KZ.01 1 0.0609 0.656 0.98 0.00 0 0.02 0.00
#> TCGA.EC.A1QX.01 4 0.4829 0.253 0.48 0.02 0 0.50 0.00
#> TCGA.BS.A0UL.01 2 0.0000 0.865 0.00 1.00 0 0.00 0.00
#> TCGA.B5.A11O.01 5 0.3983 0.985 0.34 0.00 0 0.00 0.66
#> TCGA.QS.A5YR.01 1 0.1732 0.617 0.92 0.00 0 0.00 0.08
#> TCGA.EO.A3L0.01 4 0.4302 0.230 0.00 0.48 0 0.52 0.00
#> TCGA.DF.A2KR.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DF.A2KV.01 2 0.4558 0.683 0.00 0.74 0 0.18 0.08
#> TCGA.B5.A11Y.01 2 0.1216 0.852 0.00 0.96 0 0.02 0.02
#> TCGA.EO.A3AS.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.3463 0.663 0.02 0.12 0 0.84 0.02
#> TCGA.AJ.A23O.01 4 0.3852 0.650 0.02 0.22 0 0.76 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.A5.A3LO.01 2 0.2474 0.550 0.00 0.88 0 0.04 0.00 0.08
#> TCGA.AP.A0LM.01 6 0.3578 0.000 0.00 0.34 0 0.00 0.00 0.66
#> TCGA.D1.A101.01 1 0.4282 0.476 0.56 0.00 0 0.02 0.42 0.00
#> TCGA.FI.A2D0.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 5 0.2581 0.698 0.12 0.00 0 0.00 0.86 0.02
#> TCGA.AX.A0IZ.01 1 0.4094 0.679 0.74 0.00 0 0.08 0.18 0.00
#> TCGA.B5.A3FA.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.4244 0.672 0.20 0.08 0 0.72 0.00 0.00
#> TCGA.B5.A11N.01 2 0.0000 0.590 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 5 0.4765 0.532 0.30 0.00 0 0.02 0.64 0.04
#> TCGA.D1.A17B.01 5 0.0000 0.706 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.AX.A06H.01 5 0.5020 0.360 0.38 0.00 0 0.02 0.56 0.04
#> TCGA.A5.A0GQ.01 5 0.1267 0.700 0.06 0.00 0 0.00 0.94 0.00
#> TCGA.D1.A16E.01 1 0.3076 0.694 0.76 0.00 0 0.00 0.24 0.00
#> TCGA.DF.A2KZ.01 1 0.2793 0.700 0.80 0.00 0 0.00 0.20 0.00
#> TCGA.EC.A1QX.01 1 0.3864 -0.144 0.52 0.00 0 0.48 0.00 0.00
#> TCGA.BS.A0UL.01 2 0.0937 0.590 0.00 0.96 0 0.00 0.00 0.04
#> TCGA.B5.A11O.01 5 0.1814 0.683 0.10 0.00 0 0.00 0.90 0.00
#> TCGA.QS.A5YR.01 1 0.3198 0.647 0.74 0.00 0 0.00 0.26 0.00
#> TCGA.EO.A3L0.01 2 0.5285 -0.127 0.00 0.48 0 0.42 0.00 0.10
#> TCGA.DF.A2KR.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.DF.A2KV.01 2 0.6833 0.149 0.18 0.46 0 0.08 0.00 0.28
#> TCGA.B5.A11Y.01 2 0.2629 0.530 0.08 0.88 0 0.02 0.00 0.02
#> TCGA.EO.A3AS.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.2725 0.688 0.02 0.06 0 0.88 0.00 0.04
#> TCGA.AJ.A23O.01 4 0.4574 0.568 0.04 0.26 0 0.68 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.A5.A3LO.01 2 0.2769 0.6472 0.00 0.86 0.00 0.00 0.02 0.08 0.04
#> TCGA.AP.A0LM.01 6 0.1433 0.0000 0.00 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.D1.A101.01 1 0.3685 0.4005 0.66 0.00 0.00 0.02 0.32 0.00 0.00
#> TCGA.FI.A2D0.01 3 0.0000 0.9950 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 5 0.2654 0.7345 0.10 0.00 0.00 0.02 0.86 0.00 0.02
#> TCGA.AX.A0IZ.01 1 0.1664 0.6940 0.92 0.00 0.00 0.06 0.02 0.00 0.00
#> TCGA.B5.A3FA.01 3 0.0000 0.9950 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.5740 0.4015 0.24 0.16 0.00 0.56 0.02 0.00 0.02
#> TCGA.B5.A11N.01 2 0.0504 0.6782 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BS.A0UA.01 5 0.5735 0.4923 0.34 0.00 0.00 0.08 0.52 0.02 0.04
#> TCGA.D1.A17B.01 5 0.1671 0.7405 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.AX.A06H.01 5 0.5831 0.3421 0.42 0.00 0.00 0.08 0.44 0.02 0.04
#> TCGA.A5.A0GQ.01 5 0.1928 0.7097 0.08 0.00 0.00 0.00 0.90 0.00 0.02
#> TCGA.D1.A16E.01 1 0.1166 0.7383 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.DF.A2KZ.01 1 0.1664 0.7395 0.92 0.00 0.00 0.02 0.06 0.00 0.00
#> TCGA.EC.A1QX.01 1 0.4244 -0.1132 0.54 0.04 0.00 0.42 0.00 0.00 0.00
#> TCGA.BS.A0UL.01 2 0.2016 0.6709 0.00 0.90 0.00 0.04 0.00 0.06 0.00
#> TCGA.B5.A11O.01 5 0.2569 0.7109 0.14 0.00 0.00 0.00 0.84 0.00 0.02
#> TCGA.QS.A5YR.01 1 0.1928 0.7090 0.90 0.00 0.00 0.02 0.08 0.00 0.00
#> TCGA.EO.A3L0.01 2 0.4107 0.5508 0.00 0.70 0.00 0.24 0.04 0.00 0.02
#> TCGA.DF.A2KR.01 3 0.0000 0.9950 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KV.01 7 0.2422 0.0000 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.B5.A11Y.01 2 0.3058 0.5680 0.00 0.82 0.00 0.00 0.00 0.08 0.10
#> TCGA.EO.A3AS.01 3 0.0000 0.9950 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.0504 0.9797 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.AX.A2IN.01 4 0.3744 0.3204 0.00 0.08 0.00 0.78 0.00 0.02 0.12
#> TCGA.AJ.A23O.01 2 0.4278 -0.0414 0.04 0.50 0.00 0.46 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.A5.A3LO.01 2 0.2025 0.7196 0.00 0.88 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.AP.A0LM.01 6 0.1765 0.0000 0.00 0.12 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.D1.A101.01 1 0.5197 0.2683 0.58 0.02 0.00 0.02 0.06 0.00 0.02 0.30
#> TCGA.FI.A2D0.01 3 0.0471 0.9816 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D1.A1NS.01 8 0.4081 0.6071 0.16 0.00 0.00 0.00 0.16 0.00 0.00 0.68
#> TCGA.AX.A0IZ.01 1 0.3845 0.4068 0.66 0.00 0.00 0.06 0.28 0.00 0.00 0.00
#> TCGA.B5.A3FA.01 3 0.0000 0.9954 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A2G6.01 4 0.3314 0.5432 0.08 0.10 0.00 0.80 0.02 0.00 0.00 0.00
#> TCGA.B5.A11N.01 2 0.0808 0.7361 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.BS.A0UA.01 1 0.5190 -0.0211 0.42 0.00 0.00 0.00 0.26 0.00 0.00 0.32
#> TCGA.D1.A17B.01 8 0.2862 0.7652 0.10 0.00 0.00 0.00 0.08 0.00 0.00 0.82
#> TCGA.AX.A06H.01 1 0.4622 0.3292 0.56 0.00 0.00 0.00 0.30 0.00 0.00 0.14
#> TCGA.A5.A0GQ.01 8 0.1557 0.7626 0.06 0.00 0.00 0.00 0.00 0.00 0.02 0.92
#> TCGA.D1.A16E.01 1 0.2348 0.6008 0.88 0.00 0.00 0.02 0.04 0.00 0.00 0.06
#> TCGA.DF.A2KZ.01 1 0.1341 0.6013 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.EC.A1QX.01 4 0.4636 0.2478 0.40 0.04 0.00 0.52 0.04 0.00 0.00 0.00
#> TCGA.BS.A0UL.01 2 0.2020 0.7303 0.00 0.90 0.00 0.02 0.00 0.02 0.06 0.00
#> TCGA.B5.A11O.01 8 0.2888 0.6672 0.16 0.00 0.00 0.00 0.04 0.00 0.00 0.80
#> TCGA.QS.A5YR.01 1 0.1091 0.6048 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.EO.A3L0.01 2 0.5403 0.1452 0.00 0.50 0.00 0.36 0.04 0.00 0.08 0.02
#> TCGA.DF.A2KR.01 3 0.0000 0.9954 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DF.A2KV.01 7 0.0808 0.0000 0.00 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.B5.A11Y.01 2 0.3185 0.6881 0.00 0.82 0.00 0.00 0.06 0.04 0.08 0.00
#> TCGA.EO.A3AS.01 3 0.0000 0.9954 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A6NU.01 3 0.0000 0.9954 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A2IN.01 4 0.4471 0.3391 0.00 0.02 0.00 0.70 0.16 0.10 0.00 0.02
#> TCGA.AJ.A23O.01 4 0.5371 0.3899 0.02 0.22 0.00 0.62 0.00 0.02 0.08 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node024 , Node031-leaf , Node032-leaf , Node033-leaf , Node034-leaf , Node035-leaf , Node036-leaf , Node041 , Node042 , Node043 , Node051 , Node052 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["05"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 66 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.998 0.999 0.5009 0.500 0.500
#> 3 3 0.738 0.809 0.902 0.3133 0.798 0.615
#> 4 4 0.832 0.940 0.950 0.1396 0.779 0.456
#> 5 5 0.768 0.677 0.833 0.0531 0.983 0.930
#> 6 6 0.755 0.680 0.801 0.0329 0.862 0.508
#> 7 7 0.759 0.683 0.801 0.0231 0.977 0.884
#> 8 8 0.790 0.588 0.768 0.0196 0.950 0.734
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.B5.A5OE.01 2 0.000 1.000 0.00 1.00
#> TCGA.AP.A3K1.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A0ZZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.AP.A5FX.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A3FZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.DI.A1NN.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A2HK.01 1 0.141 0.981 0.98 0.02
#> TCGA.D1.A17K.01 1 0.000 0.998 1.00 0.00
#> TCGA.DI.A0WH.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A1NW.01 2 0.000 1.000 0.00 1.00
#> TCGA.AJ.A3QS.01 2 0.000 1.000 0.00 1.00
#> TCGA.EY.A2OQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.A5.A7WK.01 2 0.000 1.000 0.00 1.00
#> TCGA.BS.A0U9.01 1 0.000 0.998 1.00 0.00
#> TCGA.A5.A2K2.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GJ.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A3DG.01 2 0.000 1.000 0.00 1.00
#> TCGA.EY.A1GC.01 2 0.000 1.000 0.00 1.00
#> TCGA.FI.A2F8.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A0YV.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A16S.01 1 0.141 0.981 0.98 0.02
#> TCGA.E6.A1LZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.H5.A2HR.01 2 0.000 1.000 0.00 1.00
#> TCGA.FI.A3PV.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A18C.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GP.01 2 0.000 1.000 0.00 1.00
#> TCGA.DI.A2QU.01 2 0.000 1.000 0.00 1.00
#> TCGA.2E.A9G8.01 1 0.000 0.998 1.00 0.00
#> TCGA.FI.A2EX.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A1NU.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A11U.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3BD.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A3FV.01 2 0.000 1.000 0.00 1.00
#> TCGA.EO.A3B1.01 2 0.000 1.000 0.00 1.00
#> TCGA.EO.A2CH.01 2 0.000 1.000 0.00 1.00
#> TCGA.AP.A0LF.01 1 0.141 0.981 0.98 0.02
#> TCGA.5B.A90C.01 1 0.000 0.998 1.00 0.00
#> TCGA.AW.A1PO.01 2 0.000 1.000 0.00 1.00
#> TCGA.B5.A3FD.01 2 0.000 1.000 0.00 1.00
#> TCGA.AJ.A3TW.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A4KR.01 2 0.000 1.000 0.00 1.00
#> TCGA.BS.A0V8.01 1 0.000 0.998 1.00 0.00
#> TCGA.BG.A0YU.01 2 0.000 1.000 0.00 1.00
#> TCGA.D1.A15V.01 1 0.000 0.998 1.00 0.00
#> TCGA.FI.A3PX.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A3G6.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A2ON.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A214.01 1 0.000 0.998 1.00 0.00
#> TCGA.EY.A1GO.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A3G1.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A3GI.01 1 0.000 0.998 1.00 0.00
#> TCGA.PG.A7D5.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A2H8.01 1 0.000 0.998 1.00 0.00
#> TCGA.B5.A3FB.01 1 0.000 0.998 1.00 0.00
#> TCGA.KP.A3W1.01 2 0.000 1.000 0.00 1.00
#> TCGA.B5.A0KB.01 2 0.000 1.000 0.00 1.00
#> TCGA.A5.A0GR.01 2 0.000 1.000 0.00 1.00
#> TCGA.AX.A3G7.01 2 0.000 1.000 0.00 1.00
#> TCGA.D1.A3JP.01 2 0.000 1.000 0.00 1.00
#> TCGA.EO.A3KW.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A2QN.01 1 0.000 0.998 1.00 0.00
#> TCGA.D1.A3DH.01 2 0.000 1.000 0.00 1.00
#> TCGA.AJ.A3NH.01 1 0.000 0.998 1.00 0.00
#> TCGA.AX.A1CN.01 1 0.000 0.998 1.00 0.00
#> TCGA.EO.A1Y8.01 1 0.000 0.998 1.00 0.00
#> TCGA.AJ.A3EM.01 1 0.000 0.998 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B5.A5OE.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AP.A3K1.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.D1.A0ZZ.01 2 0.595 0.311 0.00 0.64 0.36
#> TCGA.AP.A5FX.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.AX.A3FZ.01 3 0.583 0.587 0.00 0.34 0.66
#> TCGA.DI.A1NN.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.AX.A2HK.01 3 0.000 0.813 0.00 0.00 1.00
#> TCGA.D1.A17K.01 1 0.480 0.795 0.78 0.00 0.22
#> TCGA.DI.A0WH.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.D1.A1NW.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AJ.A3QS.01 3 0.540 0.672 0.00 0.28 0.72
#> TCGA.EY.A2OQ.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.A5.A7WK.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.BS.A0U9.01 1 0.583 0.707 0.66 0.00 0.34
#> TCGA.A5.A2K2.01 1 0.540 0.760 0.72 0.00 0.28
#> TCGA.EY.A1GJ.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.D1.A3DG.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.EY.A1GC.01 3 0.540 0.674 0.00 0.28 0.72
#> TCGA.FI.A2F8.01 3 0.000 0.813 0.00 0.00 1.00
#> TCGA.BG.A0YV.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.D1.A16S.01 3 0.000 0.813 0.00 0.00 1.00
#> TCGA.E6.A1LZ.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.H5.A2HR.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.FI.A3PV.01 3 0.000 0.813 0.00 0.00 1.00
#> TCGA.BG.A18C.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.EY.A1GP.01 3 0.400 0.761 0.00 0.16 0.84
#> TCGA.DI.A2QU.01 3 0.583 0.587 0.00 0.34 0.66
#> TCGA.2E.A9G8.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.FI.A2EX.01 1 0.583 0.707 0.66 0.00 0.34
#> TCGA.D1.A1NU.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.B5.A11U.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.AJ.A3BD.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AX.A3FV.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.EO.A3B1.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.EO.A2CH.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AP.A0LF.01 3 0.000 0.813 0.00 0.00 1.00
#> TCGA.5B.A90C.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.AW.A1PO.01 3 0.583 0.587 0.00 0.34 0.66
#> TCGA.B5.A3FD.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AJ.A3TW.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.EY.A4KR.01 2 0.630 -0.142 0.00 0.52 0.48
#> TCGA.BS.A0V8.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.BG.A0YU.01 2 0.540 0.516 0.00 0.72 0.28
#> TCGA.D1.A15V.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.FI.A3PX.01 1 0.502 0.784 0.76 0.00 0.24
#> TCGA.AX.A3G6.01 1 0.583 0.707 0.66 0.00 0.34
#> TCGA.EY.A2ON.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.EY.A214.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.EY.A1GO.01 3 0.000 0.813 0.00 0.00 1.00
#> TCGA.AX.A3G1.01 1 0.540 0.760 0.72 0.00 0.28
#> TCGA.AX.A3GI.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.PG.A7D5.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AX.A2H8.01 1 0.556 0.745 0.70 0.00 0.30
#> TCGA.B5.A3FB.01 1 0.583 0.707 0.66 0.00 0.34
#> TCGA.KP.A3W1.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.B5.A0KB.01 3 0.502 0.710 0.00 0.24 0.76
#> TCGA.A5.A0GR.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AX.A3G7.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.D1.A3JP.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.EO.A3KW.01 1 0.540 0.760 0.72 0.00 0.28
#> TCGA.AJ.A2QN.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.D1.A3DH.01 2 0.000 0.930 0.00 1.00 0.00
#> TCGA.AJ.A3NH.01 3 0.153 0.779 0.04 0.00 0.96
#> TCGA.AX.A1CN.01 1 0.000 0.884 1.00 0.00 0.00
#> TCGA.EO.A1Y8.01 3 0.000 0.813 0.00 0.00 1.00
#> TCGA.AJ.A3EM.01 1 0.583 0.707 0.66 0.00 0.34
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B5.A5OE.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AP.A3K1.01 1 0.1211 0.960 0.96 0.00 0.00 0.04
#> TCGA.D1.A0ZZ.01 3 0.0000 0.924 0.00 0.00 1.00 0.00
#> TCGA.AP.A5FX.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AX.A3FZ.01 3 0.0000 0.924 0.00 0.00 1.00 0.00
#> TCGA.DI.A1NN.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HK.01 4 0.1637 0.830 0.00 0.00 0.06 0.94
#> TCGA.D1.A17K.01 4 0.3801 0.846 0.22 0.00 0.00 0.78
#> TCGA.DI.A0WH.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NW.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3QS.01 3 0.2345 0.909 0.00 0.00 0.90 0.10
#> TCGA.EY.A2OQ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.A5.A7WK.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BS.A0U9.01 4 0.2011 0.890 0.08 0.00 0.00 0.92
#> TCGA.A5.A2K2.01 4 0.3400 0.883 0.18 0.00 0.00 0.82
#> TCGA.EY.A1GJ.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GC.01 3 0.1637 0.918 0.00 0.00 0.94 0.06
#> TCGA.FI.A2F8.01 4 0.0707 0.859 0.00 0.00 0.02 0.98
#> TCGA.BG.A0YV.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 3 0.2345 0.909 0.00 0.00 0.90 0.10
#> TCGA.E6.A1LZ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.H5.A2HR.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FI.A3PV.01 4 0.0707 0.859 0.00 0.00 0.02 0.98
#> TCGA.BG.A18C.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GP.01 3 0.3172 0.896 0.00 0.00 0.84 0.16
#> TCGA.DI.A2QU.01 3 0.1637 0.918 0.00 0.00 0.94 0.06
#> TCGA.2E.A9G8.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 4 0.2011 0.889 0.08 0.00 0.00 0.92
#> TCGA.D1.A1NU.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.B5.A11U.01 1 0.1211 0.960 0.96 0.00 0.00 0.04
#> TCGA.AJ.A3BD.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FV.01 3 0.2647 0.866 0.00 0.12 0.88 0.00
#> TCGA.EO.A3B1.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EO.A2CH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AP.A0LF.01 4 0.1637 0.830 0.00 0.00 0.06 0.94
#> TCGA.5B.A90C.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 3 0.0000 0.924 0.00 0.00 1.00 0.00
#> TCGA.B5.A3FD.01 3 0.2011 0.893 0.00 0.08 0.92 0.00
#> TCGA.AJ.A3TW.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 3 0.1637 0.914 0.00 0.06 0.94 0.00
#> TCGA.BS.A0V8.01 1 0.1211 0.960 0.96 0.00 0.00 0.04
#> TCGA.BG.A0YU.01 3 0.0000 0.924 0.00 0.00 1.00 0.00
#> TCGA.D1.A15V.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.FI.A3PX.01 4 0.3801 0.846 0.22 0.00 0.00 0.78
#> TCGA.AX.A3G6.01 4 0.2921 0.897 0.14 0.00 0.00 0.86
#> TCGA.EY.A2ON.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EY.A214.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 3 0.2647 0.908 0.00 0.00 0.88 0.12
#> TCGA.AX.A3G1.01 4 0.3400 0.883 0.18 0.00 0.00 0.82
#> TCGA.AX.A3GI.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A2H8.01 4 0.3400 0.883 0.18 0.00 0.00 0.82
#> TCGA.B5.A3FB.01 4 0.2921 0.897 0.14 0.00 0.00 0.86
#> TCGA.KP.A3W1.01 3 0.3610 0.793 0.00 0.20 0.80 0.00
#> TCGA.B5.A0KB.01 3 0.3172 0.886 0.00 0.00 0.84 0.16
#> TCGA.A5.A0GR.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AX.A3G7.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D1.A3JP.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KW.01 4 0.3400 0.883 0.18 0.00 0.00 0.82
#> TCGA.AJ.A2QN.01 1 0.0707 0.977 0.98 0.00 0.00 0.02
#> TCGA.D1.A3DH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NH.01 4 0.0707 0.859 0.00 0.00 0.02 0.98
#> TCGA.AX.A1CN.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 4 0.0707 0.859 0.00 0.00 0.02 0.98
#> TCGA.AJ.A3EM.01 4 0.3172 0.892 0.16 0.00 0.00 0.84
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.B5.A5OE.01 2 0.0609 0.9888 0.00 0.98 0.00 0.00 0.02
#> TCGA.AP.A3K1.01 1 0.6359 0.5706 0.52 0.00 0.00 0.26 0.22
#> TCGA.D1.A0ZZ.01 3 0.3109 0.1821 0.00 0.00 0.80 0.00 0.20
#> TCGA.AP.A5FX.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FZ.01 3 0.3561 -0.0993 0.00 0.00 0.74 0.00 0.26
#> TCGA.DI.A1NN.01 1 0.2732 0.7877 0.84 0.00 0.00 0.00 0.16
#> TCGA.AX.A2HK.01 4 0.5487 0.5349 0.00 0.00 0.28 0.62 0.10
#> TCGA.D1.A17K.01 4 0.4433 0.6848 0.06 0.00 0.00 0.74 0.20
#> TCGA.DI.A0WH.01 1 0.6265 0.5945 0.54 0.00 0.00 0.24 0.22
#> TCGA.D1.A1NW.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3QS.01 3 0.1648 0.4750 0.00 0.00 0.94 0.04 0.02
#> TCGA.EY.A2OQ.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.A5.A7WK.01 2 0.0609 0.9888 0.00 0.98 0.00 0.00 0.02
#> TCGA.BS.A0U9.01 4 0.3852 0.7157 0.02 0.00 0.00 0.76 0.22
#> TCGA.A5.A2K2.01 4 0.2077 0.7761 0.04 0.00 0.00 0.92 0.04
#> TCGA.EY.A1GJ.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 2 0.0609 0.9888 0.00 0.98 0.00 0.00 0.02
#> TCGA.EY.A1GC.01 5 0.4262 0.9341 0.00 0.00 0.44 0.00 0.56
#> TCGA.FI.A2F8.01 4 0.4637 0.6657 0.00 0.00 0.16 0.74 0.10
#> TCGA.BG.A0YV.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 3 0.2797 0.4504 0.00 0.00 0.88 0.06 0.06
#> TCGA.E6.A1LZ.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.H5.A2HR.01 2 0.0609 0.9888 0.00 0.98 0.00 0.00 0.02
#> TCGA.FI.A3PV.01 4 0.4637 0.6657 0.00 0.00 0.16 0.74 0.10
#> TCGA.BG.A18C.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GP.01 3 0.2331 0.4557 0.00 0.00 0.90 0.02 0.08
#> TCGA.DI.A2QU.01 5 0.4262 0.9341 0.00 0.00 0.44 0.00 0.56
#> TCGA.2E.A9G8.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 4 0.0000 0.7790 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A1NU.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11U.01 1 0.6265 0.5945 0.54 0.00 0.00 0.24 0.22
#> TCGA.AJ.A3BD.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3FV.01 5 0.4829 0.8664 0.00 0.02 0.48 0.00 0.50
#> TCGA.EO.A3B1.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.EO.A2CH.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.AP.A0LF.01 4 0.4818 0.6508 0.00 0.00 0.18 0.72 0.10
#> TCGA.5B.A90C.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 3 0.4060 -0.4357 0.00 0.00 0.64 0.00 0.36
#> TCGA.B5.A3FD.01 3 0.4675 -0.5571 0.00 0.02 0.60 0.00 0.38
#> TCGA.AJ.A3TW.01 1 0.4558 0.7586 0.74 0.00 0.00 0.08 0.18
#> TCGA.EY.A4KR.01 3 0.1648 0.4271 0.00 0.02 0.94 0.00 0.04
#> TCGA.BS.A0V8.01 1 0.6610 0.4823 0.46 0.00 0.00 0.28 0.26
#> TCGA.BG.A0YU.01 3 0.4060 -0.4357 0.00 0.00 0.64 0.00 0.36
#> TCGA.D1.A15V.01 1 0.2929 0.7839 0.82 0.00 0.00 0.00 0.18
#> TCGA.FI.A3PX.01 4 0.4854 0.6333 0.06 0.00 0.00 0.68 0.26
#> TCGA.AX.A3G6.01 4 0.2873 0.7741 0.02 0.00 0.00 0.86 0.12
#> TCGA.EY.A2ON.01 1 0.4558 0.7586 0.74 0.00 0.00 0.08 0.18
#> TCGA.EY.A214.01 1 0.4558 0.7586 0.74 0.00 0.00 0.08 0.18
#> TCGA.EY.A1GO.01 3 0.3390 0.4298 0.00 0.00 0.84 0.06 0.10
#> TCGA.AX.A3G1.01 4 0.4254 0.6937 0.04 0.00 0.00 0.74 0.22
#> TCGA.AX.A3GI.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2H8.01 4 0.3690 0.7229 0.02 0.00 0.00 0.78 0.20
#> TCGA.B5.A3FB.01 4 0.2873 0.7673 0.02 0.00 0.00 0.86 0.12
#> TCGA.KP.A3W1.01 3 0.5425 -0.0726 0.00 0.42 0.52 0.00 0.06
#> TCGA.B5.A0KB.01 3 0.1648 0.4624 0.00 0.00 0.94 0.04 0.02
#> TCGA.A5.A0GR.01 2 0.0609 0.9888 0.00 0.98 0.00 0.00 0.02
#> TCGA.AX.A3G7.01 2 0.0609 0.9888 0.00 0.98 0.00 0.00 0.02
#> TCGA.D1.A3JP.01 2 0.0609 0.9888 0.00 0.98 0.00 0.00 0.02
#> TCGA.EO.A3KW.01 4 0.2754 0.7660 0.04 0.00 0.00 0.88 0.08
#> TCGA.AJ.A2QN.01 1 0.6541 0.5197 0.48 0.00 0.00 0.26 0.26
#> TCGA.D1.A3DH.01 2 0.0000 0.9902 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3NH.01 4 0.3390 0.7248 0.00 0.00 0.06 0.84 0.10
#> TCGA.AX.A1CN.01 1 0.0000 0.8002 1.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 4 0.4818 0.6508 0.00 0.00 0.18 0.72 0.10
#> TCGA.AJ.A3EM.01 4 0.1216 0.7825 0.02 0.00 0.00 0.96 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.B5.A5OE.01 6 0.2793 0.8555 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.AP.A3K1.01 4 0.5438 0.4749 0.28 0.16 0.00 0.56 0.00 0.00
#> TCGA.D1.A0ZZ.01 5 0.2512 0.6739 0.00 0.06 0.06 0.00 0.88 0.00
#> TCGA.AP.A5FX.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FZ.01 5 0.0547 0.7206 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.DI.A1NN.01 1 0.3073 0.8297 0.84 0.08 0.00 0.08 0.00 0.00
#> TCGA.AX.A2HK.01 3 0.2260 0.6288 0.00 0.00 0.86 0.14 0.00 0.00
#> TCGA.D1.A17K.01 4 0.2725 0.6724 0.04 0.06 0.02 0.88 0.00 0.00
#> TCGA.DI.A0WH.01 4 0.5267 0.3952 0.32 0.12 0.00 0.56 0.00 0.00
#> TCGA.D1.A1NW.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3QS.01 3 0.4576 0.2997 0.00 0.04 0.56 0.00 0.40 0.00
#> TCGA.EY.A2OQ.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A5.A7WK.01 6 0.2793 0.8555 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.BS.A0U9.01 4 0.2882 0.6668 0.02 0.10 0.02 0.86 0.00 0.00
#> TCGA.A5.A2K2.01 4 0.4887 0.5899 0.02 0.16 0.12 0.70 0.00 0.00
#> TCGA.EY.A1GJ.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 6 0.2793 0.8555 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.EY.A1GC.01 5 0.5685 0.6305 0.00 0.30 0.12 0.02 0.56 0.00
#> TCGA.FI.A2F8.01 3 0.3076 0.5788 0.00 0.00 0.76 0.24 0.00 0.00
#> TCGA.BG.A0YV.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 3 0.4806 0.3354 0.00 0.06 0.56 0.00 0.38 0.00
#> TCGA.E6.A1LZ.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.H5.A2HR.01 6 0.2793 0.8555 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.FI.A3PV.01 3 0.2941 0.5958 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.BG.A18C.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GP.01 3 0.5490 0.3473 0.00 0.18 0.56 0.00 0.26 0.00
#> TCGA.DI.A2QU.01 5 0.5749 0.6225 0.00 0.32 0.12 0.02 0.54 0.00
#> TCGA.2E.A9G8.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 4 0.4810 0.4825 0.00 0.12 0.22 0.66 0.00 0.00
#> TCGA.D1.A1NU.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11U.01 4 0.5438 0.4749 0.28 0.16 0.00 0.56 0.00 0.00
#> TCGA.AJ.A3BD.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A3FV.01 5 0.4282 0.6330 0.00 0.42 0.02 0.00 0.56 0.00
#> TCGA.EO.A3B1.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EO.A2CH.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AP.A0LF.01 3 0.2454 0.6251 0.00 0.00 0.84 0.16 0.00 0.00
#> TCGA.5B.A90C.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 5 0.0547 0.7337 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.B5.A3FD.01 5 0.2581 0.7150 0.00 0.12 0.00 0.00 0.86 0.02
#> TCGA.AJ.A3TW.01 1 0.3928 0.7563 0.76 0.08 0.00 0.16 0.00 0.00
#> TCGA.EY.A4KR.01 5 0.6629 0.2362 0.00 0.12 0.28 0.00 0.50 0.10
#> TCGA.BS.A0V8.01 4 0.4926 0.5267 0.24 0.12 0.00 0.64 0.00 0.00
#> TCGA.BG.A0YU.01 5 0.0547 0.7337 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.D1.A15V.01 1 0.3321 0.8176 0.82 0.10 0.00 0.08 0.00 0.00
#> TCGA.FI.A3PX.01 4 0.3007 0.6709 0.04 0.08 0.02 0.86 0.00 0.00
#> TCGA.AX.A3G6.01 4 0.5184 0.6226 0.02 0.20 0.12 0.66 0.00 0.00
#> TCGA.EY.A2ON.01 1 0.3928 0.7563 0.76 0.08 0.00 0.16 0.00 0.00
#> TCGA.EY.A214.01 1 0.3928 0.7563 0.76 0.08 0.00 0.16 0.00 0.00
#> TCGA.EY.A1GO.01 3 0.5747 0.3194 0.00 0.20 0.50 0.00 0.30 0.00
#> TCGA.AX.A3G1.01 4 0.1092 0.6815 0.02 0.00 0.02 0.96 0.00 0.00
#> TCGA.AX.A3GI.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A2H8.01 4 0.2345 0.6660 0.02 0.06 0.02 0.90 0.00 0.00
#> TCGA.B5.A3FB.01 4 0.5043 0.6236 0.02 0.18 0.12 0.68 0.00 0.00
#> TCGA.KP.A3W1.01 6 0.6331 0.0546 0.00 0.20 0.02 0.00 0.38 0.40
#> TCGA.B5.A0KB.01 3 0.4482 0.3331 0.00 0.04 0.60 0.00 0.36 0.00
#> TCGA.A5.A0GR.01 6 0.2793 0.8555 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.AX.A3G7.01 6 0.2793 0.8555 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.D1.A3JP.01 6 0.2793 0.8555 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.EO.A3KW.01 4 0.4607 0.6196 0.02 0.18 0.08 0.72 0.00 0.00
#> TCGA.AJ.A2QN.01 4 0.4360 0.5197 0.26 0.06 0.00 0.68 0.00 0.00
#> TCGA.D1.A3DH.01 6 0.0000 0.8683 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3NH.01 3 0.4845 0.1995 0.00 0.06 0.54 0.40 0.00 0.00
#> TCGA.AX.A1CN.01 1 0.0000 0.9071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 3 0.2941 0.5977 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.AJ.A3EM.01 4 0.4887 0.5899 0.02 0.16 0.12 0.70 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.B5.A5OE.01 6 0.0000 0.917 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AP.A3K1.01 4 0.2745 0.540 0.00 0.16 0.00 0.82 0.00 0.00 0.02
#> TCGA.D1.A0ZZ.01 7 0.4701 0.291 0.02 0.00 0.04 0.00 0.44 0.00 0.50
#> TCGA.AP.A5FX.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FZ.01 5 0.2259 0.521 0.00 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.DI.A1NN.01 2 0.3047 0.659 0.00 0.72 0.00 0.28 0.00 0.00 0.00
#> TCGA.AX.A2HK.01 3 0.2509 0.748 0.02 0.00 0.88 0.06 0.00 0.00 0.04
#> TCGA.D1.A17K.01 4 0.3525 0.551 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.DI.A0WH.01 4 0.4431 0.407 0.04 0.24 0.00 0.68 0.00 0.00 0.04
#> TCGA.D1.A1NW.01 6 0.2213 0.923 0.04 0.00 0.04 0.00 0.00 0.90 0.02
#> TCGA.AJ.A3QS.01 7 0.5115 0.591 0.00 0.00 0.38 0.00 0.14 0.00 0.48
#> TCGA.EY.A2OQ.01 6 0.2563 0.921 0.04 0.00 0.04 0.00 0.00 0.88 0.04
#> TCGA.A5.A7WK.01 6 0.0000 0.917 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BS.A0U9.01 4 0.4408 0.538 0.44 0.00 0.02 0.52 0.00 0.00 0.02
#> TCGA.A5.A2K2.01 4 0.5229 0.567 0.18 0.00 0.12 0.64 0.00 0.00 0.06
#> TCGA.EY.A1GJ.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 6 0.0000 0.917 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GC.01 5 0.4622 0.609 0.38 0.00 0.02 0.00 0.56 0.00 0.04
#> TCGA.FI.A2F8.01 3 0.1886 0.787 0.00 0.00 0.88 0.12 0.00 0.00 0.00
#> TCGA.BG.A0YV.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 7 0.5295 0.609 0.04 0.00 0.34 0.00 0.08 0.00 0.54
#> TCGA.E6.A1LZ.01 6 0.2563 0.921 0.04 0.00 0.04 0.00 0.00 0.88 0.04
#> TCGA.H5.A2HR.01 6 0.1006 0.898 0.00 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.FI.A3PV.01 3 0.1886 0.787 0.00 0.00 0.88 0.12 0.00 0.00 0.00
#> TCGA.BG.A18C.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GP.01 7 0.4264 0.630 0.02 0.00 0.22 0.00 0.06 0.00 0.70
#> TCGA.DI.A2QU.01 5 0.4622 0.609 0.38 0.00 0.02 0.00 0.56 0.00 0.04
#> TCGA.2E.A9G8.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 4 0.5386 0.486 0.10 0.00 0.24 0.60 0.00 0.00 0.06
#> TCGA.D1.A1NU.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11U.01 4 0.3244 0.506 0.00 0.18 0.00 0.78 0.00 0.00 0.04
#> TCGA.AJ.A3BD.01 6 0.2563 0.921 0.04 0.00 0.04 0.00 0.00 0.88 0.04
#> TCGA.AX.A3FV.01 5 0.5717 0.569 0.28 0.00 0.00 0.00 0.54 0.12 0.06
#> TCGA.EO.A3B1.01 6 0.2563 0.921 0.04 0.00 0.04 0.00 0.00 0.88 0.04
#> TCGA.EO.A2CH.01 6 0.2563 0.921 0.04 0.00 0.04 0.00 0.00 0.88 0.04
#> TCGA.AP.A0LF.01 3 0.1928 0.782 0.00 0.00 0.90 0.08 0.00 0.00 0.02
#> TCGA.5B.A90C.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 5 0.0863 0.679 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.B5.A3FD.01 5 0.1006 0.678 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.AJ.A3TW.01 2 0.3525 0.462 0.00 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 7 0.6179 0.549 0.00 0.00 0.14 0.00 0.26 0.10 0.50
#> TCGA.BS.A0V8.01 4 0.2512 0.605 0.04 0.10 0.00 0.86 0.00 0.00 0.00
#> TCGA.BG.A0YU.01 5 0.0863 0.679 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.D1.A15V.01 2 0.3294 0.602 0.00 0.66 0.00 0.34 0.00 0.00 0.00
#> TCGA.FI.A3PX.01 4 0.3525 0.551 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.AX.A3G6.01 4 0.4295 0.549 0.06 0.00 0.14 0.74 0.00 0.00 0.06
#> TCGA.EY.A2ON.01 2 0.3525 0.462 0.00 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.EY.A214.01 2 0.3525 0.462 0.00 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 7 0.3902 0.631 0.04 0.00 0.16 0.00 0.04 0.00 0.76
#> TCGA.AX.A3G1.01 4 0.2745 0.656 0.16 0.00 0.02 0.82 0.00 0.00 0.00
#> TCGA.AX.A3GI.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 6 0.2213 0.923 0.04 0.00 0.04 0.00 0.00 0.90 0.02
#> TCGA.AX.A2H8.01 4 0.3968 0.544 0.44 0.00 0.02 0.54 0.00 0.00 0.00
#> TCGA.B5.A3FB.01 4 0.3494 0.592 0.02 0.00 0.12 0.80 0.00 0.00 0.06
#> TCGA.KP.A3W1.01 6 0.3566 0.685 0.00 0.00 0.02 0.00 0.16 0.78 0.04
#> TCGA.B5.A0KB.01 3 0.4978 -0.513 0.00 0.00 0.50 0.00 0.12 0.00 0.38
#> TCGA.A5.A0GR.01 6 0.0504 0.909 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.AX.A3G7.01 6 0.0000 0.917 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A3JP.01 6 0.1363 0.885 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.EO.A3KW.01 4 0.4604 0.613 0.18 0.00 0.06 0.70 0.00 0.00 0.06
#> TCGA.AJ.A2QN.01 4 0.3449 0.583 0.08 0.14 0.00 0.78 0.00 0.00 0.00
#> TCGA.D1.A3DH.01 6 0.2563 0.921 0.04 0.00 0.04 0.00 0.00 0.88 0.04
#> TCGA.AJ.A3NH.01 3 0.3370 0.697 0.06 0.00 0.78 0.16 0.00 0.00 0.00
#> TCGA.AX.A1CN.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 3 0.1928 0.784 0.02 0.00 0.90 0.08 0.00 0.00 0.00
#> TCGA.AJ.A3EM.01 4 0.5536 0.530 0.18 0.00 0.16 0.60 0.00 0.00 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.B5.A5OE.01 6 0.3303 0.7855 0.02 0.00 0.00 0.00 0.00 0.76 0.20 0.02
#> TCGA.AP.A3K1.01 4 0.3746 0.3330 0.00 0.04 0.00 0.64 0.00 0.00 0.00 0.32
#> TCGA.D1.A0ZZ.01 7 0.4399 -0.0354 0.00 0.00 0.02 0.00 0.44 0.00 0.50 0.04
#> TCGA.AP.A5FX.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FZ.01 5 0.1341 0.8499 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.DI.A1NN.01 2 0.3774 0.6546 0.00 0.70 0.00 0.22 0.00 0.00 0.00 0.08
#> TCGA.AX.A2HK.01 3 0.1275 0.7108 0.00 0.00 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.D1.A17K.01 4 0.2807 0.4728 0.06 0.00 0.04 0.86 0.00 0.00 0.02 0.02
#> TCGA.DI.A0WH.01 4 0.4437 0.3793 0.00 0.16 0.00 0.62 0.00 0.00 0.00 0.22
#> TCGA.D1.A1NW.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3QS.01 3 0.4554 0.1272 0.00 0.00 0.48 0.00 0.10 0.00 0.42 0.00
#> TCGA.EY.A2OQ.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A5.A7WK.01 6 0.3615 0.7795 0.02 0.00 0.00 0.00 0.00 0.74 0.20 0.04
#> TCGA.BS.A0U9.01 4 0.3102 0.4496 0.08 0.00 0.02 0.82 0.00 0.00 0.08 0.00
#> TCGA.A5.A2K2.01 8 0.4983 0.5781 0.04 0.00 0.02 0.36 0.00 0.00 0.04 0.54
#> TCGA.EY.A1GJ.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3DG.01 6 0.3615 0.7795 0.02 0.00 0.00 0.00 0.00 0.74 0.20 0.04
#> TCGA.EY.A1GC.01 1 0.3198 0.6812 0.72 0.00 0.00 0.00 0.26 0.00 0.02 0.00
#> TCGA.FI.A2F8.01 3 0.1275 0.7160 0.00 0.00 0.94 0.04 0.00 0.00 0.00 0.02
#> TCGA.BG.A0YV.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 3 0.5216 0.0737 0.00 0.00 0.44 0.00 0.10 0.00 0.42 0.04
#> TCGA.E6.A1LZ.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.H5.A2HR.01 6 0.4534 0.6582 0.02 0.00 0.00 0.00 0.04 0.62 0.30 0.02
#> TCGA.FI.A3PV.01 3 0.1275 0.7160 0.00 0.00 0.94 0.04 0.00 0.00 0.00 0.02
#> TCGA.BG.A18C.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GP.01 7 0.7016 0.2485 0.10 0.00 0.26 0.00 0.08 0.00 0.38 0.18
#> TCGA.DI.A2QU.01 1 0.3198 0.6812 0.72 0.00 0.00 0.00 0.26 0.00 0.02 0.00
#> TCGA.2E.A9G8.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 4 0.6007 -0.4085 0.02 0.00 0.32 0.34 0.00 0.00 0.02 0.30
#> TCGA.D1.A1NU.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A11U.01 4 0.4538 0.3203 0.00 0.12 0.00 0.56 0.00 0.00 0.00 0.32
#> TCGA.AJ.A3BD.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A3FV.01 1 0.5529 0.3754 0.42 0.00 0.00 0.00 0.24 0.00 0.32 0.02
#> TCGA.EO.A3B1.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EO.A2CH.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AP.A0LF.01 3 0.1275 0.7108 0.00 0.00 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.5B.A90C.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 5 0.0471 0.9082 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.B5.A3FD.01 5 0.0471 0.9299 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.AJ.A3TW.01 2 0.4199 0.5496 0.00 0.60 0.00 0.32 0.00 0.00 0.00 0.08
#> TCGA.EY.A4KR.01 7 0.5024 0.3277 0.02 0.00 0.10 0.00 0.20 0.04 0.64 0.00
#> TCGA.BS.A0V8.01 4 0.3299 0.4816 0.00 0.06 0.00 0.76 0.00 0.00 0.00 0.18
#> TCGA.BG.A0YU.01 5 0.0471 0.9299 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.D1.A15V.01 2 0.4244 0.5988 0.00 0.64 0.00 0.24 0.00 0.00 0.00 0.12
#> TCGA.FI.A3PX.01 4 0.2914 0.4713 0.08 0.00 0.04 0.84 0.00 0.00 0.04 0.00
#> TCGA.AX.A3G6.01 8 0.5305 0.3187 0.02 0.00 0.20 0.28 0.00 0.00 0.00 0.50
#> TCGA.EY.A2ON.01 2 0.4199 0.5496 0.00 0.60 0.00 0.32 0.00 0.00 0.00 0.08
#> TCGA.EY.A214.01 2 0.4199 0.5496 0.00 0.60 0.00 0.32 0.00 0.00 0.00 0.08
#> TCGA.EY.A1GO.01 7 0.6910 0.2701 0.08 0.00 0.22 0.00 0.08 0.00 0.40 0.22
#> TCGA.AX.A3G1.01 4 0.2680 0.4400 0.02 0.00 0.02 0.84 0.00 0.00 0.00 0.12
#> TCGA.AX.A3GI.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AX.A2H8.01 4 0.2807 0.4728 0.06 0.00 0.04 0.86 0.00 0.00 0.02 0.02
#> TCGA.B5.A3FB.01 8 0.5068 0.1324 0.00 0.00 0.20 0.38 0.00 0.00 0.00 0.42
#> TCGA.KP.A3W1.01 7 0.5589 -0.2886 0.04 0.00 0.00 0.00 0.10 0.38 0.46 0.02
#> TCGA.B5.A0KB.01 3 0.4511 0.1992 0.00 0.00 0.52 0.00 0.10 0.00 0.38 0.00
#> TCGA.A5.A0GR.01 6 0.3728 0.7251 0.02 0.00 0.00 0.00 0.00 0.68 0.28 0.02
#> TCGA.AX.A3G7.01 6 0.3303 0.7855 0.02 0.00 0.00 0.00 0.00 0.76 0.20 0.02
#> TCGA.D1.A3JP.01 6 0.3942 0.6613 0.02 0.00 0.00 0.00 0.00 0.62 0.34 0.02
#> TCGA.EO.A3KW.01 8 0.4983 0.5781 0.04 0.00 0.02 0.36 0.00 0.00 0.04 0.54
#> TCGA.AJ.A2QN.01 4 0.2862 0.4952 0.00 0.08 0.00 0.82 0.00 0.00 0.00 0.10
#> TCGA.D1.A3DH.01 6 0.0000 0.8343 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3NH.01 3 0.2864 0.6214 0.02 0.00 0.84 0.06 0.00 0.00 0.00 0.08
#> TCGA.AX.A1CN.01 2 0.0000 0.8309 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EO.A1Y8.01 3 0.1275 0.7160 0.00 0.00 0.94 0.04 0.00 0.00 0.00 0.02
#> TCGA.AJ.A3EM.01 8 0.5404 0.5775 0.04 0.00 0.06 0.32 0.00 0.00 0.04 0.54
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node05. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["051"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 37 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.797 0.950 0.977 0.4911 0.517 0.517
#> 3 3 1.000 0.982 0.992 0.3785 0.778 0.581
#> 4 4 0.840 0.668 0.810 0.0935 0.965 0.893
#> 5 5 0.760 0.767 0.774 0.0722 0.850 0.524
#> 6 6 0.721 0.546 0.732 0.0456 0.961 0.809
#> 7 7 0.798 0.799 0.815 0.0357 0.940 0.675
#> 8 8 0.839 0.729 0.810 0.0224 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.AP.A3K1.01 2 0.469 0.891 0.10 0.90
#> TCGA.AP.A5FX.01 2 0.000 0.961 0.00 1.00
#> TCGA.DI.A1NN.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A2HK.01 2 0.469 0.891 0.10 0.90
#> TCGA.D1.A17K.01 2 0.000 0.961 0.00 1.00
#> TCGA.DI.A0WH.01 2 0.000 0.961 0.00 1.00
#> TCGA.BS.A0U9.01 2 0.000 0.961 0.00 1.00
#> TCGA.A5.A2K2.01 2 0.469 0.891 0.10 0.90
#> TCGA.EY.A1GJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.FI.A2F8.01 2 0.000 0.961 0.00 1.00
#> TCGA.BG.A0YV.01 1 0.000 1.000 1.00 0.00
#> TCGA.D1.A16S.01 1 0.000 1.000 1.00 0.00
#> TCGA.FI.A3PV.01 2 0.000 0.961 0.00 1.00
#> TCGA.BG.A18C.01 2 0.000 0.961 0.00 1.00
#> TCGA.2E.A9G8.01 1 0.000 1.000 1.00 0.00
#> TCGA.FI.A2EX.01 2 0.990 0.272 0.44 0.56
#> TCGA.D1.A1NU.01 1 0.000 1.000 1.00 0.00
#> TCGA.B5.A11U.01 2 0.000 0.961 0.00 1.00
#> TCGA.AP.A0LF.01 2 0.469 0.891 0.10 0.90
#> TCGA.5B.A90C.01 1 0.000 1.000 1.00 0.00
#> TCGA.AJ.A3TW.01 1 0.000 1.000 1.00 0.00
#> TCGA.BS.A0V8.01 2 0.000 0.961 0.00 1.00
#> TCGA.D1.A15V.01 1 0.000 1.000 1.00 0.00
#> TCGA.FI.A3PX.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A3G6.01 2 0.000 0.961 0.00 1.00
#> TCGA.EY.A2ON.01 1 0.000 1.000 1.00 0.00
#> TCGA.EY.A214.01 2 0.000 0.961 0.00 1.00
#> TCGA.AX.A3G1.01 2 0.000 0.961 0.00 1.00
#> TCGA.AX.A3GI.01 1 0.000 1.000 1.00 0.00
#> TCGA.AX.A2H8.01 2 0.000 0.961 0.00 1.00
#> TCGA.B5.A3FB.01 2 0.000 0.961 0.00 1.00
#> TCGA.EO.A3KW.01 1 0.000 1.000 1.00 0.00
#> TCGA.AJ.A2QN.01 2 0.000 0.961 0.00 1.00
#> TCGA.AJ.A3NH.01 2 0.000 0.961 0.00 1.00
#> TCGA.AX.A1CN.01 1 0.000 1.000 1.00 0.00
#> TCGA.EO.A1Y8.01 2 0.000 0.961 0.00 1.00
#> TCGA.AJ.A3EM.01 2 0.000 0.961 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AP.A3K1.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.AP.A5FX.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.DI.A1NN.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.AX.A2HK.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.D1.A17K.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.DI.A0WH.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.BS.A0U9.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.A5.A2K2.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.EY.A1GJ.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.FI.A2F8.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.BG.A0YV.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.D1.A16S.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.FI.A3PV.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.BG.A18C.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.2E.A9G8.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.FI.A2EX.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.D1.A1NU.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.B5.A11U.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.AP.A0LF.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.5B.A90C.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.AJ.A3TW.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.BS.A0V8.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.D1.A15V.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.FI.A3PX.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.AX.A3G6.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.EY.A2ON.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.EY.A214.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.AX.A3G1.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.AX.A3GI.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.AX.A2H8.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.B5.A3FB.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.EO.A3KW.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.AJ.A2QN.01 2 0.00 1.000 0 1.00 0.00
#> TCGA.AJ.A3NH.01 3 0.54 0.611 0 0.28 0.72
#> TCGA.AX.A1CN.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.EO.A1Y8.01 3 0.00 0.968 0 0.00 1.00
#> TCGA.AJ.A3EM.01 2 0.00 1.000 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AP.A3K1.01 3 0.000 0.944 0.00 0.00 1.00 0.00
#> TCGA.AP.A5FX.01 2 0.201 0.407 0.00 0.92 0.00 0.08
#> TCGA.DI.A1NN.01 1 0.000 0.788 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HK.01 3 0.265 0.919 0.00 0.00 0.88 0.12
#> TCGA.D1.A17K.01 2 0.485 0.458 0.00 0.60 0.00 0.40
#> TCGA.DI.A0WH.01 2 0.471 0.468 0.00 0.64 0.00 0.36
#> TCGA.BS.A0U9.01 2 0.485 0.458 0.00 0.60 0.00 0.40
#> TCGA.A5.A2K2.01 3 0.000 0.944 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GJ.01 1 0.000 0.788 1.00 0.00 0.00 0.00
#> TCGA.FI.A2F8.01 3 0.201 0.934 0.00 0.00 0.92 0.08
#> TCGA.BG.A0YV.01 1 0.471 0.817 0.64 0.00 0.00 0.36
#> TCGA.D1.A16S.01 1 0.495 0.790 0.56 0.00 0.00 0.44
#> TCGA.FI.A3PV.01 3 0.201 0.934 0.00 0.00 0.92 0.08
#> TCGA.BG.A18C.01 2 0.000 0.465 0.00 1.00 0.00 0.00
#> TCGA.2E.A9G8.01 1 0.000 0.788 1.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 3 0.000 0.944 0.00 0.00 1.00 0.00
#> TCGA.D1.A1NU.01 1 0.485 0.812 0.60 0.00 0.00 0.40
#> TCGA.B5.A11U.01 2 0.000 0.465 0.00 1.00 0.00 0.00
#> TCGA.AP.A0LF.01 3 0.000 0.944 0.00 0.00 1.00 0.00
#> TCGA.5B.A90C.01 1 0.000 0.788 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3TW.01 1 0.000 0.788 1.00 0.00 0.00 0.00
#> TCGA.BS.A0V8.01 2 0.471 0.468 0.00 0.64 0.00 0.36
#> TCGA.D1.A15V.01 1 0.471 0.817 0.64 0.00 0.00 0.36
#> TCGA.FI.A3PX.01 3 0.234 0.874 0.00 0.00 0.90 0.10
#> TCGA.AX.A3G6.01 2 0.485 0.458 0.00 0.60 0.00 0.40
#> TCGA.EY.A2ON.01 1 0.485 0.812 0.60 0.00 0.00 0.40
#> TCGA.EY.A214.01 2 0.201 0.407 0.00 0.92 0.00 0.08
#> TCGA.AX.A3G1.01 2 0.485 0.458 0.00 0.60 0.00 0.40
#> TCGA.AX.A3GI.01 1 0.485 0.812 0.60 0.00 0.00 0.40
#> TCGA.AX.A2H8.01 4 0.634 -0.238 0.00 0.46 0.06 0.48
#> TCGA.B5.A3FB.01 2 0.000 0.465 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KW.01 1 0.485 0.812 0.60 0.00 0.00 0.40
#> TCGA.AJ.A2QN.01 2 0.485 0.458 0.00 0.60 0.00 0.40
#> TCGA.AJ.A3NH.01 4 0.754 0.343 0.00 0.20 0.34 0.46
#> TCGA.AX.A1CN.01 1 0.201 0.737 0.92 0.00 0.00 0.08
#> TCGA.EO.A1Y8.01 3 0.201 0.934 0.00 0.00 0.92 0.08
#> TCGA.AJ.A3EM.01 2 0.485 0.458 0.00 0.60 0.00 0.40
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AP.A3K1.01 3 0.603 0.719 0.22 0.20 0.58 0.00 0.00
#> TCGA.AP.A5FX.01 4 0.173 0.829 0.08 0.00 0.00 0.92 0.00
#> TCGA.DI.A1NN.01 5 0.104 0.908 0.04 0.00 0.00 0.00 0.96
#> TCGA.AX.A2HK.01 3 0.104 0.684 0.00 0.04 0.96 0.00 0.00
#> TCGA.D1.A17K.01 2 0.368 0.817 0.00 0.72 0.00 0.28 0.00
#> TCGA.DI.A0WH.01 2 0.509 0.718 0.04 0.56 0.00 0.40 0.00
#> TCGA.BS.A0U9.01 2 0.368 0.817 0.00 0.72 0.00 0.28 0.00
#> TCGA.A5.A2K2.01 3 0.603 0.719 0.22 0.20 0.58 0.00 0.00
#> TCGA.EY.A1GJ.01 5 0.104 0.908 0.04 0.00 0.00 0.00 0.96
#> TCGA.FI.A2F8.01 3 0.000 0.697 0.00 0.00 1.00 0.00 0.00
#> TCGA.BG.A0YV.01 1 0.429 0.872 0.54 0.00 0.00 0.00 0.46
#> TCGA.D1.A16S.01 1 0.473 0.901 0.58 0.02 0.00 0.00 0.40
#> TCGA.FI.A3PV.01 3 0.000 0.697 0.00 0.00 1.00 0.00 0.00
#> TCGA.BG.A18C.01 4 0.233 0.854 0.02 0.08 0.00 0.90 0.00
#> TCGA.2E.A9G8.01 5 0.104 0.908 0.04 0.00 0.00 0.00 0.96
#> TCGA.FI.A2EX.01 3 0.603 0.719 0.22 0.20 0.58 0.00 0.00
#> TCGA.D1.A1NU.01 1 0.499 0.902 0.60 0.04 0.00 0.00 0.36
#> TCGA.B5.A11U.01 4 0.173 0.865 0.00 0.08 0.00 0.92 0.00
#> TCGA.AP.A0LF.01 3 0.603 0.719 0.22 0.20 0.58 0.00 0.00
#> TCGA.5B.A90C.01 5 0.000 0.896 0.00 0.00 0.00 0.00 1.00
#> TCGA.AJ.A3TW.01 5 0.000 0.896 0.00 0.00 0.00 0.00 1.00
#> TCGA.BS.A0V8.01 2 0.539 0.685 0.06 0.54 0.00 0.40 0.00
#> TCGA.D1.A15V.01 1 0.429 0.872 0.54 0.00 0.00 0.00 0.46
#> TCGA.FI.A3PX.01 3 0.653 0.667 0.28 0.24 0.48 0.00 0.00
#> TCGA.AX.A3G6.01 2 0.454 0.794 0.02 0.64 0.00 0.34 0.00
#> TCGA.EY.A2ON.01 1 0.418 0.906 0.60 0.00 0.00 0.00 0.40
#> TCGA.EY.A214.01 4 0.173 0.829 0.08 0.00 0.00 0.92 0.00
#> TCGA.AX.A3G1.01 2 0.475 0.812 0.04 0.66 0.00 0.30 0.00
#> TCGA.AX.A3GI.01 1 0.499 0.902 0.60 0.04 0.00 0.00 0.36
#> TCGA.AX.A2H8.01 2 0.595 0.275 0.02 0.50 0.42 0.06 0.00
#> TCGA.B5.A3FB.01 4 0.233 0.856 0.02 0.08 0.00 0.90 0.00
#> TCGA.EO.A3KW.01 1 0.499 0.902 0.60 0.04 0.00 0.00 0.36
#> TCGA.AJ.A2QN.01 2 0.475 0.812 0.04 0.66 0.00 0.30 0.00
#> TCGA.AJ.A3NH.01 3 0.533 -0.206 0.02 0.44 0.52 0.02 0.00
#> TCGA.AX.A1CN.01 5 0.342 0.713 0.08 0.00 0.00 0.08 0.84
#> TCGA.EO.A1Y8.01 3 0.000 0.697 0.00 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3EM.01 2 0.368 0.817 0.00 0.72 0.00 0.28 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AP.A3K1.01 3 0.4328 -0.313 0.02 0.00 0.52 0.00 0.00 0.46
#> TCGA.AP.A5FX.01 4 0.4926 0.721 0.00 0.14 0.00 0.72 0.08 0.06
#> TCGA.DI.A1NN.01 5 0.2631 0.949 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.AX.A2HK.01 3 0.3318 0.156 0.00 0.00 0.82 0.02 0.02 0.14
#> TCGA.D1.A17K.01 2 0.3315 0.741 0.00 0.78 0.00 0.00 0.02 0.20
#> TCGA.DI.A0WH.01 2 0.0937 0.739 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.BS.A0U9.01 2 0.4380 0.705 0.00 0.70 0.00 0.00 0.08 0.22
#> TCGA.A5.A2K2.01 3 0.4328 -0.313 0.02 0.00 0.52 0.00 0.00 0.46
#> TCGA.EY.A1GJ.01 5 0.2631 0.949 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.FI.A2F8.01 3 0.0000 0.307 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0YV.01 1 0.1814 0.781 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.D1.A16S.01 1 0.1635 0.797 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.FI.A3PV.01 3 0.0000 0.307 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A18C.01 4 0.3706 0.704 0.00 0.38 0.00 0.62 0.00 0.00
#> TCGA.2E.A9G8.01 5 0.2631 0.949 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.FI.A2EX.01 3 0.4328 -0.313 0.02 0.00 0.52 0.00 0.00 0.46
#> TCGA.D1.A1NU.01 1 0.4430 0.797 0.76 0.00 0.00 0.12 0.04 0.08
#> TCGA.B5.A11U.01 4 0.3409 0.765 0.00 0.30 0.00 0.70 0.00 0.00
#> TCGA.AP.A0LF.01 3 0.4328 -0.313 0.02 0.00 0.52 0.00 0.00 0.46
#> TCGA.5B.A90C.01 5 0.2793 0.944 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.AJ.A3TW.01 5 0.2793 0.944 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.BS.A0V8.01 2 0.4733 0.547 0.00 0.74 0.00 0.12 0.06 0.08
#> TCGA.D1.A15V.01 1 0.1814 0.781 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.FI.A3PX.01 6 0.6460 0.000 0.16 0.00 0.30 0.02 0.02 0.50
#> TCGA.AX.A3G6.01 2 0.4200 0.636 0.00 0.74 0.00 0.14 0.00 0.12
#> TCGA.EY.A2ON.01 1 0.0000 0.820 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A214.01 4 0.4926 0.721 0.00 0.14 0.00 0.72 0.08 0.06
#> TCGA.AX.A3G1.01 2 0.0000 0.765 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3GI.01 1 0.4733 0.790 0.74 0.00 0.00 0.12 0.06 0.08
#> TCGA.AX.A2H8.01 3 0.6885 -0.127 0.00 0.26 0.42 0.00 0.06 0.26
#> TCGA.B5.A3FB.01 4 0.4265 0.747 0.00 0.30 0.00 0.66 0.00 0.04
#> TCGA.EO.A3KW.01 1 0.4430 0.797 0.76 0.00 0.00 0.12 0.04 0.08
#> TCGA.AJ.A2QN.01 2 0.0000 0.765 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NH.01 3 0.5608 0.093 0.00 0.20 0.54 0.00 0.00 0.26
#> TCGA.AX.A1CN.01 5 0.2794 0.809 0.08 0.00 0.00 0.06 0.86 0.00
#> TCGA.EO.A1Y8.01 3 0.0000 0.307 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3EM.01 2 0.3315 0.741 0.00 0.78 0.00 0.00 0.02 0.20
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AP.A3K1.01 6 0.000 0.878 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AP.A5FX.01 4 0.231 0.747 0.00 0.06 0.00 0.88 0.06 0.00 0.00
#> TCGA.DI.A1NN.01 5 0.117 0.961 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.AX.A2HK.01 3 0.499 0.656 0.04 0.00 0.68 0.04 0.00 0.20 0.04
#> TCGA.D1.A17K.01 2 0.189 0.787 0.00 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.DI.A0WH.01 2 0.251 0.750 0.00 0.86 0.00 0.10 0.00 0.00 0.04
#> TCGA.BS.A0U9.01 2 0.320 0.765 0.00 0.80 0.14 0.00 0.00 0.00 0.06
#> TCGA.A5.A2K2.01 6 0.000 0.878 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GJ.01 5 0.117 0.961 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.FI.A2F8.01 3 0.314 0.738 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.BG.A0YV.01 1 0.117 0.897 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.D1.A16S.01 1 0.000 0.858 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FI.A3PV.01 3 0.314 0.738 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.BG.A18C.01 4 0.479 0.737 0.00 0.14 0.00 0.60 0.00 0.00 0.26
#> TCGA.2E.A9G8.01 5 0.117 0.961 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.FI.A2EX.01 6 0.000 0.878 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A1NU.01 7 0.428 0.985 0.46 0.00 0.00 0.00 0.04 0.00 0.50
#> TCGA.B5.A11U.01 4 0.424 0.784 0.00 0.10 0.00 0.68 0.00 0.00 0.22
#> TCGA.AP.A0LF.01 6 0.000 0.878 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.5B.A90C.01 5 0.216 0.946 0.06 0.00 0.02 0.00 0.90 0.00 0.02
#> TCGA.AJ.A3TW.01 5 0.166 0.950 0.06 0.00 0.00 0.02 0.92 0.00 0.00
#> TCGA.BS.A0V8.01 2 0.496 0.565 0.00 0.64 0.02 0.18 0.00 0.00 0.16
#> TCGA.D1.A15V.01 1 0.166 0.893 0.92 0.00 0.00 0.02 0.06 0.00 0.00
#> TCGA.FI.A3PX.01 6 0.586 0.466 0.28 0.00 0.08 0.04 0.00 0.56 0.04
#> TCGA.AX.A3G6.01 2 0.454 0.508 0.00 0.62 0.10 0.00 0.00 0.00 0.28
#> TCGA.EY.A2ON.01 1 0.186 0.862 0.92 0.00 0.00 0.02 0.02 0.00 0.04
#> TCGA.EY.A214.01 4 0.286 0.728 0.00 0.04 0.00 0.86 0.06 0.00 0.04
#> TCGA.AX.A3G1.01 2 0.136 0.792 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.AX.A3GI.01 7 0.428 0.985 0.46 0.00 0.00 0.00 0.04 0.00 0.50
#> TCGA.AX.A2H8.01 3 0.339 0.502 0.00 0.20 0.76 0.00 0.00 0.00 0.04
#> TCGA.B5.A3FB.01 4 0.518 0.758 0.00 0.08 0.04 0.58 0.00 0.00 0.30
#> TCGA.EO.A3KW.01 7 0.471 0.970 0.46 0.00 0.02 0.00 0.04 0.00 0.48
#> TCGA.AJ.A2QN.01 2 0.136 0.792 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.AJ.A3NH.01 3 0.354 0.635 0.00 0.10 0.80 0.00 0.00 0.02 0.08
#> TCGA.AX.A1CN.01 5 0.186 0.864 0.00 0.00 0.04 0.02 0.92 0.00 0.02
#> TCGA.EO.A1Y8.01 3 0.314 0.738 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.AJ.A3EM.01 2 0.189 0.787 0.00 0.88 0.12 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.AP.A3K1.01 6 0.1341 0.7982 0.00 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.AP.A5FX.01 4 0.4995 0.6188 0.36 0.00 0.00 0.52 0.00 0.04 0.08 0.00
#> TCGA.DI.A1NN.01 5 0.0000 0.9645 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A2HK.01 3 0.5026 0.4245 0.22 0.00 0.64 0.00 0.00 0.04 0.06 0.04
#> TCGA.D1.A17K.01 2 0.0471 0.7234 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A0WH.01 2 0.4882 0.6721 0.18 0.60 0.00 0.20 0.00 0.00 0.02 0.00
#> TCGA.BS.A0U9.01 2 0.1557 0.7117 0.00 0.92 0.02 0.00 0.00 0.00 0.06 0.00
#> TCGA.A5.A2K2.01 6 0.1341 0.7982 0.00 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.EY.A1GJ.01 5 0.0000 0.9645 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2F8.01 3 0.2114 0.7293 0.00 0.00 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.BG.A0YV.01 8 0.1091 0.8242 0.00 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.D1.A16S.01 8 0.0471 0.7958 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.FI.A3PV.01 3 0.2114 0.7293 0.00 0.00 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.BG.A18C.01 4 0.1563 0.6537 0.10 0.00 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.2E.A9G8.01 5 0.0000 0.9645 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FI.A2EX.01 6 0.1557 0.7905 0.00 0.00 0.06 0.00 0.00 0.92 0.02 0.00
#> TCGA.D1.A1NU.01 7 0.3198 0.9276 0.00 0.00 0.00 0.00 0.02 0.00 0.72 0.26
#> TCGA.B5.A11U.01 4 0.0000 0.7248 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AP.A0LF.01 6 0.1804 0.7961 0.00 0.00 0.08 0.00 0.00 0.90 0.02 0.00
#> TCGA.5B.A90C.01 5 0.0471 0.9582 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.AJ.A3TW.01 5 0.1091 0.9291 0.06 0.00 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.BS.A0V8.01 2 0.6101 0.5752 0.22 0.50 0.02 0.18 0.00 0.00 0.08 0.00
#> TCGA.D1.A15V.01 8 0.2864 0.8204 0.08 0.00 0.00 0.00 0.06 0.00 0.02 0.84
#> TCGA.FI.A3PX.01 6 0.7040 -0.0336 0.24 0.00 0.10 0.00 0.00 0.30 0.06 0.30
#> TCGA.AX.A3G6.01 2 0.5181 0.3994 0.08 0.48 0.02 0.40 0.00 0.00 0.02 0.00
#> TCGA.EY.A2ON.01 8 0.4119 0.7031 0.08 0.00 0.00 0.00 0.02 0.02 0.14 0.74
#> TCGA.EY.A214.01 4 0.4370 0.6203 0.40 0.00 0.00 0.52 0.00 0.00 0.08 0.00
#> TCGA.AX.A3G1.01 2 0.3299 0.7461 0.18 0.76 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.AX.A3GI.01 7 0.3291 0.9358 0.00 0.00 0.00 0.00 0.02 0.00 0.70 0.28
#> TCGA.AX.A2H8.01 3 0.3690 0.3062 0.02 0.42 0.56 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FB.01 4 0.0941 0.7177 0.00 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.EO.A3KW.01 7 0.4887 0.8951 0.04 0.00 0.02 0.00 0.02 0.02 0.62 0.28
#> TCGA.AJ.A2QN.01 2 0.3299 0.7461 0.18 0.76 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3NH.01 3 0.1765 0.6877 0.00 0.12 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CN.01 5 0.2265 0.8979 0.08 0.00 0.00 0.00 0.88 0.00 0.02 0.02
#> TCGA.EO.A1Y8.01 3 0.2114 0.7293 0.00 0.00 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.AJ.A3EM.01 2 0.0941 0.7170 0.02 0.96 0.02 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: Node051. Child nodes: Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02121-leaf , Node02122-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node02341-leaf , Node02342-leaf , Node04111-leaf , Node04112-leaf , Node04311-leaf , Node04312-leaf , Node04313-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0511"]
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 '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 1.000 1.000 0.5389 0.462 0.462
#> 3 3 0.872 0.967 0.975 0.2423 0.872 0.722
#> 4 4 0.769 0.893 0.860 0.1283 0.923 0.769
#> 5 5 0.923 0.928 0.969 0.1089 0.897 0.600
#> 6 6 0.885 0.836 0.952 0.0443 0.962 0.750
#> 7 7 0.910 0.756 0.928 0.0323 0.974 0.778
#> 8 8 0.910 0.650 0.898 0.0232 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 5
There is also optional best \(k\) = 2 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.DI.A1NN.01 2 0 1 0 1
#> TCGA.EY.A1GJ.01 2 0 1 0 1
#> TCGA.BG.A0YV.01 1 0 1 1 0
#> TCGA.D1.A16S.01 1 0 1 1 0
#> TCGA.2E.A9G8.01 2 0 1 0 1
#> TCGA.D1.A1NU.01 2 0 1 0 1
#> TCGA.5B.A90C.01 1 0 1 1 0
#> TCGA.AJ.A3TW.01 1 0 1 1 0
#> TCGA.D1.A15V.01 1 0 1 1 0
#> TCGA.EY.A2ON.01 1 0 1 1 0
#> TCGA.AX.A3GI.01 2 0 1 0 1
#> TCGA.EO.A3KW.01 2 0 1 0 1
#> TCGA.AX.A1CN.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DI.A1NN.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.EY.A1GJ.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.BG.A0YV.01 3 0.0892 1.000 0.02 0.00 0.98
#> TCGA.D1.A16S.01 3 0.0892 1.000 0.02 0.00 0.98
#> TCGA.2E.A9G8.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.D1.A1NU.01 2 0.0892 0.986 0.00 0.98 0.02
#> TCGA.5B.A90C.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.AJ.A3TW.01 1 0.2959 0.911 0.90 0.00 0.10
#> TCGA.D1.A15V.01 1 0.0892 0.937 0.98 0.00 0.02
#> TCGA.EY.A2ON.01 1 0.2959 0.911 0.90 0.00 0.10
#> TCGA.AX.A3GI.01 2 0.0892 0.986 0.00 0.98 0.02
#> TCGA.EO.A3KW.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AX.A1CN.01 1 0.0892 0.937 0.98 0.00 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DI.A1NN.01 2 0.462 0.836 0.00 0.66 0.00 0.34
#> TCGA.EY.A1GJ.01 2 0.479 0.842 0.00 0.62 0.00 0.38
#> TCGA.BG.A0YV.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D1.A16S.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.2E.A9G8.01 2 0.479 0.842 0.00 0.62 0.00 0.38
#> TCGA.D1.A1NU.01 2 0.201 0.619 0.00 0.92 0.00 0.08
#> TCGA.5B.A90C.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3TW.01 4 0.671 0.972 0.36 0.00 0.10 0.54
#> TCGA.D1.A15V.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EY.A2ON.01 4 0.694 0.972 0.36 0.00 0.12 0.52
#> TCGA.AX.A3GI.01 2 0.000 0.681 0.00 1.00 0.00 0.00
#> TCGA.EO.A3KW.01 2 0.479 0.842 0.00 0.62 0.00 0.38
#> TCGA.AX.A1CN.01 1 0.000 1.000 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DI.A1NN.01 2 0.173 0.907 0.00 0.92 0.00 0.00 0.08
#> TCGA.EY.A1GJ.01 2 0.000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.BG.A0YV.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.D1.A16S.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.2E.A9G8.01 2 0.000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A1NU.01 5 0.000 0.744 0.00 0.00 0.00 0.00 1.00
#> TCGA.5B.A90C.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3TW.01 4 0.000 0.879 0.00 0.00 0.00 1.00 0.00
#> TCGA.D1.A15V.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2ON.01 4 0.275 0.880 0.08 0.00 0.04 0.88 0.00
#> TCGA.AX.A3GI.01 5 0.311 0.748 0.00 0.20 0.00 0.00 0.80
#> TCGA.EO.A3KW.01 2 0.000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A1CN.01 1 0.000 1.000 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.DI.A1NN.01 6 0.2454 0.000 0.0 0.16 0 0.00 0.0 0.84
#> TCGA.EY.A1GJ.01 2 0.0547 0.974 0.0 0.98 0 0.00 0.0 0.02
#> TCGA.BG.A0YV.01 3 0.0000 1.000 0.0 0.00 1 0.00 0.0 0.00
#> TCGA.D1.A16S.01 3 0.0000 1.000 0.0 0.00 1 0.00 0.0 0.00
#> TCGA.2E.A9G8.01 2 0.0000 0.987 0.0 1.00 0 0.00 0.0 0.00
#> TCGA.D1.A1NU.01 5 0.0000 0.591 0.0 0.00 0 0.00 1.0 0.00
#> TCGA.5B.A90C.01 1 0.1814 0.910 0.9 0.00 0 0.00 0.0 0.10
#> TCGA.AJ.A3TW.01 4 0.0000 0.967 0.0 0.00 0 1.00 0.0 0.00
#> TCGA.D1.A15V.01 1 0.0000 0.956 1.0 0.00 0 0.00 0.0 0.00
#> TCGA.EY.A2ON.01 4 0.0937 0.967 0.0 0.00 0 0.96 0.0 0.04
#> TCGA.AX.A3GI.01 5 0.3819 0.570 0.0 0.28 0 0.00 0.7 0.02
#> TCGA.EO.A3KW.01 2 0.0000 0.987 0.0 1.00 0 0.00 0.0 0.00
#> TCGA.AX.A1CN.01 1 0.0000 0.956 1.0 0.00 0 0.00 0.0 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DI.A1NN.01 6 0.1363 0.000 0.00 0.04 0.00 0.00 0.02 0.94 0.00
#> TCGA.EY.A1GJ.01 2 0.1166 0.941 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.BG.A0YV.01 3 0.0000 0.967 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A16S.01 3 0.0863 0.967 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.2E.A9G8.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A1NU.01 5 0.1671 0.697 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.5B.A90C.01 7 0.3139 0.000 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.AJ.A3TW.01 4 0.0000 0.844 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A15V.01 1 0.0000 0.971 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A2ON.01 4 0.2422 0.844 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.AX.A3GI.01 5 0.2912 0.689 0.00 0.14 0.00 0.00 0.82 0.04 0.00
#> TCGA.EO.A3KW.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A1CN.01 1 0.0504 0.971 0.98 0.00 0.00 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DI.A1NN.01 6 0.3333 0.000 0.00 0.00 0.00 0.50 0.00 0.5 0.00 0.0
#> TCGA.EY.A1GJ.01 2 0.3083 0.625 0.00 0.66 0.00 0.34 0.00 0.0 0.00 0.0
#> TCGA.BG.A0YV.01 3 0.2856 0.807 0.00 0.00 0.78 0.00 0.00 0.2 0.02 0.0
#> TCGA.D1.A16S.01 3 0.0000 0.807 0.00 0.00 1.00 0.00 0.00 0.0 0.00 0.0
#> TCGA.2E.A9G8.01 2 0.0000 0.817 0.00 1.00 0.00 0.00 0.00 0.0 0.00 0.0
#> TCGA.D1.A1NU.01 5 0.2114 0.552 0.00 0.00 0.00 0.16 0.84 0.0 0.00 0.0
#> TCGA.5B.A90C.01 7 0.0808 0.000 0.04 0.00 0.00 0.00 0.00 0.0 0.96 0.0
#> TCGA.AJ.A3TW.01 8 0.0000 0.731 0.00 0.00 0.00 0.00 0.00 0.0 0.00 1.0
#> TCGA.D1.A15V.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.0 0.00 0.0
#> TCGA.EY.A2ON.01 8 0.2938 0.731 0.00 0.00 0.00 0.00 0.00 0.3 0.00 0.7
#> TCGA.AX.A3GI.01 5 0.3095 0.563 0.00 0.24 0.00 0.00 0.74 0.0 0.02 0.0
#> TCGA.EO.A3KW.01 2 0.0000 0.817 0.00 1.00 0.00 0.00 0.00 0.0 0.00 0.0
#> TCGA.AX.A1CN.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.0 0.00 0.0
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: Node05. Child nodes: Node0111-leaf , Node0112-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0131-leaf , Node0132-leaf , Node0211 , Node0212 , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234 , Node0241-leaf , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0411 , Node0412-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431 , Node0432-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["052"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 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 0.789 0.817 0.931 0.4767 0.498 0.498
#> 3 3 1.000 0.972 0.967 0.4195 0.700 0.460
#> 4 4 0.923 0.784 0.923 0.0721 0.956 0.860
#> 5 5 0.786 0.699 0.848 0.0604 0.980 0.933
#> 6 6 0.758 0.688 0.809 0.0457 0.963 0.873
#> 7 7 0.761 0.617 0.755 0.0333 0.938 0.757
#> 8 8 0.765 0.657 0.815 0.0269 0.970 0.846
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.B5.A5OE.01 1 0.000 0.962 1.00 0.00
#> TCGA.D1.A0ZZ.01 2 0.000 0.851 0.00 1.00
#> TCGA.AX.A3FZ.01 1 0.000 0.962 1.00 0.00
#> TCGA.D1.A1NW.01 1 0.000 0.962 1.00 0.00
#> TCGA.AJ.A3QS.01 1 0.000 0.962 1.00 0.00
#> TCGA.EY.A2OQ.01 1 0.000 0.962 1.00 0.00
#> TCGA.A5.A7WK.01 2 0.855 0.641 0.28 0.72
#> TCGA.D1.A3DG.01 2 0.990 0.343 0.44 0.56
#> TCGA.EY.A1GC.01 2 0.000 0.851 0.00 1.00
#> TCGA.E6.A1LZ.01 1 0.000 0.962 1.00 0.00
#> TCGA.H5.A2HR.01 1 1.000 -0.279 0.50 0.50
#> TCGA.EY.A1GP.01 2 0.000 0.851 0.00 1.00
#> TCGA.DI.A2QU.01 2 0.000 0.851 0.00 1.00
#> TCGA.AJ.A3BD.01 1 0.000 0.962 1.00 0.00
#> TCGA.AX.A3FV.01 1 0.000 0.962 1.00 0.00
#> TCGA.EO.A3B1.01 1 0.000 0.962 1.00 0.00
#> TCGA.EO.A2CH.01 2 1.000 0.164 0.50 0.50
#> TCGA.AW.A1PO.01 2 0.000 0.851 0.00 1.00
#> TCGA.B5.A3FD.01 2 0.000 0.851 0.00 1.00
#> TCGA.EY.A4KR.01 1 0.000 0.962 1.00 0.00
#> TCGA.BG.A0YU.01 2 0.000 0.851 0.00 1.00
#> TCGA.EY.A1GO.01 2 0.000 0.851 0.00 1.00
#> TCGA.PG.A7D5.01 2 0.855 0.641 0.28 0.72
#> TCGA.KP.A3W1.01 1 0.000 0.962 1.00 0.00
#> TCGA.B5.A0KB.01 1 0.000 0.962 1.00 0.00
#> TCGA.A5.A0GR.01 1 0.000 0.962 1.00 0.00
#> TCGA.AX.A3G7.01 1 0.000 0.962 1.00 0.00
#> TCGA.D1.A3JP.01 1 0.000 0.962 1.00 0.00
#> TCGA.D1.A3DH.01 1 0.000 0.962 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B5.A5OE.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.D1.A0ZZ.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.AX.A3FZ.01 1 0.2537 0.928 0.92 0.00 0.08
#> TCGA.D1.A1NW.01 3 0.2537 0.963 0.08 0.00 0.92
#> TCGA.AJ.A3QS.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.EY.A2OQ.01 3 0.2537 0.963 0.08 0.00 0.92
#> TCGA.A5.A7WK.01 3 0.2537 0.924 0.00 0.08 0.92
#> TCGA.D1.A3DG.01 3 0.2066 0.924 0.00 0.06 0.94
#> TCGA.EY.A1GC.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.E6.A1LZ.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.H5.A2HR.01 3 0.2947 0.961 0.06 0.02 0.92
#> TCGA.EY.A1GP.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.DI.A2QU.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.AJ.A3BD.01 3 0.2537 0.963 0.08 0.00 0.92
#> TCGA.AX.A3FV.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.EO.A3B1.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.EO.A2CH.01 3 0.2947 0.961 0.06 0.02 0.92
#> TCGA.AW.A1PO.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.B5.A3FD.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.EY.A4KR.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.BG.A0YU.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.EY.A1GO.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.PG.A7D5.01 3 0.2537 0.924 0.00 0.08 0.92
#> TCGA.KP.A3W1.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.B5.A0KB.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.A5.A0GR.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.AX.A3G7.01 3 0.2537 0.963 0.08 0.00 0.92
#> TCGA.D1.A3JP.01 1 0.0000 0.986 1.00 0.00 0.00
#> TCGA.D1.A3DH.01 3 0.2537 0.963 0.08 0.00 0.92
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B5.A5OE.01 1 0.0000 0.9379 1.00 0.00 0.00 0.00
#> TCGA.D1.A0ZZ.01 2 0.4624 0.4244 0.00 0.66 0.00 0.34
#> TCGA.AX.A3FZ.01 4 0.4624 -0.2158 0.34 0.00 0.00 0.66
#> TCGA.D1.A1NW.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.AJ.A3QS.01 1 0.1211 0.9339 0.96 0.00 0.00 0.04
#> TCGA.EY.A2OQ.01 3 0.0707 0.9808 0.00 0.00 0.98 0.02
#> TCGA.A5.A7WK.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.D1.A3DG.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GC.01 2 0.0000 0.8176 0.00 1.00 0.00 0.00
#> TCGA.E6.A1LZ.01 1 0.0000 0.9379 1.00 0.00 0.00 0.00
#> TCGA.H5.A2HR.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.EY.A1GP.01 4 0.5000 -0.5667 0.00 0.50 0.00 0.50
#> TCGA.DI.A2QU.01 2 0.0000 0.8176 0.00 1.00 0.00 0.00
#> TCGA.AJ.A3BD.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.AX.A3FV.01 1 0.3172 0.8048 0.84 0.00 0.00 0.16
#> TCGA.EO.A3B1.01 1 0.1211 0.9339 0.96 0.00 0.00 0.04
#> TCGA.EO.A2CH.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.AW.A1PO.01 2 0.0000 0.8176 0.00 1.00 0.00 0.00
#> TCGA.B5.A3FD.01 2 0.0000 0.8176 0.00 1.00 0.00 0.00
#> TCGA.EY.A4KR.01 1 0.1211 0.9339 0.96 0.00 0.00 0.04
#> TCGA.BG.A0YU.01 2 0.0000 0.8176 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GO.01 2 0.5000 -0.0109 0.00 0.50 0.00 0.50
#> TCGA.PG.A7D5.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.KP.A3W1.01 1 0.0000 0.9379 1.00 0.00 0.00 0.00
#> TCGA.B5.A0KB.01 1 0.3610 0.7942 0.80 0.00 0.00 0.20
#> TCGA.A5.A0GR.01 1 0.0000 0.9379 1.00 0.00 0.00 0.00
#> TCGA.AX.A3G7.01 3 0.0000 0.9953 0.00 0.00 1.00 0.00
#> TCGA.D1.A3JP.01 1 0.0707 0.9375 0.98 0.00 0.00 0.02
#> TCGA.D1.A3DH.01 3 0.0707 0.9808 0.00 0.00 0.98 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.B5.A5OE.01 5 0.000 0.808 0.00 0.00 0.00 0.00 1.00
#> TCGA.D1.A0ZZ.01 2 0.000 0.570 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3FZ.01 4 0.173 0.000 0.00 0.00 0.00 0.92 0.08
#> TCGA.D1.A1NW.01 3 0.141 0.866 0.06 0.00 0.94 0.00 0.00
#> TCGA.AJ.A3QS.01 5 0.329 0.778 0.12 0.00 0.00 0.04 0.84
#> TCGA.EY.A2OQ.01 3 0.454 0.632 0.34 0.00 0.64 0.02 0.00
#> TCGA.A5.A7WK.01 3 0.244 0.840 0.06 0.00 0.90 0.04 0.00
#> TCGA.D1.A3DG.01 3 0.244 0.840 0.06 0.00 0.90 0.04 0.00
#> TCGA.EY.A1GC.01 2 0.483 0.747 0.48 0.50 0.00 0.02 0.00
#> TCGA.E6.A1LZ.01 5 0.000 0.808 0.00 0.00 0.00 0.00 1.00
#> TCGA.H5.A2HR.01 3 0.000 0.868 0.00 0.00 1.00 0.00 0.00
#> TCGA.EY.A1GP.01 2 0.173 0.522 0.00 0.92 0.00 0.08 0.00
#> TCGA.DI.A2QU.01 2 0.483 0.747 0.48 0.50 0.00 0.02 0.00
#> TCGA.AJ.A3BD.01 3 0.141 0.866 0.06 0.00 0.94 0.00 0.00
#> TCGA.AX.A3FV.01 5 0.543 0.221 0.08 0.00 0.00 0.32 0.60
#> TCGA.EO.A3B1.01 5 0.329 0.778 0.12 0.00 0.00 0.04 0.84
#> TCGA.EO.A2CH.01 3 0.000 0.868 0.00 0.00 1.00 0.00 0.00
#> TCGA.AW.A1PO.01 2 0.429 0.756 0.46 0.54 0.00 0.00 0.00
#> TCGA.B5.A3FD.01 2 0.429 0.756 0.46 0.54 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 5 0.329 0.778 0.12 0.00 0.00 0.04 0.84
#> TCGA.BG.A0YU.01 2 0.429 0.756 0.46 0.54 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 2 0.173 0.522 0.00 0.92 0.00 0.08 0.00
#> TCGA.PG.A7D5.01 3 0.244 0.840 0.06 0.00 0.90 0.04 0.00
#> TCGA.KP.A3W1.01 5 0.000 0.808 0.00 0.00 0.00 0.00 1.00
#> TCGA.B5.A0KB.01 5 0.642 0.182 0.18 0.00 0.00 0.36 0.46
#> TCGA.A5.A0GR.01 5 0.000 0.808 0.00 0.00 0.00 0.00 1.00
#> TCGA.AX.A3G7.01 3 0.141 0.866 0.06 0.00 0.94 0.00 0.00
#> TCGA.D1.A3JP.01 5 0.165 0.804 0.02 0.00 0.00 0.04 0.94
#> TCGA.D1.A3DH.01 3 0.454 0.632 0.34 0.00 0.64 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.B5.A5OE.01 5 0.0547 0.732 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.D1.A0ZZ.01 1 0.1092 0.952 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.AX.A3FZ.01 4 0.0547 0.000 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.D1.A1NW.01 3 0.0000 0.768 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AJ.A3QS.01 5 0.4380 0.697 0.00 0.00 0.00 0.08 0.70 0.22
#> TCGA.EY.A2OQ.01 3 0.5793 0.440 0.00 0.20 0.58 0.02 0.00 0.20
#> TCGA.A5.A7WK.01 3 0.4282 0.566 0.00 0.02 0.56 0.00 0.00 0.42
#> TCGA.D1.A3DG.01 3 0.4282 0.566 0.00 0.02 0.56 0.00 0.00 0.42
#> TCGA.EY.A1GC.01 2 0.5509 0.850 0.30 0.54 0.00 0.00 0.00 0.16
#> TCGA.E6.A1LZ.01 5 0.0547 0.732 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.H5.A2HR.01 3 0.0937 0.768 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EY.A1GP.01 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QU.01 2 0.5509 0.850 0.30 0.54 0.00 0.00 0.00 0.16
#> TCGA.AJ.A3BD.01 3 0.0000 0.768 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AX.A3FV.01 5 0.5822 0.223 0.00 0.08 0.00 0.28 0.58 0.06
#> TCGA.EO.A3B1.01 5 0.4380 0.697 0.00 0.00 0.00 0.08 0.70 0.22
#> TCGA.EO.A2CH.01 3 0.0937 0.768 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.AW.A1PO.01 2 0.3409 0.903 0.30 0.70 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FD.01 2 0.3409 0.903 0.30 0.70 0.00 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 5 0.4380 0.697 0.00 0.00 0.00 0.08 0.70 0.22
#> TCGA.BG.A0YU.01 2 0.3409 0.903 0.30 0.70 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 3 0.2981 0.711 0.00 0.02 0.82 0.00 0.00 0.16
#> TCGA.KP.A3W1.01 5 0.0547 0.732 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.B5.A0KB.01 5 0.6613 0.227 0.00 0.04 0.00 0.36 0.40 0.20
#> TCGA.A5.A0GR.01 5 0.0000 0.735 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AX.A3G7.01 3 0.0000 0.768 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D1.A3JP.01 5 0.3475 0.723 0.00 0.00 0.00 0.06 0.80 0.14
#> TCGA.D1.A3DH.01 3 0.6525 0.335 0.00 0.20 0.46 0.04 0.00 0.30
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.B5.A5OE.01 5 0.3496 0.3655 0.00 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.D1.A0ZZ.01 1 0.3519 0.9659 0.74 0.22 0.00 0.00 0.00 0.04 0.00
#> TCGA.AX.A3FZ.01 4 0.2376 0.0000 0.00 0.00 0.00 0.86 0.02 0.00 0.12
#> TCGA.D1.A1NW.01 3 0.0000 0.7234 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3QS.01 5 0.1166 0.5816 0.00 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.EY.A2OQ.01 6 0.4127 0.8651 0.00 0.00 0.36 0.00 0.04 0.60 0.00
#> TCGA.A5.A7WK.01 3 0.7087 0.2965 0.10 0.00 0.42 0.12 0.00 0.30 0.06
#> TCGA.D1.A3DG.01 3 0.7087 0.2965 0.10 0.00 0.42 0.12 0.00 0.30 0.06
#> TCGA.EY.A1GC.01 2 0.3061 0.8677 0.00 0.84 0.00 0.02 0.00 0.06 0.08
#> TCGA.E6.A1LZ.01 5 0.3496 0.3655 0.00 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.H5.A2HR.01 3 0.0000 0.7234 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GP.01 1 0.2708 0.9831 0.78 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QU.01 2 0.3061 0.8677 0.00 0.84 0.00 0.02 0.00 0.06 0.08
#> TCGA.AJ.A3BD.01 3 0.0000 0.7234 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FV.01 7 0.3670 0.0000 0.10 0.00 0.00 0.00 0.14 0.00 0.76
#> TCGA.EO.A3B1.01 5 0.1166 0.5816 0.00 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.EO.A2CH.01 3 0.0000 0.7234 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AW.A1PO.01 2 0.0000 0.9141 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FD.01 2 0.0000 0.9141 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 5 0.0863 0.5876 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.BG.A0YU.01 2 0.0000 0.9141 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 1 0.2708 0.9831 0.78 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 3 0.2572 0.6140 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.KP.A3W1.01 5 0.3496 0.3655 0.00 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.B5.A0KB.01 5 0.3685 0.0406 0.02 0.00 0.00 0.00 0.66 0.00 0.32
#> TCGA.A5.A0GR.01 5 0.3047 0.4656 0.00 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.AX.A3G7.01 3 0.0000 0.7234 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3JP.01 5 0.1664 0.5741 0.02 0.00 0.00 0.00 0.92 0.00 0.06
#> TCGA.D1.A3DH.01 6 0.3841 0.8615 0.00 0.00 0.28 0.00 0.04 0.68 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.B5.A5OE.01 5 0.5528 0.2403 0.04 0.00 0.00 0.00 0.56 0.02 0.24 0.14
#> TCGA.D1.A0ZZ.01 1 0.4077 0.8716 0.76 0.10 0.00 0.00 0.00 0.08 0.04 0.02
#> TCGA.AX.A3FZ.01 4 0.0808 0.0000 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.D1.A1NW.01 3 0.0000 0.9225 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AJ.A3QS.01 5 0.1563 0.5237 0.00 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.EY.A2OQ.01 6 0.2114 0.8914 0.00 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.A5.A7WK.01 8 0.2534 1.0000 0.00 0.00 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.D1.A3DG.01 8 0.2534 1.0000 0.00 0.00 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.EY.A1GC.01 2 0.4914 0.7205 0.00 0.68 0.00 0.04 0.00 0.06 0.16 0.06
#> TCGA.E6.A1LZ.01 5 0.5528 0.2403 0.04 0.00 0.00 0.00 0.56 0.02 0.24 0.14
#> TCGA.H5.A2HR.01 3 0.1275 0.9147 0.02 0.00 0.94 0.00 0.00 0.00 0.04 0.00
#> TCGA.EY.A1GP.01 1 0.1563 0.9380 0.90 0.10 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DI.A2QU.01 2 0.4422 0.7608 0.00 0.74 0.00 0.04 0.00 0.06 0.10 0.06
#> TCGA.AJ.A3BD.01 3 0.0000 0.9225 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AX.A3FV.01 7 0.3551 0.0000 0.00 0.00 0.00 0.06 0.22 0.00 0.72 0.00
#> TCGA.EO.A3B1.01 5 0.1563 0.5237 0.00 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.EO.A2CH.01 3 0.2132 0.8873 0.04 0.00 0.88 0.00 0.00 0.00 0.08 0.00
#> TCGA.AW.A1PO.01 2 0.0471 0.8499 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B5.A3FD.01 2 0.0471 0.8499 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A4KR.01 5 0.1563 0.5237 0.00 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.BG.A0YU.01 2 0.0471 0.8499 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EY.A1GO.01 1 0.1563 0.9380 0.90 0.10 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PG.A7D5.01 3 0.3185 0.8260 0.04 0.00 0.82 0.00 0.00 0.00 0.08 0.06
#> TCGA.KP.A3W1.01 5 0.5528 0.2403 0.04 0.00 0.00 0.00 0.56 0.02 0.24 0.14
#> TCGA.B5.A0KB.01 5 0.4350 -0.0314 0.02 0.00 0.00 0.06 0.62 0.00 0.30 0.00
#> TCGA.A5.A0GR.01 5 0.3404 0.3435 0.00 0.00 0.00 0.00 0.72 0.00 0.24 0.04
#> TCGA.AX.A3G7.01 3 0.0000 0.9225 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D1.A3JP.01 5 0.1275 0.4886 0.02 0.00 0.00 0.00 0.94 0.00 0.04 0.00
#> TCGA.D1.A3DH.01 6 0.2623 0.8901 0.00 0.00 0.10 0.00 0.00 0.84 0.00 0.06
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
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