Data set for cola analysis. The original source is from https://gdc.cancer.gov/about-data/publications/gbm_exp.
RDS files generated by cola (use readRDS() to load into R (>= 3.6.0)):
HTML reports for cola analysis:
Following code performs the analysis.
Prepare the input matrix:
library(cola)
library(RColorBrewer)
m = read.table("unifiedScaled.txt", header = TRUE, row.names = 1, check.names = FALSE)
m = as.matrix(m)
subtype = read.table("TCGA_unified_CORE_ClaNC840.txt", sep = "\t", header = TRUE,
check.names = FALSE, stringsAsFactors = FALSE)
subtype = structure(unlist(subtype[1, -(1:2)]), names = colnames(subtype)[-(1:2)])
subtype_col = structure(seq_len(4), names = unique(subtype))
m = m[, names(subtype)]
m = adjust_matrix(m)
Perform the consensus partitioning:
register_NMF()
set.seed(123)
rl = run_all_consensus_partition_methods(
m,
mc.cores = 4,
anno = data.frame(subtype = subtype),
anno_col = list(subtype = subtype_col)
)
saveRDS(rl, file = "TCGA_GBM_subgroup.rds")
cola_report(rl, output_dir = "TCGA_GBM_subgroup_cola_report", mc.cores = 4)