vignettes/vignette_example.R

In jokergoo/cola: A Framework for Consensus Partitioning

library(cola)

data = read.table("~/cola_test/unifiedScaled.txt", header = TRUE, row.names = 1, check.names = FALSE)
data = as.matrix(data)

subtype = read.table("~/cola_test/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)])

data = data[, names(subtype)]

data = adjust_matrix(data)
rl = run_all_consensus_partition_methods(data, top_n = c(1000, 2000, 3000, 4000), 
	max_k = 6, mc.cores = 4, anno = data.frame(subtype = subtype), 
	anno_col = list(subtype = structure(seq_len(4), names = unique(subtype))))
saveRDS(rl, file = "~/cola_test/TCGA_subgroup.rds")


cola_report(rl, output_dir = "~/cola_test/tcga_cola_rl_report")