OVmae.R

library(curatedTCGAData)
curatedTCGAData("OV")
mae <- curatedTCGAData("OV", assays=c("mRNAArray", "RNASeq2GeneNorm", "RNASeqGene"), dry.run = FALSE)
library(TCGAutils)
keep <- TCGAsampleSelect(colnames(mae), 11)
mae <- mae[, keep, ]
mae <- intersectColumns(mae)
mae <- intersectRows(mae)

library(org.Hs.eg.db)
entrez.ids <- mapIds(org.Hs.eg.db, keys=rownames(mae[[1]]), keytype = "SYMBOL", column="ENTREZID")


library(consensusOV)
consensus.subtypes <- lapply(experiments(mae), function(x) get.subtypes(x, method = "consensusOV", entrez.ids = entrez.ids))

## set higher threshold for ambiguous subtypes in get.subtypes
## also consider limma-voom transformation of RNA-seq datasets