Takes in a geneset list to write out a gmt file.

writeGMT(filename, genesets, names = NULL, descriptions = NULL)

Arguments

file

filename to write file to; note if pre-existing, this will APPEND to that file

name

character vector of names for each geneset

description

character vector of descriptions for each geneset

geneset

list where each component is a character vector of the geneset

Value

None; written file as specified

Examples

names <- c("MP_fc1.5", "TE_fc1.5")
desc <- c("MP Signature with Fold-Change > 1.5 and Norm.Counts > 200",
          "TE Signature with Fold-Change > 1.5 and Norm.Counts > 200")
genesets <- list(MP = sigs.l$MP$SYMBOL[!is.na(sigs.l$MP$SYMBOL)],
                 TE = sigs.l$TE$SYMBOL[!is.na(sigs.l$TE$SYMBOL)])
genesetsENS <- list(MP = sigs.l$MP$ENSEMBL, TE = sigs.l$TE$ENSEMBL)
writeGMT("../genesets/mpte_SYMBOL.gmt", names, desc, genesets)
writeGMT("../genesets/mpte_ENSEMBL.gmt", names, desc, genesetsENS)