R/write_geneSets_to_gmt.R

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

write_geneSets_to_gmt <-
function (gs, fileName = "gene_sets.gmt") 
{
    gs_name <- names(gs)
    link <- unlist(lapply(gs, function(x) attr(x, "link")))
    geneSet <- lapply(gs, function(x) paste0(x, collapse = "\t"))
    tmp <- paste(gs_name, link, geneSet, sep = "\t")
    cat(tmp[1], file = fileName, append = FALSE, sep = "\n")
    for (k in 2:length(tmp)) cat(tmp[k], file = fileName, append = TRUE, 
        sep = "\n")
    invisible(NULL)
}