R/get_geneSets_from_local_files.R

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

get_geneSets_from_local_files <-
function (ffiles) 
{
    ffunction <- function(x) {
        geneSets_tmp <- readLines(x)
        geneSets_tmp <- strsplit(geneSets_tmp, "\t")
        nnames <- sapply(geneSets_tmp, function(x) x[1])
        link <- sapply(geneSets_tmp, function(x) x[2])
        geneSets_tmp <- lapply(geneSets_tmp, function(x) x[3:length(x)])
        for (k in 1:length(geneSets_tmp)) {
            attr(geneSets_tmp[[k]], "link") <- link[k]
            attr(geneSets_tmp[[k]], "collection") <- x
        }
        names(geneSets_tmp) <- nnames
        return(geneSets_tmp)
    }
    geneSets <- ffunction(ffiles[1])
    if (length(ffiles) > 1) 
        for (k in 2:length(ffiles)) geneSets <- c(geneSets, ffunction(ffiles[k]))
    invisible(geneSets)
}