R/gmt_to_list.R

In gdario/gdamisc: Utility functions for analyzing the output of gsa.py

##' Read a GMT file into a list
##'
##' This function reads a GMT file into an R list. At the moment
##' no type checking is performed, and all the elements in the
##' GMT file are assumed to be of type character. This may change
##' in the future, but it is important to be aware of this,
##' especially when working with ENTREZ ids.
##' @title Read a GMT file into a list
##' @param gmt_file full path to the GMT file
##' @return an R list where each component is a gene set
##' @seealso \code{list_to_gmt}
##' @author Giovanni d'Ario
##' @export
gmt_to_list <- function(gmt_file) {
    gmt <- scan(gmt_file, sep = "\n", what = "character")
    gmt <- lapply(gmt, strsplit, split = "\t")
    unlist(gmt, recursive = FALSE)
}