function for reading gmt files as data frames with 1st column gene set id, 2nd column gene id.

read_gmt.r

library(foreach)
library(stringr)
library(biomaRt)

read_gmt <- function(gmt_file){
  
  conn <- file(gmt_file,open="r")
  all_lines <-readLines(conn)
  result <- foreach(line = str_split(all_lines, "\t"), .combine = bind_rows) %do% {
    data_frame(id = line[1], gene_id = line[-c(1,2)])
  }
  close(conn)

  return(result)
}