R/msigdb.R

In jhart99/gseasier: Run the GSEA java pacakage from inside R

# Copyright ---------------------------------------------------------------
# 2013 The Scripps Research Institute Author: Jonathan Ross Hart

# Author ------------------------------------------------------------------
# Jonathan Ross Hart(jonathan@jonathanrosshart.com)

# Description -------------------------------------------------------------
# Function for reading msigdb gmt files

# Input -------------------------------------------------------------------
# msigdb formatted gmt file

# Methods -------------------------------------------------

# Outputs -------------------------------------------------
# returns a data frame of sigs with genes



# Library imports ---------------------------------------------------------

#' Loads signatures from GMT formatted files from msigdb
#'
#' @param filename The GMT file to read
#' @param path The path to the GMT file
#'
#' @return A data frame of the signatures, signature class, definitions, and genes.
#' @examples
#' sigs <- loadSigs("test.gmt", ".")
loadSig <- function(filename, path = ".") {
  sig.file <- file(paste0(path, "/", filename), "rt")
  sig.text <- readLines(sig.file)
  close(sig.file)

  split.lines <- strsplit(sig.text, "\t")
  sig <- unlist(lapply(split.lines, "[", 1))
  definitions <- unlist(lapply(split.lines, "[", 2))
  genes <- lapply(split.lines, "[", c(-1, -2))

  genes <- data.frame(ragged.list.melt(genes), stringsAsFactors = F)
  genes <- data.frame(lapply(genes, type.convert, as.is = T))
  genes$sig <- sig[genes$i]
  genes$def <- definitions[genes$i]
  filename <- paste(unlist(strsplit(filename, "\\."))[c(1, 2)], collapse = ".")
  data.frame(sig = genes$sig,
             class = filename,
             def = genes$def,
             gene = genes[, 2])
}