R/read.gct.R

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

# Copyright ---------------------------------------------------------------
# 2018 The Scripps Research Institute Author: Jonathan Ross Hart

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

# Description -------------------------------------------------------------
# A demonstration of the gene signature overlap routines.

# Input -------------------------------------------------------------------
# msigdb formatted gmt files or yuor own gmt formatted gene sets

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

# Outputs -------------------------------------------------

# a table of comparisons between two sets of gene sets with odds ratios and
# p.values

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

# acquire the msigdb files from Broad directly at
# http://software.broadinstitute.org/gsea/downloads.jsp

# this part will work with either set of genes.  Meaning you can use entrez ids
# or gene names as you prefer.

#' Title
#'
#' @param filename
#'
#' @return
#' @export
#'
#' @examples
read.gct <- function(filename) {
  read.table(filename, skip = 2, header = T, sep = "\t", quote = "")
}