R/write.sn.rnk.R

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

# Copyright ---------------------------------------------------------------
# 2013-2014 The Scripps Research Institute Author: Jonathan Ross Hart

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

# Description -------------------------------------------------------------
# Write a rank file from expression data for preranked GSEA

# Input -------------------------------------------------------------------
# expression.data

# Methods -------------------------------------------------
# write.rnk

# Outputs -------------------------------------------------
# rank file

write.sn.rnk <- function(expression.data, out.file) {
  file.handle <- file(out.file, "wt")
  writeLines("#", file.handle)
  rnk.table <- data.frame(gene = rownames(expression.data),
                          expr = expression.data$sn)
  rnk.table <- rnk.table[order(rnk.table$expr), ]
  rnk.table <- rnk.table[!is.na(rnk.table$expr), ]
  write.table(rnk.table, file = file.handle, sep = "\t",
              row.names = F, quote = F)
  close(file.handle)
}