# HG changeset patch
# User dktanwar
# Date 1513649311 18000
# Node ID 9e75d29c2409e28b3252fe7a90b74c7d353eb759
# Parent  91eed1b5c0091a343da62a1a725b73b52aea75c7
Uploaded

diff -r 91eed1b5c009 -r 9e75d29c2409 16_fgsea/GSEA.R
--- a/16_fgsea/GSEA.R	Tue Dec 12 21:19:55 2017 -0500
+++ b/16_fgsea/GSEA.R	Mon Dec 18 21:08:31 2017 -0500
@@ -12,6 +12,7 @@
 library("getopt")
 library("fgsea")
 library("Rcpp")
+library("data.table")
 
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
 
@@ -35,8 +36,11 @@
 # cat("\n output: ", options$output)
 
 # Rank file
-ranks <- read.table(options$input1, header=F, colClasses = c("character", "numeric"))
-ranks <- setNames(ranks[,2], ranks[,1])
+ranks <- fread(options$input1, header=T, stringsAsFactors = F)
+ranks <- data.frame(ranks)
+r <- ranks[abs(ranks$logFC) >= 0.5 & ranks$PValue <= 0.05,]
+r <- r[,c(1, 2)]
+ranks <- setNames(r[,2], r[,1])
 
 # Pathways database
 pathways <- gmtPathways(options$input2)