Mercurial > repos > dktanwar > fgsea_test
changeset 0:3a53b8e91ede draft
Uploaded
author | dktanwar |
---|---|
date | Mon, 18 Dec 2017 21:09:41 -0500 (2017-12-19) |
parents | |
children | 23f1abdec8d1 |
files | GSEA.R |
diffstat | 1 files changed, 61 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GSEA.R Mon Dec 18 21:09:41 2017 -0500 @@ -0,0 +1,61 @@ +## How to execute this tool +# $Rscript GSEA.R --input ranked_genes_list.rnk --input Mus_musculus_GSEA_GO_sets_all_symbols_highquality_April_2015.gmt +# --output GSEA_results.txt --output + +# Send R errors to stderr +options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)}) + +# Avoid crashing Galaxy with an UTF8 error on German LC settings +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +# Import library +library("getopt") +library("fgsea") +library("Rcpp") +library("data.table") + +options(stringAsfactors = FALSE, useFancyQuotes = FALSE) + +# Take in trailing command line arguments +args <- commandArgs(trailingOnly = TRUE) + +# Get options using the spec as defined by the enclosed list +# Options are read from the default: commandArgs(TRUE) +option_specification = matrix(c( + 'input1', 'i1', 2, 'character', + 'input2', 'i2', 2, 'character', + 'output', 'o', 2, 'character' +), byrow = TRUE, ncol = 4); + +# Parse options +options = getopt(option_specification); + +# Print options to stderr for debugging +# cat("\n input: ", options$input1) +# cat("\n input: ", options$input2) +# cat("\n output: ", options$output) + +# Rank file +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) + +# running analysis +fgseaRes <- fgsea(pathways, ranks, minSize=10, maxSize=500, nperm=1000) +res <- as.data.frame(fgseaRes[order(pval), ], stringsAsFactors = F) + +# save results +write.table(x = res[,1:7], file = options$output, quote = F, row.names = F, sep = "\t") +# +# topPathwaysUp <- fgseaRes[ES > 0][head(order(pval), n=10), pathway] +# topPathwaysDown <- fgseaRes[ES < 0][head(order(pval), n=10), pathway] +# topPathways <- c(topPathwaysUp, rev(topPathwaysDown)) +# +# pdf(paste0(options$output, ".pdf"), width = 8.5, height = 11) +# plotGseaTable(pathways[topPathways], ranks, fgseaRes,gseaParam = 0.5) +# z <- dev.off() \ No newline at end of file