comparison 16_fgsea/GSEA.R @ 2:9e75d29c2409 draft default tip

Uploaded

1:91eed1b5c009

# Import library
library("getopt")
library("fgsea")
library("Rcpp")

options(stringAsfactors = FALSE, useFancyQuotes = FALSE)

# Take in trailing command line arguments
args <- commandArgs(trailingOnly = TRUE)

# cat("\n input: ", options$input1)
# cat("\n input: ", options$input2)
# cat("\n output: ", options$output)

# Rank file
ranks <- read.table(options$input1, header=F, colClasses = c("character", "numeric"))
ranks <- setNames(ranks[,2], ranks[,1])

# Pathways database
pathways <- gmtPathways(options$input2)

# running analysis

2:9e75d29c2409

# 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)

# 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