############################################################
#
# author: Ludwig Geistlinger
# last update: 2018-04-16
#
# descr: differential expression analysis of RNA-seq data
#
# call: Rscript de_rseq.R <exprs.file>
# <cdat.file>
# <rdat.file>
# <de.method>
# <out.file>
#
# choose <de.method> out of {'limma', 'edgeR', 'DESeq'}
############################################################
if(length(commandArgs()) != 10)
{
message(paste("usage: Rscript de_rseq.R <exprs.file> <cdat.file>",
"<rdat.file> <de.method> <out.file>"))
quit(save="no")
}
message("Loading EnrichmentBrowser")
suppressPackageStartupMessages(library(EnrichmentBrowser))
exprs.file <- commandArgs()[6]
cdat.file <- commandArgs()[7]
rdat.file <- commandArgs()[8]
de.method <- commandArgs()[9]
out.file <- commandArgs()[10]
message("Reading data ...")
se <- readSE(exprs.file, cdat.file, rdat.file)
message("DE analysis ...")
se <- deAna(se, de.method=de.method)
de.tbl <- rowData(se)[,sapply(c("FC.COL", "PVAL.COL", "ADJP.COL"), configEBrowser)]
de.tbl <- cbind(names(se), de.tbl)
colnames(de.tbl) <- c("GENE.ID", "log2FC", "RAW.PVAL", "ADJ.PVAL")
write.table(de.tbl, file=out.file, row.names=FALSE, quote=FALSE, sep="\t")
message("DE table written to ", out.file)
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