#!/usr/bin/env Rscript library(edgeR) RawCounts <- read.delim("count_matrix.txt", row.names = "gene_id") group <- read.table("SampleGroups.txt", header=TRUE, sep="\t", row.names=1) dgecomplete <- DGEList(RawCounts, group = group$Condition) logcpm <- cpm(dgecomplete, log=TRUE) filtData <- filterByExpr(dgecomplete) dgecomplete <- dgecomplete[filtData, keep.lib.sizes=FALSE] dgecomplete <- calcNormFactors(dgecomplete) dgecomplete <- estimateDisp(y = dgecomplete) fit <- glmQLFit(y=dgecomplete) qlf <- glmQLFTest(fit, coef = 2) diff_results <- topTags(qlf, n=Inf) write.csv(diff_results, file="edgeR_diff_genes.csv") write.csv(as.data.frame(logcpm), file="edgeR_normcounts.csv")