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Diffstat (limited to 'day2/ex3-R/script.R')
| -rw-r--r-- | day2/ex3-R/script.R | 16 |
1 files changed, 16 insertions, 0 deletions
diff --git a/day2/ex3-R/script.R b/day2/ex3-R/script.R new file mode 100644 index 0000000..fcbf6e1 --- /dev/null +++ b/day2/ex3-R/script.R @@ -0,0 +1,16 @@ +library(edgeR) + +# It's easier to read environment variables than parse command line arguments +counts <- read.delim(Sys.getenv("counts"), row.names=1) +out <- Sys.getenv("out") + +group <- rep(c("A", "B"), each = 2) +design <- model.matrix(~group) +dge <- DGEList(counts=counts) +keep <- filterByExpr(dge, design) +dge <- dge[keep,,keep.lib.sizes=FALSE] +dge <- calcNormFactors(dge) +logCPM <- cpm(dge, log=TRUE, prior.count=3) +fit <- lmFit(logCPM, design) +fit <- eBayes(fit, trend=TRUE) +write.table(topTable(fit, coef=ncol(design)), file = out) |