DESeq

Code taken from the DESeq vignette for my own convenience.

library("DESeq")

exampleFile = system.file ("extra/TagSeqExample.tab",package="DESeq")

countsTable = read.delim(exampleFile, header=TRUE, stringsAsFactors=TRUE)

rownames(countsTable) = countsTable$gene

countsTable = countsTable[ , -1]

conds = c("T","T","T","Tb","N","N")

cds = newCountDataSet (countsTable, conds)

cds = cds[,-1]

cds = estimateSizeFactors(cds)

sizeFactors(cds)

cds <- estimateVarianceFunctions( cds )

res <- nbinomTest( cds, "N", "T" )

resSig <- res[ res$padj < .1, ]

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