## ----setup, echo = FALSE------------------------------------------------------ library(BiocStyle) knitr::opts_chunk$set(tidy = FALSE, cache = TRUE, autodep = TRUE) ## ----samples------------------------------------------------------------------ dataFilesDir = system.file("extdata", package = "pasilla", mustWork=TRUE) pasillaSampleAnno = read.csv(file.path(dataFilesDir, "pasilla_sample_annotation.csv")) pasillaSampleAnno ## ----dirextData--------------------------------------------------------------- dir(system.file("extdata", package = "pasilla", mustWork=TRUE), pattern = ".txt$") ## ----ecs---------------------------------------------------------------------- gffFile = file.path(dataFilesDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff") ## ----read, message = FALSE, warning = FALSE----------------------------------- library("DEXSeq") dxd = DEXSeqDataSetFromHTSeq( countfiles = file.path(dataFilesDir, paste(pasillaSampleAnno$file, "txt", sep=".")), sampleData = pasillaSampleAnno, design= ~ sample + exon + condition:exon, flattenedfile = gffFile) dxd ## ----dxd---------------------------------------------------------------------- genesforsubset = readLines(file.path(dataFilesDir, "geneIDsinsubset.txt")) dxd = dxd[geneIDs( dxd ) %in% genesforsubset,] ## ----save, eval = FALSE------------------------------------------------------- # save(dxd, file = file.path("..", "data", "pasillaDEXSeqDataSet.RData")) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()