## ----style, echo = FALSE, results = 'asis'-------------------------------------------------------- BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))) ## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE-------------------------------------------- suppressPackageStartupMessages({ library(airway) library(DESeq2) }) ## ----airway--------------------------------------------------------------------------------------- library("airway") data(airway) airway ## main components of SummarizedExperiment head(assay(airway)) colData(airway) rowRanges(airway) ## e.g., coordinated subset to include dex 'trt' samples airway[, airway$dex == "trt"] ## e.g., keep only rows with non-zero counts airway <- airway[rowSums(assay(airway)) != 0, ] ## ----DESeqDataSet--------------------------------------------------------------------------------- library(DESeq2) dds <- DESeqDataSet(airway, design = ~ cell + dex) ## ----DESeq-workflow------------------------------------------------------------------------------- dds <- DESeq(dds) dds ## ----DESeq-result--------------------------------------------------------------------------------- res <- results(dds) res