## ----风格，echo = false，结果='Asis'-----------------------------------------------------生物焦质:: markdown（）选项（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”）））## ----设置，echo = false，消息= false，警告= false -------------------------------------- suppresspackagestartupmessages（{图书馆（气道）图书馆（deseq2）}）## ----气道------------------------------------------------------------------------------------------------- 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