## ----style, echo = FALSE, results = 'asis'-------------------------------------------------------- BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), error=FALSE) ## ----load-data------------------------------------------------------------------------------------ library("airway") data(airway) ## ----play----------------------------------------------------------------------------------------- library("airway") data(airway) se <- airway se ## ------------------------------------------------------------------------------------------------- library("DESeq2") dds <- DESeqDataSet(se, design = ~ cell + dex) ## ------------------------------------------------------------------------------------------------- dds$dex <- relevel(dds$dex, "untrt") ## ------------------------------------------------------------------------------------------------- dds <- DESeq(dds) ## ------------------------------------------------------------------------------------------------- (res <- results(dds)) ## ------------------------------------------------------------------------------------------------- mcols(res, use.names=TRUE) ## ------------------------------------------------------------------------------------------------- summary(res) ## ----plotcounts, fig.width=5, fig.height=5-------------------------------------------------------- topGene <- rownames(res)[which.min(res$padj)] plotCounts(dds, gene=topGene, intgroup=c("dex")) ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()