## ----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”）），缓存= as.logical（sys.getenv（“knitr_cache”，“true”）），错误= false）## ----加载 -数据 - - - - - - - - - - - - - - - - - - - - - - - - ---------------------------------图书馆（“气道”）数据（气道）## ----玩 - - - - - - - - - - - - - - - - - - - - - - - --------------------------------------图书馆（“航空公司”）数据（呼吸道）SE < - Airway Se ## ---------------------------------------------------------------------------------------------------------图书馆（“deseq2”）DDS < - deseqdataset（SE，Design =〜Cell + Dex）## ------------------------------------------------------------------------------------------------------------ DDS $ DEX < - 相关性（DDS $ DEX，“UNTRT”）## ----------------------------------------------------------------------------------------------------------------------- - DDS < - DESQ（DDS）## ---------------------------------------------------------------------------------------------------------------（res < - 结果（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()