## ----设置，回声=假-------------------------------------------- suppresspackageStartUpMessages（{库（deseq2）库（org.hs.eg.db）}）goldatafile < - system.file（package =“sydney2016”，“extdata”，“Airway”-coldata.tab“）assayfile < - system.file（package =”sydney2016“，”extdata“，”airway-assay.tab“）## ----依赖关系，eval = false -------------------------------------------＃源（“https://biocidodder.org/bioclite。r“）＃bioclite（c（”deseq2“，”org.hs.eg.db“））## ---- Sydney2016，eval = false ---------------------------------------------------------------- - -->悉尼2016年 - Filepaths，eval= false -------------------------------＃system.file（package =“sydney2016”，“extdata“）## ---- eval = false ---------------------------------------------------------------------------＃goldatafile < - file.chooose（）＃find'airway-coldata.tab'## ------------------------------------------------------------------------------------- Coldata < - Read.Table（ColdAtafile）Coldata ## ---- eval = False --------------------------------------------------- #sssayfile < - file.chooose（）＃find'airway-assay.tab'## ------------------------------------------------------------------读数< - 阅读。 - read.table（Assayfile）头（测定）## ---------------------------------------------------------------------------------------------------------------------------------- - - - - - - - - - - - - - - - - - - - - - - - 阴谋（密度（Rowmeans（Asinh（Asinh））））## ---------------------------------------------------------------- - d < - dist（t（aSINH（ASINH）））情节（cmdscale(d), pch=19, cex=2) plot(cmdscale(d), pch=19, cex=2, col=colData$cell) plot(cmdscale(d), pch=19, cex=2, col=colData$dex) ## ------------------------------------------------------------------------ library(DESeq2) dds <- DESeqDataSetFromMatrix(assay, colData, ~ cell + dex) ## ------------------------------------------------------------------------ dds <- DESeq(dds) dds ## ------------------------------------------------------------------------ result <- results(dds) result ridx <- head(order(result$padj), 10) top = result[ridx,] top ## ------------------------------------------------------------------------ library(org.Hs.eg.db) top$Symbol <- mapIds(org.Hs.eg.db, rownames(top), "SYMBOL", "ENSEMBL") top ## ------------------------------------------------------------------------ sessionInfo()