# #——风格,回声= FALSE,结果=“黑名单”,消息= FALSE -------------------- BiocStyle:减价()knitr: opts_chunk设置美元(整洁= FALSE,警告= FALSE,消息= FALSE) # #——回声= FALSE,结果=“隐藏”,消息= FALSE --------------------------- 库(org.Hs.eg.db)图书馆(剂量)图书馆(ReactomePA ) ## ------------------------------------------------------------------------ 库(ReactomePA)数据(geneList) de < -名字(geneList) (abs (geneList) > 1.5)头(de) x < - enrichPathway(基因= de pvalueCutoff = 0.05,可读= T)头(as.data.frame (x )) ## ---- 无花果。身高= 4,fig.width = 7 ------------------------------------------- barplot (x, showCategory = 8) # #——无花果。身高= 6,fig.width = 8 ------------------------------------------- dotplot (x, showCategory = 15) # #——无花果。身高= 16,fig.width = 20, eval = FALSE ----------------------------- # enrichMap (x,布局= igraph:: layout.kamada。Kawai, vertex.label.cex = 1) ## ----身高= 12,fig.width = 12, eval = FALSE ----------------------------- # cnetplot (x, categorySize =“pvalue foldChange = geneList) # #——无花果。身高= 8,fig.width = 13, eval = FALSE ------------------------------ # 需要(clusterProfiler) #数据(gcSample) # res < - compareCluster (gcSample、有趣=“enrichPathway”)#地块(res ) ## ------------------------------------------------------------------------ y < - gsePathway (geneList nPerm = 1000, minGSSize = 120, pvalueCutoff = 0.2, pAdjustMethod =“黑洞”,verbose = FALSE) res < - as.data.frame (y)头(res) # #——无花果。身高= 16,fig.width = 16, eval = FALSE ----------------------------- # enrichMap (y) # #——无花果。身高= 7,fig.width = 10 ------------------------------------------ gseaplot (y, geneSetID = " r - hsa - 69242 ") ## ---- 无花果。身高= 16,fig.width = 16, eval = FALSE ----------------------------- # viewPathway(“E2F介导的DNA复制的监管”,读= TRUE, foldChange = geneList) # #——回声= FALSE ---------------------------------------------------------- sessionInfo ()