# #——风格,回声= FALSE,结果=“黑名单”,消息= FALSE -------------------- 美元knitr: opts_chunk集(整洁= FALSE,警告= FALSE,消息= FALSE) # #——回声= FALSE,结果=“隐藏”,消息= FALSE --------------------------- CRANpkg (pkg){凹口< < -功能-“https://CRAN.R-project.org/package”fmt <”(% s) (% s = % s)“sprintf (fmt,包裹,凹口,包裹)}Biocpkg < -函数(pkg) {sprintf(“(% s) (//www.anjoumacpherson.com/packages/%s)”,包裹,pkg)}库(org.Hs.eg.db)库(剂量)库(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= 6,fig.width = 12 ------------------------------------------ barplot (x, showCategory = 8) # #——无花果。身高= 6,fig.width = 12 ------------------------------------------ dotplot (x, showCategory = 15) # #——无花果。身高= 10,fig.width = 10 ----------------------------------------- emapplot (x) # #——无花果。身高= 8,fig.width = 8 ------------------------------------------- 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”)# dotplot (res ) ## ------------------------------------------------------------------------ y < - gsePathway (geneList nPerm = 10000, pvalueCutoff = 0.2, pAdjustMethod =“黑洞”,verbose = FALSE) res < - as.data.frame (y)头(res) # #——无花果。身高= 8,fig.width = 8 ------------------------------------------- = " pvalue emapplot (y,颜色 ") ## ---- 无花果。身高= 7,fig.width = 10 ------------------------------------------ gseaplot (y, geneSetID = " r - hsa - 69242 ") ## ---- 无花果。身高= 8,fig.width = 8 ------------------------------------------- viewPathway(“E2F介导的DNA复制的监管”,读= TRUE, foldChange = geneList)