## ----style, echo=FALSE, results="asis", message=FALSE-------------------- BiocStyle::markdown() knitr::opts_chunk$set(tidy = FALSE, warning = FALSE, message = FALSE) ## ----echo=FALSE, results='hide', message=FALSE--------------------------- library(org.Hs.eg.db) library(DOSE) library(ReactomePA) ## ------------------------------------------------------------------------ library(ReactomePA) data(geneList) de <- names(geneList)[abs(geneList) > 1.5] head(de) x <- enrichPathway(gene=de,pvalueCutoff=0.05, readable=T) head(as.data.frame(x)) ## ----fig.height=4, fig.width=7------------------------------------------- barplot(x, showCategory=8) ## ----fig.height=6, fig.width=8------------------------------------------- dotplot(x, showCategory=15) ## ----fig.height=16, fig.width=20, eval=FALSE----------------------------- ## enrichMap(x, layout=igraph::layout.kamada.kawai, vertex.label.cex = 1) ## ----fig.height=12, fig.width=12, eval=FALSE----------------------------- ## cnetplot(x, categorySize="pvalue", foldChange=geneList) ## ----fig.height=8, fig.width=13, eval=FALSE------------------------------ ## require(clusterProfiler) ## data(gcSample) ## res <- compareCluster(gcSample, fun="enrichPathway") ## plot(res) ## ------------------------------------------------------------------------ y <- gsePathway(geneList, nPerm=1000, minGSSize=120, pvalueCutoff=0.2, pAdjustMethod="BH", verbose=FALSE) res <- as.data.frame(y) head(res) ## ----fig.height=16, fig.width=16, eval=FALSE----------------------------- ## enrichMap(y) ## ----fig.height=7, fig.width=10------------------------------------------ gseaplot(y, geneSetID = "1280215") ## ----fig.height=16, fig.width=16, eval=FALSE----------------------------- ## viewPathway("E2F mediated regulation of DNA replication", readable=TRUE, foldChange=geneList) ## ----echo=FALSE---------------------------------------------------------- sessionInfo()