## ----style, echo=FALSE, results="asis", message=FALSE-------------------- knitr::opts_chunk$set(tidy = FALSE, warning = FALSE, message = FALSE) ## ----echo=FALSE, results='hide', message=FALSE--------------------------- CRANpkg <- function (pkg) { cran <- "https://CRAN.R-project.org/package" fmt <- "[%s](%s=%s)" sprintf(fmt, pkg, cran, pkg) } Biocpkg <- function (pkg) { sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg) } 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=6, fig.width=12------------------------------------------ barplot(x, showCategory=8) ## ----fig.height=6, fig.width=12------------------------------------------ dotplot(x, showCategory=15) ## ----fig.height=10, fig.width=10----------------------------------------- emapplot(x) ## ----fig.height=8, fig.width=8------------------------------------------- cnetplot(x, categorySize="pvalue", foldChange=geneList) ## ----fig.height=8, fig.width=13, eval=FALSE------------------------------ # require(clusterProfiler) # data(gcSample) # res <- compareCluster(gcSample, fun="enrichPathway") # dotplot(res) ## ------------------------------------------------------------------------ y <- gsePathway(geneList, nPerm=10000, pvalueCutoff=0.2, pAdjustMethod="BH", verbose=FALSE) res <- as.data.frame(y) head(res) ## ----fig.height=8, fig.width=8------------------------------------------- emapplot(y, color="pvalue") ## ----fig.height=7, fig.width=10------------------------------------------ gseaplot(y, geneSetID = "R-HSA-69242") ## ----fig.height=8, fig.width=8------------------------------------------- viewPathway("E2F mediated regulation of DNA replication", readable=TRUE, foldChange=geneList)