## ----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(DOSE) library(org.Hs.eg.db) library(clusterProfiler) ## ------------------------------------------------------------------------ library(DOSE) data(geneList) gene <- names(geneList)[abs(geneList) > 1.5] head(gene) x <- enrichDO(gene = gene, ont = "DO", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe = names(geneList), minGSSize = 5, maxGSSize = 500, qvalueCutoff = 0.05, readable = FALSE) head(x) ## ------------------------------------------------------------------------ x <- setReadable(x, 'org.Hs.eg.db') head(x) ## ------------------------------------------------------------------------ gene2 <- names(geneList)[abs(geneList) < 3] ncg <- enrichNCG(gene2) head(ncg) ## ------------------------------------------------------------------------ dgn <- enrichDGN(gene) head(dgn) snp <- c("rs1401296", "rs9315050", "rs5498", "rs1524668", "rs147377392", "rs841", "rs909253", "rs7193343", "rs3918232", "rs3760396", "rs2231137", "rs10947803", "rs17222919", "rs386602276", "rs11053646", "rs1805192", "rs139564723", "rs2230806", "rs20417", "rs966221") dgnv <- enrichDGNv(snp) head(dgnv) ## ----fig.height=6, fig.width=7------------------------------------------- barplot(x, showCategory=10) ## ----fig.width=6--------------------------------------------------------- dotplot(x) ## ----fig.width=18, fig.height=18, eval=FALSE----------------------------- # cnetplot(x, categorySize="pvalue", foldChange=geneList) ## ----fig.width=10, fig.height=6, eval=FALSE------------------------------ # upsetplot(x) ## ----fig.height=10, fig.width=10, eval=FALSE----------------------------- # enrichMap(x) ## ----fig.width=7, fig.height=7------------------------------------------- library(clusterProfiler) data(gcSample) cdo <- compareCluster(gcSample, fun="enrichDO") plot(cdo)