## ----echo = FALSE, message = FALSE-------------------------------------------- library(knitr) knitr::opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, warning = FALSE, fig.align = "center") ## ----------------------------------------------------------------------------- library(KEGGREST) pathway2gene = keggLink("pathway", "hsa") head(pathway2gene) ## ----------------------------------------------------------------------------- kegg_pathways = split(gsub("hsa:", "", names(pathway2gene)), gsub("path:", "", pathway2gene)) ## ----------------------------------------------------------------------------- library(rGREAT) gr = randomRegions(genome = "hg19") great(gr, kegg_pathways, "hg19") ## ----------------------------------------------------------------------------- pn = keggList("pathway/hsa") head(pn) ## ----------------------------------------------------------------------------- lt = getKEGGPathways("hsa") lt[1:2] ## ----------------------------------------------------------------------------- library(reactome.db) gs = as.list(reactomePATHID2EXTID) great(gr, gs, "hg19") ## ----------------------------------------------------------------------------- sessionInfo()