## ---- echo=FALSE, results="hide", warning=FALSE, message=FALSE---------------- library(GenomicInteractionNodes) library(rtracklayer) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) knitr::opts_chunk$set(warning=FALSE, message=FALSE) ## ----devtoolsInstallation, eval=FALSE----------------------------------------- # library(devtools) # install_github("jianhong/GenomicInteractionNodes") ## ----BiocManagerInstallation, eval=FALSE-------------------------------------- # library(BiocManager) # install("GenomicInteractionNodes") ## ----quickStart--------------------------------------------------------------- ## load library library(GenomicInteractionNodes) library(rtracklayer) library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## for human hg19 library(org.Hs.eg.db) ## used to convert gene_id to gene_symbol library(GO.db) ## used for enrichment analysis ## import the interactions from bedpe file p <- system.file("extdata", "WT.2.bedpe", package = "GenomicInteractionNodes") #### please try to replace the connection to your file path interactions <- import(con=p, format="bedpe") ## define the nodes nodes <- detectNodes(interactions) names(nodes) lapply(nodes, head, n=2) ## annotate the nodes by gene promoters node_regions <- nodes$node_regions node_regions <- annotateNodes(node_regions, txdb=TxDb.Hsapiens.UCSC.hg19.knownGene, orgDb=org.Hs.eg.db, upstream=2000, downstream=500) head(node_regions, n=2) ## Gene Ontology enrichment analysis enrich <- enrichmentAnalysis(node_regions, orgDb=org.Hs.eg.db) names(enrich$enriched) names(enrich$enriched_in_compound) res <- enrich$enriched$BP res <- res[order(res$fdr), ] head(res, n=2) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()