# #——回声= FALSE -------------------------------------------------------------- # 这些设置使装饰图案漂亮knitr: opts_chunk设置美元(= "持有",结果消息= FALSE) # #——加载regionDB ---------------------------------------------------------- 库(LOLA) dbPath =系统。文件(“extdata”、“hg19”、包=“洛拉”)regionDB = loadRegionDB (dbPath) # #——看看regionDB的元素 --------------------------------------- 名称(regionDB) # #——加载示例用户集和宇宙 --------------------------------------- 数据(“sample_input”,包=“洛拉”)# userSets数据加载(“sample_universe”,包=“洛拉”)#负载userUniverse # #——运行计算 ------------------------------------------------------ locResults = runLOLA (userSets userUniverse regionDB,核= 1 ) ## ----------------------------------------------------------------------------- (locResults colnames (locResults)头 ) ## ----------------------------------------------------------------------------- locResults[秩序(支持,减少= TRUE ),] ## ----------------------------------------------------------------------------- locResults[秩序(maxRnk,减少= TRUE ),] ## ---- 写的结果 ------------------------------------------------------------ writeCombinedEnrichment (locResults倒转褶皱= " lolaResults ") ## ---- 写分割结果 ------------------------------------------------------ writeCombinedEnrichment (locResults倒转褶皱=“lolaResults includeSplits = TRUE) # #——提取重叠 ------------------------------------------------------ oneResult = locResults [2] extractEnrichmentOverlaps (oneResult、userSets regionDB) # #,抓住个别地区集 ------------------------------------------ getRegionSet (regionDB集合= " ucsc_example ",filnames ="vistaEnhancers.bed") ## ----从磁盘抓取单个区域集-------------------------------- getRegionSet(dbPath, collections="ucsc_example"， filnames ="vistaEnhancers.bed")