writeCombinedEnrichment {LOLA} | R Documentation |
Function for writing output all at once: combinedResults is an table generated by "locationEnrichment()" or by rbinding category/location results. Writes all enrichments to a single file, and also spits out the same data divided into groups based on userSets, and Databases, just for convenience. disable this with an option.
writeCombinedEnrichment( combinedResults, outFolder = NULL, includeSplits = TRUE )
combinedResults |
enrichment results object |
outFolder |
location to write results on disk |
includeSplits |
also include individual files for each user set and database? |
No return value.
dbPath = system.file("extdata", "hg19", package="LOLA") regionDB = loadRegionDB(dbLocation=dbPath) data("sample_universe", package="LOLA") data("sample_input", package="LOLA") getRegionSet(regionDB, collections="ucsc_example", filenames="vistaEnhancers.bed") getRegionSet(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed") getRegionFile(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed") res = runLOLA(userSets, userUniverse, regionDB, cores=1) locResult = res[2,] extractEnrichmentOverlaps(locResult, userSets, regionDB) writeCombinedEnrichment(locResult, "temp_outfolder") userSetsRedefined = redefineUserSets(userSets, userUniverse) resRedefined = runLOLA(userSetsRedefined, userUniverse, regionDB, cores=1) g = plotTopLOLAEnrichments(resRedefined)