getRegionSet {LOLA} | R Documentation |
If you want to work with a LOLA regionDB region set individually, this function can help you. It can extract individual (or subsets of) region sets from either loaded regionDBs, loaded with loadRegionDB(), or from a database on disk, where only the region sets of interest will be loaded.
getRegionSet(regionDB, filenames, collections = NULL)
regionDB |
A region database loaded with loadRegionDB(). |
filenames |
Filename(s) of a particular region set to grab. |
collections |
(optional) subset of collections to list |
A GRanges object derived from the specified file in the regionDB.
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)