getRegionSet: Grab a single region set from a database, specified by...

In sheffien/LOLA: Locus overlap analysis for enrichment of genomic ranges

Description

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.

Usage

getRegionSet(regionDB, filenames, collections = NULL)

Arguments

regionDB	A region database loaded with loadRegionDB().
filenames	Filename(s) of a particular region set to grab.
collections	(optional) subset of collections to list

Value

A GRanges object derived from the specified file in the regionDB.

Examples

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)

sheffien/LOLA documentation built on Sept. 3, 2020, 8:29 p.m.