getRegionFile: Grab the filename for a a single region set from a database...

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

Description

Like getRegionSet but returns a filename instead of a GRanges object. Given a local filename, returns a complete absolulte path so you can read that file in.

Usage

getRegionFile(dbLocation, filenames, collections = NULL)

Arguments

dbLocation	folder of regionDB
filenames	Filename(s) of a particular region set to grab.
collections	(optional) subset of collections to list

Value

A filename 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)

nsheff/LOLA documentation built on Sept. 8, 2020, 11:50 a.m.