extractEnrichmentOverlaps: Given a single row from an enrichment table calculation,...

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

Description

Given a single row from an enrichment table calculation, finds the set of overlaps between the user set and the test set. You can then use these, for example, to get sequences for those regions.

Usage

extractEnrichmentOverlaps(locResult, userSets, regionDB)

Arguments

locResult	Results from runLOLA function
userSets	User sets passed to the runLOLA function
regionDB	Region database used

Value

userSets overlapping the supplied database entry.

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.