LOLA (version 1.2.2)

extractEnrichmentOverlaps: 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.

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")

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)