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

Description Usage Arguments Value Examples

View source: R/postEnrichment.R

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

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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

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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 May 7, 2018, 12:58 a.m.