extractEnrichmentOverlaps {LOLA} | R Documentation

## 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")
    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)

[Package LOLA version 1.18.1 Index]