redefineUserSets {LOLA} | R Documentation

## This function will take the user sets, overlap with the universe, and redefine the user sets as the set of regions in the user universe that overlap at least one region in user sets. this makes for a more appropriate statistical enrichment comparison, as the user sets are actually exactly the same regions found in the universe otherwise, you can get some weird artifacts from the many-to-many relationship between user set regions and universe regions.

### Description

This function will take the user sets, overlap with the universe, and redefine the user sets as the set of regions in the user universe that overlap at least one region in user sets. this makes for a more appropriate statistical enrichment comparison, as the user sets are actually exactly the same regions found in the universe otherwise, you can get some weird artifacts from the many-to-many relationship between user set regions and universe regions.

### Usage

    redefineUserSets(userSets, userUniverse, cores = 1)

### Arguments

`userSets` | Regions of interest
`userUniverse` | Regions tested for inclusion in userSets
`cores` | Number of processors

### Value

userSets redefined in terms of userUniverse

### 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 1.14.0 Index]