getRegionSet {LOLA} | R Documentation

## Grab a single region set from a database, specified by filename.

### Description

If you want to work with a LOLA regionDB region set individually, this function can help you. It can extract individual (or subsets of) region sets from either loaded regionDBs, loaded with loadRegionDB(), or from a database on disk, where only the region sets of interest will be loaded.

### Usage

    getRegionSet(regionDB, filenames, collections = NULL)

### Arguments

`regionDB` | A region database loaded with loadRegionDB().
`filenames` | Filename(s) of a particular region set to grab.
`collections` | (optional) subset of collections to list

### Value

A GRanges object derived from the specified file in the regionDB.

### 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]