writeCombinedEnrichment {LOLA} | R Documentation

## Function for writing output all at once: combinedResults is an table generated by "locationEnrichment()" or by rbinding category/location results. Writes all enrichments to a single file, and also spits out the same data divided into groups based on userSets, and Databases, just for convenience. disable this with an option.

### Description

Function for writing output all at once: combinedResults is an table generated by "locationEnrichment()" or by rbinding category/location results. Writes all enrichments to a single file, and also spits out the same data divided into groups based on userSets, and Databases, just for convenience. disable this with an option.

### Usage

    writeCombinedEnrichment(combinedResults, outFolder = NULL,
      includeSplits = TRUE)

### Arguments

`combinedResults` | enrichment results object
`outFolder` | location to write results on disk
`includeSplits` | also include individual files for each user set and database?

### Value

No return value.

### 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]