runLOLA {LOLA} | R Documentation

## Enrichment Calculation

### Description

Workhorse function that calculates overlaps between userSets, and then uses a fisher's exact test rank them by significance of the overlap.

### Usage

    runLOLA(
      userSets,
      userUniverse,
      regionDB,
      minOverlap = 1,
      cores = 1,
      redefineUserSets = FALSE,
      direction = "enrichment"
    )

### Arguments

`userSets` | Regions of interest
`userUniverse` | Regions tested for inclusion in userSets
`regionDB` | Region DB to check for overlap, from loadRegionDB()
`minOverlap` | (Default:1) Minimum bases required to count an overlap
`cores` | Number of processors
`redefineUserSets` | run redefineUserSets() on your userSets?
`direction` | Defaults to "enrichment", but may also accept "depletion", which will swap the direction of the fisher test (use 'greater' or less' value passed to the 'alternative' option of fisher.test)

### Value

Data.table with enrichment results. Rows correspond to individual pairwise fisher's tests comparing a single userSet with a single databaseSet. The columns in this data.table are: userSet and dbSet: index into their respective input region sets. pvalueLog: -log10(pvalue) from the fisher's exact result; oddsRatio: result from the fisher's exact test; support: number of regions in userSet overlapping databaseSet; rnkPV, rnkOR, rnkSup: rank in this table of p-value, oddsRatio, and Support respectively. The –value is the negative natural log of the p-value returned from a one-sided fisher's exact test. maxRnk, meanRnk: max and mean of the 3 previous ranks, providing a combined ranking system. b, c, d: 3 other values completing the 2x2 contingency table (with support). The remaining columns describe the dbSet for the row.

If you have the qvalue package installed from bioconductor, runLOLA will add a q-value transformation to provide FDR scores automatically.

### 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 1.20.0 Index]