LOLA (version 1.2.2)

runLOLA: 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)

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?

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; logOddsRatio: result from the fisher's exact test; support: number of regions in userSet overlapping databaseSet; rnkPV, rnkLO, rnkSup: rank in this table of p-value, logOddsRatio, 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")

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)