writeCombinedEnrichment: Function for writing output all at once: combinedResults is...

In sheffien/LOLA: Locus overlap analysis for enrichment of genomic ranges

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)

sheffien/LOLA documentation built on Sept. 3, 2020, 8:29 p.m.