plotTopLOLAEnrichments {LOLA}R Documentation

Given some results (you grab the top ones on your own), this plots a barplot visualizing their odds ratios.

Description

Given some results (you grab the top ones on your own), this plots a barplot visualizing their odds ratios.

Usage

plotTopLOLAEnrichments(data)

Arguments

data

A results table returned from runLOLA()

Value

Returns a ggplot2 plot object.

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 1.12.0 Index]