inst/doc/usingLOLACore.R

In LOLA: Locus overlap analysis for enrichment of genomic ranges

## ---- eval = FALSE------------------------------------------------------------
#  library("LOLA")
#  
#  regionDB = loadRegionDB("LOLACore/hg19")
#  
#  regionSetA = readBed("lola_vignette_data/setA_100.bed")
#  regionSetB = readBed("lola_vignette_data/setB_100.bed")
#  regionSetC = readBed("lola_vignette_data/setC_100.bed")
#  activeDHS = readBed("lola_vignette_data/activeDHS_universe.bed")

## ---- eval = FALSE------------------------------------------------------------
#  userSets = GRangesList(regionSetA, regionSetB, regionSetC)
#  locResults = runLOLA(userSets, activeDHS, regionDB, cores=1)

## ---- eval = FALSE------------------------------------------------------------
#  locResults[1:10,]

## ---- eval = FALSE------------------------------------------------------------
#  locResults[order(meanRnk, decreasing=FALSE),][1:20,]
#  locResults[order(maxRnk, decreasing=FALSE),][1:20,]
#  locResults[collection=="sheffield_dnase", ][order(maxRnk, decreasing=FALSE),]
#  
#  locResults[userSet==2,][order(maxRnk, decreasing=FALSE),][1:10,]
#  locResults[userSet==3,][order(maxRnk, decreasing=FALSE),][1:10,]
#  
#  locResults[userSet==1,][collection=="sheffield_dnase", ][1:15,]
#  locResults[userSet==2,][collection=="sheffield_dnase", ][1:15,]
#  locResults[userSet==3,][collection=="sheffield_dnase", ][1:15,]

## ---- eval = FALSE------------------------------------------------------------
#  writeCombinedEnrichment(locResults, outFolder= "lolaResults", includeSplits=TRUE)