inst/doc/choosingUniverse.R

In LOLA: Locus overlap analysis for enrichment of genomic ranges

## ---- eval = FALSE------------------------------------------------------------
#  activeDHS = unlist(regionDB$regionGRL[which(regionDB$regionAnno$collection == "sheffield_dnase")])
#  activeDHS = disjoin(activeDHS)
#  activeDHS

## ---- eval = FALSE------------------------------------------------------------
#  restrictedUniverse = unlist(userSets)

## ---- eval = FALSE------------------------------------------------------------
#  locResults = runLOLA(userSets, activeDHS, regionDB, cores=1)
#  locResultsRestricted = runLOLA(userSets, restrictedUniverse, regionDB, cores=1)

## ---- eval = FALSE------------------------------------------------------------
#  locResults[userSet==2,][order(maxRnk, decreasing=FALSE),][1:10,]
#  locResultsRestricted[userSet==2,][order(maxRnk, decreasing=FALSE),][1:10,]
#  
#  locResults[userSet==3,][order(maxRnk, decreasing=FALSE),][1:10,]
#  locResultsRestricted[userSet==3,][order(maxRnk, decreasing=FALSE),][1:10,]