## ----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,]

