## ---- 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)