## ---- echo=FALSE-------------------------------------------------------------- # These settings make the vignette prettier knitr::opts_chunk$set(results="hold", message=FALSE) ## ----Load a regionDB---------------------------------------------------------- library("LOLA") dbPath = system.file("extdata", "hg19", package="LOLA") regionDB = loadRegionDB(dbPath) ## ----Look at the elements of a regionDB--------------------------------------- names(regionDB) ## ----Load sample user sets and universe--------------------------------------- data("sample_input", package="LOLA") # load userSets data("sample_universe", package="LOLA") # load userUniverse ## ----Run the calculation------------------------------------------------------ locResults = runLOLA(userSets, userUniverse, regionDB, cores=1) ## ----------------------------------------------------------------------------- colnames(locResults) head(locResults) ## ----------------------------------------------------------------------------- locResults[order(support, decreasing=TRUE),] ## ----------------------------------------------------------------------------- locResults[order(maxRnk, decreasing=TRUE),] ## ----Write results------------------------------------------------------------ writeCombinedEnrichment(locResults, outFolder= "lolaResults") ## ----Write split results------------------------------------------------------ writeCombinedEnrichment(locResults, outFolder= "lolaResults", includeSplits=TRUE) ## ----Extracting overlaps------------------------------------------------------ oneResult = locResults[2,] extractEnrichmentOverlaps(oneResult, userSets, regionDB) ## ----Grabbing individual region sets------------------------------------------ getRegionSet(regionDB, collections="ucsc_example", filenames="vistaEnhancers.bed") ## ----Grabbing individual region sets from disk-------------------------------- getRegionSet(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed")