All functions
buildRestrictedUniverse	If you want to test for differential enrichment within your usersets, you can restrict the universe to only regions that are covered in at least one of your sets. This function helps you build just such a restricted universe
checkUniverseAppropriateness	Check universe appropriateness
cleanws	cleanws takes multi-line, code formatted strings and just formats them as simple strings
countOverlapsAnyRev	Just a reverser. Reverses the order of arguments and passes them untouched to countOverlapsAny -- so you can use it with lapply.
extractEnrichmentOverlaps	Given a single row from an enrichment table calculation, finds the set of overlaps between the user set and the test set. You can then use these, for example, to get sequences for those regions.
getRegionFile	Grab the filename for a a single region set from a database specified by filename.
getRegionSet	Grab a single region set from a database, specified by filename.
lapplyAlias	Function to run lapply or mclapply, depending on the option set in getOption("mc.cores"), which can be set with setLapplyAlias().
listRegionSets	Lists the region sets for given collection(s) in a region database on disk.
listToGRangesList	converts a list of GRanges into a GRangesList; strips all metadata.
loadRegionDB	Helper function to annotate and load a regionDB, a folder with subfolder collections of regions.
LOLA	Genome locus overlap analysis.
mergeRegionDBs	Given two regionDBs, (lists returned from loadRegionDB()), This function will combine them into a single regionDB. This will enable you to combine, for example, LOLA Core databases with custom databases into a single analysis.
nlist	Named list function.
plotTopLOLAEnrichments	Given some results (you grab the top ones on your own), this plots a barplot visualizing their odds ratios.
readBed	Imports bed files and creates GRanges objects, using the fread() function from data.table.
readCollection	Given a bunch of region set files, read in all those flat (bed) files and create a GRangesList object holding all the region sets. This function is used by readRegionGRL to process annotation objects.
readCollectionAnnotation	Read collection annotation
readCollectionFiles	Given a database and a collection, this will create the region annotation data.table; either giving a generic table based on file names, or by reading in the annotation data.
readRegionGRL	This function takes a region annotation object and reads in the regions, returning a GRangesList object of the regions.
readRegionSetAnnotation	Given a folder containing region collections in subfolders, this function will either read the annotation file if one exists, or create a generic annotation file.
redefineUserSets	This function will take the user sets, overlap with the universe, and redefine the user sets as the set of regions in the user universe that overlap at least one region in user sets. this makes for a more appropriate statistical enrichment comparison, as the user sets are actually exactly the same regions found in the universe otherwise, you can get some weird artifacts from the many-to-many relationship between user set regions and universe regions.
replaceFileExtension	This will change the string in filename to have a new extension
runLOLA	Enrichment Calculation
sampleGRL	Function to sample regions from a GRangesList object, in specified proportion
setLapplyAlias	To make parallel processing a possibility but not required, I use an lapply alias which can point at either the base lapply (for no multicore), or it can point to mclapply, and set the options for the number of cores (what mclapply uses). With no argument given, returns intead the number of cpus currently selected.
setSharedDataDir	setSharedDataDir Sets global variable specifying the default data directory.
splitDataTable	Efficiently split a data.table by a column in the table
splitFileIntoCollection	This function will take a single large bed file that is annotated with a column grouping different sets of similar regions, and split it into separate files for use with the LOLA collection format.
data	An example set of regions, sampled from the example database.
data	A reduced GRanges object from the example regionDB database
write.tsv	Wrapper of write.table that provides defaults to write a simple .tsv file. Passes additional arguments to write.table
writeCombinedEnrichment	Function for writing output all at once: combinedResults is an table generated by "locationEnrichment()" or by rbinding category/location results. Writes all enrichments to a single file, and also spits out the same data divided into groups based on userSets, and Databases, just for convenience. disable this with an option.
writeDataTableSplitByColumn	Given a data table and a factor variable to split on, efficiently divides the table and then writes the different splits to separate files, named with filePrepend and numbered according to split.