LOLA                    Genome locus overlap analysis.
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.
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.
userSets                An example set of regions, sampled from the
                        example database.
userUniverse            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.
