| buildRestrictedUniverse | If you want to test for differential enrichment within your... |
| checkUniverseAppropriateness | Check universe appropriateness |
| cleanws | cleanws takes multi-line, code formatted strings and just... |
| countOverlapsAnyRev | Just a reverser. Reverses the order of arguments and passes... |
| extractEnrichmentOverlaps | Given a single row from an enrichment table calculation,... |
| getRegionFile | Grab the filename for a a single region set from a database... |
| getRegionSet | Grab a single region set from a database, specified by... |
| lapplyAlias | Function to run lapply or mclapply, depending on the option... |
| listRegionSets | Lists the region sets for given collection(s) in a region... |
| listToGRangesList | converts a list of GRanges into a GRangesList; strips all... |
| loadRegionDB | Helper function to annotate and load a regionDB, a folder... |
| LOLA | Genome locus overlap analysis. |
| mergeRegionDBs | Given two regionDBs, (lists returned from loadRegionDB()),... |
| nlist | Named list function. |
| plotTopLOLAEnrichments | Given some results (you grab the top ones on your own), this... |
| readBed | Imports bed files and creates GRanges objects, using the... |
| readCollection | Given a bunch of region set files, read in all those flat... |
| readCollectionAnnotation | Read collection annotation |
| readCollectionFiles | Given a database and a collection, this will create the... |
| readRegionGRL | This function takes a region annotation object and reads in... |
| readRegionSetAnnotation | Given a folder containing region collections in subfolders,... |
| redefineUserSets | This function will take the user sets, overlap with the... |
| replaceFileExtension | This will change the string in filename to have a new... |
| runLOLA | Enrichment Calculation |
| sampleGRL | Function to sample regions from a GRangesList object, in... |
| setLapplyAlias | To make parallel processing a possibility but not required, I... |
| setSharedDataDir | setSharedDataDir Sets global variable specifying the default... |
| splitDataTable | Efficiently split a data.table by a column in the table |
| splitFileIntoCollection | This function will take a single large bed file that is... |
| userSets | An example set of regions, sampled from the example database. |
| userUniverse | A reduced GRanges object from the example regionDB database |
| writeCombinedEnrichment | Function for writing output all at once: combinedResults is... |
| writeDataTableSplitByColumn | Given a data table and a factor variable to split on,... |
| write.tsv | Wrapper of write.table that provides defaults to write a... |
