Man pages for LOLA
Location overlap analysis for enrichment of genomic ranges

buildRestrictedUniverseIf you want to test for differential enrichment within your...
checkUniverseAppropriatenessCheck universe appropriateness
cleanwscleanws takes multi-line, code formatted strings and just...
countOverlapsAnyRevJust a reverser. Reverses the order of arguments and passes...
extractEnrichmentOverlapsGiven a single row from an enrichment table calculation,...
getRegionSetGrab a single region set from a database, specified by...
lapplyAliasFunction to run lapply or mclapply, depending on the option...
listRegionSetsLists the region sets for given collection(s) in a region...
listToGRangesListconverts a list of GRanges into a GRangesList; strips all...
loadRegionDBHelper function to annotate and load a regionDB, a folder...
LOLAProvides functions for genome location overlap analysis.
mergeRegionDBsGiven two regionDBs, (lists returned from loadRegionDB()),...
nlistNamed list function.
readBedImports bed files and creates GRanges objects, using the...
readCollectionGiven a bunch of region set files, read in all those flat...
readCollectionAnnotationRead collection annotation
readCollectionFilesGiven a database and a collection, this will create the...
readRegionGRLThis function takes a region annotation object and reads in...
readRegionSetAnnotationGiven a folder containing region collections in subfolders,...
redefineUserSetsThis function will take the user sets, overlap with the...
replaceFileExtensionThis will change the string in filename to have a new...
runLOLAEnrichment Calculation
sampleGRLFunction to sample regions from a GRangesList object, in...
setLapplyAliasTo make parallel processing a possibility but not required, I...
setSharedDataDirsetSharedDataDir Sets global variable specifying the default...
splitDataTableEfficiently split a data.table by a column in the table
splitFileIntoCollectionThis function will take a single large bed file that is...
userSetsAn example set of regions, sampled from the example database.
userUniverseA reduced GRanges object from the example regionDB database
writeCombinedEnrichmentFunction for writing output all at once: combinedResults is...
writeDataTableSplitByColumnGiven a data table and a factor variable to split on,...
write.tsvWrapper of write.table that provides defaults to write a...
LOLA documentation built on May 31, 2017, 11:23 a.m.