LOLA: Location overlap analysis for enrichment of genomic ranges

Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This make is possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.

Author
Nathan Sheffield <http://www.databio.org> [aut, cre], Christoph Bock [cre]
Date of publication
None
Maintainer
Nathan Sheffield <nathan@code.databio.org>
License
GPL-3
Version
1.4.0
URLs

View on Bioconductor

Man pages

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,...
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
Provides functions for genome location overlap analysis.
mergeRegionDBs
Given two regionDBs, (lists returned from loadRegionDB()),...
nlist
Named list function.
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...

Files in this package

LOLA/DESCRIPTION
LOLA/NAMESPACE
LOLA/NEWS
LOLA/R
LOLA/R/LOLA.R
LOLA/R/calcLocEnrichment.R
LOLA/R/data.R
LOLA/R/examples
LOLA/R/examples/example.R
LOLA/R/examples/example2.R
LOLA/R/loadRegionDB.R
LOLA/R/postEnrichment.R
LOLA/R/splitFileIntoCollection.R
LOLA/R/utility.R
LOLA/README.md
LOLA/build
LOLA/build/vignette.rds
LOLA/data
LOLA/data/sample_input.RData
LOLA/data/sample_universe.RData
LOLA/inst
LOLA/inst/CITATION
LOLA/inst/doc
LOLA/inst/doc/choosingUniverse.R
LOLA/inst/doc/choosingUniverse.Rmd
LOLA/inst/doc/choosingUniverse.html
LOLA/inst/doc/gettingStarted.R
LOLA/inst/doc/gettingStarted.Rmd
LOLA/inst/doc/gettingStarted.html
LOLA/inst/doc/usingLOLACore.R
LOLA/inst/doc/usingLOLACore.Rmd
LOLA/inst/doc/usingLOLACore.html
LOLA/inst/extdata
LOLA/inst/extdata/examples
LOLA/inst/extdata/examples/combined_regions.bed
LOLA/inst/extdata/hg19
LOLA/inst/extdata/hg19/ucsc_example
LOLA/inst/extdata/hg19/ucsc_example/collection.txt
LOLA/inst/extdata/hg19/ucsc_example/index.txt
LOLA/inst/extdata/hg19/ucsc_example/regions
LOLA/inst/extdata/hg19/ucsc_example/regions/cpgIslandExt.bed
LOLA/inst/extdata/hg19/ucsc_example/regions/laminB1Lads.bed
LOLA/inst/extdata/hg19/ucsc_example/regions/numtSAssembled.bed
LOLA/inst/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed
LOLA/inst/extdata/hg19/ucsc_example/regions/vistaEnhancers_colNames.bed
LOLA/inst/extdata/hg19/ucsc_example/sizes.txt
LOLA/inst/extdata/multi
LOLA/inst/extdata/multi/collection1
LOLA/inst/extdata/multi/collection1/collection.txt
LOLA/inst/extdata/multi/collection1/index.txt
LOLA/inst/extdata/multi/collection1/regions
LOLA/inst/extdata/multi/collection1/regions/cpgIslandExt.bed
LOLA/inst/extdata/multi/collection1/regions/laminB1Lads.bed
LOLA/inst/extdata/multi/collection1/regions/vistaEnhancers.bed
LOLA/inst/extdata/multi/collection1/sizes.txt
LOLA/inst/extdata/multi/collection2
LOLA/inst/extdata/multi/collection2/index.txt
LOLA/inst/extdata/multi/collection2/regions
LOLA/inst/extdata/multi/collection2/regions/cpgIslandExt.bed
LOLA/inst/extdata/multi/collection2/regions/laminB1Lads.bed
LOLA/inst/extdata/multi/collection2/regions/vistaEnhancers.bed
LOLA/inst/extdata/multi/collection2/sizes.txt
LOLA/inst/scripts
LOLA/inst/scripts/LOLA
LOLA/inst/web
LOLA/inst/web/index.html
LOLA/inst/web/webComponents
LOLA/inst/web/webComponents/ajax-loader.gif
LOLA/inst/web/webComponents/d3.min.js
LOLA/inst/web/webComponents/gridstyle.css
LOLA/man
LOLA/man/LOLA.Rd
LOLA/man/buildRestrictedUniverse.Rd
LOLA/man/checkUniverseAppropriateness.Rd
LOLA/man/cleanws.Rd
LOLA/man/countOverlapsAnyRev.Rd
LOLA/man/extractEnrichmentOverlaps.Rd
LOLA/man/getRegionSet.Rd
LOLA/man/lapplyAlias.Rd
LOLA/man/listRegionSets.Rd
LOLA/man/listToGRangesList.Rd
LOLA/man/loadRegionDB.Rd
LOLA/man/mergeRegionDBs.Rd
LOLA/man/nlist.Rd
LOLA/man/readBed.Rd
LOLA/man/readCollection.Rd
LOLA/man/readCollectionAnnotation.Rd
LOLA/man/readCollectionFiles.Rd
LOLA/man/readRegionGRL.Rd
LOLA/man/readRegionSetAnnotation.Rd
LOLA/man/redefineUserSets.Rd
LOLA/man/replaceFileExtension.Rd
LOLA/man/runLOLA.Rd
LOLA/man/sampleGRL.Rd
LOLA/man/setLapplyAlias.Rd
LOLA/man/setSharedDataDir.Rd
LOLA/man/splitDataTable.Rd
LOLA/man/splitFileIntoCollection.Rd
LOLA/man/userSets.Rd
LOLA/man/userUniverse.Rd
LOLA/man/write.tsv.Rd
LOLA/man/writeCombinedEnrichment.Rd
LOLA/man/writeDataTableSplitByColumn.Rd
LOLA/tests
LOLA/tests/testthat
LOLA/tests/testthat.R
LOLA/tests/testthat/test_all.R
LOLA/vignettes
LOLA/vignettes/choosingUniverse.Rmd
LOLA/vignettes/gettingStarted.Rmd
LOLA/vignettes/usingLOLACore.Rmd