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.

AuthorNathan Sheffield <http://www.databio.org> [aut, cre], Christoph Bock [cre]
Date of publicationNone
MaintainerNathan Sheffield <nathan@code.databio.org>
LicenseGPL-3
Version1.4.0
http://databio.org/lola

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

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