LOLA: Location overlap analysis for enrichment of genomic ranges
Version 1.6.0

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.

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AuthorNathan Sheffield <http://www.databio.org> [aut, cre], Christoph Bock [cre]
Bioconductor views ChIPSeq FunctionalGenomics GeneRegulation GeneSetEnrichment GenomeAnnotation MethylSeq Sequencing SystemsBiology
Date of publicationNone
MaintainerNathan Sheffield <nathan@code.databio.org>
LicenseGPL-3
Version1.6.0
URL http://databio.org/lola
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("LOLA")

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...

Functions

LOLA Man page
LOLA-package Man page
buildRestrictedUniverse Man page Source code
checkUniverseAppropriateness Man page Source code
cleanws Man page Source code
countFileLines Source code
countOverlapsAny Source code
countOverlapsAnyRev Man page Source code
countOverlapsRev Source code
dtToGr Source code
dtToGrInternal Source code
enforceEdgeCharacter Source code
enforceTrailingSlash Source code
extractEnrichmentOverlaps Man page Source code
getRegionSet Man page Source code
lapplyAlias Man page Source code
listRegionSets Man page Source code
listToGRangesList Man page Source code
loadRegionDB Man page Source code
mergeRegionDBs Man page Source code
nlist Man page Source code
readBed Man page Source code
readCollection Man page Source code
readCollectionAnnotation Man page Source code
readCollectionFiles Man page Source code
readRegionGRL Man page Source code
readRegionSetAnnotation Man page Source code
redefineUserSets Man page Source code
replaceFileExtension Man page Source code
runLOLA Man page Source code
sampleGRL Man page Source code
setLapplyAlias Man page Source code
setSharedDataDir Man page Source code
splitDataTable Man page Source code
splitFileIntoCollection Man page Source code
userSets Man page
userUniverse Man page
write.tsv Man page Source code
writeCombinedEnrichment Man page Source code
writeDataTableSplitByColumn Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/LOLA.R
R/calcLocEnrichment.R
R/data.R
R/examples
R/examples/example.R
R/examples/example2.R
R/loadRegionDB.R
R/postEnrichment.R
R/splitFileIntoCollection.R
R/utility.R
README.md
build
build/vignette.rds
data
data/sample_input.RData
data/sample_universe.RData
inst
inst/CITATION
inst/doc
inst/doc/choosingUniverse.R
inst/doc/choosingUniverse.Rmd
inst/doc/choosingUniverse.html
inst/doc/gettingStarted.R
inst/doc/gettingStarted.Rmd
inst/doc/gettingStarted.html
inst/doc/usingLOLACore.R
inst/doc/usingLOLACore.Rmd
inst/doc/usingLOLACore.html
inst/extdata
inst/extdata/examples
inst/extdata/examples/combined_regions.bed
inst/extdata/hg19
inst/extdata/hg19/ucsc_example
inst/extdata/hg19/ucsc_example/collection.txt
inst/extdata/hg19/ucsc_example/index.txt
inst/extdata/hg19/ucsc_example/regions
inst/extdata/hg19/ucsc_example/regions/cpgIslandExt.bed
inst/extdata/hg19/ucsc_example/regions/laminB1Lads.bed
inst/extdata/hg19/ucsc_example/regions/numtSAssembled.bed
inst/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed
inst/extdata/hg19/ucsc_example/regions/vistaEnhancers_colNames.bed
inst/extdata/hg19/ucsc_example/sizes.txt
inst/extdata/multi
inst/extdata/multi/collection1
inst/extdata/multi/collection1/collection.txt
inst/extdata/multi/collection1/index.txt
inst/extdata/multi/collection1/regions
inst/extdata/multi/collection1/regions/cpgIslandExt.bed
inst/extdata/multi/collection1/regions/laminB1Lads.bed
inst/extdata/multi/collection1/regions/vistaEnhancers.bed
inst/extdata/multi/collection1/sizes.txt
inst/extdata/multi/collection2
inst/extdata/multi/collection2/index.txt
inst/extdata/multi/collection2/regions
inst/extdata/multi/collection2/regions/cpgIslandExt.bed
inst/extdata/multi/collection2/regions/laminB1Lads.bed
inst/extdata/multi/collection2/regions/vistaEnhancers.bed
inst/extdata/multi/collection2/sizes.txt
inst/scripts
inst/scripts/LOLA
inst/web
inst/web/index.html
inst/web/webComponents
inst/web/webComponents/ajax-loader.gif
inst/web/webComponents/d3.min.js
inst/web/webComponents/gridstyle.css
man
man/LOLA.Rd
man/buildRestrictedUniverse.Rd
man/checkUniverseAppropriateness.Rd
man/cleanws.Rd
man/countOverlapsAnyRev.Rd
man/extractEnrichmentOverlaps.Rd
man/getRegionSet.Rd
man/lapplyAlias.Rd
man/listRegionSets.Rd
man/listToGRangesList.Rd
man/loadRegionDB.Rd
man/mergeRegionDBs.Rd
man/nlist.Rd
man/readBed.Rd
man/readCollection.Rd
man/readCollectionAnnotation.Rd
man/readCollectionFiles.Rd
man/readRegionGRL.Rd
man/readRegionSetAnnotation.Rd
man/redefineUserSets.Rd
man/replaceFileExtension.Rd
man/runLOLA.Rd
man/sampleGRL.Rd
man/setLapplyAlias.Rd
man/setSharedDataDir.Rd
man/splitDataTable.Rd
man/splitFileIntoCollection.Rd
man/userSets.Rd
man/userUniverse.Rd
man/write.tsv.Rd
man/writeCombinedEnrichment.Rd
man/writeDataTableSplitByColumn.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_all.R
vignettes
vignettes/choosingUniverse.Rmd
vignettes/gettingStarted.Rmd
vignettes/usingLOLACore.Rmd
LOLA documentation built on May 20, 2017, 9:33 p.m.