regioneR: Association analysis of genomic regions based on permutation tests
Version 1.8.0

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

Browse man pages Browse package API and functions Browse package files

AuthorAnna Diez-Villanueva <adiez@imppc.org>, Roberto Malinverni <rmalinverni@carrerasresearch.org> and Bernat Gel <bgel@imppc.org>
Bioconductor views ChIPSeq CopyNumberVariation DNASeq Genetics MethylSeq
Date of publicationNone
MaintainerBernat Gel <bgel@imppc.org>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("regioneR")

Man pages

characterToBSGenome: characterToBSGenome
circularRandomizeRegions: Circular Randomize Regions
commonRegions: Common Regions
createFunctionsList: Create Functions List
createRandomRegions: Create Random Regions
emptyCacheRegioneR: Empty Cache regioneR
extendRegions: Extend Regions
filterChromosomes: filterChromosomes
getChromosomesByOrganism: getChromosomesByOrganism
getGenome: getGenome
getGenomeAndMask: getGenomeAndMask
getMask: getMask
joinRegions: Join Regions
listChrTypes: filterChromosomes listChrTypes
localZScore: Local z-score
maskFromBSGenome: maskFromBSGenome
meanDistance: Mean Distance
meanInRegions: Mean In Regions
mergeRegions: Merge Regions
numOverlaps: Number Of Overlaps
overlapGraphicalSummary: Overlap Graphical Summary
overlapPermTest: Permutation Test for Overlap
overlapRegions: Overlap Regions
permTest: Permutation Test
plot.localZScoreResults: Plot localZscore results
plot.localZScoreResultsList: Plot a list of localZscore results
plot.permTestResults: Function for plotting the results from a 'permTestResults'...
plot.permTestResultsList: Function for plotting the results from a...
plotRegions: Plot Regions
print.permTestResults: Print permTestResults objects
randomizeRegions: Randomize Regions
recomputePermTest: Recompute Permutation Test
resampleRegions: Resample Regions
splitRegions: Split Regions
subtractRegions: Subtract Regions
summary.permTestResults: Summary of permTestResults objects
summary.permTestResultsList: Summary of permTestResultsList objects
toDataframe: toDataframe
toGRanges: toGRanges
uniqueRegions: Unique Regions

Functions

Curry Source code
characterToBSGenome Man page
circularRandomizeRegions Man page Source code
commonRegions Man page Source code
copySeqLevels Source code
createFunctionsList Man page Source code
createRandomRegions Man page Source code
emptyCacheRegioneR Man page Source code
extendRegions Man page Source code
filterChromosomes Man page Source code
getChromosomesByOrganism Man page Source code
getGenome Man page
getGenomeAndMask Man page
getMask Man page
joinRegions Man page Source code
listChrTypes Man page Source code
localZScore Man page Source code
maskFromBSGenome Man page
meanDistance Man page Source code
meanInRegions Man page Source code
mergeRegions Man page Source code
numOverlaps Man page Source code
overlapGraphicalSummary Man page Source code
overlapPermTest Man page Source code
overlapRegions Man page Source code
permTest Man page Source code
plot.localZScoreResults Man page Source code
plot.localZScoreResultsList Man page Source code
plot.permTestResults Man page Source code
plot.permTestResultsList Man page Source code
plotRegions Man page Source code
print.permTestResults Man page Source code
private_randomizeRegions Source code
randomizeFastWithNoOverlappingControl Source code
randomizeRegions Man page Source code
recomputePermTest Man page Source code
removeOverlapping Source code
resampleRegions Man page Source code
spinChromosome Source code
splitRegions Man page Source code
subtractRegions Man page Source code
summary.permTestResults Man page Source code
summary.permTestResultsList Man page Source code
toDataframe Man page Source code
toGRanges Man page Source code
uniqueRegions Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/characterToBSGenome.R
R/circularRandomizeRegions.R
R/commonRegions.R
R/createFunctionsList.R
R/createRandomRegions.R
R/emptyCacheRegioneR.R
R/extendRegions.R
R/filterChromosomes.R
R/getChromosomesByOrganism.R
R/getGenome.R
R/getGenomeAndMask.R
R/getMask.R
R/joinRegions.R
R/listChrTypes.R
R/localZScore.R
R/maskFromBSGenome.R
R/meanDistance.R
R/meanInRegions.R
R/mergeRegions.R
R/numOverlaps.R
R/overlapGraphicalSummary.R
R/overlapPermTest.R
R/overlapRegions.R
R/permTest.R
R/plot.localZScoreResults.R
R/plot.localZScoreResultsList.R
R/plot.permTestResults.R
R/plot.permTestResultsList.R
R/plotRegions.R
R/print.permTestResults.R
R/randomizeRegions.R
R/recomputePermTest.R
R/resampleRegions.R
R/splitRegions.R
R/subtractRegions.R
R/summary.permTestResults.R
R/summary.permTestResultsList.R
R/toDataframe.R
R/toGRanges.R
R/uniqueRegions.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/regioneR.R
inst/doc/regioneR.Rnw
inst/doc/regioneR.pdf
inst/extdata
inst/extdata/all.genes.bed
inst/extdata/my.altered.regions.bed
inst/extdata/my.special.genes.bed
man
man/characterToBSGenome.Rd
man/circularRandomizeRegions.Rd
man/commonRegions.Rd
man/createFunctionsList.Rd
man/createRandomRegions.Rd
man/emptyCacheRegioneR.Rd
man/extendRegions.Rd
man/filterChromosomes.Rd
man/getChromosomesByOrganism.Rd
man/getGenome.Rd
man/getGenomeAndMask.Rd
man/getMask.Rd
man/joinRegions.Rd
man/listChrTypes.Rd
man/localZScore.Rd
man/maskFromBSGenome.Rd
man/meanDistance.Rd
man/meanInRegions.Rd
man/mergeRegions.Rd
man/numOverlaps.Rd
man/overlapGraphicalSummary.Rd
man/overlapPermTest.Rd
man/overlapRegions.Rd
man/permTest.Rd
man/plot.localZScoreResults.Rd
man/plot.localZScoreResultsList.Rd
man/plot.permTestResults.Rd
man/plot.permTestResultsList.Rd
man/plotRegions.Rd
man/print.permTestResults.Rd
man/randomizeRegions.Rd
man/recomputePermTest.Rd
man/resampleRegions.Rd
man/splitRegions.Rd
man/subtractRegions.Rd
man/summary.permTestResults.Rd
man/summary.permTestResultsList.Rd
man/toDataframe.Rd
man/toGRanges.Rd
man/uniqueRegions.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_evaluationFunctions.R
tests/testthat/test_genomesAndMasks.R
tests/testthat/test_numOverlaps.R
tests/testthat/test_permTest.R
tests/testthat/test_randomizationFunctions.R
vignettes
vignettes/figures
vignettes/figures/Example1_fig1.pdf
vignettes/figures/Example2_fig1.pdf
vignettes/figures/Example2_fig2.pdf
vignettes/figures/Example2_fig3.pdf
vignettes/figures/Example2_fig4.pdf
vignettes/figures/mask_test_regioneR_small.pdf
vignettes/figures/regular_genes_5000perm.pdf
vignettes/figures/special_genes_5000perm.pdf
vignettes/figures/speed_test_regioneR_small.pdf
vignettes/regioneR.Rnw
regioneR documentation built on May 20, 2017, 9:37 p.m.