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regioneR (version 1.4.0)

Association analysis of genomic regions based on permutation tests

Description

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

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Version

Version

1.4.0

License

Artistic-2.0

Maintainer

Bernat Gel

Last Published

February 15th, 2017

Functions in regioneR (1.4.0)

getChromosomesByOrganism

getChromosomesByOrganism

characterToBSGenome

characterToBSGenome

createFunctionsList

Create Functions List

createRandomRegions

Create Random Regions

filterChromosomes

filterChromosomes

emptyCacheRegioneR

Empty Cache regioneR

circularRandomizeRegions

Circular Randomize Regions

getGenomeAndMask

getGenomeAndMask

Number Of Overlaps

maskFromBSGenome

maskFromBSGenome

Mean In Regions

filterChromosomes listChrTypes

plot.permTestResults

Function for plotting the results from a permTestResults object.

overlapPermTest

Permutation Test for Overlap

overlapGraphicalSummary

Overlap Graphical Summary

plot.permTestResultsList

Function for plotting the results from a permTestResultsList object when more than one evaluation function was used.

Overlap Regions

Permutation Test

print.permTestResults

Print permTestResults objects

plot.localZScoreResults

Plot localZscore results

plot.localZScoreResultsList

Plot a list of localZscore results

subtractRegions

Subtract Regions

resampleRegions

Resample Regions

summary.permTestResults

Summary of permTestResults objects

summary.permTestResultsList

Summary of permTestResultsList objects

randomizeRegions

Randomize Regions

recomputePermTest

Recompute Permutation Test