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MMDiff2 (version 1.0.2)

Statistical Testing for ChIP-Seq data sets

Description

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

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Version

Version

1.0.2

License

Artistic-2.0

Maintainer

Gabriele Schweikert

Last Published

February 15th, 2017

Functions in MMDiff2 (1.0.2)

estimateFragmentCenters

estimate center of fragments
Cfp1-Peaks

Peaks for Cfp1-data set
compDists

Compute distances between Peaks
MMD

DBAmmd Object for Cfp1 example
compPvals

compute p-values
ui.MMDiff2

ui component for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks
getPeakReads

Get reads from indexed bam files for defined regions
plotDISTS4Peak

plotDISTS4Peak
runShinyMMDiff2

Shiny Application for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks
DBAmmd-class

Class DBAmmd
reportResults

report results
server.MMDiff2

Shiny server code for interactive visualization of MMD distances, peak plots, and MMD distances by sample.
DBAmmd-Accessors

Extract data from DBAmmd objects
plotPeak

plot Peak
plotDists

plotDists
compHists

Compute Peak histograms
metaData

Generics for DBAmmd-Class
mm9-Genes

mm9-Genes