# Statistical Testing for ChIP-Seq data sets

## Documentation for package ‘MMDiff2’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

Cfp1-Peaks | Peaks for Cfp1-data set
compDists | Compute distances between Peaks
compHists | Compute Peak histograms
compPvals | compute p-values
Contrast | Generics for DBAmmd-Class
Contrast-method | Extract data from DBAmmd objects
Counts | Generics for DBAmmd-Class
Counts-method | Extract data from DBAmmd objects
DBAmmd | Class DBAmmd
DBAmmd-Accessors | Extract data from DBAmmd objects
DBAmmd-class | Class DBAmmd
Dists | Generics for DBAmmd-Class
Dists-method | Extract data from DBAmmd objects
estimateFragmentCenters | estimate center of fragments
Genome | Generics for DBAmmd-Class
Genome-method | Extract data from DBAmmd objects
getPeakReads | Get reads from indexed bam files for defined regions
Hists | Generics for DBAmmd-Class
Hists-method | Extract data from DBAmmd objects
metaData | Generics for DBAmmd-Class
metaData-method | Extract data from DBAmmd objects
mm9-Genes | mm9-Genes
MMD | DBAmmd Object for Cfp1 example
numPeaks | Generics for DBAmmd-Class
numPeaks-method | Extract data from DBAmmd objects
numSamples | Generics for DBAmmd-Class
numSamples-method | Extract data from DBAmmd objects
plotDists | plotDists
plotDISTS4Peak | plotDISTS4Peak
plotPeak | plot Peak
Reads | Generics for DBAmmd-Class
Reads-method | Extract data from DBAmmd objects
Regions | Generics for DBAmmd-Class
Regions-method | Extract data from DBAmmd objects
reportResults | report results
runShinyMMDiff2 | Shiny Application for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks
Samples | Generics for DBAmmd-Class
Samples-method | Extract data from DBAmmd objects
server.MMDiff2 | Shiny server code for interactive visualization of MMD distances, peak plots, and MMD distances by sample.
setContrast | Generics for DBAmmd-Class
setContrast-method | Extract data from DBAmmd objects
setRegions | Generics for DBAmmd-Class
setRegions-method | Extract data from DBAmmd objects
ui.MMDiff2 | ui component for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks