Statistical Testing for ChIP-Seq data sets

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Documentation for package ‘MMDiff2’ version 1.36.0

• 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