Statistical Testing for ChIP-Seq data sets


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Documentation for package ‘MMDiff2’ version 1.12.0

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