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 |