aggregatePeaks          Aggregate Interactions to Interaction Peaks
aggregatePeaks_regions
                        Aggregate Interactions to Interaction Peaks by
                        Distance in bp
annotateInts            Annotate Interactions
baitmap2baited_genes    Convert baitmap to baited_genes
boxplotsCapC            Boxplots of summarized interactions data.
getMatrix               Create Interaction Matrices
loadCdList              Loads List with Interaction Tables
loadGrl                 Load Intervals into a GenomicRangesList
makeBedGraphs           Create Bedgraphs From ChicagoData
makeIntsTable           Create Interactions Table
makeOneGeneOnePeak      Make one-Gene-one-Peak Interaction Tables.
makeQCplots             Quality Control Plots
plotAggregatePeaks      Plot Aggregate Interaction Profiles
plotInteractions        Plot Lineplots of Interactions
plotSigIntsStats        Plot Interaction Statistics
quantifyWithinPeaks     Quantification of Reads and Scores within
                        oneGeneOnePeak or AggregatedPeak Interactions.
rmap2rmapgr             Convert .rmap to the GenomicRanges object
                        'rmapgr'
runChicagoForPostChicago
                        Run Chicago and save ChicagoData objects.
