calculateRPM            calculate read per million (RPM)
contrCoverage           Get the coverage for 3C-seq data from the
                        control
contrInteractionRegions
                        get interaction regions from the control
contrRPM                get read per million (RPM) for the control
enzyme.db               Rebase The Restriction Enzyme Database
expCoverage             Get the coverage for 3C-seq data from the
                        experiment
expInteractionRegions   get interaction regions from the experiment
expRPM                  get read per million (RPM) for the experiment
export3Cseq2bedGraph    export interaction regions to the 'bedGraph'
                        format
exportInteractions2text
                        export interaction regions to the tab separated
                        format
generate3CseqReport     generate reports for analysis results from
                        r3Cseq
getCoverage             Coverage for 3C-seq data
getInteractions         assign p-value and fold change to candidate
                        interaction regions
getReadCountPerRestrictionFragment
                        get read count per restriction fragment for
                        3C-seq data
getViewpoint            get the viewpoint of 3C-seq data
my.data                 a simple example of r3Cseq object
plot3Cecdf              Plot the empirical distribution of interaction
                        regions
plotInteractionsNearViewpoint
                        Plot candidate interaction regions near the
                        viewpoint
plotInteractionsPerChromosome
                        Plot interaction regions per each chromosome of
                        interest
plotOverviewInteractions
                        Plot the overview of interaction regions for
                        the genome-wide
r3Cseq-class            r3Cseq objects
