Myb_prom_FB             Myb_prom_FB a data set for the example of
                        r3Cseq analysis
Myb_prom_FL             Myb_prom_FL a data set for the example of
                        r3Cseq analysis
calculateBatchRPM       calculate read per million (RPM) for replicates
                        analysis
calculateRPM            calculate read per million (RPM)
contrCoverage           This method has been removed.
contrInteractionRegions
                        get interaction regions from the control
contrRPM                get read per million (RPM) for the control
contrRawData            Accessors for the 'contrRawData' slot of a
                        r3Cseq object.
contrReadCount          get read count per region for the control
enzymeDb                Rebase The Restriction Enzyme Database
expCoverage             This method has been removed.
expInteractionRegions   get interaction regions from the experiment
expRPM                  get read per million (RPM) for the experiment
expRawData              Accessors for the 'expRawData' slot of a r3Cseq
                        object.
expReadCount            get read count per region for the experiment
export3Cseq2bedGraph    export interaction regions to the 'bedGraph'
                        format
export3CseqRawReads2bedGraph
                        export the interaction signal from the raw
                        reads to the 'bedGraph' format
exportBatchInteractions2text
                        export identified interaction regions to the
                        tab separated format for replicates analysis
exportInteractions2text
                        export identified interaction regions to the
                        tab separated format
generate3CseqReport     generate reports for analysis results from
                        r3Cseq
getBatchInteractions    calculate z-score, assign p-value and q-value
                        for each interaction region for replicates data
                        sets
getBatchRawReads        Get aligned reads from the replicates BAM files
getBatchReadCountPerRestrictionFragment
                        count reads for replicates analysis
getBatchReadCountPerWindow
                        count reads per window size for replicates
                        analysis
getContrInteractionsInRefseq
                        identified significant interaction regions for
                        RefSeq genes
getCoverage             This method has been removed.
getExpInteractionsInRefseq
                        identified significant interaction regions for
                        RefSeq genes
getInteractions         calculate z-score, assign p-value and q-value
                        for each interaction region
getRawReads             Get aligned reads from the BAM file
getReadCountPerRestrictionFragment
                        count reads per resitrcition fragment
getReadCountPerWindow   count reads per window size
getViewpoint            get the viewpoint of 3C-seq data
hg18refGene             hg18's refGenes
hg19refGene             hg19's refGenes
mm10refGene             mm10's refGenes
mm9refGene              mm9's refGenes
plot3Cecdf              This method has been removed.
plotDomainogramNearViewpoint
                        Plot domainogram of interaction regions near
                        the viewpoint
plotInteractionsNearViewpoint
                        Plot identified interaction regions near the
                        viewpoint
plotInteractionsPerChromosome
                        Plot interaction regions per each chromosome of
                        interest
plotOverviewInteractions
                        Plot overview of identified interaction regions
                        for genome-wide
r3Cseq-class            r3Cseq objects
r3CseqCommon-class      r3CseqCommon objects
r3CseqInBatch-class     r3CseqInBatch objects
rn5refGene              rn5's refGenes
