FourC                   FourC-class
addFragments            Add the restriction fragment information
addPeaks                Add peaks based on z-scores and adjusted
                        p-values
addViewpointFrags       Add the information of the viewpoint fragments
combineFragEnds         Combine the counts of both fragment ends.
countFragmentOverlaps   Count fragment overlaps
countFragmentOverlapsSecondCutter
                        Count fragment overlaps when sequencing was
                        performed from the second cutting site
distFitMonotone         Fit the distance dependency
distFitMonotoneSymmetric
                        Fit the distance dependency
fc                      FourC object with counts
fcf                     FourC object with z-scores
findViewpointFragments
                        Find the fragments to which the viewpoint
                        primers map.
getAllResults           FourCSeq analysis results
getDifferences          Detect differences
getDistAroundVp         getDistAroundVp
getNormalizationFactors
                        Get normalization factors for each fragment
getReferenceSeq         Function to read reference sequences
getZScores              Calculate z-scores using the residuals of the
                        general trend fit.
normalizeRPM            Normalize count data to rpm
plotDifferences         Plot differences
plotFits                Plot fit results.
plotNormalizationFactors
                        Plot the estimated normalization factors.
plotScatter             plotScatter
plotZScores             Plot z-score results.
smoothCounts            Smooth the counts of neighboring fragments
smoothHitPerCent        Smooth the hits of neighboring fragments
writeTrackFiles         Write track files of an selected 'assay'
