Data4Cseq               Creating a Data4Cseq object
Data4Cseq-class         Class '"Data4Cseq"'
checkRestrictionEnzymeSequence
                        Remove invalid 4C-seq reads from a SAM file
chooseNearCisFragments
                        Choose fragments in a provided region around
                        the viewpoint
createVirtualFragmentLibrary
                        Create a virtual fragment library from a
                        provided genome and two restriction enzymes
drawDigestionFragmentHistogram
                        Visualize digestion fragments with a histogram
drawHeatmap             Draw a heatmap-like multi-scale contact profile
exportVisualizationFragmentData
                        Export near-cis fragment data of a 'Data4Cseq'
                        object
getReadDistribution     Calculate the read distribution for a 4C-seq
                        experiment
giveEnzymeSequence      Provide the corresponding enzyme sequence for
                        an enzyme name
importVisualizationFragmentData
                        Import visualization data from a file
liverData               Example 4C-seq data set of fetal liver data
liverDataRaw            Example 4C-seq data set of fetal liver data
normalizeFragmentData   Normalize near-cis fragment data read count
plotTransInteractions   Visualize trans interaction intervals
prepare4CseqData        Alignment and filtering of raw 4C-seq data
printBEDFragmentLibrary
                        Print a BED-file fragment library
printWigFile            Print a wig file from 4C-seq read data
readPointsOfInterestFile
                        Read a file with coordinates of marker points
readsToFragments        Determine fragment coverage of a 4C-seq
                        fragment library
simulateDigestion       Simulate the digestion of a genome
visualizeViewpoint      Draw a near-cis coverage plot for 4C-seq data
