COUPLINGset-class       COUPLINGset class and internal functions
MEDIPS-package          (MeD)IP-seq data analysis
MEDIPS.CpGenrich        Calculates CpG enrichment of provided short
                        reads compared to the reference genome.
MEDIPS.addCNV           Function to run a copy number variation
                        analysis.
MEDIPS.correlation      Calculates pairwise Pearson correlations
                        between provided MEDIPS SETs
MEDIPS.couplingVector   Calculates the sequence pattern densities at
                        genome wide windows.
MEDIPS.createROIset     Creates a MEDIPS ROI SET by reading a suitable
                        input file
MEDIPS.createSet        Creates a MEDIPS SET by reading a suitable
                        input file
MEDIPS.exportWIG        Exports count, rpkm, or sequence pattern
                        densities into a wiggle file.
MEDIPS.getAnnotation    Funtion to fetch annotations from biomaRt.
MEDIPS.mergeFrames      Merges genomic coordinates of neighboring
                        windows into one supersized window
MEDIPS.mergeSets        Creates one merged MEDIPS SET out of two.
MEDIPS.meth             Funtion summarizes coverage profiles for given
                        MEDIPS SETs and allows to calculate differental
                        coverage and copy number vartiation, if
                        applicable.
MEDIPS.plotCalibrationPlot
                        Creates the calibration plot.
MEDIPS.plotSaturation   Function plots the results of the
                        MEDIPS.saturationAnalysis function.
MEDIPS.plotSeqCoverage
                        Function plots the results of the
                        MEDIPS.seqCoverage function.
MEDIPS.saturation       Function calculates the
                        saturation/reproducibility of the provided
                        IP-Seq data.
MEDIPS.selectROIs       Selects row-wise subsets of a result table as
                        returned by the MEDIPS.meth function.
MEDIPS.selectSig        Selects windows which show significant
                        differential coverage between two MEDIPS SETs
                        from a resultTable (as returned by the function
                        MEDIPS.meth).
MEDIPS.seqCoverage      The function identifies the number of CpGs (or
                        any other predefined sequence pattern) covered
                        by the given short reads.
MEDIPS.setAnnotation    Funtion to annotate a matrix of genomic
                        coordinates (i.e. a result table) by a given
                        annotation object.
MEDIPSroiSet-class      MEDIPSroiSet class and internal functions
MEDIPSset-class         MEDIPSset class and internal functions