MEDIPS-package          MeDIP-Seq data analysis
MEDIPS.CpGenrich        Calculates the enrichment of provided CpG rich
                        regions compared to the reference genome.
MEDIPS.annotate         Funtion to annotate given genomic coordinates.
MEDIPS.calibrationCurve
                        Function that calculates the calibration curve
MEDIPS.couplingVector   Calculates the sequence pattern densities for
                        genome wide bins.
MEDIPS.coverageAnalysis
                        The function identifies the number of CpGs (or
                        any other predefined sequence pattern) covered
                        by the given short reads.
MEDIPS.exportWIG        Exports reads per million, relative methylation
                        score or sequence pattern density into a wiggle
                        file.
MEDIPS.genomeVector     Calculates the genome wide short read coverage
                        on a user specified resolution
MEDIPS.getPositions     Identifies genomic sequence pattern positions
                        within the reference genome.
MEDIPS.mergeFrames      Merges genomic coordinates of overlapping
                        frames into one supersized frame
MEDIPS.methylProfiling
                        Funtion calculates mean methylation values
                        (rpm, rms) and ams values, ratios, variances,
                        and pvalues comparing two MEDIPS SETs for user
                        supplied regions of interests (ROIs) or genome
                        wide frames.
MEDIPS.normalize        Function that normalizes raw signals by local
                        sequence pattern (e.g. CpG) densities.
MEDIPS.plotCalibrationPlot
                        Plots the results of the
                        MEDIPS.calibrationCurve function.
MEDIPS.plotCoverage     Function plots the results of the
                        MEDIPS.coverageAnalysis function.
MEDIPS.plotSaturation   Function plots the results of the
                        MEDIPS.saturationAnalysis function.
MEDIPS.readAlignedSequences
                        Creates a MEDIPS SET by reading a suitable
                        input file
MEDIPS.saturationAnalysis
                        Function calculates the
                        saturation/reproducibility of the provided
                        MeDIP-Seq data.
MEDIPS.selectSignificants
                        Selects candidate ROIs that show significant
                        differential methylation between two MEDIPS
                        SETs.
MEDIPSset-class         Class "MEDIPSset"
