SL9                     Example data selected from a set of Illumina
                        sequencing experiments.
alignmentClass-class    Class "alignmentClass"
alignmentData-class     Class "alignmentData"
alignmentMeth-class     Class "alignmentMeth"
averageMethylationRegions
                        Plots the average distribution of methylation
                        (taken from an alignmentMeth object) over a set
                        of coordinates (and optionally a surrounding
                        region).
classifySeg             A method for defining a genome segment map by
                        an empirical Bayesian classification method
findChunks              Identifies 'chunks' of data within a set of
                        aligned reads.
getCounts               Gets counts from alignment data from a set of
                        genome segments.
getOverlaps             Identifies overlaps between two sets of genomic
                        coordinates
heuristicSeg            A (fast) heuristic method for creation of a
                        genome segment map.
lociData-class          Class "lociData"
lociLikelihoods         Evaluates the posterior likelihoods of each
                        region defined by a segmentation map as a
                        locus.
mergeMethSegs           Merges neighbouring methylation loci with the
                        same pattern of expression.
methData-class          Class "methData"
plotGenome              Plots the alignment of sequence tags on the
                        genome given an 'aligmentData' object and
                        (optionally) a set of segments found.
plotMeth                Plots a map of cytosine methylation (and
                        optionally, methylation loci).
plotMethDistribution    Plots the distribution of methylation on the
                        genome.
processAD               Processes an 'alignmentData' or 'alignmentMeth'
                        object into a 'segData' or 'segMeth' object for
                        segmentation.
readGeneric             Functions for processing files of various
                        formats into an 'alignmentData' object.
readMeths               A function for reading data from the YAMA
                        methylation aligner (or similarly parsed data)
                        from which to identify methylation loci and/or
                        differentially methylated regions.
segClass-class          Class "segClass"
segData-class           Class "segData"
segMeth-class           Class "segMeth"
segmentSeq-package      Segmentation of the genome based on multiple
                        samples of high-throughput sequencing data.
