SL9                     Example data selected from a set of Illumina
                        sequencing experiments.
alignmentClass-class    Class "alignmentClass"
alignmentData-class     Class "alignmentData"
alignmentMeth-class     Class "alignmentMeth"
averageProfiles         Computes and plots the average distribution of
                        aligned reads (taken from an alignmentData
                        object) or methylation (taken from an
                        alignmentMeth object) over a set of coordinates
                        (and optionally the surrounding regions).
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
givenExpression         Adjusts posterior likelihoods of differential
                        expression by the likelihood that a locus is
                        expressed.
hSL                     Preprocessed 'lociData' object containing
                        likelihoods of methylation at each locus.
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"
normaliseNC             A function providing adjustment of cytosine
                        methylated/unmethylated counts based on a
                        nonconversion rate.
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.
selectLoci              Filters a 'lociData' object based on given
                        selection criteria.
summariseLoci           Summarise the expected number of loci in a
                        'lociData' object.
thresholdFinder         Determines threshold for the proportion of
                        methylation at which a methylation locus may be
                        identified.
