SL9                     Example data selected from a set of Illumina
                        sequencing experiments.
alignmentData-class     Class "alignmentData"
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.
plotGenome              Plots the alignment of sequence tags on the
                        genome given an 'aligmentData' object and
                        (optionally) a set of segments found.
processAD               Processes an 'alignmentData' object into a
                        'segData' object for segmentation.
readGeneric             Functions for processing files of various
                        formats into an 'alignmentData' object.
segData-class           Class "segData"
segmentSeq-package      Segmentation of the genome based on multiple
                        samples of high-throughput sequencing data.
