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
filterSegments          Filters an set of segments (given an ordering
                        on the segments) such that no segments overlap.
findChunks              Identifies 'chunks' of data within an
                        'alignmentData' object.
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.
lociLikelihoods         Evaluates the posterior likelihoods of each
                        region defined by a segmentation map as a
                        locus.
mergeSD                 Merges multiple 'segData' objects.
plotGenome              Plots the alignment of sequence tags on the
                        genome given an 'aligmentData' object and
                        (optionally) a set of segments found.
postSeg-class           baySeq - classes
processAD               Processes an 'alignmentData' object into a
                        'segData' object for segmentation.
processTags             Convenience function for processing
                        tab-delimited files in a certain format into an
                        'alignmentData' object.
segData-class           Class "segData"
segmentSeq-package      Segmentation of the genome based on multiple
                        samples of high-throughput sequencing data.
