alignmentData-class     Class "alignmentData"
filterSegments          Filters an set of segments (given an ordering
                        on the segments) such that no segments overlap.
getCounts               Gets counts from alignment data from a set of
                        genome segments.
getPriors               Finds a set of priors for a 'segData' object.
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.
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.
segmentSequences        Takes the 'segData' object and uses it to
                        define segments on the genome.
