Takes high-throughput sequencing data and uses it to define segments of the genome to which a high density of reads align.

Documentation for package ‘segmentSeq’ version 1.0.1

segmentSeq-package	Segmentation of the genome based on multiple samples of high-throughput sequencing data.
alignmentData	Class "alignmentData"
alignmentData-class	Class "alignmentData"
dim-method	Class "alignmentData"
dim-method	Class "segData"
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.
initialize-method	Class "alignmentData"
initialize-method	Class "segData"
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	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.
show-method	Class "alignmentData"
show-method	Class "segData"
[-method	Class "alignmentData"
[-method	Class "segData"