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


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Documentation for package ‘segmentSeq’ version 1.0.1

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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"