Methods for identifying small RNA loci from high-throughput sequencing data


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Documentation for package ‘segmentSeq’ version 1.2.0

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segmentSeq-package Segmentation of the genome based on multiple samples of high-throughput
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
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
processAD Processes an 'alignmentData' object into a 'segData' object for
processTags Convenience function for processing tab-delimited files in a certain
segData-class Class "segData"
segmentSeq Segmentation of the genome based on multiple samples of high-throughput
show-method Class "alignmentData"
show-method Class "segData"
similaritySeg Takes the 'segData' object and uses it to define segments on the
SL10 Example data selected from a set of Illumina sequencing experiments.
SL26 Example data selected from a set of Illumina sequencing experiments.
SL32 Example data selected from a set of Illumina sequencing experiments.
SL9 Example data selected from a set of Illumina sequencing experiments.
[-method Class "alignmentData"
[-method Class "segData"