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

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Documentation for package ‘segmentSeq’ version 1.4.0

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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"
cbind Class "alignmentData"
cbind-method Class "alignmentData"
classifySeg A method for defining a genome segment map by an empirical Bayesian classification method
dim-method Class "alignmentData"
dim-method baySeq - classes
dim-method Class "segData"
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.
initialize-method Class "alignmentData"
initialize-method Class "segData"
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 baySeq - classes
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 Segmentation of the genome based on multiple samples of high-throughput sequencing data.
show-method Class "alignmentData"
show-method baySeq - classes
show-method Class "segData"
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 baySeq - classes
[-method Class "segData"