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

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Documentation for package ‘segmentSeq’ version 1.6.2

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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 Class "lociData"
dim-method Class "segData"
findChunks Identifies 'chunks' of data within a set of aligned reads.
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"
lociData Class "lociData"
lociData-class Class "lociData"
lociLikelihoods Evaluates the posterior likelihoods of each region defined by a segmentation map as a locus.
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.
readBAM Functions for processing files of various formats into an 'alignmentData' object.
readGeneric Functions for processing files of various formats 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 Class "lociData"
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 Class "lociData"
[-method Class "segData"