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

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Documentation for package ‘segmentSeq’ version 2.42.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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segmentSeq-package	Segmentation of the genome based on multiple samples of high-throughput sequencing data.
alignmentClass	Class "alignmentClass"
alignmentClass-class	Class "alignmentClass"
alignmentData	Class "alignmentData"
alignmentData-class	Class "alignmentData"
alignmentMeth	Class "alignmentMeth"
alignmentMeth-class	Class "alignmentMeth"
averageProfiles	Computes and plots the average distribution of aligned reads (taken from an alignmentData object) or methylation (taken from an alignmentMeth object) over a set of coordinates (and optionally the surrounding regions).
c-method	Class "lociData"
cbind-method	Class "alignmentClass"
cbind-method	Class "alignmentData"
cbind-method	Class "alignmentMeth"
classifySeg	A method for defining a genome segment map by an empirical Bayesian classification method
dim-method	Class "alignmentClass"
dim-method	Class "alignmentData"
dim-method	Class "alignmentMeth"
dim-method	Class "lociData"
dim-method	Class "methData"
dim-method	Class "segClass"
dim-method	Class "segData"
dim-method	Class "segMeth"
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
givenExpression	Adjusts posterior likelihoods of differential expression by the likelihood that a locus is expressed.
heuristicSeg	A (fast) heuristic method for creation of a genome segment map.
hSL	Preprocessed 'lociData' object containing likelihoods of methylation at each locus.
initialize-method	Class "alignmentClass"
initialize-method	Class "alignmentData"
initialize-method	Class "alignmentMeth"
initialize-method	Class "segClass"
initialize-method	Class "segData"
initialize-method	Class "segMeth"
lociData	Class "lociData"
lociData-class	Class "lociData"
lociLikelihoods	Evaluates the posterior likelihoods of each region defined by a segmentation map as a locus.
mergeMethSegs	Merges neighbouring methylation loci with the same pattern of expression.
methData	Class "methData"
methData-class	Class "methData"
normaliseNC	A function providing adjustment of cytosine methylated/unmethylated counts based on a nonconversion rate.
plotAverageProfile	Computes and plots the average distribution of aligned reads (taken from an alignmentData object) or methylation (taken from an alignmentMeth object) over a set of coordinates (and optionally the surrounding regions).
plotGenome	Plots the alignment of sequence tags on the genome given an 'aligmentData' object and (optionally) a set of segments found.
plotMeth	Plots a map of cytosine methylation (and optionally, methylation loci).
plotMethDistribution	Plots the distribution of methylation on the genome.
processAD	Processes an 'alignmentData' or 'alignmentMeth' object into a 'segData' or 'segMeth' 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.
readMeths	A function for reading data from the YAMA methylation aligner (or similarly parsed data) from which to identify methylation loci and/or differentially methylated regions.
segClass	Class "segClass"
segClass-class	Class "segClass"
segData	Class "segData"
segData-class	Class "segData"
segmentSeq	Segmentation of the genome based on multiple samples of high-throughput sequencing data.
segMeth	Class "segMeth"
segMeth-class	Class "segMeth"
selectLoci	Filters a 'lociData' object based on given selection criteria.
show-method	Class "alignmentClass"
show-method	Class "alignmentData"
show-method	Class "alignmentMeth"
show-method	Class "lociData"
show-method	Class "methData"
show-method	Class "segClass"
show-method	Class "segData"
show-method	Class "segMeth"
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.
summariseLoci	Summarise the expected number of loci in a 'lociData' object.
thresholdFinder	Determines threshold for the proportion of methylation at which a methylation locus may be identified.
[-method	Class "alignmentClass"
[-method	Class "alignmentData"
[-method	Class "alignmentMeth"
[-method	Class "lociData"
[-method	Class "methData"
[-method	Class "segClass"
[-method	Class "segData"
[-method	Class "segMeth"