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

## Documentation for package ‘segmentSeq’ version 2.18.0

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

## Help Pages

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"