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

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Documentation for package ‘segmentSeq’ version 2.10.0

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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).
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.
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"