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segmentSeq (version 2.6.0)

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

Description

High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.

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Version

Version

2.6.0

License

GPL-3

Maintainer

Thomas J Hardcastle

Last Published

February 15th, 2017

Functions in segmentSeq (2.6.0)

alignmentMeth-class

Class "alignmentMeth"

Class "methData"

alignmentData-class

Class "alignmentData"

Class "lociData"

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).

Class "segClass"

plotMethDistribution

Plots the distribution of methylation on the genome.

Identifies overlaps between two sets of genomic coordinates

Identifies `chunks' of data within a set of aligned reads.

Merges neighbouring methylation loci with the same pattern of expression.

A (fast) heuristic method for creation of a genome segment map.

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.

Processes an `alignmentData' or `alignmentMeth' object into a `segData' or `segMeth' object for segmentation.

Summarise the expected number of loci in a `lociData' object.

alignmentClass-class

Class "alignmentClass"

Plots a map of cytosine methylation (and optionally, methylation loci).

Class "segMeth"

Functions for processing files of various formats into an `alignmentData' object.

Class "segData"

Gets counts from alignment data from a set of genome segments.

segmentSeq-package

Segmentation of the genome based on multiple samples of high-throughput sequencing data.

A method for defining a genome segment map by an empirical Bayesian classification method

Example data selected from a set of Illumina sequencing experiments.

Plots the alignment of sequence tags on the genome given an `aligmentData' object and (optionally) a set of segments found.

Filters a `lociData' object based on given selection criteria.

lociLikelihoods

Evaluates the posterior likelihoods of each region defined by a segmentation map as a locus.