mergeMethSegs


    A <code><a rd-options="" href="/link/methData?package=segmentSeq&version=2.6.0" data-mini-rdoc="segmentSeq::methData">methData</a></code> object defining the loci to be merged.
  

segs


    An <code><a rd-options="" href="/link/alignmentMeth?package=segmentSeq&version=2.6.0" data-mini-rdoc="segmentSeq::alignmentMeth">alignmentMeth</a></code> object from which the loci have been derived.
  


    The maximum gap below which neighbouring loci may be merged.
  


Within a region of cytosine methylation, there may be some cytosines
which show no evidence of methylation. The presence of these cytosines
may lead to the region being split into multiple methylation loci. This
function merges neighbouring loci if the pattern of expression is the
same in each locus, and if they are not separated by too great a genomic
distance.


manip

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.

Thomas J Hardcastle

segmentSeq

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

mergeMethSegs function

A <code><a href="methData" rd-options="">methData</a></code> object defining the loci to be merged.

An <code><a href="alignmentMeth" rd-options="">alignmentMeth</a></code> object from which the loci have been derived.

The maximum gap below which neighbouring loci may be merged.

Within a region of cytosine methylation, there may be some cytosines
which show no evidence of methylation. The presence of these cytosines
may lead to the region being split into multiple methylation loci. This
function merges neighbouring loci if the pattern of expression is the
same in each locus, and if they are not separated by too great a genomic
distance.

mergeMethSegs: Merges neighbouring methylation loci with the same pattern of expression.

Description

Usage

Arguments

Value

See Also