segMeth-class: Class "segMeth"

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

Description

The segMeth class inherits from the segClass class and contains data about potential segments on the genome, together with counts for each of those segments.

Objects from the class

Objects can be created by calls of the form new("segMeth", ..., seglens). However, more usually they will be created by calling the processAD function.

Slots

coordinates:

A GRanges object defining the coordinates of the segments.

replicates:

Object of class "factor". The replicate structure for the samples.

locLikelihoods:

Object of class "DataFrame" describing estimated likelihoods that each region defined in ‘coordinates’ is a locus in each replicate group.

Cs:

Object of class matrix. Contains the number of methylated cytosines (which are sequenced as a ‘C’) observed for each sample in each potential segment.

Ts:

Object of class matrix. Contains the number of unmethylated cytosines (which are sequenced as a ‘T’) observed for each sample in each potential segment.

nonconversion:

Object of class "numeric". The (estimated) nonconversion rate (see Details) for each of the libraries.

Details

The @coordinates slot contains information on each of the potential segments; specifically, chromosome, start and end of the segment, together. Each row of the @coordinates slot should correspond to the same row of the @C and @T slots.

The nonconversion slot is an estimate of the rate (for each library) at which an unmethylated cytosine has failed to be converted by sodium bisulphite treatment into thymine, and is thus recorded (incorrectly) as methylated. In some cases, this can be estimated from considering observed methylation rates on regions known to be unmethylated (e.g., chloroplasts) or by introducing unmethylated control sequences.

In almost all cases objects of this class should be produced by the processAD function.

Methods

Methods 'new', 'dim', '[' and 'show' have been defined for this class.

Author(s)

Thomas J. Hardcastle

See Also

processAD, the function that will most often be used to create objects of this class. segClass, from which this class inherits.

segmentSeq documentation built on Nov. 8, 2020, 5:18 p.m.