segMeth-class {segmentSeq} | R Documentation

## Class "segMeth"

### 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.

[Package segmentSeq version 2.28.0 Index]