segClass-class {segmentSeq} | R Documentation

## Class "segClass"

### Description

The `segClass` class contains data about potential segments on the genome.

### Objects from the class

Objects can be created by calls of the form `new("segClass", ..., 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.

### 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 `@data` slot.

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. `segData`, which inherits from this class. `segMeth`, which inherits from this class.

[Package segmentSeq version 2.28.0 Index]