R: Class '"ploidysuper"' and Subclasses

ploidysuper-class {polysat} | R Documentation

## Class `"ploidysuper"` and Subclasses

### Description

These classes contain ploidy data indexed by sample, locus, both, or neither. They are intended to go in the `Ploidies` slot of `"gendata"` objects.

### Objects from the Class

`"ploidysuper"` is a virtual class: No objects may be created from it.

Objects of the subclasses `"ploidymatrix"`, `"ploidysample"`, `"ploidylocus"`, and `"ploidyone"` can be created with the call `new(ploidyclass, samples, loci, ...)`, where `ploidyclass` is a character string of one of the class names, and `samples` and `loci` are character vectors naming samples and loci, respectively. The latter two arguments are optional depending on the class (whether ploidies are indexed by sample and/or locus). The typical user will not have to create an object in this way, because other functions in polysat will do it for you.

### Slots

`pld`:

  The only slot for objects of these classes. For `"ploidymatrix"`, this is a matrix of integers, indexed in the first dimension by sample name and in the second dimension by locus name. Each element represents the ploidy at a given sample and locus. For `"ploidysample"` and `"ploidylocus"`, the slot is an integer vector, named by sample or locus and indicating the ploidy at each sample or locus, respectively. For `"ploidyone"`, the slot contains a single integer representing the ploidy for the entire dataset.

### Methods

pld

  `signature(object= "ploidymatrix")`: Returns the contents of `object@pld`: a matrix of ploidies indexed by sample and locus. The `samples` and `loci` arguments can be used, optionally, to only return a subset of ploidies.

### Author(s)

Lindsay V. Clark

### See Also

`reformatPloidies`, `pld`, `plCollapse`, `gendata`

### Examples

    showClass("ploidysuper")

[Package polysat version 1.7-6 Index]