ploidysuper-class {polysat}

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")