Class "ploidysuper" and Subclasses
These classes contain ploidy data indexed by sample, locus, both, or
neither. They are intended to go in the
Ploidies slot of
Objects from the Class
"ploidysuper" is a virtual
class: No objects may be created from it.
Objects of the subclasses
"ploidyone" can be created with the
new(ploidyclass, samples, loci, ...), where
ploidyclass is a character string of one of the class names, 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.
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
"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.
signature(object= "ploidymatrix"): Returns the contents of
object@pld: a matrix of ploidies indexed by sample and locus. The
lociarguments can be used, optionally, to only return a subset of ploidies.
Lindsay V. Clark
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