"ploidysuper" and SubclassesThese classes contain ploidy data indexed by sample, locus, both, or
neither. They are intended to go in the Ploidies slot of
"gendata" objects.
"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.
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.
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.
Lindsay V. Clark
reformatPloidies, pld,
plCollapse, gendata