geno_qty_array: S3 class for arrays holding probabilities and likelihoods of...
In eriqande/fullsniplings: Full sibling reconstruction from SNP data

S3 class for arrays holding probabilities and likelihoods of different genotypes at different loci

This is the main S3 class for arrays that hold things like the likelihoods of the pair of parental genotypes given all their offspring, or the likelihood of an individual's genotypes given his observed phenotype. Or, I suppose they could even be indicators of SNP genotypes in an individual, or normalized probabilities, etc. Several different objects inherit from this one. I mostly have this because I wanted to learn more about S3 objects and I wanted to have an easy way of printing these to get information.

Every object that inherits from this class is a numeric (or possibly an integer) matrix. However, they are typically all objects that would be more naturally represented by higher dimensional arrays, but we don't do that because the operations that we will end up doing on them are typically column and row multiplies, etc, and it is easier in Rcpp to just deal with matrices.

But, it would be nice to know about the underlying natural higher dimensional array. These properties are stored in these objects. The attributes these objects have are:

dim: They have a 2-D dim b/c they are matrices
class: They may have variable classes, but they all inherit from the geno_qty_array
gqa_dim: The dimension attributes that would be natural to have for the object.
gqa_dimnames: The dimnames on those gqa_dims. Note that these are not technically required, but printing won't work very well without them, and you really should have some names on those dimensions.
gqa_description: A little blurb about what kinds of quantities this object is storing.