VanRaden GRM

[timothymillar]

Implement the VanRaden genomic relationship matrix (VanRaden 2008). This is typically calculated from dosages for biallelic markers and has been generalized to autopolyploids (fixed ploidy). One consideration is the specification of "base"/"ancestral"/"founder" allele frequencies. These are often estimated from the sample population but this assumes a population under HWE. I can't see a sensible default for estimating these so it's probably best to default to an array (a new variable) which must be pre-populated.