per_kid_marriage_likelihoods: Compute the likelihood of the genotypes of a marriage given...
In eriqande/fullsniplings: Full sibling reconstruction from SNP data

Description Usage Arguments Value

It is advantageous to precompute and store some quantities for pedigree analysis with SNPs. One of those quantities is the likelihood of the genotypes of the two parents that produced a child, conditional only on that one child's genotype. This is convenient because the likelihood of the two parents' genotypes given all of their offspring will be the product of the single-offspring likelihoods. When genotyping error is present, that has to be thrown into the mix as well. However, here we assume that the individual offspring genotype likelihoods have already been computed given their observed genotypes.

1	per_kid_marriage_likelihoods(offspring_likelihoods, transmission_probs)

`offspring_likelihoods`	This is a 3 x L x N array of likelihoods of the individual's true genotypes given their observed genotypes. This sort of array is returned by the function `get_indiv_geno_lik`.
`transmission_probs`	a 3 x 3 x 3 matrix of probs of kid genotypes given parent genotypes. Such an array is returned by `trans_probs`. See the documentation thereof for a description.

This returns a 3 x 3 x L x N array of the parent genotypes (9 states) at each of the L loci for each of the N offspring. Although these are ostensible likelihoods of "marriages" (think of them as marriage nodes), it will be beneficial to regard these quantities of properties of the individual offspring moreso than as properties of the marriage nodes.

eriqande/fullsniplings documentation built on May 16, 2019, 8:45 a.m.