turns long format genotypes into a matrix of integer-code genotypes

turns long format genotypes into a matrix of integer-code genotypes

create_integer_genotype_matrix(LG, AF)

Arguments

LG

the genotypes in long format. It must have the columns Indiv (unique IDs of the individuals), Locus, gene_copy (must be 1 or 2 denoting which of the two gene copies in a diploid each allele is), and Allele, which must be a character. If there are any missing genotypes in the data frame, they must appear as NAs in the Allele column.

AF

The data frame of allele frequencies that was passed to create_ckmr() to create the ckmr object that will be used for computing genotype probabilities. It must have columns Chrom, Pos, Locus, Allele, LocIdx, AlleIdx, and Freq.