This function separates a genotype matrix into two data frames based on population assignments.
It's designed to work with the batches or windows processed by process_vcf_in_batches and process_vcf_in_windows.
separateByPopulations(
sep_gt,
pop1_names,
pop2_names,
ploidy = 2,
rm_ref_alleles = TRUE
)A list containing two data frames, one for each population.
A genotype matrix similar to the @sep_gt slot of a vcfR object.
A character vector of individual names for the first population.
A character vector of individual names for the second population.
Logical, whether variants that only have the reference allele should be removed from the respective subpopulations data frame. (Default = TRUE)