get_map_genotypes {polyfreqs} | R Documentation |
INTERNAL: Calculates the MAP estimate of the genotypes for autopolyploid individuals using the posterior mode of the marginal posterior distribtuion of genotypes for each individual at each locus.
get_map_genotypes(tM, burnin = 20, geno_dir = "genotypes")
tM |
Total reads matrix: matrix containing the total number of reads mapping to each locus for each individual. |
burnin |
Percent of the posterior samples to discard as burn-in (default=20). |
geno_dir |
File path to directory containing the posterior samples of genotypes output by |
The easiest way to get these estimates is to set the genotypes
argument to TRUE
when running polyfreqs
.
A matrix containing the maximum a posteriori estimates for all individuals at each locus. The MAP estimate of the genotype is simply the posterior mode.