get_map_genotypes {polyfreqs}R Documentation

Maximum a posteriori (MAP) estmation of autopolyploid genotypes

Description

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.

Usage

get_map_genotypes(tM, burnin = 20, geno_dir = "genotypes")

Arguments

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 polyfreqs (default = "genotypes").

Details

The easiest way to get these estimates is to set the genotypes argument to TRUE when running polyfreqs.

Value

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.


[Package polyfreqs version 1.0.2 Index]