get_map_genotypes

Total reads matrix: matrix containing the total number of reads mapping to each locus for each individual.

Percent of the posterior samples to discard as burn-in (default=20).

burnin

File path to directory containing the posterior samples of genotypes output by <code><a rd-options="" href="/link/polyfreqs?package=polyfreqs&version=1.0.2" data-mini-rdoc="polyfreqs::polyfreqs">polyfreqs</a></code> (default = "genotypes").

geno_dir


<em>INTERNAL</em>: 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.


Implements a Gibbs sampling algorithm to perform Bayesian inference
on biallelic SNP frequencies, genotypes and heterozygosity (observed and
expected) in a population of autopolyploids. See the published paper in
Molecular Ecology Resources: Blischak et al. (2016) <doi:10.1111/1755-0998.12493>.

Paul Blischak

polyfreqs

Bayesian Population Genomics in Autopolyploids

get_map_genotypes function

File path to directory containing the posterior samples of genotypes output by <code><a rd-options='' href='polyfreqs'>polyfreqs</a></code> (default = "genotypes").

get_map_genotypes: Maximum a posteriori (MAP) estmation of autopolyploid genotypes

Description

Usage

Arguments

Value

Details