get_hyper_weights

ploidy

The number of reference alleles in the individual.

Obtains the mixing weights for the mixing distributions
of <code><a rd-options="" href="/link/get_bivalent_probs?package=updog&version=1.2.0" data-mini-rdoc="updog::get_bivalent_probs">get_bivalent_probs</a></code> to return a hypergeometric
distribution where <code>ploidy</code> is the population size,
<code>ell</code> is the number of success states in the population,
and <code>ploidy / 2</code> is the number of draws. If these
are the mixing weights in the population, then there is no
preferential pairing.

Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allelic bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow the specification
of many different genotype distributions. An experimental
function that takes into account varying levels of relatedness
is implemented in mupdog(). Also provided are functions to
simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as
functions to calculate oracle genotyping error rates, oracle_mis(), and
correlation with the true genotypes, oracle_cor(). These latter two
functions are useful for read depth calculations. Run
browseVignettes(package = "updog") in R for example usage. See
Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and
Gerard and Ferrao (2019) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.

David Gerard

updog

Flexible Genotyping for Polyploids

get_hyper_weights function

Obtains the mixing weights for the mixing distributions
of <code><a rd-options='' href='get_bivalent_probs'>get_bivalent_probs</a></code> to return a hypergeometric
distribution where <code>ploidy</code> is the population size,
<code>ell</code> is the number of success states in the population,
and <code>ploidy / 2</code> is the number of draws. If these
are the mixing weights in the population, then there is no
preferential pairing.

get_hyper_weights: Return mixture weights needed to obtain a hypergeometric distribution.

Description

Usage

Arguments

Value

Examples