get_inner_weights

The ploidy of the species. Assumed to be the same for each
individual.

ploidy

The mode if <code>model = "ash"</code>. If not provided,
<code>flexdog</code> will estimate the mode. This is the starting point of
the allele frequency if <code>model = "hw"</code>. This should be
<code>NULL</code> for all other options of <code>model</code>.

mode

The (i,k)th element is \(1(k \in F(a, i)) / |F(a,i)|\).

internal

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.

get_inner_weights: Compute inner weights for updating the mixing proportions when using ash model.

Description

Usage

Arguments

Value