get_wik_mat

The vector of current prior probabilities of each genotype.

probk_vec

A vector of counts of reads of the reference allele.

refvec

sizevec

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

ploidy

The starting value of the sequencing error rate.

bias

The starting value of the overdispersion parameter.

E-step in <code><a rd-options="" href="/link/flexdog?package=updog&version=1.1.3" data-mini-rdoc="updog::flexdog">flexdog</a></code>.

internal

Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allelic bias, overdispersion, and sequencing
error. The main function is flexdog(), which allows 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_wik_mat function

E-step in <code><a rd-options='' href='flexdog'>flexdog</a></code>.

get_wik_mat: E-step in `flexdog`.

Description

Usage

Arguments

Value

See Also