obj_for_weighted_lbb

A vector of length 2. The first term is the current mean of the
underlying beta. The second term is the current overdispersion parameter.

parvec

ploidy

A vector of length <code>ploidy + 1</code> that contains the weights
for each component beta-binomial.

weight_vec

Objective function for updating the beta-binomial genotype distribution when
<code>model = "bb"</code> in <code><a rd-options="" href="/link/flex_update_pivec?package=updog&version=1.1.3" data-mini-rdoc="updog::flex_update_pivec">flex_update_pivec</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

obj_for_weighted_lbb function

Objective function for updating the beta-binomial genotype distribution when
<code>model = "bb"</code> in <code><a rd-options='' href='flex_update_pivec'>flex_update_pivec</a></code>.

Objective function for updating the beta-binomial genotype distribution when
<code>model = "bb"</code> in <code><a rd-options='' href='flex_update_pivec'>flex_update_pivec</a></code>. — obj_for_weighted_lbb

Objective function for updating the beta-binomial genotype distribution when
<code>model = "bb"</code> in <code><a rd-options='' href='flex_update_pivec'>flex_update_pivec</a></code>.

Objective function for updating the beta-binomial genotype distribution when
<code>model = "bb"</code> in <code><a rd-options="" href="/link/flex_update_pivec?package=updog&version=1.1.3" data-mini-rdoc="updog::flex_update_pivec">flex_update_pivec</a></code>.

obj_for_weighted_lbb: Objective function for updating the beta-binomial genotype distribution when `model = "bb"` in `flex_update_pivec`.

Description

Usage

Arguments

Value