update_dr

<code>colSums(wik_mat)</code> from <code><a rd-options="" href="/link/flexdog?package=updog&version=1.2.0" data-mini-rdoc="updog::flexdog">flexdog</a></code>.
This is the sum of current posterior probabilities of each individual
having genotype k.

weight_vec

model

A list of anything else needed to be passed.
E.g. if <code>model = "ash"</code>,
then <code>inner_weights</code> needs to be passed through <code>control</code>
(see <code><a rd-options="" href="/link/get_inner_weights?package=updog&version=1.2.0" data-mini-rdoc="updog::get_inner_weights">get_inner_weights</a></code> for how to get this matrix).

control

Same as <code><a rd-options="" href="/link/update_pp_f1?package=updog&version=1.2.0" data-mini-rdoc="updog::update_pp_f1">update_pp_f1</a></code> but I exclusively use the EM (instead of also Brent's method),
and I allow for priors on the mixing proportions.

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.

David Gerard

updog

Flexible Genotyping for Polyploids

update_dr function

<code>colSums(wik_mat)</code> from <code><a rd-options='' href='flexdog'>flexdog</a></code>.
This is the sum of current posterior probabilities of each individual
having genotype k.

A list of anything else needed to be passed.
E.g. if <code>model = "ash"</code>,
then <code>inner_weights</code> needs to be passed through <code>control</code>
(see <code><a rd-options='' href='get_inner_weights'>get_inner_weights</a></code> for how to get this matrix).

Same as <code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code> but I exclusively use the EM (instead of also Brent's method),
and I allow for priors on the mixing proportions.

Same as <code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code> but I exclusively use the EM (instead of also Brent's method),
and I allow for priors on the mixing proportions. — update_dr

Same as <code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code> but I exclusively use the EM (instead of also Brent's method),
and I allow for priors on the mixing proportions.

Same as <code><a rd-options="" href="/link/update_pp_f1?package=updog&version=1.2.0" data-mini-rdoc="updog::update_pp_f1">update_pp_f1</a></code> but I exclusively use the EM (instead of also Brent's method),
and I allow for priors on the mixing proportions.

update_dr: Same as `update_pp_f1` but I exclusively use the EM (instead of also Brent's method), and I allow for priors on the mixing proportions.

Description

Usage

Arguments

Value

See Also