pp_brent_obj

The mixing weight of the first component.

firstmixweight

The rows index the components and the columns
index the segregation amount. Should only have two rows.

probmat

The distribution of the other parent.

pvec

weight_vec

The mixing weight on the uniform component.

alpha

Objective function when doing Brent's method in
<code><a rd-options="" href="/link/update_pp_f1?package=updog&version=1.1.3" data-mini-rdoc="updog::update_pp_f1">update_pp_f1</a></code> when one parent only has
two mixing components.

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

pp_brent_obj function

Objective function when doing Brent's method in
<code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code> when one parent only has
two mixing components.

Objective function when doing Brent's method in
<code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code> when one parent only has
two mixing components. — pp_brent_obj

Objective function when doing Brent's method in
<code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code> when one parent only has
two mixing components.

Objective function when doing Brent's method in
<code><a rd-options="" href="/link/update_pp_f1?package=updog&version=1.1.3" data-mini-rdoc="updog::update_pp_f1">update_pp_f1</a></code> when one parent only has
two mixing components.

pp_brent_obj: Objective function when doing Brent's method in `update_pp_f1` when one parent only has two mixing components.

Description

Usage

Arguments

Value