get_conv_inner_weights

One of the parents segregation probability vector.

psegprob

The other parent's segregation matrix.

psegmat

Get the inner weights used for the em update 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 there are more than two bivalent components for one of the parents.

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_conv_inner_weights function

Get the inner weights used for the em update in <code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code>
when there are more than two bivalent components for one of the parents.

Get the inner weights used for the em update in <code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code>
when there are more than two bivalent components for one of the parents. — get_conv_inner_weights

Get the inner weights used for the em update in <code><a rd-options='' href='update_pp_f1'>update_pp_f1</a></code>
when there are more than two bivalent components for one of the parents.

Get the inner weights used for the em update 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 there are more than two bivalent components for one of the parents.

get_conv_inner_weights: Get the inner weights used for the em update in `update_pp_f1` when there are more than two bivalent components for one of the parents.

Description

Usage

Arguments

Value

See Also