uni_obj_const

pivec

The mixing weight for the uniform component.
This should be small (say, less tahn 10^-3).

alpha

A vector of weights. Each element of <code>weight_vec</code> corresponds
to a column of <code>lmat</code>.

weight_vec

A matrix of inner weights. The columns are the "individuals" and the rows are the "classes."

lmat

A vector of penalties on the pi's (corresponding to the rows
of <code>lmat</code>).
This can either be of length 1, in which case the same penalty is applied
to each of the pi's. Or it can be the same length of <code>pivec</code>, in
which case a different penalty is applied to each of the pi's. Larger
penalties generally increase the value of the pi's, not shrink them.

lambda

Objective function optimized by <code><a rd-options="" href="/link/uni_em_const?package=updog&version=1.2.0" data-mini-rdoc="updog::uni_em_const">uni_em_const</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 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

uni_obj_const function

Objective function optimized by <code><a rd-options='' href='uni_em_const'>uni_em_const</a></code>.

Objective function optimized by <code><a rd-options='' href='uni_em_const'>uni_em_const</a></code>. — uni_obj_const

Objective function optimized by <code><a rd-options='' href='uni_em_const'>uni_em_const</a></code>.

Objective function optimized by <code><a rd-options="" href="/link/uni_em_const?package=updog&version=1.2.0" data-mini-rdoc="updog::uni_em_const">uni_em_const</a></code>.

uni_obj_const: Objective function optimized by `uni_em_const`.

Description

Usage

Arguments

Value