pen_bias

The current value of bias parameter. Must be
greater than 0. A value of 1 means no bias.

The prior mean of the log-bias parameter.

mu_h

The prior variance (not standard deviation)
of the log-bias parameter. Set to to <code>Inf</code> to return <code>0</code>.

sigma2_h

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.

pen_bias: Penalty on bias parameter.

Description

Usage

Arguments

Value