pen_seq_error

The current value of sequencing error rate.
Must be between 0 and 1.

The prior mean of the logit sequencing error rate.

mu_eps

The prior variance (not standard deviation)
of the logit sequencing error rate. Set this to <code>Inf</code> to
return <code>0</code>.

sigma2_eps

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.

pen_seq_error: Penalty on sequencing error rate.

Description

Usage

Arguments

Value