post_prob

dosage

ploidy

The variational variance (not standard deviation).

sigma2

alpha

The individual's overdispersion parameter.

Variational posterior probability of having <code>dosage</code> A alleles
when the ploidy is <code>ploidy</code>, the allele frequency is
<code>alpha</code>, the individual-specific overdispersion parameter is
<code>rho</code>, the variational mean is <code>mu</code>, and the variational
variance is <code>sigma2</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 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

post_prob function

Variational posterior probability of having <code>dosage</code> A alleles
when the ploidy is <code>ploidy</code>, the allele frequency is
<code>alpha</code>, the individual-specific overdispersion parameter is
<code>rho</code>, the variational mean is <code>mu</code>, and the variational
variance is <code>sigma2</code>. — post_prob

Variational posterior probability of having <code>dosage</code> A alleles
when the ploidy is <code>ploidy</code>, the allele frequency is
<code>alpha</code>, the individual-specific overdispersion parameter is
<code>rho</code>, the variational mean is <code>mu</code>, and the variational
variance is <code>sigma2</code>.

post_prob: Variational posterior probability of having `dosage` A alleles when the ploidy is `ploidy`, the allele frequency is `alpha`, the individual-specific overdispersion parameter is `rho`, the variational mean is `mu`, and the variational variance is `sigma2`.

Description

Usage

Arguments

Value