obj_for_mu_sigma2

A vector, the ith element is the variational posterior mean of individual i for the SNP.

A vector, the ith element is the variational posterior variance of individual i for the SNP.

sigma2

A matrix that contains the standard normal quantile of the beta-binomial cdf at dosage k for individual i.
The rows index the individuals and the columns index the dosages.

phifk_mat

The inverse of the underlying correlation matrix.

cor_inv

A matrix of log-densities of the beta binomial. The rows index the individuals and the columns index the allele dosage.
Allele dosage goes from -1 to ploidy, so there are ploidy + 2 elements.

log_bb_dense

Objective function when updating mu and sigma2.

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.

obj_for_mu_sigma2: Objective function when updating mu and sigma2.

Description

Usage

Arguments

Value