obj_for_rho

The inbreeding coefficient for the individual.

A vector of posterior means. The jth element is the
posterior mean of SNP j for the individual.

A vector of posterior variances. The jth element
is the posterior variance of SNP j for the individual.

sigma2

A vector of allele frequencies. The jth element
is the allele frequency for SNP j.

alpha

A matrix of log posterior densities. The
rows index the SNPs and the columns index the dosage.

log_bb_dense

ploidy

Objective function when updating a single inbreeding coefficient.

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_rho: Objective function when updating a single inbreeding coefficient.

Description

Usage

Arguments

Value