get_bivalent_probs

<p>The ploidy of the individual. Should be even
and greater than 0.</p>

ploidy

<p>Returns segregation probabilities, pairing representation
and number of ref alleles given the ploidy.</p>

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

get_bivalent_probs: Returns segregation probabilities, pairing representation and number of ref alleles given the ploidy.

Description

Usage

Arguments

Value

Examples