get_q_array

Return the probabilities of an offspring's genotype given its
parental genotypes for all possible combinations of parental and
offspring genotypes. This is for species with polysomal inheritance
and bivalent, non-preferential pairing.

Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allele bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow the specification
of many different genotype distributions. 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 (2020) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.

David Gerard

updog

Flexible Genotyping for Polyploids

get_q_array function

<dl><dt>ploidy</dt>
<dd>A positive integer. The ploidy of the species.</dd></dl>

Arguments

Author

Return the probabilities of an offspring's genotype given its
parental genotypes for all possible combinations of parental and
offspring genotypes. This is for species with polysomal inheritance
and bivalent, non-preferential pairing. — get_q_array

<dl>

<dt>ploidy</dt>
<dd>A positive integer. The ploidy of the species.</dd>

</dl>

Return the probabilities of an offspring's genotype given its
parental genotypes for all possible combinations of parental and
offspring genotypes. This is for species with polysomal inheritance
and bivalent, non-preferential pairing.

get_q_array: Return the probabilities of an offspring's genotype given its parental genotypes for all possible combinations of parental and offspring genotypes. This is for species with polysomal inheritance and bivalent, non-preferential pairing.

Description

Usage

Value

Arguments

Author

Examples