updog

updog-package

<img src="figures/logo.png?package=updog&version=2.1.6" style="float: right" alt="logo" width="120">
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) tools:::Rd_expr_doi("10.1534/genetics.118.301468") and Gerard and Ferrao (2020) tools:::Rd_expr_doi("10.1093/bioinformatics/btz852") for details on the implemented methods.

internal

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

Flexible Genotyping for Polyploids

updog-package function

Maintainer: David Gerard <a href="/link/gerard.1787%40gmail.com?package=updog&version=2.1.6" data-mini-rdoc="updog::gerard.1787@gmail.com">gerard.1787@gmail.com</a> (<a href="https://orcid.org/0000-0001-9450-5023">ORCID</a>)

Author

<img src='figures/logo.png' style='float: right' alt='logo' width='120' />
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) tools:::Rd_expr_doi("10.1534/genetics.118.301468") and Gerard and Ferrao (2020) tools:::Rd_expr_doi("10.1093/bioinformatics/btz852") for details on the implemented methods.

updog: Flexible Genotyping for Polyploids — updog-package

Maintainer: David Gerard <a href='mailto:gerard.1787@gmail.com'>gerard.1787@gmail.com</a> (<a href='https://orcid.org/0000-0001-9450-5023'>ORCID</a>)

updog-package: updog: Flexible Genotyping for Polyploids

Description

Arguments

Author

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