updog: Flexible Genotyping for Polyploids

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 also Gerard et al. (2018) <doi:10.1101/281550> for details on the implemented methods.

Version: 1.0.0
Depends: R (≥ 3.4.0)
Imports: Rcpp (≥ 0.12.16), RcppArmadillo, assertthat, foreach, doParallel, ggplot2, ggthemes, stringr
LinkingTo: Rcpp, RcppArmadillo
Suggests: covr, testthat, SuppDists, Rmpfr, CVXR, knitr, rmarkdown, tidyverse
Published: 2018-07-10
Author: David Gerard ORCID iD [aut, cre]
Maintainer: David Gerard <gerard.1787 at gmail.com>
BugReports: http://github.com/dcgerard/updog/issues
License: GPL-3
NeedsCompilation: yes
Citation: updog citation info
Materials: README NEWS
CRAN checks: updog results

Downloads:

Reference manual: updog.pdf
Vignettes: Oracle Calculations
Parallelized Genotyping using Updog
Simulate Next-Generation Sequencing Data
Example Use of Updog
Package source: updog_1.0.0.tar.gz
Windows binaries: r-devel: updog_1.0.0.zip, r-release: updog_1.0.0.zip, r-oldrel: updog_1.0.0.zip
OS X binaries: r-release: updog_1.0.0.tgz, r-oldrel: updog_1.0.0.tgz

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