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.

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Description file content

Package
updog
Title
Flexible Genotyping for Polyploids
Version
1.0.0
Date
2018-06-11
Description
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) for details on the implemented methods.
Depends
R (>= 3.4.0)
License
GPL-3
BugReports
http://github.com/dcgerard/updog/issues
Encoding
UTF-8
LazyData
true
RoxygenNote
6.0.1
LinkingTo
Rcpp, RcppArmadillo
Imports
Rcpp (>= 0.12.16), RcppArmadillo, assertthat, foreach, doParallel, ggplot2, ggthemes, stringr
Suggests
covr, testthat, SuppDists, Rmpfr, CVXR, knitr, rmarkdown, tidyverse
VignetteBuilder
knitr
NeedsCompilation
yes
Packaged
2018-07-09 14:14:56 UTC; david
Author
David Gerard [aut, cre] ()
Maintainer
David Gerard
Repository
CRAN
Date/Publication
2018-07-10 16:20:03 UTC

install.packages('updog')

1.0.0

12 days ago

David Gerard

GPL-3

Depends on

R (>= 3.4.0)

Imports

Rcpp (>= 0.12.16), RcppArmadillo, assertthat, foreach, doParallel, ggplot2, ggthemes, stringr

Suggests

covr, testthat, SuppDists, Rmpfr, CVXR, knitr, rmarkdown, tidyverse

Discussions