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
- 1.0.1
- 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)
- 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
- 2018-07-27 16:38:38 UTC; david
- Author
- David Gerard [aut, cre] ()
- Maintainer
- David Gerard
- Repository
- CRAN
- Date/Publication
- 2018-07-27 17:50:06 UTC
