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

install.packages('updog')
1.0.1
6 months 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