Package: updog
Title: Flexible Genotyping for Polyploids
Version: 1.0.1
Date: 2018-06-11
Authors@R: person("David", "Gerard", email = "gerard.1787@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9450-5023"))
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) <doi:10.1101/281550> 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] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-27 17:50:06 UTC
Built: R 3.4.4; x86_64-apple-darwin15.6.0; 2018-07-28 13:49:45 UTC; unix
Archs: updog.so.dSYM
