Skip to content

Home

Jump to bottom Edit New page
Paul Blischak edited this page Sep 20, 2015 · 16 revisions

polyfreqs is an R package for the estimation of biallelic SNP frequencies, genotypes and heterozygosity (observed and expected; Hardy [2015]) in populations of autopolyploids. It uses a hierarchical Bayesian model to integrate over genotype uncertainty using high throughput sequencing read counts as data (similar to the diploid model of Buerkle and Gompert [2013]). The package implements a Gibbs sampler to draw from the joint posterior distribution of allele frequencies and genotypes. The model is described in our paper which is currently in review but can be found as a preprint on bioRxiv: Blischak et al.

Dependencies

polyfreqs uses C++ code to implement its Gibbs sampling algorithm which will usually require the installation of additional software (depending on the operating system [OS] being used). Windows users will need to install Rtools. MacOSX users will need to install the Xcode Command Line Tools. Linux users will need an up-to-date version of the GNU C Compiler (gcc), which typically comes installed with most Linux distributions.

polyfreqs relies on two other R packages: Rcpp and RcppArmadillo. These are both available on CRAN and can be installed in the usual way using install.packages():

install.packages("Rcpp")
install.packages("RcppArmadillo")

Note that Rcpp and RcppArmadillo also require the compilation of C++ code so make sure that the necessary compilers are installed appropriately for your OS.

Installation

Installing polyfreqs can be done using the devtools package and the install_github() command. Install devtools using install.packages("devtools"). polyfreqs can then be installed as follows:

devtools::install_github("pblischak/polyfreqs")

References

  • Blischak PD, Kubatko LS, Wolfe AD. 2015. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids. In revision. bioRxiv, doi: http://dx.doi.org/10.1101/021907.

  • Buerkle CA and Gompert Z. 2013. Population genomics based on low coverage sequencing: how low should we go? Molecular Ecology, 22, 3028--3035.

  • Hardy, OJ. 2015. Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate. Molecular Ecology Resources, doi: 10.1111/1755-0998.12431.

next

Add a custom footer
Clone this wiki locally