polyfreqs is an R package for the estimation of biallelic SNP frequencies, genotypes and heterozygosity in autopolyploid taxa using high throughput sequencing data. It should work for diploids as well but I have not tested this.
NEW: polyfreqs now has a Google Groups page. Please feel free to join the group and post any questions that you may have about the software. [Google Groups link]
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 Compiler Collection (gcc) and the r-base-dev package. polyfreqs relies on the R package Rcpp which is a good place to start too for figuring what you will need. Note that Rcpp also requires the compilation of C++ code so make sure that the necessary compilers are installed appropriately for your OS. You can install Rcpp directly from CRAN in the usual way using the install.packages()
command:
install.packages("Rcpp")
polyfreqs v1.0.0 is now on CRAN: link.
You can now install it like you would any other R package:
install.packages("polyfreqs")
Installing the latest developmental release of 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")
Example code and tutorials for running polyfreqs can be found in the vignette. For more details on the model underlying polyfreqs please see the associated paper in Molecular Ecology Resources: Blischak et al. The Supplemental Material also has a walk through for analyzing a data set collected for autotetraploid potato (Solanum tuberosum).
Release notes
-
v1.0.1 -- Removed dependency on the RcppArmadillo
sample()
function by coding our own version (nonunif_int()
in the sample_g.cpp source file). The Gibbs sampler should run a bit faster now. -
v1.0.0 -- First release. Now available on CRAN.