polyfreqs

An R package for Bayesian population genomics in autopolyploids

polyfreqs is an R package for the estimation of biallelic SNP frequencies, genotypes and heterozygosity in autopolyploid taxa using high throughput sequencing data.

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) and the r-base-dev package.
Looking at the requirements for Rcpp is a good place to start too.

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")

Documentation

Example code and tutorials for running polyfreqs can be found in the wiki. For more details on the model underlying polyfreqs please see the associated preprint on bioRxiv: Blischak et al.

Help topics

• get_map_genotypes
  Maximum
• point_Hexp
  Estimation of expected heterozygosity
• point_Hobs
  Estimation of observed heterozygosity
• polyfreqs
  Bayesian population genomics in autopolyploids
• polyfreqs_pps
  Posterior predictive model checks for polyfreqs
• ref_reads
  Reference reads matrix
• sim_reads
  Simulation of sequencing read counts and genotypes
• simple_freqs
  Point estimation of allele frequencies based on read counts
• total_reads
  Total reads matrix