Polysat

polysat is an R package for polyploid microsatellite analysis in ecological genetics. The first publicly available version, 0.1, is available on CRAN as of June 2010.

What polysat does

• Assumes allele copy number ambiguity in partial heterozygotes
• Handles data of any ploidy, including mixed ploidy samples
• Stores genotype data in a simple format that can be easily manipulated to exclude or add samples and loci
• Imports and exports data in ABI GeneMapper Genotypes Table, GenoDive, Structure, SPAGeDi, ATetra, Tetrasat/Tetra, and binary presence/absence formats.
• Calculates pairwise distances between individuals using a stepwise mutation model or infinite alleles model
• Counts alleles to assist user in estimating ploidy
• Estimates allele frequencies and calculates pairwise F_ST based on these estimates. Mixed ploidy population size is measured in genomes rather than individuals.

Author and Maintainer

User:Lindsay V. Clark

Obtaining polysat

If you don't already have R, download it from CRAN and install it.

At the prompt in the R console, type:

install.packages("combinat")

install.packages("polysat")

library(polysat)

Documentation

Tutorial manual: Most users will want to read this first to get a general idea of how to use the package. It is organized by topic, each topic containing an explanation followed by examples using the data provided with the package. All example code from this manual is also available in the demo directory of the package, or can be extracted from the *.Rnw (Sweave) version of the manual in the doc directory of the package.

Reference manual: This is an alphabetized collection of all of the help files provided with the package. It contains more details about each function, as well as additional examples. Advanced R users may want to skip the tutorial manual and go straight to the reference manual, although the introduction to "How genotypes are stored in polysat" in the tutorial manual may still be a worthwhile read.

How to cite polysat

We are going to submit a Computer Program Note to Molecular Ecology Resources:

Clark, L and Jasieniuk, M. POLYSAT: an R package for polyploid microsatellite analysis. Molecular Ecology Resources (in review).

Wish List

Since polysat is so new, I am very interested in getting feedback!

This section lists additional functionality that I'm thinking of adding to polysat. If you have any additional requests, or would like to "vote" for one of the items below to be a top priority, just send me an email! If you have created your own functions to interface with the package and would like to be added as a contributor, I am open to that as well.

• Store all information pertinent to a particular dataset in one object, instead of several. The object could be a list, so that you would have mydata$Genotypes, mydata$Popinfo, mydata$Missing, mydata$Usatnts, mydata$Ploidy, etc. Functions would take the entire list as an argument and access the appropriate items. (Another option is to create a class similar to the genind class in adegenet, but with genotypes still formatted as they are in polysat.) This could help prevent a lot of user mistakes, but on the other hand it would mean more typing in order to view and edit your data.
• Make a graphical front end for the package. I lack the programming expertise to do this, but if I find myself with some free time on my hands I could learn. I'm definitely open to collaboration on this one!
• Some sort of iterative computation in order to better estimate allele frequencies.
• More population statistics (Weir and Cockerham 1984, etc.).

Source code

For advanced R users, here is the source code for the functions in the package, so that you may tweak them or create new functions for your own use:

Media: polysat_0.1_functions.R.txt