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

Clark, LV and Jasieniuk, M, 2011. POLYSAT: an R package for polyploid microsatellite analysis. Molecular Ecology Resources (in review).

Wish List

Since I have just recently released polysat, 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. I am experimenting with creating one or more S4 classes to contain the slots @Genotypes, @PopInfo, @PopNames, @Missing, @Usatnts, and @Ploidies. This should increase user friendliness and prevent a lot of errors.
• Some sort of iterative computation in order to better estimate allele frequencies. (Very high on the to-do list since Molecular Ecology Resources wants to see it added to the package.)
• 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!
• More population statistics (Weir and Cockerham 1984, etc.).
• Use allele frequency estimations to randomly generate unambiguous genotypes for a dataset with partial heterozygotes. These could then be passed to software such as adegenet that allows for polyploidy but not allele copy number ambiguity.
• Parentage analysis
• A method (other than genetic distance distributions as in GenoType) to quantitatively distinguish asexual and sexual progeny. I'm doing a study on apomixis in blackberries so I have a bunch of notes jotted down on this, although I at least temporarily abandoned the idea.

Frequently asked questions

If you have never used R before, particularly if you find command-line software to be intimidating, you may need to spend a day or two just learning R before you even touch polysat. (Look for the Introduction to R manual on the CRAN website.) I have tried to make polysat as user-friendly as possible, but that cannot substitute for a basic understanding of how R works. Trust me, learning R is worth it! R is very powerful and efficient software for data analysis, and if you take the time to learn it for the sake of using polysat, you may find yourself using R in other areas of your research.

If you email me questions about polysat, I will happily and promptly answer them. But if more than one or two of your questions have to do with basic comprehension of R, I am just going to direct you to read the manual more carefully. If you are not sure how something works, try experimenting to see if it does what you think it does.

I will start putting the most frequently asked questions (yes, even the basic R questions) into this section once a few more people contact me (so that I have a better sense of what the most common questions are going to be).

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

External links

• You can rate and review polysat on Crantastic. (I am of course also open to questions and comments via email.)
• CRAN page with source and binary downloads.