Polysat

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* '''In <code>read.GeneMapper</code> I got the error "line 2 did not have X elements".'''  Each line of the file needs to have the same number of tab stops.  You can add these manually in a text editor, or if you open and save the file in a spreadsheet program it should automatically insert the right number of tab stops.
* '''In <code>read.GeneMapper</code> I got the error "line 2 did not have X elements".'''  Each line of the file needs to have the same number of tab stops.  You can add these manually in a text editor, or if you open and save the file in a spreadsheet program it should automatically insert the right number of tab stops.
* '''I tried to do PCoA (cmdscale) but got the error "NA values not allowed in d."'''  If you only have one or two loci, you will need to exclude all individuals with missing data from your analysis.  If you have three or more loci and still see this error, you may need to exclude individuals that are missing genotypes at multiple loci.
* '''I tried to do PCoA (cmdscale) but got the error "NA values not allowed in d."'''  If you only have one or two loci, you will need to exclude all individuals with missing data from your analysis.  If you have three or more loci and still see this error, you may need to exclude individuals that are missing genotypes at multiple loci.
 +
* '''Do all populations need to have the same number of individuals?  Do the samples have to be ordered by population?'''  No and no.  [[Media:polysat_tables.txt | Example code]]
== Known issues ==
== Known issues ==

Revision as of 09:26, 11 October 2012

polysat is an R package for polyploid microsatellite analysis in ecological genetics. Version 1.2-1 is available on CRAN as of June 2011. Development version 1.3-0 is available via this webpage as of May 2012 (see below).
Screenshot of polysat from RGui
Screenshot of polysat from RGui

Since the paper on polysat was recently published in the May 2011 issue of Molecular Ecology Resources, a lot of people are now using it for the first time. This is occasionally bringing up issues that I didn't find when I tested the software myself. If you think you have found a bug, please feel free to let me know about it! If I fix the bug but am not immediately ready to release a new version of polysat, I will send you the corrected source code so that you can proceed with your analysis in the meantime.

Contents

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, POPDIST, and binary presence/absence formats.
  • Calculates pairwise distances between individuals using a stepwise mutation model or infinite alleles model.
  • Calculates Shannon and Simpson indexes of genotype diversity.
  • Counts alleles to assist user in estimating ploidy.
  • Estimates allele frequencies in autopolyploids using either an iterative or non-iterative algorithm. Calculates pairwise FST based on these estimates. Mixed ploidy population size is measured in genomes rather than individuals.
  • Exports allele frequencies in SPAGeDi and adegenet formats.
  • Easily extensible; ordinary users can write new functions to interface with the package.

Author and Maintainer

User:Lindsay V. Clark

Note that I have changed institutions since the paper was published! If you email me at my UC Davis address you might not get a response for awhile. If you replace "ucdavis.edu" with "illinois.edu", that is my new email address.

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 starts with a broad tutorial to familiarize users with the package, then goes into more detail about how data are stored in polysat and which analyses are appropriate for autopolyploid and allopolyploid data.

R code from tutorial manual: You can copy and paste this code into the R console in order to follow along with the tutorial, or edit it to work with your own data. Emacs Speaks Statistics is a really handy program for editing this type of file and sending lines directly to R, but you can also use a simpler text editor such as Notepad to view and edit this file.

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.

Development version

Version 1.3 changes how ploidy information is stored in polysat. In versions 1.2 and earlier, each sample was assigned one ploidy. In version 1.3, ploidy may be indexed by sample, locus (different copy numbers for different loci), both (for example, if some markers are on sex chromosomes), or neither (if you just want one ploidy value for the entire dataset). From the user's perspective, the biggest change is that there is a new function called reformatPloidies that can switch between these indexing schemes. In terms of the code, there are widespread but minor changes. Due to the likelihood that the changes introduced new bugs, I am going to keep 1.3 as a development version for a few months before putting it on CRAN.

You may want to use version 1.3 if you:

  • want ploidy to vary by locus as described above
  • are using genbinary objects (there are a couple bug fixes)
  • are using the genotypeDiversity function (there are bug fixes as well as an improved Simpson index that is corrected for sample size)
  • are just beginning to analyze your data and want your dataset to be compatible with future versions
  • really love polysat and want to beta test the latest version.

Windows binary

Linux source

Tutorial manual

Reference manual

Download the binary or source to your R working directory, then use:

install.packages("polysat_1.3-0.zip", repos=NULL)

or

install.packages("polysat_1.3-0.tar.gz", repos=NULL)

depending on your operating system.

Graphical Front End for Import/Export

I have made a limited graphical front end (GUI) for interacting with polysat versions 1.0 to 1.2. It may be expanded in the future. Currently, it can assist the user with importing and exporting data to and from text files, as well as editing the dataset. The GUI does not yet perform any analyses (distance matrices, allele frequencies) but creates a "genambig" object, named genobject, that can be used for analysis from the R command prompt.

Notes on use of the GUI: Media: polysat_front_end_notes101017.txt

To obtain the GUI:

  1. If you haven't already, follow the instructions above for installing polysat.
  2. Install the package tcltk2. (Type install.packages("tcltk2") at the R prompt.)
  3. Save a copy of the following file to your computer: Media: polysat_front_end101017.R.txt
  4. Every time you want to launch the GUI, load the text file using the source function. For example: source("C:/Users/lvclark/Desktop/polysat_front_end101017.R.txt")

Note that the GUI has not gone through the same quality control (i.e. extensive checks on CRAN) that polysat itself has. I am offering it here "as is".

How to cite polysat

Clark, LV and Jasieniuk, M, 2011. POLYSAT: an R package for polyploid microsatellite analysis. Molecular Ecology Resources 11(3): 562-566. DOI: 10.1111/j.1755-0998.2011.02985.x

Wish List

This section lists additional functionality that I'm thinking of adding to polysat. If you have any additional requests (please be specific), 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.

  • For allopolyploids, assign alleles to one genome or the other based on what genotypes are found in the population. (This is a complex problem and not on the to-do list for my dissertation, but could be very useful. Want to hire me to do this as a post-doc?) Use these allele assignments to re-code allopolyploid data into autopolyploid data by splitting each locus into two or more loci.
  • On a related note, test whether genotype distributions in a population are consistent with autopolyploid or allopolyploid inheritance.
  • Given probabilities of unambiguous genotypes (genotypeProbs function), randomly generate an unambiguous dataset. This could then be passed to software such as adegenet that allows for polyploidy but not allele copy number ambiguity.
  • More population statistics (Weir and Cockerham 1984, etc.).
  • Parentage analysis
  • Options for handling data where allele copy number is known. At the same time, I will probably make it so that different loci can have different ploidies (for sex chromosomes, SSRs that only amplify in one homeologous genome, etc.).
  • Estimate selfing rate under polysomic inheritance, based on observed and expected frequencies of fully heterozygous genotypes. I wrote a function to do this, but the results were imprecise due to stochastic effects in simulated datasets. I can email you the source code and documentation if you would like to tinker with it.
  • A scoring system to determine whether an offspring was sexually or asexually produced, as seen in my poster at PAG XIX. I have all the code for this, but basically my PI and I are awaiting peer-review on the methodology before I release it as part of polysat.
  • Some relatedness coefficients for unambiguous genotypes, to be used with meandistance.matrix2.


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 An 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 are not sure how something works, try experimenting to see if it does what you think it does.

If you get an error message or if the software behaves in an unexpected way, I'm happy to help you figure out what went wrong. (Particularly since several users have helped me to find bugs in this way.) In this case, please send your dataset (or a subset of your data that you don't mind sharing) and code that can be used to duplicate the error.

  • Is missing data allowed in polysat? Yes it is! For the Structure, GenoDive, SPAGeDi, and Tetrasat/Tetra formats, you can code the missing data as you normally would for that format. For the GeneMapper format, you can either delete rows with missing data, or fill in a -9 in the first allele column for that row.
  • I have made my PCA plot. Can I add a label for each sample? Yes. See ?text.
  • In read.GeneMapper I got the error "line 2 did not have X elements". Each line of the file needs to have the same number of tab stops. You can add these manually in a text editor, or if you open and save the file in a spreadsheet program it should automatically insert the right number of tab stops.
  • I tried to do PCoA (cmdscale) but got the error "NA values not allowed in d." If you only have one or two loci, you will need to exclude all individuals with missing data from your analysis. If you have three or more loci and still see this error, you may need to exclude individuals that are missing genotypes at multiple loci.
  • Do all populations need to have the same number of individuals? Do the samples have to be ordered by population? No and no. Example code

Known issues

Current version (1.2-1)

  • Locus names should not contain a period. For now this is going to remain a "feature" of polysat.
  • There is a problem with "genbinary" objects if a particular locus has only one allele for the whole dataset. I've found the bug, so contact me if you have this issue and need the bug fix.
  • Rounding errors in R can cause errors when the Simpson or Shannon indices are used. ("p should sum to 1.") This will be fixed in version 1.3.

Older versions

  • Bruvo.distance: In version 1.2-0 and earlier, if both genotypes are missing, returns 0 rather than NA.
  • read.GenoDive: The function does not expect a "Clones" column, and will simply take sample names from whichever column is second. (Version 1.2-0 and earlier)
  • If one locus name is a shorter version of another locus name, e.g. "ABC1" and "ABC12", there will be some issues with the "genbinary" class and with the allele frequency functions. (Version 1.2-0 and earlier)
  • In version 1.1, write.GeneMapper has problems when genotypes have more alleles than the maximum ploidy in the dataset.
  • editGenotypes in version 1.0-0 rearranges the genotypes if the samples and loci are not in alphabetical order.
  • In version 0.1, read.SPAGeDi will not work with missing=0, missing=00, etc. This should not be an issue in version 1.0 because of the change in data structure. (In either version, even if the missing data symbol is at the default, -9, the software still knows that zero indicates missing data in a SPAGeDi file.)

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:

Current version (1.2-1)

Older versions

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.
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