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| <code>polysat</code> is an [[R_Statistics|R]] package for polyploid microsatellite analysis in ecological genetics. Version 1.2-0 is available on CRAN as of May 2011. [[Image:polysat_screenshot_101021.jpg | thumb | right | 450px | Screenshot of polysat from RGui ]] | | <code>polysat</code> is an [[R_Statistics|R]] package for polyploid microsatellite analysis in ecological genetics. [[Image:polysat_screenshot_101021.jpg | thumb | right | 450px | Screenshot of polysat from RGui ]] |
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| == What polysat does ==
| | This is the old website for polysat. Please find the new site at https://github.com/lvclark/polysat/wiki. |
| * Assumes allele copy number ambiguity in partial heterozygotes.
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| * Handles data of any ploidy, including mixed ploidy samples.
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| * Stores genotype data in a simple format that can be easily manipulated to exclude or add samples and loci.
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| * Imports and exports data in [http://www.appliedbiosystems.com/genemapper ABI GeneMapper Genotypes Table], [http://www.bentleydrummer.nl/software/software/GenoDive.html GenoDive], [http://pritch.bsd.uchicago.edu/structure.html Structure], [http://ebe.ulb.ac.be/ebe/Software.html SPAGeDi], [http://www.vub.ac.be/APNA/ATetra.html ATetra], [http://markwith.freehomepage.com/tetrasat.html Tetrasat]/[http://ecology.bnu.edu.cn/zhangdy/TETRA/TETRA.htm Tetra], [http://gbi.agrsci.dk/~bernt/popgen/ POPDIST], and binary presence/absence formats.
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| * Calculates pairwise distances between individuals using a stepwise mutation model or infinite alleles model.
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| * Calculates Shannon and Simpson indexes of genotype diversity.
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| * Counts alleles to assist user in estimating ploidy.
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| * Estimates allele frequencies in autopolyploids using either an iterative or non-iterative algorithm. Calculates pairwise F<sub>ST</sub> based on these estimates. Mixed ploidy population size is measured in genomes rather than individuals.
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| * Exports allele frequencies in SPAGeDi and [http://adegenet.r-forge.r-project.org/ adegenet] formats.
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| * Easily extensible; ordinary users can write new functions to interface with the package.
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| == Author and Maintainer ==
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| [[User:Lindsay V. Clark]]
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| == Obtaining polysat ==
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| If you don't already have R, download it from [http://cran.r-project.org CRAN] and install it.
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| At the prompt in the R console, type:
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| <code>install.packages("combinat")</code>
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| <code>install.packages("polysat")</code>
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| <code>library(polysat)</code>
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| == Documentation ==
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| [[Media: Polysattutorial_1.2.pdf | 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.
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| [[Media: polysat1-2tutorialcode.R.txt | 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. [http://ess.r-project.org/ 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.
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| [[Media: Polysat-manual_1.2.pdf | 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.
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| == Graphical Front End for Import/Export ==
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| I have made a limited graphical front end (GUI) for interacting with <code>polysat</code>. 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 <code>"genambig"</code> object, named <code>genobject</code>, that can be used for analysis from the R command prompt.
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| Notes on use of the GUI: [[Media: polysat_front_end_notes101017.txt]]
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| To obtain the GUI:
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| # If you haven't already, follow the instructions above for installing <code>polysat</code>.
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| # Install the package <code>tcltk2</code>. (Type <code>install.packages("tcltk2")</code> at the R prompt.)
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| # Save a copy of the following file to your computer: [[Media: polysat_front_end101017.R.txt]]
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| # Every time you want to launch the GUI, load the text file using the <code>source</code> function. For example: <code>source("C:/Users/lvclark/Desktop/polysat_front_end101017.R.txt")</code>
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| Note that the GUI has not gone through the same quality control (i.e. extensive checks on CRAN) that <code>polysat</code> itself has. I am offering it here "as is".
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| == How to cite polysat ==
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| Clark, LV and Jasieniuk, M, 2011. POLYSAT: an R package for polyploid microsatellite analysis. ''Molecular Ecology Resources'' 11(3): 562-566. DOI: [[doi:10.1111/j.1755-0998.2011.02985.x | 10.1111/j.1755-0998.2011.02985.x]]
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| == Upcoming in Version 1.3 ==
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| Below are some functions that I am adding because I will be using them in my dissertation work. They are in various stages of development. If you have an immediate need for something on this list, email me and I may be able to send you the source code and documentation.
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| * A scoring system to determine whether an offspring was sexually or asexually produced, as seen in [[Media:LVCpag2011.pdf | my poster at PAG XIX]].
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| * Some relatedness coefficients for unambiguous genotypes, to be used with <code>meandistance.matrix2</code>.
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| == Wish List ==
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| 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.
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| * 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.
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| * On a related note, test whether genotype distributions in a population are consistent with autopolyploid or allopolyploid inheritance.
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| * Given probabilities of unambiguous genotypes (<code>genotypeProbs</code> function), randomly generate an unambiguous dataset. This could then be passed to software such as <code>adegenet</code> that allows for polyploidy but not allele copy number ambiguity.
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| * More population statistics (Weir and Cockerham 1984, etc.).
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| * Parentage analysis
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| * 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.).
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| * 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.
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| * <code>Bruvo.distance</code> under the genome addition or genome loss models, rather than having virtual alleles equal to infinity.
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| == Frequently asked questions ==
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| 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 <code>polysat</code>. (Look for the ''An Introduction to R'' manual on the CRAN website.) I have tried to make <code>polysat</code> 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 <code>polysat</code>, 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.
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| * '''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 <code>-9</code> in the first allele column for that row.
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| * '''I have made my PCA plot. Can I add a label for each sample?''' Yes. See <code>?text</code>.
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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.
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| * '''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.
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| == Known issues ==
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| ===Current version (1.2-0)===
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| * No known issues. (Email me if you find any.)
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| ===Older versions===
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| * In version 1.1, <code>write.GeneMapper</code> has problems when genotypes have more alleles than the maximum ploidy in the dataset.
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| * <code>editGenotypes</code> in version 1.0 rearranges the genotypes if the samples and loci are not in alphabetical order.
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| * In version 0.1, <code>read.SPAGeDi</code> will not work with <code>missing=0</code>, <code>missing=00</code>, 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.)
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| == Source code ==
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| 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:
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| === Current version (1.1-0) ===
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| *[[Media: classes_generics_methods_polysat_1-0-1.R.txt]]
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| *[[Media: class_conversion_polysat_1-0.R.txt]]
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| *[[Media: dataimport_polysat_1-1.R.txt]]
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| *[[Media: dataexport_polysat_1-2.R.txt]]
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| *[[Media: individual_distance_polysat_1-2.R.txt]]
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| *[[Media: population_stats_polysat_1-2.R.txt]]
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| === Older versions ===
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| *[[Media: dataexport_polysat_1-1.R.txt]]
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| *[[Media: individual_distance_polysat_1-0.R.txt]]
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| *[[Media: population_stats_polysat_1-1.R.txt]]
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| *[[Media: polysat_0.1_functions.R.txt]]
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| *[[Media: dataimport_polysat_1-0.R.txt]]
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| *[[Media: dataexport_polysat_1-0.R.txt]]
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| *[[Media: population_stats_polysat_1-0a.R.txt]]
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| == External links ==
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| * You can rate and review polysat on [http://crantastic.org/packages/polysat Crantastic]. (I am of course also open to questions and comments via [[Special:Emailuser/Lindsay_V._Clark|email]].)
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| * [http://cran.r-project.org/web/packages/polysat/ CRAN] page with source and binary downloads.
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