Hi VojtÄch, The stable development version of the poppr package available on github (https://github.com/grunwaldlab/poppr/tree/devel) can handle polyploid SSR data based on Bruvo's distance. Download instructions are available here: https://github.com/grunwaldlab/poppr/tree/devel#for-the-bleeding-edge-development-version.
Best, Nik and Zhian On May 30, 2014, at 6:39 AM, Gilles Benjamin Leduc <g...@hi.is> wrote: > > Hi, > > I'm also curently developing a R package: https://github.com/giby/Linarius > that can be used for triploid⦠actually it is designed for mixed ploidy > levels. But right now, I focus on AFLP. As I told you there is much more > thing availlable for microsatelites. > Benjamin > > Le Vendredi 30 Mai 2014 09:17 GMT, VojtÄch Zeisek <vo...@trapa.cz> a écrit: > >> Hello, >> thank You both. poppr looks interesting, I need to explore it more. >> Adegenet is famous package. I didn't know it can also handle triploid data. >> I >> found problem when importing data to it. Functions of import2genind group >> (read.genetix, read.structure, read.fstat and read.genepop) are only for >> diploid data. So I used read.loci. The input file was easy: first line with >> names of markers etc, first row with names of samples, second row with >> populations and from third row alleles. I coded alleles in this way > >> 123/234/345, so that each individual has 3 alleles. Missing alleles are just >> NA. >> ssrs3n.loci <- read.loci("ssrs3n.txt", header=TRUE, loci.sep="\t", >> allele.sep="/", col.pop=2, col.loci=3:10, row.names=1) >> ssrs3n.loci >> Allelic data frame: 130 individuals >> 8 loci >> 1 additional variable >> ssrs3n.genind <- loci2genind(ssrs3n.loci) >> ssrs3n.genind >> >> ##################### >> ### Genind object ### >> ##################### >> - genotypes of individuals - >> >> S4 class: genind >> @call: df2genind(X = as.matrix(x[, attr(x, "locicol")]), sep = "/", >> pop = pop) >> >> @tab: 130 x 115 matrix of genotypes >> >> @ind.names: vector of 130 individual names >> @loc.names: vector of 8 locus names >> @loc.nall: number of alleles per locus >> @loc.fac: locus factor for the 115 columns of @tab >> @all.names: list of 8 components yielding allele names for each locus >> @ploidy: 2 >> @type: codom >> >> Optional contents: >> @pop: factor giving the population of each individual >> @pop.names: factor giving the population of each individual >> >> @other: - empty - >> >> As You can see, it was imported as diploid and I haven't found way how >> import >> it as triploid data. Imported data matrix seems to be wrong. When I used >> input >> file formatted in the same way for diploids, it works perfectly... >> Any ideas how to fix that? >> Thank You in advance, >> VojtÄch Zeisek >> >> Dne Pá 30. kvÄtna 2014 03:34:49 jste napsal(a): >>> Hi there, >>> >>> yes, adegenet handles any (constant) ploidy for most purposes. For input >>> formats etc. please see the tutorial on basics, section 'documents' on: >>> http://adegenet.r-forge.r-project.org/ >>> >>> Please feel free to use the adegenet forum for adegenet-related questions. >>> Cheers >>> Thibaut >>> >>> ________________________________________ >>> From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] >>> on behalf of Gilles Benjamin Leduc [g...@hi.is] Sent: 29 May 2014 17:12 >>> To: VojtÄch Zeisek >>> Cc: mailinglist R >>> Subject: Re: [R-sig-phylo] Triploid microsatellites? >>> >>> Hi, >>> >>> Yes it is possible in R, there is a package created for related purposes: >>> poppr or something like that⦠The dev version on github should be >>> preferred. I have seen several R work with polyploids and microsatelites, >>> unfortunately⦠I work with ALFP :p Benjamin >>> >>> Le Jeudi 29 Mai 2014 13:40 GMT, VojtÄch Zeisek <vo...@trapa.cz> a écrit: >>>> Hello, >>>> I wonder if it is possible to handle triploid microsatellite (yes, all >>>> individuals are regular 3n) data in adegenet and another R packages. And >>>> if so, how to enter the data. Any experiences and/or Ideas are very> > >>>> welcomed. :-) Structure and BAPS are working well. >>>> Yours sincerely, >>>> VojtÄch Zeisek >> -- >> VojtÄch Zeisek >> http://trapa.cz/en/ >> >> Department of Botany, Faculty of Science >> Charles University in Prague >> Benátská 2, Prague, 12801, CZ >> http://botany.natur.cuni.cz/en/ >> >> Institute of Botany, Academy of Science >> Zámek 1, Průhonice, 25243, CZ >> http://www.ibot.cas.cz/en/ >> >> Czech Republic > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ Niklaus J. Grünwald Research Plant Pathologist | Horticultural Crops Research Laboratory | USDA ARS Professor (courtesy) | Department of Botany and Plant Pathology | Oregon State University 3420 NW Orchard Ave. | Corvallis, OR 97330 | USA | Tel 541.738-4049 | Fax 541.738-4025 grunwaldlab.cgrb.oregonstate.edu | phytophthora-id.org | oregonstate.edu/instruct/dce/phytophthora | phytophthora-smallrna-db.cgrb.oregonstate.edu [[alternative HTML version deleted]]
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