Hi, thank You, it is very nice package, I really like it. Together with APE, Adegenet, Pegas, etc it is very powerful combination. Best, Vojtěch
Dne Pá 30. května 2014 08:43:01 jste napsal(a): > Hi Vojtěch, > > 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-devel > opment-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, Vojtěch 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, > >> Vojtěch Zeisek > >> > >> Dne Pá 30. května 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: Vojtěch 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, Vojtěch 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, > >>>> Vojtěch Zeisek > > > > _______________________________________________ > > 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 -- Vojtěch 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
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