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 <[email protected]> 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: [email protected] [[email protected]]
> > on behalf of Gilles Benjamin Leduc [[email protected]] 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 <[email protected]> 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
> --
> 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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