Hi, yes, thank You, adegenet uses some functions from pegas. I thought it is mainly for DNA data. I have problems with AMOVA and HW test.
amova(ssrs3n.dist~ssrs3n.pops, data=NULL, nperm=1000, is.squared=TRUE)
Analysis of Molecular Variance
Call: amova(formula = ssrs3n.dist ~ ssrs3n.pops, data = NULL, nperm = 1000,
is.squared = TRUE)
SSD MSD df
ssrs3n.pops NA NA 8
Error NA NA 121
Total NA NA 129
Variance components:
sigma2 P.value
ssrs3n.pops
Error
Variance coefficients:
a
14.23846
I don't get, why I have NAs everywhere.
ssrs3n.hwe.test <- hw.test(ssrs3n.loci, B=100000)
Error in expand.genotype(Nall, ploidy = ploidy, matrix = TRUE) :
object 'ans' not found
Calls: hw.test -> lapply -> FUN -> expand.genotype
When I run it with diploid microsatellites, it works fine. But I think those
two procedures should work with any ploidy level. I tried to set B=0 for
hw.test, but it is the same... Do I miss some basic point?
Sincerely,
Vojtěch
Dne Pá 30. května 2014 11:31:31 jste napsal(a):
> Hi Vojtěch,
>
> You can also have a look at pegas: it includes a vignette detailing how
> to read allelic/genotypic data files and converting from/to adegenet:
>
> library(pegas)
> vignette("ReadingFiles")
>
> Most functions in pegas will accept any level of ploidy.
>
> HTH
>
> Emmanuel
>
> Le 30/05/2014 05:34, Jombart, Thibaut a écrit :
> > 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
--
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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