[adegenet-forum] adegenet-forum Digest, Vol 80, Issue 5
Zhian Kamvar
zkamvar at gmail.com
Wed Apr 8 16:56:01 CEST 2015
Vikram,
This is off-topic for this forum. This is a forum for the adegenet package.
Please submit questions about general methods or handling things across packages to the R-SIG-genetics group: https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
This specific issue is a poppr related issue (a bug) and should be submitted to the poppr forum: https://groups.google.com/forum/#!forum/poppr
Cheers,
Zhian
> On Apr 8, 2015, at 03:00 , adegenet-forum-request at lists.r-forge.r-project.org wrote:
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> Today's Topics:
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> 1. amova on genind object (using poppr) (Vikram Chhatre)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 7 Apr 2015 17:45:32 -0400
> From: Vikram Chhatre <crypticlineage at gmail.com>
> To: "adegenet-forum at lists.r-forge.r-project.org"
> <adegenet-forum at lists.r-forge.r-project.org>
> Subject: [adegenet-forum] amova on genind object (using poppr)
> Message-ID:
> <CAJZnH0=KRjOb5UyMqvGeaF7KGWX1O7jVURJew6Xhv+ZW-8i9Mw at mail.gmail.com>
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>
> I am trying to do amova on individual loci within a genind object created
> from a structure formatted data set.
>
> Steps I have followed so far:
>
> mygenind <- import2genind(.....)
>
> myhier <- read.table('myhier.txt', header=T)
> head(myhier)
>
> Pop Reg
> 1 1 1
> 2 1 1
> 3 2 1
> 4 2 1
> 5 3 2
> 6 3 2
> 7 4 2
> 8 4 2
> 9 4 2
>
> mygenclone <- as.genclone(mygenind)
>
> sethierarchy(mygenclone) <- myhier
>
> mygenclone_seploc <- seploc(mygenclone, truenames=TRUE, res.type('genind',
> 'matrix'))
>
> amova_res <- poppr.amova(mygenclone_seploc, ~Reg/Pop, within=TRUE)
>
> Error: mygenclone_seploc must be a genind object.
>
> ------------
> Has anyone seen this error before? If anyone knows a workaround, I would
> appreciate hearing about it. The statistic works fine for 'over all loci',
> but I need to obtain per locus estimates.
>
> Thanks for any feedback.
> Vikram
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