[adegenet-forum] adegenet-forum Digest, Vol 80, Issue 5

[Jombart, Thibaut]

Hi guys, 

I'd like to emphasize Zhian's comment, as the R-sig-genetics is going to become more and more useful in the near future. A bunch of very good, nice and reactive people have subscribed recently, so it will likely become a more lively forum of discussion. Meaning that the adegenet forum is going to be more strictly reserved for adegenet-related issues.

https://stat.ethz.ch/mailman/listinfo/r-sig-genetics

All the best
Thibaut 

________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Zhian Kamvar [zkamvar at gmail.com]
Sent: 08 April 2015 15:56
To: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] adegenet-forum Digest, Vol 80, Issue 5

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>
> Content-Type: text/plain; charset="utf-8"
>
> 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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