Dear Thibaut and Diane, <div><br></div><div>I was thinking... considering that leaves' genotypes are parental generation and seeds are progeny 1 and so they are different individuals (despite the fact that the seeds are physically all together on the same plant), maybe you could just put any genotype as a single ind, instead of creating a super-gen.ind-pop-object which in this case would be rather a "gen.fam" (family, each pop is mother plant and children). If you put them separately, you would have a lot of individuals in a pop with a high inbreeding coefficient and overlapping generations (light years far from HW equilibrium), but as long as you are interested in pop structure, maybe this is better than a pop composed by multi-related-genotyped individuals. Or do you think it doesn't make that much difference?</div>
<div><br></div><div>(sorry for the nerdy explicit content of this post)</div><div>Cheers</div><div><br></div><div>Valeria</div><div><br><div class="gmail_quote">On 22 November 2011 11:26, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello,<br>
<br>
yes; what you need to do is have a factor defining "plants" and use it when constructing your genpop object, so that leaves and seeds of a given plant will give allele frequencies in the plant, considered as a "population" (i.e. a group of genotypes).<br>
<br>
Then you can run multivariate analyses on the obtained genpop.<br>
<br>
Cheers<br>
<br>
Thibaut<br>
________________________________________<br>
From: Diane Bailleul [<a href="mailto:diane.bailleul@u-psud.fr">diane.bailleul@u-psud.fr</a>]<br>
Sent: 22 November 2011 10:14<br>
To: Jombart, Thibaut<br>
Cc: <a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at">adegenet-forum@r-forge.wu-wien.ac.at</a><br>
Subject: Re: [adegenet-forum] possibility to use adegenet on seeds data<br>
<div class="HOEnZb"><div class="h5"><br>
Hi and thanks for your answer.<br>
I've got proper genotypes for seeds and leaves. The only difference is<br>
that I've got one leaf for each plant and several seeds for the same<br>
plant. And the genotypes of the seeds that belong to the same plant can<br>
be similar, or not.<br>
I'd like to perform a PCA on my data to see if there's a genetic<br>
structuration of my big populations.<br>
If I transform each bunch of seeds per plant in a genpop object (if I<br>
understand correctly what you suggest), will I be able to mix these<br>
genpop objects with the leaves informations in a genind object ?<br>
<br>
Le 11/21/2011 12:44 PM, Jombart, Thibaut a écrit :<br>
> Hello,<br>
><br>
> I know some users have used adegenet to analyse plant data... anyone care to share his/her experience?<br>
><br>
> I am not sure about what your seed data look like. Is it a mixture of alleles? Or do you have proper genotypes? In the second case, then I would consider genotypes as 'individuals' (genind object), and seeds as 'populations'. You would probably carry out most of your analyses at a 'population' (seed level) using a genpop object. Having a look at the vignette "adegenet-basics" (type vignette("adegenet-basics")) may help for genind/genpop conversions.<br>
><br>
> Cheers<br>
><br>
> Thibaut<br>
><br>
> ________________________________________<br>
> From: <a href="mailto:adegenet-forum-bounces@r-forge.wu-wien.ac.at">adegenet-forum-bounces@r-forge.wu-wien.ac.at</a> [<a href="mailto:adegenet-forum-bounces@r-forge.wu-wien.ac.at">adegenet-forum-bounces@r-forge.wu-wien.ac.at</a>] on behalf of Bailleul [<a href="mailto:diane.bailleul@u-psud.fr">diane.bailleul@u-psud.fr</a>]<br>
> Sent: 19 November 2011 21:45<br>
> To: <a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at">adegenet-forum@r-forge.wu-wien.ac.at</a><br>
> Subject: [adegenet-forum] possibility to use adegenet on seeds data<br>
><br>
> Good afternoon,<br>
><br>
> I'm sorry to bother you but I've read the adegenet documentation and I can't find the answer to my question.<br>
><br>
> I've got a data set of genotypes of plant samples of leaves and seeds divided between different populations.<br>
><br>
> For leaves, each genotype is an plant. But for seeds, I've got 2 or 8 differents genotypes of 2 or 8 seeds for the same individual.<br>
><br>
> The data set is divided as followed : populationX/plantX/seedX for seeds or populationX/plantX for leaves.<br>
><br>
> Can I use the adegenet package to analyse my data ? Is there is any risk that each seed will be considered as one plant ?<br>
><br>
> Thanks for your answer,<br>
><br>
> Diane<br>
><br>
<br>
<br>
--<br>
Diane Bailleul<br>
Doctorante<br>
Université Paris-Sud 11 - Faculté des Sciences d'Orsay<br>
Unité Ecologie, Systématique et Evolution<br>
Département Biodiversité, Systématique et Evolution<br>
UMR 8079 - UPS CNRS AgroParisTech<br>
Porte 320, premier étage, Bâtiment 360<br>
91405 ORSAY CEDEX FRANCE<br>
(0033) 01.69.15.56.64<br>
<br>
<br>
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