[adegenet-forum] possibility to use adegenet on seeds data

[Jombart, Thibaut]

Hello, 
I am not sure I get what you want to do, but why would you use DPCOA for part of the data and then compare the results obtained by another method?
Cheers
Thibaut
________________________________________
From: Diane Bailleul [diane.bailleul at u-psud.fr]
Sent: 23 November 2011 09:49
To: valeria montano
Cc: Jombart, Thibaut; adegenet-forum at r-forge.wu-wien.ac.at
Subject: Re: [adegenet-forum] possibility to use adegenet on seeds data

Dear Valeria,
Despite the fact I've got seeds, i.e. generation+1, I'm interested in generation 0. I'd like to compare the PCA on the genotypes with a DPCOA on the assigned individuals (i.e. the plants that bears seeds and not the seeds).
But otherwise, it would be simplier to perform the analysis the way you suggest.
Perhaps it doesn't change anything ... Has anybody got a previous and similar experience ?

Le 11/22/2011 6:30 PM, valeria montano a écrit :
Dear Thibaut and Diane,

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?

(sorry for the nerdy explicit content of this post)
Cheers

Valeria

On 22 November 2011 11:26, Jombart, Thibaut <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>> wrote:
Hello,

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).

Then you can run multivariate analyses on the obtained genpop.

Cheers

Thibaut
________________________________________
From: Diane Bailleul [diane.bailleul at u-psud.fr<mailto:diane.bailleul at u-psud.fr>]
Sent: 22 November 2011 10:14
To: Jombart, Thibaut
Cc: adegenet-forum at r-forge.wu-wien.ac.at<mailto:adegenet-forum at r-forge.wu-wien.ac.at>
Subject: Re: [adegenet-forum] possibility to use adegenet on seeds data

Hi and thanks for your answer.
I've got proper genotypes for seeds and leaves. The only difference is
that I've got one leaf for each plant and several seeds for the same
plant. And the genotypes of the seeds that belong to the same plant can
be similar, or not.
I'd like to perform a PCA on my data to see if there's a genetic
structuration of my big populations.
If I transform each bunch of seeds per plant in a genpop object (if I
understand correctly what you suggest), will I be able to mix these
genpop objects with the leaves informations in a genind object ?

Le 11/21/2011 12:44 PM, Jombart, Thibaut a écrit :
> Hello,
>
> I know some users have used adegenet to analyse plant data... anyone care to share his/her experience?
>
> 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.
>
> Cheers
>
> Thibaut
>
> ________________________________________
> From: adegenet-forum-bounces at r-forge.wu-wien.ac.at<mailto:adegenet-forum-bounces at r-forge.wu-wien.ac.at> [adegenet-forum-bounces at r-forge.wu-wien.ac.at<mailto:adegenet-forum-bounces at r-forge.wu-wien.ac.at>] on behalf of Bailleul [diane.bailleul at u-psud.fr<mailto:diane.bailleul at u-psud.fr>]
> Sent: 19 November 2011 21:45
> To: adegenet-forum at r-forge.wu-wien.ac.at<mailto:adegenet-forum at r-forge.wu-wien.ac.at>
> Subject: [adegenet-forum] possibility to use adegenet on seeds data
>
> Good afternoon,
>
> I'm sorry to bother you but I've read the adegenet documentation and I can't find the answer to my question.
>
> I've got a data set of genotypes of plant samples of leaves and seeds divided between different populations.
>
> 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.
>
> The data set is divided as followed : populationX/plantX/seedX for seeds or populationX/plantX for leaves.
>
> Can I use the adegenet package to analyse my data ? Is there is any risk that each seed will be considered as one plant ?
>
> Thanks for your answer,
>
> Diane
>


--
Diane Bailleul
Doctorante
Université Paris-Sud 11 - Faculté des Sciences d'Orsay
Unité Ecologie, Systématique et Evolution
Département Biodiversité, Systématique et Evolution
UMR 8079 - UPS CNRS AgroParisTech
Porte 320, premier étage, Bâtiment 360
91405 ORSAY CEDEX FRANCE
(0033) 01.69.15.56.64


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--
Diane Bailleul
Doctorante
Université Paris-Sud 11 - Faculté des Sciences d'Orsay
Unité Ecologie, Systématique et Evolution
Département Biodiversité, Systématique et Evolution
UMR 8079 - UPS CNRS AgroParisTech
Porte 320, premier étage, Bâtiment 360
91405 ORSAY CEDEX FRANCE
(0033) 01.69.15.56.64