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

[Jombart, Thibaut]

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]
Sent: 22 November 2011 10:14
To: Jombart, Thibaut
Cc: 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 [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Bailleul [diane.bailleul at u-psud.fr]
> Sent: 19 November 2011 21:45
> To: 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
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