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

[Jombart, Thibaut]

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