[adegenet-forum] Can AFLP data be applied to adegenet?

[Yu-Huang Wang]

Yu-Huang Wang wrote:
> Dear Dr. Jombart,
>  
> I used AFLP to study the landscape genetics of spiny rat.  I tried to 
> identify the position of  its genetic boundaries and overlay the 
> boundaries with potential dispersal barriers (highway, river, etc.).
> I have tried 'wombsoft' but there is still some subjectivity of 
> defining genetic bandwidth.  I read through the manual of adegenet.
> It seems that AFLP data can not be used for the sPCA in adegenet.  
> Will you include the function of using AFLP data for adegenet in the 
> near future?
>  
> Best regards,
>  
> Yu-Huang Wang
> PhD. Candidate
> Dep. Life Science
> Tung-Hai University
> Taichung City
> Taiwan
>  
>  
Dear Yu-Huang,
 
Thanks for your interest in adegenet and the sPCA. their are no theoretical
reason why the sPCA could not be used with AFLP, but you may be right about
the current implementation: AFLP may not be read as easliy as other data.
One way is to read your data inside R as a genotypes X alleles matrix,
containing 1 where the genotype possesses the given allele, and 0 elsewhere.
Then you can use this as input to the 'genind' constructor (see ?genind) to
get a genind object. And then, provided your xy coordinates are sorted the
same way as your genotypes, the sPCA can be used without problem.
 
Your question is interesting, and may be (will surely be) asked by other
users. It would be nice if you could post your next questions on the
adegenet-forum, which is dedicated to these topics:
adegenet-forum at lists.r-forge.r-project.org
 
As soon as I have time, I will add a section in the tutorial about reading
AFLP in adegenet. If you have any problem, please do not hesitate to post on
the ML.
 
Best regards,
 
Thibaut.

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