[adegenet-forum] FST genlight

[Guillaume Robert]

Hi and thank you for your response,

I have around 400k SNPs, but I could reduce my set, focusing on coding regions.

What is the maximum number of SNPs that a genind object could handle? (I've got 32Go of RAM)
________________________________________
De : Thierry Gosselin <thierrygosselin at icloud.com>
Envoyé : mardi 4 avril 2017 15:31
À : Thibaut Jombart; Guillaume Robert
Cc : adegenet-forum at lists.r-forge.r-project.org
Objet : Re: [adegenet-forum] FST genlight

Hi Guillaume and Thibault,

How many markers in the genlight object ?

Cheers,
Thierry

> On Apr 4, 2017, at 09:19, Thibaut Jombart <thibautjombart at gmail.com> wrote:
>
> I think Jérome Goudet was thinking of implementing this at some point,
> but I don't know where this ended. This is not implemented as it is in
> adegenet. PR welcome ;)
>
> Cheers
> Thibaut
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
> Head of RECON: repidemicsconsortium.org
> sites.google.com/site/thibautjombart/
> github.com/thibautjombart
> Twitter: @TeebzR
> +44(0)20 7594 3658
>
>
> On 4 April 2017 at 12:58, Guillaume Robert <guillaume.robert at inra.fr> wrote:
>> Hi,
>>
>>
>> I use adegenet to perform FST analysis for a big set of SNPs markers.
>>
>>
>> I've already loaded my data in a genlight object, but I haven't found how to
>> do a FST computation for each SNP.
>>
>> (the method described in the "basic tutorial" is for genind object)
>>
>>
>> Would anyone know if it's possible, and how?
>>
>>
>> Thanks,
>>
>>
>> Guillaume
>>
>>
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