[adegenet-forum] FST genlight

[Guillaume Robert]

Thank you very much Thierry for the advices, I will give a try to your package ;)

Guillaume
________________________________________
De : Thibaut Jombart <thibautjombart at gmail.com>
Envoyé : mardi 4 avril 2017 16:24
À : Thierry Gosselin
Cc : Guillaume Robert; adegenet-forum at lists.r-forge.r-project.org
Objet : Re: [adegenet-forum] FST genlight

Looks cool! :)

--
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 15:22, Thierry Gosselin <thierrygosselin at icloud.com> wrote:
> several solutions: SNPRelate, hierfstat, strataG, diveRsity and GENODIVE.
>
> But I prefer my package ;) why? (check this link)
> assigner
> vignette
> bug report
>
> I haven’t tested my package above 200K markers, curious to see how it goes
> with 400K!
>
> It uses genlight and many other input files.
> I would start by just asking for the overall Fst, then if it finish without
> bug or error.
>
> Example with genlight object:
>
> library(assigner) #Install instructions on my github
>
> fst.test <- stackr::tidy_genomic_data(data = genlight.data) %>%
>   assigner::fst_WC84(data = ., verbose = TRUE)
>
> After, you could use other arguments: pairwise, confidence intervals and
> subsampling.
>
> There is also a function for Nei’s Gst, G’st and Jost’s D
>
> Cheers
> Thierry
>
> On Apr 4, 2017, at 09:45, Guillaume Robert <guillaume.robert at inra.fr> wrote:
>
> 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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