[adegenet-forum] FST genlight

[Thierry Gosselin]

several solutions: SNPRelate, hierfstat, strataG, diveRsity and GENODIVE.

But I prefer my package ;) why? (check this link) <https://www.dropbox.com/s/fl4s30enh6nnxiy/fst_comparisons.nb.html?dl=0>
assigner <https://github.com/thierrygosselin/assigner>
vignette <https://github.com/thierrygosselin/assigner/blob/master/vignettes/fst_confidence_intervals.Rmd>
bug <https://github.com/thierrygosselin/assigner/blob/master/FEATURES.md#contributions> 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 <https://github.com/thierrygosselin/assigner>

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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