<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">several solutions: SNPRelate, hierfstat, strataG, diveRsity and GENODIVE.</div><div class=""><br class=""></div><div class="">But I prefer my package ;) <a href="https://www.dropbox.com/s/fl4s30enh6nnxiy/fst_comparisons.nb.html?dl=0" class="">why? (check this link)</a></div><div class=""><a href="https://github.com/thierrygosselin/assigner" class="">assigner</a></div><div class=""><div class=""><a href="https://github.com/thierrygosselin/assigner/blob/master/vignettes/fst_confidence_intervals.Rmd" class="">vignette</a></div><div class=""><a href="https://github.com/thierrygosselin/assigner/blob/master/FEATURES.md#contributions" class="">bug</a> report</div></div><div class=""><br class=""></div>I haven’t tested my package above 200K markers, curious to see how it goes with 400K!<div class=""><br class=""></div><div class="">It uses <b class="">genlight</b> and many other input files.</div><div class="">I would start by just asking for the overall Fst, then if it finish without bug or error.</div><div class=""><br class=""></div><div class="">Example with genlight object:</div><div class=""><br class=""></div><div class=""><div class="">library(assigner) #Install instructions on my <a href="https://github.com/thierrygosselin/assigner" class="">github</a></div><div class=""><br class=""></div><div class="">fst.test <- stackr::tidy_genomic_data(data = genlight.data) %>% </div><div class=""> assigner::fst_WC84(data = ., verbose = TRUE) </div></div><div class=""><br class=""></div><div class="">After, you could use other arguments: pairwise, confidence intervals and subsampling.</div><div class=""><br class=""></div><div class=""><div class="">There is also a function for Nei’s Gst, G’st and Jost’s D</div></div><div class=""><br class=""></div><div class="">Cheers</div><div class="">Thierry</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 4, 2017, at 09:45, Guillaume Robert <<a href="mailto:guillaume.robert@inra.fr" class="">guillaume.robert@inra.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi and thank you for your response,<br class=""><br class="">I have around 400k SNPs, but I could reduce my set, focusing on coding regions.<br class=""><br class="">What is the maximum number of SNPs that a genind object could handle? (I've got 32Go of RAM)<br class="">________________________________________<br class="">De : Thierry Gosselin <<a href="mailto:thierrygosselin@icloud.com" class="">thierrygosselin@icloud.com</a>><br class="">Envoyé : mardi 4 avril 2017 15:31<br class="">À : Thibaut Jombart; Guillaume Robert<br class="">Cc : <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" class="">adegenet-forum@lists.r-forge.r-project.org</a><br class="">Objet : Re: [adegenet-forum] FST genlight<br class=""><br class="">Hi Guillaume and Thibault,<br class=""><br class="">How many markers in the genlight object ?<br class=""><br class="">Cheers,<br class="">Thierry<br class=""><br class=""><blockquote type="cite" class="">On Apr 4, 2017, at 09:19, Thibaut Jombart <<a href="mailto:thibautjombart@gmail.com" class="">thibautjombart@gmail.com</a>> wrote:<br class=""><br class="">I think Jérome Goudet was thinking of implementing this at some point,<br class="">but I don't know where this ended. This is not implemented as it is in<br class="">adegenet. PR welcome ;)<br class=""><br class="">Cheers<br class="">Thibaut<br class=""><br class="">--<br class="">Dr Thibaut Jombart<br class="">Lecturer, Department of Infectious Disease Epidemiology, Imperial College London<br class="">Head of RECON: <a href="http://repidemicsconsortium.org" class="">repidemicsconsortium.org</a><br class=""><a href="http://sites.google.com/site/thibautjombart/" class="">sites.google.com/site/thibautjombart/</a><br class="">github.com/thibautjombart<br class="">Twitter: @TeebzR<br class="">+44(0)20 7594 3658<br class=""><br class=""><br class="">On 4 April 2017 at 12:58, Guillaume Robert <guillaume.robert@inra.fr> wrote:<br class=""><blockquote type="cite" class="">Hi,<br class=""><br class=""><br class="">I use adegenet to perform FST analysis for a big set of SNPs markers.<br class=""><br class=""><br class="">I've already loaded my data in a genlight object, but I haven't found how to<br class="">do a FST computation for each SNP.<br class=""><br class="">(the method described in the "basic tutorial" is for genind object)<br class=""><br class=""><br class="">Would anyone know if it's possible, and how?<br class=""><br class=""><br class="">Thanks,<br class=""><br class=""><br class="">Guillaume<br class=""><br class=""><br class="">_______________________________________________<br class="">adegenet-forum mailing list<br class="">adegenet-forum@lists.r-forge.r-project.org<br class="">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br class=""></blockquote>_______________________________________________<br class="">adegenet-forum mailing list<br class="">adegenet-forum@lists.r-forge.r-project.org<br class="">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br class=""></blockquote><br class=""></div></div></blockquote></div><br class=""></div></body></html>